Note: Descriptions are shown in the official language in which they were submitted.
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DESIGN, SYNTHESIS AND USE OF SPECIFIC
POLYAMIDE DNA-BINDING LIGANDS
The U.S. Government has certain rights in this invention pursuant to Grant
Nos. GM
26453, 27681 and 47530 awarded by the National Institute of Health.
CROSS REFERENCE TO RELATED APPLICAT10NS
1o This application is a continuation-in-part of PCT/L7S97103332 filed
February 20, 1997,
Serial No. 08/853,522 filed May 8, 1997 and PCTIL1S 97/12722 filed July 21,
1997 which are
continuation-in-part applications of Serial No. 08/837,524, filed April 21,
1997, Serial No.
08/607,078, filed February 26, 1996, provisional application Serial No.
60/042,022, f led April
16, 1997 and provisional application Serial No. 60/043,444, filed April 8,
1997.
BACKGROUND OF THE INVENTION
Field of the Invention
2o This invention relates to polyamides which bind to predetermined sequences
in the minor
groove of double stranded DNA.
Description of the Related Art
The design of synthetic ligands that read the information stored in the DNA
double helix
has been a long standing goal of chemistry. Cell-permeable small molecules
which target
predetermined DNA sequences are useful for the regulation of gene-expression.
Oligodeoxynucleotides that recognize the major groove of double-helical DNA
via triple-helix
formation bind to a broad range of sequences with high affinity and
specificity. Although
oligonucleotides and their analogs have been shown to interfere with gene
expression, the triple
helix approach is limited to purine tracks and suffers from poor cellular
uptake. The
development of pairing rules for minor groove binding polyamides derived from
N-
methylpyrrole (Py) and N-methylimidazole (Im) amino acids provides another
code to control
sequence specificity. An ImlPy pair distinguishes G~C from C~G and both of
these from A~T or
,35 T~A base pairs. Wade, W.S., Mrksich, M. & Dervan, P.B. describes the
design of peptides that
bind in the minor groove of DNA at 5'-(A,T)G(A,T)C(A,T)-3' sequences by a
dimeric side-by-
side motif. J. Am. Chem. Soc. 114, 8783-8794 (1992); Mrksich, M. et al.
describes antiparallel
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side-by-side motif for sequence specific-recognition in the minor groove of
DNA by the
designed peptide I -methyliinidazole-2-carboxamidenetropsin. Proc. Natl. Acad.
Sci. USA 89,
7586-7590 (1992); Trauger, J.W., Baird, E. E. Dervan, P.B. describes the
recognition of DNA by
designed ligands at subnanomolar concentrations. Nature 382, 559-561 (1996). A
Py/Py pair
specifies A~T from G~C but does not distinguish A~T from T~A. Pelton, J.G. &
Wemmer, D.E.
describes the structural characterization of a 2-1 distamycin A-
d(CGCAAATTTGGC) complex
by two-dimensional NMR. Proc. Natl. Acad. Sci. USA 86, 5723-5727 (1989);
White, S., Baird,
E. E. & Dervan, P.B. Describes the effects of the A~T/T~A degeneracy of
pyrrole-imidazole
polyamide recognition in the minor groove of DNA. Biochemistry 35, 12532-12537
(1996);
l0 White, S., Baird, E. E. & Dervan, P. B. describes the pairing rules for
recognition in the minor
groove of DNA by pyrrole-imidazole polyamides. Chem. c~ Biol. 4, 569-578
(1997); White, S.,
Baird, E. E. & Dervan, P.B. describes the S'-3' N-C orientation preference for
polyamide
binding in the minor groove. New methods of designing selective compounds and
the resulting
specific polyamide binding ligands that are designed to target an identified
sequence of double
stranded DNA are needed to overcome the A~T/T~A degeneracy of pyrrole-
imidazole
polyamide recognition.
SUMMARY OF THE INVENTION
It has been found that a new aromatic amino acid, 3-hydroxy-N-methylpyrrole
(Hp)
when incorporated into a polyamide and paired opposite Py, provides the means
to discriminate
A~T from T~A. Unexpectedly, the replacement of a single hydrogen atom on the
pyrrole with a
hydroxy group in a Hp/Py pair regulates the affinity and the specificity of a
polyamide by an
order of magnitude. Utilizing Hp together with Py and Im in polyamides to form
four aromatic
amino acid pairs (Im/Py, Py/Im, Hp/Py, and Py/Hp) provides a code to
distinguish all four
Watson-Crick base pairs in the minor groove of DNA.
3o The present invention provides a method for designing specific polyamides
suitable for
use as DNA-binding ligands, as well as compositions comprising such
polyamides, that are
selective for an identified target sequence of double stranded DNA.
Preferably, the designed
specific polyamides are characterized by a dissociation constant of less than
1 nM, as measured
by DNase I footprint titration, and greater than ten-fold selectivity for the
identified target
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sequence over related mismatch sequences, based on the ratio of the
corresponding dissociation
constants measured by DNase I footprint titrations.
The invention encompasses improved polyamides for binding to the minor groove
of
double stranded ("duplex") DNA. The polyamides are in the form of a hairpin
comprising two
groups of at least three consecutive carboxamide residues, the two groups
covalently linked by
an aliphatic amino acid residue, preferably ~y-aminobutyric acid or 2,4
diaminobutyric acid, the
consecutive carboxamide residues of the first group pairing in an antiparallel
manner with the
consecutive carboxamide residues of the second group in the minor groove of
double stranded
to DNA. The improvement relates to the inclusion of a binding pair of Hp/Py
carboxamides in the
polyamide to bind to a T~A base pair in the minor groove of double stranded
DNA or Py/Hp
carboxamide binding pair in the polyamide to bind to an A~T base pair in the
minor groove of
double stranded DNA. The improved polyamides have at least three consecutive
carboxamide
pairs for binding to at least three DNA base pairs in the minor groove of a
duplex DNA sequence
that has at least one A~T or T~A DNA base pair, the improvement comprising
selecting a Hp/Py
carboxamide pair to correspond to a T~A base pair in the minor groove or a
Py/Hp carboxamide
pair to bind to an A~T DNA base pair in the minor groove. Preferably the
binding of the
carboxamide pairs to the DNA base pairs modulates the expression of a gene.
In general, the method provides specific polyamides suitable for use as DNA-
binding
ligands that are selective for identified target sequences of double stranded
DNA having a
coding strand sequence of the form 5'-WN1N2 . . , NmW-3' where N is a
nucleotide chosen
from the group A, T, C and G, W is a nucleotide chosen from the group A and T,
and with the
coresponding paired antiparallel strand 3'-W'N' 1N'2 , , , N'mW'-5' where N'
is a nucleotide
chosen from the group T, A, G and C respectively to form Watson-Crick pase
pairs, W is a
nucleotide chosen from the group T and A respectively to form Watson-Crick
pase pairs, and m
is an integer having a value from 3 to 6 inclusive.
The preferred corresponding designed specific polyamides resulting from this
invention
are of the form
X 1 X2 . . . Xm-y-X(m + 1 ) . . . X(2m-1 )X2m-~-Dp
wherein X l , X2, Xm, X(m + 1 ), X(2m - 1 )~ ~d X2m are carboxamide residues
forming
carboxamide binding pairs Xl/X2m~ X2/X(2m-1)~ Xm/X(m + 1), and y is y-
aminobuytic acid or
2,4 diaminobutyric acid and Dp is dimethylaminopropylamide,
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and where
carboxamide binding pair X I /X2m corresponds to base pair N I ~N' l,
carboxamide binding pair X2/X~2m-1) corresponds to base pair N2~N'2,
carboxamide binding pair Xm/X~m+1 ) corresponds to base pair Nm~N'm.
In general, the specific polyamide DNA-binding ligands were designed by using
a
method that comprises the steps of identifying the target DNA sequence 5'-
WNIN2 . , . NmW-
3'; representing the identified sequence as 5'-Wab . . . xW-3', wherein a is a
first nucleotide to
be bound by the X I carboxamide residue, b is a second nucleotide to be bound
by the X2
to carboxamide residue, and x is the corresponding nucleotide to be bound by
the Xm carboxamide
residue; defining a as A, G, C, or T to correspond to the first nucleotide to
be bound by a
carboxamide residue in the identified six base pair sequence.
Carboxamide residues were selected sequentially as follows: Im was selected as
the X 1
carboxamide residue and Py as the X2m carboxamide residue if a was G. Py was
selected as
the X I carboxamide residue and Im as the X2m carboxamide residue if a was C.
Hp was
selected as the Xl carboxamide residue and Py as the X2m carboxamide residue
if a was T. Py
was selected as the Xl carboxamide residue and Hp as the X2m carboxamide
residue if a .was
A.
The remaining carboxamide residues were selected in the same fashion. Im was
selected
as the X2 carboxamide residue and Py as the X2m-1 carboxamide residue if b was
G. Py was
selected as the X2 carboxamide residue and Im as the X2m-1 carboxamide residue
if b was C.
Hp was selected as the X2 carboxamide residue and Py as the X2m_ 1 carboxamide
residue if b
was T. Py was selected as the X2 carboxamide residue and Hp as the X2m-1
carboxamide
residue if b was A.
The selection of carboxamide residues was continued through m iterations. In
the last
iteration, Im was selected as the Xm carboxamide residue and Py as the Xm+1
carboxamide
3o residue if x was G. Py was selected as the Xm carboxamide residue and Im as
the Xm+1
carboxamide residue if x was C. Hp was selected as the Xm carboxamide residue
and Py as the
Xm+1 carboxamide residue if x was T. Py was selected as the Xm carboxamide
residue and Hp
as the Xm+1 carboxamide residue if x was A.
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In one preferred embodiment, the polyamide includes at least four consecutive
carboxamide pairs for binding to at least four base pairs in a duplex DNA
sequence. In another
preferred embodiment, the polyamide includes at least five consecutive
carboxamide pairs for
binding to at least five base pairs in a duplex DNA sequence. In yet another
preferred
embodiment, the polyamide includes at least six consecutive carboxamide pairs
for binding to at
least six base pairs in a duplex DNA sequence. In one preferred embodiment,
the improved
polyamides have four carboxamide binding pairs that will distinguish A~T, T~A,
C~G and G~C
to base pairs in the minor groove of a duplex DNA sequence. The duplex DNA
sequence can be a
regulatory sequence, such as a promoter sequence or an enhancer sequence, or a
gene sequence,
such as a coding sequence or a non-coding sequence. Preferably, the duplex DNA
sequence is a
promoter sequence.
More specifically, "polyamidc" refers to a polymer of polyamide subunits of
the formula.
R1
Y! X N R3 N
X
O ~n O y~ ~ R4
~N
2 O
a b
c
where R1 is chosen from H, NH2, SH, Cl, Br, F, N-acetyl, or N-formyl
where R2 is C 1 _ 100 alkyl (preferably C 1 _ 10 alkyl such as methyl, ethyl,
isopropyl), C 1 _
100 alkylamine (preferably C 1 _ l p alkylamine such as ethylamine), C 1-100
alkyldiamine
(preferably C1-10 alkyldiamine such as N,N-dimethylpropylamine), a C1-100
alkylcarboxylate
(preferably a C 1-10 alkylcarboxylate such as-CH2COOH), C 1 _ 100 alkenyl
(preferably C 1 _ I O
alkenyl such as CH2CH=CH2), or a C 1 _ 100 alkynyl (preferably C 1-10 alkynyl
such as -
CH2C---CH3), or a C1_100L, where L groups can be independently chosen from but
is not
limited to arylboronic acids, biotins, polyhistidines comprised from about 2
to 8 amino acids,
haptens to which an antibody binds, solid phase supports,
oligodeoxynucleotide, N-
ethylnitrosourea, fluorescein, bromoacetamide, iodoacetamide, DL-a-lipoic
acid, acridine,
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captothesin, pyrene, mitomycin, texas red, anthracene, anthrinilic acid,
avidin, DAPI, isosulfan
blue, malachite green, psoralen, ethyl red, 4-(psoraen-$-yloxy}-butyrate,
tartaric acid, (+)-a.-
tocopheral. Most preferably R2 is H, (CH2)mCH3, (CH2)mNH2, (CH2)mSH, (CH2)mOH,
(CH2)m~52~ (CH2)mORS, (CH2)mSRS, where RS - (CH2)mCH3, (CH2)m~2~
(CH2)mSH, (CH2)mOH and m is an integer from 0 to 6.
where R3 is chosen from H, NH2, OH, SH, Br, Cl, F, OMe, CH20H, CH2SH, CH2NH2.
where R4 is -NH(CH2)0-100~6R~ or NI-I(CH2}pC0 NH(CH2}0-100~6R~ or NHR6
or NH(CH2)pCONHR6. Where R6 and R~ are independently chosen from H, Cl, NO, N-
acetyl,
benzyl, C 1 _ 100 alkyl, C 1-100 alkylamine, C 1-100 alkyldiamine, C 1-100
alkylcarboxylate, C 1 _
1 o 100 alkenyl, a C 1 _ 100 alkynyl, or a C 1-1 OOL~ where L groups can be
independently chosen from
but is not limited to arylboranic acids, biotins, polyhistidines comprised
from about 2 to 8 amino
acids, haptens to which an antibody binds, solid phase supports,
oligodeoxynucleotide, N-
ethylnitrosourea, fluorescein, bromoacetamide, iodoacetamide, DL-a-lipoic
acid, acridine,
captothesin, pyrene, mitomycin, texas red, anthracene, anthrinilic acid,
avidin, DAPI, an
oligodeoxynucleotide, isosulfan blue, malachite green, psoralen, ethyl red, 4-
(psoraen-8-yloxy)-
butyrate, tartaric acid, (+)-a-tocopheral. Where p is an integer value ranging
from 0 to 12. In the
preferred form of the present invention Rf and R~ are H, and the resulting
amine modified
polyamide is coupled to an amine reactive molecule in order to generate a
bifiznction polyamide
conjugate.Where the amine reactive molecule is chosen from but not limited to
the following:
2o aryiboronic acids, biotins, polyhistidines comprised from about 2 to 8
amino acids, haptens to
which an antibody binds , solid phase supports, an oligodeoxynucleotide, N-
ethylnitrosourea,
fluorescein, bromoacetamide, iodoacetamide, DL-a-lipoic acid, acridine,
captothesin, pyrene,
mitomycin, texas red, anthracene, anthrinilic acid, avidin, DAPI, isosulfan
blue, malachite green,
psoralen, ethyl red, 4-(psoraen-8-yloxy)-butyrate, tartaric acid, (+)-a-
tocopheral.
where X and Y are chosen from the following, N, CH, COH, CCH3, CNH2, CC1, CF.
a is an integer chosen from values of 0 or 1
b is an integer chosen integer values ranging from 1 to 5.
c is an integer value ranging from 2 to 10.
3o Hereinafter, N-methylpyrrolecarboxamide may be referred to as "Py", N-
methylimidazolecarboxamide may be referred to as "Im", y-aminobutyric acid may
referred to as
"y", (3-alanine may be referred to as "(3", glycine may be referred to as "G",
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dimethylaminopropylamide may be referred to as "Dp", and
ethylenediaminetetraacetic acid
may be referred to as "EDTA":
The preparation and the use of polyamides for binding in the minor groove of
double
s stranded DNA are extensively described in the art. This invention is an
improvement of the
existing technology that uses 3-hydroxy-N-methyIpyrrole to provide carboxamide
binding pairs
for DNA binding polyamides.
The invention encompasses polyamides having y-aminobutyric acid or a
substituted y-
1o arninobutyric acid to form a hairpin with a member of each carboxamide
pairing on each side of
it. Preferably the substituted y-aminobutyric acid is a chiral substituted y-
aminobutyric acid such
as (R)-2,4-diaminohutyric acid. In addition, the polyamides may contain an
aliphatic amino acid
residue, preferably a (3-alanine residue, in place of a Hp or Py carboxamide.
The [3-alanine
residue is represented in formulas as (3. The ~-alanine residue becomes a
member of a
t s carboxamide binding pair. The invention further includes the substitution
as a X3/(3 binding pair
for non-Im containing binding pair. Thus, binding pairs in addition to the
Im/Py, Py/Im, Hp/Py
and Py/Hp are Iml(3, ~3/Im, Py/~, ~3/PY, Hp/~, ~3/Hp, and (3/~i.
The polyamides of the invention can have additional moieties attached
covalently to the
2o polyamide. Preferably the additional moieties are attached as substituents
at the amino terminus
of the polyamide, the carboxy terminus of the polyamide, or at a chiral (R)-
2,4-diaminobutyric
acid residue. Suitable additional moieties include a detectable labeling group
such as a dye,
biotin or a hapten. Other suitable additional moieties are DNA reactive
moieties that provide for
sequence specific cleavage of the duplex DNA.
BRIEF DESCRIPTION OF THE DRAWINGS
Figure 1 illustrates the structure of polyamide 1 2 and 3.
.3o Figure 2 illustrates the pairing of polyamides to DNA base pairs.
Figure 3 illustrates the DNase footprint titration of compounds 2 and 3.
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_g_
Figure 4 illustrates a list of the structures of representative Hp containing
polyamides. '
Figure 5 schematically illustrates a method for the design of eight
carboxamide residue hairpin
polyamide compounds suitable for recognition of 6-by 5'-V~~fl'JNNW-3'
sequences in the minor
groove of double stranded DNA.
Figure 6 schematically illustrates a method for determining the position of an
aromatic amino
acid residue that should be replaced with a ~3-alanine residue in order to
enhance the DNA
binding properties of certain eight carboxamide residue hairpin polyamide
compounds.
Figure 7 schematically illustrates a method for the design of ten carboxamide
residue hairpin
polyamide compounds suitable for recognition of 7-by 5'-WNT12~1NNW-3'
sequences in the
t o minor groove of double stranded DNA.
Figure 8 schematically illustrates a method for determining the position of an
aromatic amino
acid residue that should be replaced with a (3-alanine residue in order to
enhance the DNA
binding properties of certain tcn carboxamide residue hairpin polyamide
compounds.
Figure 9 schematically illustrates a method for determining the position of an
additional
t 5 aromatic amino acid residue that should be replaced with a (3-alanine
residue in order to enhance
the DNA binding properties of certain ten carboxamide residue hairpin
poiyamide compounds.
Figure 10 schematically illustrates a method for the design of twelve
carboxamide residue
hairpin polyamide compounds suitable for recognition of 8-by S'-VJhfIJNNW-3'
sequences in
the minor groove of double stranded DNA.
20 Figure 11 schematically illustrates a method for determining the position
of an aromatic amino
acid residue that should be replaced with a ~-alanine residue in order to
enhance the DNA
binding properties of certain twelve carboxamide residue hairpin polyamide
compounds.
DETAILED DESCRIPTION OF THE INVENTION
Within this application, unless otherwise stated, definitions of the terms and
illustration
of the techniques of this application may be found in any of several well-
known references such
as: Sambrook, J., e1 al., Molecular Cloning: A Laboratory Manual, Cold Spring
Harbor
Laboratory Press (1989); Goeddel, D., ed., Gene Expression Technology, Methods
in
Enzymology, 185, Academic Press, San Diego, CA (1991); "Guide to Protein
Purification" in
Deutshcer, M.P., ed., Methods in Enzymology, Academic Press, San Diego, CA (
1989); Innis, et
al., PCR Protocols: A Guide to Methods and Applications, Academic Press, San
Diego, CA
(1990); Freshney, R.L, Culture of Animal Cells: A Manual of Basic Technique,
2"d Ed., Alan
Liss, Inc. New York, NY (1987); Murray, E.J., ed., Gene Transfer and
Expression Protocols, pp.
109-128, The Humana Press Inc., Clifton, NJ and Lewin, B., Genes Vl, Oxford
University Press,
New York (1997).
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For the purposes of this application, a promoter is a regulatory sequence of
DNA- that is
involved in the binding of RNA polymerase to initiate transcription of a gene.
A gene is a
segment of DNA involved in producing a peptide, polypeptide or protein,
including the coding
region, non-coding regions preceding ("leader") and following ("trailer") the
coding region, as
well as intervening non-coding sequences ("introns") between individual coding
segments
("exons"). Coding refers to the representation of amino acids, start and stop
signals in a three
base "triplet" code. Promoters are often upstream (" '5 to") the transcription
initiation site of the
corresponding gene. Other regulatory sequences of DNA in addition to promoters
are known,
including sequences involved with the binding of transcription factors,
including response
elements that are the DNA sequences bound by inducible factors. Enhancers
comprise yet
another group of regulatory sequences of DNA that can increase the utilization
of promoters, and
can function in either orientation (S'-3' or 3'-5') and in any location
(upstream or downstream)
relative to the promoter. Preferably, the regulatory sequence has a positive
activity, i.e., binding
of an endogeneous ligand (e.g. a transcription factor) to the regulatory
sequence increases
transcription, thereby resulting in increased expression of the corresponding
target gene. In such
a case, interference with transcription by binding a polyamide to a regulatory
sequence would
reduce or abolish expression of a gene.
The promoter may also include or be adjacent to a regulatory sequence known in
the art
as a silencer-. A silencer sequence generally has a negative regulatory effect
on expression of the
gene. In such a case, expression of a gene may be increased directly by using
a poiyamide to
prevent binding of a factor to a silencer regulatory sequence or indirectly,
by using a polyamide
to block transcription of a factor to a silencer regulatory sequence.
It is to be understood that the polyamides of this invention bind to double
stranded DNA
in a sequence specific manner. The function of a segment of DNA of a given
sequence, such as
5'-TATAAA-3', depends on its position relative to other functional regions in
the DNA
sequence. In this case, if the sequence 5'-TATAAA-3' on the coding strand of
DNA is
3o positioned about 30 base pairs upstream of the transcription start site,
the sequence forms part of
the promoter region (Lewin, Genes UI, pp. 831-835). On the other hand, if the
sequence 5'-
TATAAA-3' is downstream of the transcription start site in a coding region and
in proper
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register with the reading frame, the sequence encodes the tyrosyl and lysyl
amino acid residues
(Lewin, Genes Vl, pp. 213-215).
While not being held to one hypothesis, it is believed that the binding of the
polyamides
of this invention modulate gene expression by altering the binding of DNA
binding proteins,
such as RNA polymerase, transcription factors, TBF, TFIIIB and other proteins.
The effect on
gene expression of polyamide binding to a segment of double stranded DNA is
believed to be
related to the function, e.g., promoter, of that segment of DNA.
to
It is to be understood by one skilled in the art that the improved polyamides
of the
present invention may bind to any of the above-described DNA sequences or any
other sequence
having a desired effect upon expression of a gene. In addition, U.S. Patent
No. 5,578,444
describes numerous promoter targeting sequences from which base pair sequences
for targeting
an improved polyamide of the present invention may be identified.
It is generally understood by those skilled in the art that the basic
structure of DNA in a
living cell includes both major and a minor groove. For the purposes of
describing the present
invention, the minor groove is the narrow groove of DNA as illustrated in
common molecular
2o biology references such as Lewin, B., Genes vl, Oxford University Press,
New York (1997).
To affect gene expression in a cell, which may include causing an increase or
a decrease
in gene expression, a effective quantity of one or more polyamide is contacted
with the cell and
internalized by the cell. The cell may be contacted in vivo or in vitro.
Effective extracellular
concentrations of polyamides that can modulate gene expression range from
about 10 nanomolar
to about 1 micromolar. Gottesfeld, J.M., et al., Nature 387 202-205 (1997). To
determine
effective amounts and concentrations of polyamides in vitro, a suitable number
of cells is plated
on tissue culture plates and various quantities of one or more polyamide are
added to separate
wells. Gene expression following exposure to a polyamide can be monitored in
the cells or
3o medium by detecting the amount of the protein gene product present as
determined by various
techniques utilizing specific antibodies, including ELISA and western blot.
Alternatively, gene
expression following exposure to a polyamide can be monitored by detecting the
amount of
messenger RNA present as determined by various techniques, including northern
blot and RT-
PCR.
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Similarly, to determine effective amounts and concentrations of polyamides for
-in vivo
administration, a sample of body tissue or fluid, such as plasma, blood,
urine, cerebrospinal
~ fluid, saliva, or biopsy of skin, muscle, liver, brain or other appropriate
tissue source is analyzed.
Gene expression following exposure to a polyamide can be monitored by
detecting the amount
' of the protein gene product present as determined by various techniques
utilizing specific
antibodies, including ELISA and western blot. Alternatively, gene expression
following
exposure to a polyamide can be monitored by the detecting the amount of
messenger RNA
present as determined by various techniques, including northern blot and RT-
PCR.
The polyamides of this invention may be formulated into diagnostic and
therapeutic
compositions for in vivo or in vitro use. Representative methods of
formulation may be found in
Remington: The Science and Practice of Pharmacy, 19th ed., Mack Publishing
Co., Easton, PA
(1995).
For in vivo use, the polyamides may be incorporated into a physiologically
acceptable
pharmaceutical composition that is administered to a patient in need of
treatment or an animal
for medical or research purposes. The polyamide composition comprises
pharmaceutically
acceptable earners, excipients, adjuvants, stabilizers, and vehicles. The
composition may be in
2o solid, liquid, gel, or aerosol form. The polyamide composition of the
present invention may be
administered in various dosage forms orally, parentally, by inhalation spray,
rectally, or
topically. The term parenteral as used herein includes, subcutaneous,
intravenous,
intramuscular, intrasternal, infusion techniques or intraperitoneally.
The selection of the precise concentration, composition, and delivery regimen
is
influenced by, inter alia, the specific pharmacological properties of the
particular selected
compound, the intended use, the nature and severity of the condition being
treated or diagnosed,
the age, weight, gender, physical condition and mental acuity of the intended
recipient as well as
the route of administration. Such considerations are within the purview of the
skilled artisan.
3o Thus, the dosage regimen may vary widely, but can be determined routinely
using standard
methods.
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Polyamides of the present invention are also useful for detecting the presence
of double
stranded DNA of a specific -sequence for diagnostic or preparative purposes.
The sample
containing the double stranded DNA can be contacted by polyamide linked to a
solid substrate,
thereby isolating DNA comprising a desired sequence. Alternatively, poIyamides
linked to a
suitable detectable marker, such as biotin, a hapten, a radioisotope or a dye
molecule, can be
contacted by a sample containing double stranded DNA.
The design of bifunctional sequence specific DNA binding molecules requires
the
integration of two separate entities: recognition and functional activity.
Polyamides that
specifically bind with subnanomolar affinity to the minor groove of a
predetermined sequence of
double stranded DNA are linked to a functional molecule, providing the
corresponding
bifunctional conjugates useful in molecular biology, genomic sequencing, and
human medicine.
Polyamides of this invention can be conjugated to a variety of functional
molecules, which can
be independently chosen from but is not limited to arylboronic acids, biotins,
polyhistidines
comprised from about 2 to 8 amino acids, haptens to which an antibody binds,
solid phase
supports, oligodeoxynucleotides, N-ethylnitrosourea, fluorescein,
bromoacetamide,
iodoacetamide, DL-a-lipoic acid, acridine, captothesin, pyrene, mitomycin,
texas red,
anthracene, anthrinilic acid, avidin, DAPI, isosulfan blue, malachite green,
psoralen, ethyl red, 4-
(psoraen-8-yloxy)-butyrate, tartaric acid, (+)-~,-tocopheral, psoralen, EDTA,
methidium,
2o acridine, Ni(II)~Gly-Gly-His, TO, Dansyl, pyrene, N-bromoacetamide, and
gold particles. Such
bifunctional polyamides are useful for DNA affinity capture, covalent DNA
modification,
oxidative DNA cleavage, and DNA photocleavage. Such bifunctional polyamides
are useful for
DNA detection by providing a polyamide linked to a detectable label. Detailed
instructions for
synthesis of such bifunctional polyamides can be found in copending U.S.
provisional
application 60/043,444, the teachings of which are incorporated by reference.
DNA complexed to a labeled polyamide can then be determined using the
appropriate
detection system as is well known to one skilled in the art. For example, DNA
associated with a
polyamide linked to biotin can be detected by a streptavidin / alkaline
phosphatase system.
The present invention also describes a diagnostic system, preferably in kit
form, for
assaying for the presence of the double stranded DNA sequence bound by the
polyamide of this
invention in a body sample, such brain tissue, cell suspensions or tissue
sections, or body fluid
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samples such as CSF, blood, plasma or serum, where it is desirable to detect
the presence, and
preferably the amount, of the double stranded DNA sequence bound by the
polyamide in the
sample according to the diagnostic methods described herein.
The diagnostic system includes, in an amount sufficient to perform at least
one assay, a
specific polyamide as a separately packaged reagent. Instructions for use of
the packaged
reagents) are also typically included. As used herein, the term "package"
refers to a solid
matrix or material such as glass, plastic (e.g., polyethylene, polypropylene
or polycarbonate),
paper, foil and the like capable of holding within fixed limits a polyamide of
the present
1 o invention. Thus, for example, a package can be a glass vial used to
contain milligram quantities
of a contemplated polyamide or it can be a microliter plate well to which
microgram quantities
of a contemplated polyamide have been operatively affixed, i.e., linked so as
to be capable of
being bound by the target DNA sequence. "Instructions for use" typically
include a tangible
expression describing the reagent concentration or at least one assay method
parameter such as
the relative amounts of reagent and sample to be admixed, maintenance time
periods for reagent
or sample admixtures, temperature, buffer conditions and the like. A
diagnostic system of the
present invention preferably also includes a detectable label and a detecting
or indicating means
capable of signaling the binding of the contemplated polyamide of the present
invention to the
target DNA sequence. As noted above, numerous detectable labels, such as
biotin, and detecting
or indicating means, such as enzyme-linked (direct or indirect) streptavidin,
are well known in
the art.
As used herein, "subnanomolar affinity" means binding that is characterized by
a
dissociation constant, Kd , of less than 1 nM, as measured by DNase I
footprint titration.
Preferably, polyamides of the present invention are characterized by
subnanomolar binding
affinity for the identified target DNA sequence. As used herein, the
"selectivity" of the binding
of a polyamide to a DNA sequence is the ratio of the dissociation constant, Kd
, as measured by
DNase I footprint titration of binding the polyamide to a mismatch DNA
sequence divided by
the corresponding dissociation constant of the binding of the polyamide to the
identified target
3o DNA sequence. Preferably, polyamides of the present invention are
characterized by a
selectivity of 5 or greater, more preferably a selectivity of greater that 10.
r
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The exemplary polyamide that illustrates the compositions and methods of the
present
invention is polyamide 3 of Figure 1, ImImHpPy-y-ImPyPyPy-~3-Dp. This
polyamide was
designed according to the method of the present invention to target the
identified sequence 5'-
WGGTCW-3'. See Table 5, below, Sequence No. 36 and the corresponding sequence
of
carboxamide binding pairs. Polyamide 3 binds an identified target sequence 5'-
TGGTCA-3'
with a dissociation constant, as measured by DNase I footprint titration, of
0.48 nM, i.e., with
subnanomolar affinity as defined herein (see Table 1, below). The polyamide
binds to the
mismatch sequence 5'-TGGACA-3' with a dissociation contant of 37 nM, yielding
a selectivity,
as defined herein, of 77 (Table 1 ).
to
Figure 1 shows representative structures of polyamides. ImImPyPy-y-ImPyPyPy-~3-
Dp
(1), ImImPyPy-y-ImHpPyPy-/3-Dp (2), and ImlmHpPy-y-ImPyPyPy-(3-Dp (3). (Hp = 3-
hydroxy-N-methylpyrrole, Im = N-methylimidazole, Py = N-methylpyrrole, (3 = ~i-
alanine, y = y-
aminobutyric acid, Dp = Dimethylaminopropylamide). Polyamides were synthesized
by solid
phase methods using Boc-protected 3-methoxypyrrole, imidazole, and pyrrole
aromatic amino
acids, cleaved from the support by aminolysis, deprotected with sodium
thiophenoxide, and
purified by reversed phase HPLC. Baird, E. E. & Dervan, P. B. describes the
solid phase
synthesis of polyamides containing imidazole and pyrrole amino acids. J. Am.
Chern. Soc. 118,
6141-6146 (1996); also see PCT US 971003332. The identity and purity of the
polyamides were
2o verified by'H NMR, analytical HPLC, and matrix-assisted laser-desorption
ionization time-of
flight mass spectrometry (MALDI-TOF MS-monoisotopic): 1 1223.6 {1223.6
calculated), 2
1239.6 (1239.6 calculated); 3 1239.6 (1239.6 calculated).
Figure 2 illustrates binding models for polyamides 1-3 in complex with 5'-
TGGTCA-3'
and 5'-TGGACA-3' (A~T and T~A in fourth position highlighted). Filled and
unfilled circles
represent imidazole and pyrrole rings respectively; circles containing an H
represent 3-
hydroxypyrrole, the curved line connecting the polyamide subunits represents y-
aminobutyric
acid, the diamond represents (3-alanine, and the + represents the positively
charged
dimethylaminopropylamide tail group.
Figure 3 shows quantitative DNase I footprint titration experiments with
polyamides 2
and 3 on the 3' 3~P labeled 250-by pJK6 EcoRIIPvuII restriction fragment. Lane
1, intact DNA;
lanes 2-11 DNase I digestion products in the presence of 100, 50, 20, 10, 5,
2, l, 0.5, 0.2, 0.1 nM
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polyamide, respectively; lane 12, DNase I digestion products in the absence of
polyamide; lane
13, adenine-specific chemical sequencing. Iverson, B. L. & Dervan, P. B.
describes an adenine-
specific DNA chemical sequencing reaction. Methods ~nzymol. 15, 7823-7830
(1987). All
reactions were done in a total volume of 400 p,L. A polyamide stock solution
or Hz0 was added
to an assay buffer containing radiolabeled restriction fragment, with the
final solution conditions
of 10 mM Tris-HC1, 10 mM KC1, 10 mM MgCh, 5 mM CaCl2, pH 7Ø Solutions were
allowed to equilibrate for 4-12 h at 22 °C before initiation of
footprinting reactions.
Footprinting reactions, separation of cleavage products, and data analysis
were carried out as
described. White, S., Baird, E. E. & Dervan, P. B. Effects of the A~T/T~A
degeneracy of
to pyrrole-imidazole polyamide recognition in the minor groove of DNA.
Biochemistry 35, 12532-
12537 (1996).
Figure 4 shows the structure and equilibrium dissociation constant for
numerous
compounds of the present invention. Polyamides are shown in complex with their
respective
1s match site. Filled and unfilled circles represent imidazole (Im) and
pyrrole (Py) rings,
respectively; circles containing an H represent 3-hydroxypyrrole (Hp), the
curved line
connecting the polyamide subunits represents y-aminobutyric acid (y), the
diamond represents ~3-
alanine (~3), and the + represents the positively charged
dimethylaminopropylamide tail group
(Dp). The equilibrium dissociation constants are the average values obtained
from three DNase
2o I footprint titration experiments. The standard deviation for each set is
less than 15% of the
reported number. Assays were earned out in the presence of 10 mM Tris~HCI, 10
mM KCI, 10
mM MgCl2, and 5 mM CaClz at pH 7.0 and 22°C.
Four-ring polyamide subunits, covalently coupled to form eight-ring hairpin
structures,
2s bind specifically to 6-by target sequences at subnanomolar concentrations.
Trauger, J.W., Baird,
E. E. & Dervan, P.B. describe the recognition of DNA by designed ligands at
subnanomolar
concentrations. Nature 382, 559-561 (1996); Swalley, S. E., Baird, E. E. &
Dervan, P. B.
describe the discrimination of 5'-GGGG-3', S'-GCGC-3', and 5'-GGCC'3'
sequences in the
minor groove of DNA by eight-ring hairpin polyamides. J. Am. Chem. Soc. 119,
6953-6961
30 ( 1997). The DNA-binding affinities of three eight-ring hairpin polyamides
shown in Figure 1 as
compound 1, 2, and 3 containing pairings of Im/Py, Py/Im opposite G~C, C~G and
either Py/Py,
Hp/Py, or Py/Hp at a common single point opposite T~A and A~T has been
determined.
Equilibrium dissociation constants (K~) for ImImPyPy-y-ImPyPyPy-(3-Dp 1,
ImImPyPy-y-
ImHpPyPy-~i-Dp 2, ImImHpPy-y-ImPyPyPy-~3-Dp 3 of Figure 1 are shown in Table
1.
3s Brenowitz, M., Senear, D. F., Shea, M. A. & Ackers, G. K. describe a
quantitative DNase
footprint titration method for studying protein-DNA interactions. Methods
Enzymol. 130, 132-
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181 {1986); The Kd values were determined by quantitative DNase I footprint
titration
experiments: on a 3' 32P-labeled 250-by DNA fragment containing the target
sites, 5'-
TGGACA-3' and 5'-TGGTCA-3' which differ by a single A~T base pair in the
fourth position.
The DNase footprint gels are shown in Figure 3.
S
TABLE 1 Equilibrium dissociation constants%
Polyamidet 5'-TGG_TCA-3' 5'-TGGACA-3' KrelT
5'-T G G T C A-3' 5'-T G G 'A C A-3'
1 PyIPy + + 2.0
3'-A C C A G T-5' 3'-A C C T G T-5'
K~ = 0.077 nM Kd = 0.15 nM
5'-T G G T C A-3' S'-T G G A. C A-3'
2 PyIHp + H + H a.of~
3'-A C C Fa G T-5' 3'-A C C T G T-5'
Kd = 15 nM Kd = 0.83 nM
5'-T G G T C A-3' S'-T G G A' C A-3'
H H
3 Hp/Py + +
3'-A C C 11 G T-5' 3'-A C C T G T-5'
Kd = 0.48 nM K~ =37 nM
*The reported dissociation constants are the average values obtained from
three
DNase I footprint titration experiments. The standard deviation for each data
set is
less than 15% of the reported number. Assays were carried out in the presence
of 10
mM Tris~HCI, 10 mM KCI, 10 mM MgCl2, and 5 mM CaCl2 at pI-i 7.0 and 22
°C.
Ring pairing opposite T~A and A~T in the fourth position.
Calculated as Kd(5'-TGGACA-3')/Kd(5'-TGGTCA-3').
Based on the pairing rules for polyamide-DNA complexes both of these sequences
are a
match for control polyamide 1 which places a Py/Py pairing opposite
to A~T and T~A at both sites. It was determined that polyamide 1 (Py/Py) binds
to 5'-TGGTCA-3'
and 5'-TGGACA-3' within a factor of 2 (K~ = 0.077 or 0.15 nM respectively). In
contrast,
poiyamide 2 {Py/Hp) binds to 5'-TGGTCA-3' and 5'-TGGACA-3' with dissociation
constants
which differ by a factor of 18 (K~ = 15 nM and 0.83 nM respectively). By
reversing the pairing
in polyamide 3 (Hp/Py) the dissociation constants differ again in the opposite
direction by a
15 factor of 77 (KD = 0.48 nM and 37 nM respectively). Control experiments
performed on separate
DNA fragments; reveal that neither a S'-TGGGCA-3' or a 5'-TGG_CCA-3' site is
bound by
polyamide 2 or 3 at concentrations < 100 nM, indicating that the Hp/Py and
Py/Hp ring pairings
do not bind opposite G~C or C~G.
20 The specificity of polyamides 2 and 3 for sites which differ by a single
A~T/T~A base
pair results from small chemical changes. Replacing the Py/Py pair in 1 with a
Py/Hp pairing as
in 2, a single substitution of C3-OH for C3-H, destabilizes interaction with
5'-TGGTCA-3' by
191-fold, a free energy difference of 3.1 kcal mol-'. Interaction of 2 with 5'-
TGGACA-3' is
destabilized only 6-fold relative to 1, a free energy difference of 1.1 kcal
mol-' . Similarly,
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replacing the Py/Py pair in 1 with Hp/Py as in 3 destabilizes interaction with
S'-TGGACA-3'~by
2S2-fold, a free energy difference of 3.2 kcal mol-~. Interaction of 3 with
S'TGG_TCA-3' is
destabilized only b-fold relative to 1, a free energy difference of 1.0 kcal
mol-1.
~ s The polyamides of this invention provide for coded targeting of
predetermined DNA
sequences with affinity and specificity comparable to sequence-specific DNA
binding proteins.
I~p, Im, and Py polyamides complete the minor groove recognition code using
three aromatic
amino acids which combine to form four ring pairings (lm/Py, Py/Im, Hp/Py, and
Py/Hp) which
complement the four Watson-Crick base pairs, as shown in TABLE 2. There are a
possible 240
to four base pair sequences which contain at least 1 A~T or T~A base pair and
therefore can
advantageously use an Hp/Py, or Py/Hp carboxamide binding. Polyamides binding
to any of
these sequences can be designed in accordance with the code of TABLE 2.
TABLE 2 Pairing code for minor groove recognition_* _
Pair G~C C~G T~A A~T
Im/Py -i- - - -
PylIm - ~. - -
Hp/Py - - ..f.
Py/Hp - - -
* favored (+), disfavored (-)
IS
For certain G~C rich sequences the affinity of polyamide~DNA complexes may be
enhanced by substitution of an Im/~ pair for Im/Py at G~C and ~3/Im for PylIm
at C~G. At A~T
and T~A base pairs, either a Py/~i, ~3/Py, Hp/~i, ~i/Hp, and (3/(3 may be
used. The alternate
aliphatic/aromatic amino acid pairing code is described in Table 3.
Za
TABLE 3 Aliphatic/Aromatic substitrution for ring
pairings*
Pair Substitution
Py ...___..........R......_-........ .............................-
.._.........
Iml Im/
Py/Im (3llm
HpIPy Py/(3, ~/PY,
Hpl(3, (3/(3
PYIHP PY/I~, ~IPY,
~IHP~ ~I~
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U. S. Patent 5,578,444 describes numerous promoter region targeting sequences
from
which base pair sequences for targeting a polyamide can be identified.
PCT U.S. 97/003332 describes methods for synthesis of polyamides which are
suitable
for preparing polyamides of this invention. The use of ~3-aianine in place of
a pyrrole amino
acid in the synthetic methods provides aromatic/aliphatic pairing (Im/(3,
(3/Im, Hp/(3, (3/Hp, Py/(3,
and ~3/Py) and aliphatic/aliphatic pairing ((3/(3) substitution. The use of y-
aminobutyric acid, or a
substituted y-aminobutyric acid such as (R)-2,4 diaminobutyric acid, provides
for preferred
hairpin turns. The following examples illustrate the synthesis of polyamides
of the present
1 o invention.
The process of designing a preferred polyamide molecule X1X2X3X4-y-XSX6X7Xg
comprising eight aromatic amino acid residues of this invention is shown
schematically in
Figure 5. The polyamide design process provides a method for designing an
eight carboxamide
residue molecule comprising , four carboxamide binding pairs for detection and
binding of a
target six base pair 5'-V~NNNNW-3' sequence in the minor groove of double
stranded DNA.
The design process identifies an appropriate polyamide ligand for recognition
of a predetermined
6-bp, 5'-V~1\f~JNNW-3' sequence with subnanomolar affinity and >10-fold
specificity versus
mismatch sites. Trauger, J.W., Baird, E. E. Dervan, P.B. describes the
recognition of DNA by
2o designed Iigands at subnanomolar concentrations. Nature 382, 559-561
(1996).
In order to prepare a polyamide molecule specific for an identified six base
pair sequence
of double stranded DNA, a user starts the 8-ring polyamide design process that
implements the
minor groove recognition pairing code summarized in Table 2 above. In the
design process a 5'-
VV1\I~~INNW-3' sequence was identified. In a preferred embodiment, the
identified sequence was
located within a gene promoter. U. S. Patent 5,578,444 describes numerous
promoter region
targeting sequences from which target six base pair sequences for targeting a
polyamide can be
identified. The identified sequence was then defined as 5'-WabcdW-3' in a
stepwise process
wherein a, b, c, and d, were sequentially and independently defined as A, G,
C, or T. The
3o structure of the polyamide molecule was then correspondingly defined by
sequentially chosing
antiparallel carboxamide binding pairs according to the minor groove pairing
code summarized
in Table 2 above. Thus, if a was G, then X1 was defined as Im, and Xg was
defined as Py. If a
was C, then X 1 was defined as Py, and Xg was defined as Im. If a was T, then
X I was defined
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as Hp, and Xg was defined as Py. If a was A, then Xl was defined as Py, and Xg
was defined as
Hp,
Similarly,.b was defined as A, G, C, or T and corresponding carboxamide
binding pairs
were defined. According to the same rules, if b was G, then X2 was defined as
Im, and X7 was
' defined as Py. If b was C, then X2 was defined as Py, and X7 was defined as
Im. Likewise, if b
was T, then X2 was defined as Hp, and X7 was defined as Py. If b was A, then
X2 was defined
as Py, and X7 was defined as Hp.
to The next step was to define c as A, G, C, or T and then define
corresponding
carboxamide binding pairs. Following the same rules, if c was G, then X3 was
defined as Im,
and X6 was defined as Py. If c was C, then X3 was defined as Py, and X6 was
defined as Im.
Similarly, if c was T, then X3 was defined as Hp, and X6 was defined as Py. If
c was A, then
X3 was defined as Py, and X6 was defined as Hp. Lastly, d was defined as A, G,
C, or T and the
last corresponding carboxamide binding pair was defined. According to above
rules, if d was G,
then X4 was defined as Im, and XS was defined as Py. If d was C, then X4 was
defined as Py,
and XS was defined as Im. If d was T, then X4 was defined as Hp, and XS was
defined as Py. If
d was A, then X4 was defined as Py, and XS was defined as Hp.
2o With all eight carboxamide residues that participate in binding pairs now
defined, the
designed polyamide X1X2X3X4-y-X5X6X7Xg suitable for binding to the identified
sequence
was synthesized using known techniques. Baird, E. E. & Dervan, P. B. describes
the solid phase
synthesis of polyamides containing imidazole and pyrrole amino acids. J. Am.
Chem. Soc. 118,
6141-6146 (1996); also see PCT US 97/003332.
The binding affinity of the synthesized polyamide to the identified sequence
was
determined using a quantitative DNase footprint titration method for studying
protein-DNA
interactions described by Brenowitz, M., Senear, D. F., Shea, M. A. & Ackers,
G. K., Methods
Enzymol. 130, 132-181 (1986). If the affinity of the synthesized polyamide at
the target site
3o was not subnanomolar affinity then adding a (3-alanine (process A) was
considered in order to
- optimize the exact positions of the binding pairs of aromatic amino acids.
If the affinity of the
said polyamide at said target site was subnanomolar affinity then the sequence
specificity of the
polyamide versus mismatch sequences was determined. If the specificity versus
mismatch sites
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was not > 10-fold specificity then adding a ~3-alanine (process A
schematically shown in Figure
6) was considered, in order to optimize the positions of the aromatic amino
acids in relationship
to the base pairs in the minor groove. Specificity of the polyamide molecule
for the target
identified sequence versus mismatch sequence sites of greater than 10-fold was
considered a
successful result of design process.
The 256 polyamide molecules comprising four carboxamide binding pairs that
were
designed using this method are useful for binding to the 256 target 5'-NNNN-3'
core sequences,
and are listed in Tables 4-11. A corresponding polyamide molecule was designed
for each
1o DNA sequence (1-240) and (G1-G16) using the process outlined above and
shown schematically
in Figure 5.
If the synthesized polyamide molecule did not bind to the target identified
sequence with
subnanomolar affinity or if the synthesized. polyamide molecule did not
exhibit a specificity for
the target identified sequence versus mismatch sequence sites of greater than
10-fold, the option
of substituting an aliphatic amino acid residues for one of the carboxamide
residues was
considered. The preferred aliphatic amino acid residue is (3-alanine. At least
one aliphatic
amino acid residue such as a ~i-alanine residue provided some flexibility to
the central portion of
the polyamide molecule, acting as a "spring" to permit optimization of the
hydrogen bonding
2o between the carboxamide binding pairs and the nucleotide bases of the
double stranded DNA.
In general, it was not found to be advantageous to replace either member of
the terminal
carboxamide binding pair, Xl/Xg, with ~3-alanine. Similarly, ~i-alanine was
not substituted for
members of the binding pair, X41X5, adjacent to the y hairpin residue. ~i-
alanine residues were
not substituted for N-methylimidazole residues. The use of (3-alanine in place
of a pyrrole or 3-
hydroxypyrrole amino acid residue provides aromatic/aliphatic pairing (Im/(3,
~3lIm, Hp/(3, (3/Hp,
Py/~, and (3/Py) and aliphatic/aliphatic pairing (~/(3) substitution.
The method for selecting which pyrrole amino acid to substitute with (3-
alanine is
3o schematically illustrated in Figure 6. Selective placement of an aliphatic
(3-alanine ((3) residue
paired with either a pyrrole (Py), 3-hydroxypyrrole (Hp), or imidazole (Im)
aromatic amino acid
or another ~3-alanine residue is found to compensate for sequence composition
effects to improve
.....,.. ~ , . i ~ ..~~. ,
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recognition and binding of the minor groove of DNA by pyrrole-imidazole
polyamides of the
present invention. If an all-ring polyamide has been found to have an affinity
which is not
subnanomolar, or a specificity versus mismatch sequences which is less than 10-
fold it may be
caused by DNA sequence-composition effects which can be reduced by replacement
of an
s aromatic amino acid with an aliphatic ~-alanine residue. In a polyamide
molecule that comprises
four binding pairs it is only beneficial to place ~3-alanine in positions X2,
X3, Xb, and X~. No
more than two (3-alanine residues may be placed within a single hairpin
structure. No more than
a single (3-residue may be placed within each individual polyamide subunit,
e.g., if X2 is
replaced with ~3-alanine, then X3 cannot be replaced.
~o
These rules and others were implemented in the method schematically
illustrated in
Figure 6. This process is suitable for the refinement of the design polyamide
comprising four
binding pairs that has been designed by the method illustrated in Figure 5,
but which lacks
subnanomolar affinity or greater than 10-fold specificity at the identified
target DNA sequence.
is As in the basic design method, the designed polyamides are synthesized and
the affinity and
specificity of binding to the target DNA were determined.
For a given polyamide molecule X1X2X3X4-y-XSXfX~Xg there are five possible
outcomes for the process of substituting a ~i-alanine residue for an aromatic
amino acid residue.
2o First, there may be no position at which it is possible to add a (3-alanine
residue; in such case, a
better binding affinity or selectivity can be sought in the design and
synthesis of a polyamide
with five or six carboxamide binding pairs, described below. Second, the
process may result in a
derivative which contains a single (3-alanine substitution (such derivatives
are numbered
according to the parent numbering scheme such that a single (3-derivative of
compound 5 would
25 be called 5~3), which is sufficient to produce subnanomolar binding
affinity and >10-fold
specificity, and at which point the process is deemed complete.
Third, the process of Figure 5 may result in a polyamide which contains a
single (3-
alanine substitution which is not sufficient to produce subnanomolar binding
affinity and >10-
3o fold specificity, but where there are no additional positions in which it
is possible to substitute a
(3-alanine residue, and in such a case a polyamide with five or six
carboxamide binding pairs,
should be designed and synthesized, as described below. Fourth, the process of
Figure 5 may
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result in a polyamide that contains a single (3-alanine substitution that is
not sufficient to produce
subnanomolar binding affinity and >10-fold specificity, but where there is an
additional position
for (3-alanine substitution that does produce a polyamide with the criterion
level of affinity and
selectivity and therefore the design process is deemed complete. Polyamides
that were designed
by the process that produces polyamide molecules that contain two (3-alanine
residues are
labeled ~2 in Tables 12-19.
A fifth possibility is that substitution at a second position by the method
illustrated in
Figure G with a second (3-alanine residue is not sufficient to produce a
polyamide having the
1o subnanomolar binding affinity and >10-fold specificity, and a polyamide
with five or six
carboxamide binding pairs, should be designed and synthesized, as described
below. Tables 12-
19 list polyamides corresponding to sequences 1-240 and G1-G16 which contain
either one or
two (3-alanine residues.
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TABLE
4:
8-ring
Hairpin
Polyamides
for
recognition
of
6-by
5'-WGWNNW-3'
DNA aromatic amino acid sequence
sequence
1) 5' G T T T W-3' ImHpHpHp-y-Pypypypy
-W
2) 5'-W G T T A W-3' ImHpF~IpPy-y-HpPyPyPy
3) 5'-W G T T G W-3' ImHpHpIm-y-PyPyPyPy
4 ) 5' G T T C W-3' ImHpHpPy-y-ImPyPyPy
-W
5) 5'-W G T A T W-3' ImHpPyHp-y-pyHpPyPy
6 ) 5' G T A A W-3 ' ImHpPyPy-y-HpHpPypy
-W
7 ) 5' G T A G W-3 ' ImHpPyIm-y-pygppypy
-W
8) 5' G T A C W-3' ImHpPyPy-y-ImHpPyPy
-W
9) 5'-W G T G T W-3' ImHpImHp-y-Pypypypy
10) 5'-W G T G A W-3' ImHpImPy-y-HpPyPyPy
11) 5' G T G G W-3 ' ImHpImIm-y-PyPyPyPy
-W
12) 5' G T G C W-3' ImHpImPy-y-ImpyPypy
-W
13) 5' G T C T W-3' ImHpPyHp-y-PyImPyPy
-W
14) 5' G T C A W-3' ImHpPyPy-y-HpImPyPy
-W
15) 5' G T C G W-3' ImHpPyIm-y-PyImPyPy
-W
16) 5' G T C C W-3' ImHpPyPy-y-ImImPyPy
-W
17) 5' G A T T W-3' ImPyHpHp-y-PypyHpPy
-W
18 ) 5' G A T A W-3 ' ImPyHpPy-y-HpPyHpPy
-W
19) 5' G A T G W-3' ImPyHpIm-y-PyPyHpPy
-W
20) 5'-W G A T C W-3' ImPyHpPy-y-ImPyHpPy
21) 5'-W G A A T W-3' ImPyPyHp-y-PyHpHpPy
22) 5'-W G A A A W-3' ImPyPyPy-y-HpHpHpPy
23) 5'-W G A A G W-3' ItriPyPyIm-y-PyHpHpPy
24) 5' G A A C W-3' ImPyPyPy-y-ImHpHpPy
-W
25) 5' G A G T W-3' ImPyImHp-y-PyPyHpPy
-W
26) 5'-W G A G A W-3' ImPyImPy-y-HpPyHpPy
27) 5'-W G A G G W-3' ImPyImIm-y-Pypygppy
28) 5' G A G C W-3' ImPyImPy-y-ImPyHpPy
-W
29) 5'-W G A C T W-3' ImPyPyHp-y-PyImHpPy
30) 5'-W G A C A W-3' ImPyPyPy-y-HpImHpPy
31) 5' G A C G W-3' ImPyPyIm-y-PyImHpPy
- -W
32) 5'-W G A C C W-3'
ImPyPyPy-y-ImImHpPy
CA 02281930 1999-08-18
WO 98/37067 PCTlUS98/01714
-24-
'TABLE
5:
8-ring
Hairpin
Polyamides
for
recognition
of
6-by
S'-WGSNNW-3'
DNA aromatic amino acid sequence
sequence
33) 5'-W G G T TW-3' ImImHpHp-y-pyPypypy
34) 5'-W G G T AW-3' ImImHpPy-y-HpPyPyPy
35) 5' G G T GW-3' ImImHpIm-y-PyPyPyPy
-W
3 6 ) 5 G G T CW- 3 ' ImImHpPy-y- ImPyPyPy
'
-W
37) 5'-W G G A TW-3' ImImPyHp-y-PyHpPyPy
38) 5'-W G G A AW-3' ImImPyPy-y-HpHpPyPy
39) 5' G G A GW-3' ImImPyIm-y-PyHpPyPy
-W
40) 5' G G A CW-3' ImImPyPy-y-ImHpPyPy
-W
41) 5'-W G G G TW-3' ImImImHp-y-PyPypypy
42) 5'-W G G G AW-3' ImImImPy-y-HppyPypy
43) 5'-W G G C TW-3' ImImPyHp-y-PyImPyPy
44) 5' G G C AW-3' ImImPyPy-y-HpImPyPy
-W
45) 5'-W G C T TW-3' ImPyHpHp-y-PyPyImPy
46) 5'-W G C T AW-3' ImPyHpPy-y-HpPyImPy
47) 5' G C T GW-3' ImPyHpIm-y-PyPyImPy
-W
48) 5'-W G C T CW-3' ImPyHpPy-y-ImPyImPy
49) 5'-W G C A TW-3' ImPyPyHp-y-PyHpImPy
50) 5'-W G C A AW-3' ImPyPyPy-y-HpHpImPy
51) 5' G C A GW-3' ImPyPyIm-y-PyHpImPy
-W
52) 5'-W G C A CW-3' ImPyPyPy-y-ImHpImPy
53) 5'-W G C G TW-3' ImPyImHp-y-PypyImPy
54) 5'-W G C G AW-3' ImPyImPy-y-HpPyImPy
55) 5'-W G C C TW-3' ImPyPyHp-y-pyImImPy
56) 5'-W G C C AW-3' ImPyPyPy-y-HpImImPy
G1) 5'-W G G G GW-3' ImImImIm-y-PyPypypy
G2) 5'-W G G G CW-3'
ImImImPy-y-ImPyPyPy
G3) 5'-W G G C GW-3' ImImPyIm-y-PyImPyPy
G4) 5'-W G G C CW-3' ImImPyPy-y-ImImPyPy
G5) 5'-W G C G GW-3' ImPyImIm-y-PyPyImPy
G6) 5'-W G C G CW-3'
ImPyImPy-y-ImPyImPy
G7) 5' G C C GW-3' ImPyPyIm-y-PyImImPy
-W
G8) 5'-W G C C CW-3' ImPyPyPy-y-ImImImPy
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-25-
TABLE :
6 8-ring
Hairpin
Polyamides
for
recognition
of
6-by
5'-WTWNNW-3'
DNA aromatic amino acid sequence
sequence
57) 5'-W TT T T W-3' HpHpHpHp-y-PYPyPyPy
5 8 ) 5 ' TT T A W- 3 ' HpHpHpPy-y-HpPypypy
-W
59) 5'-W TT T G W-3' HpHpHpIm-y-PyPypypy
60) 5'-W TT T C W-3' HpHpHpPy-y-ImPyPypy
61) 5'-W TT A T W-3' HpHpPYHp-y-PyHpPyPy
62) 5'-W TT A A W-3' HpHpPYPy-y-HpHpPYPy
63) 5'-W TT A G W-3' HpHpPyIm-y-PyHpPyPy
64) 5'-W TT A C W-3' HpHpPyPy-y-ImHpPYPy
65) 5' -W TT G T W-3' HpHpImHp-y-PyPypypY
66) 5' -W TT G A W-3' HpHpImPy-y-HpPYPypy
67) 5'-W TT G G W-3' HpHpImIm-y-PYPypyPy
6 8 ) 5 ' TT G C W-3 ' HpHpImPy-y- ImPyPyPy
-W
69) 5'-W TT C T W-3' HpHpPyHp-y-PyImPYPy
70) 5' -W TT C A W-3' HpHpPYPy-y-HpImPYPy
71 ) 5 ' TT C G W- 3 ' HpHpPyIm-y-PyImPyPy
-W
72) 5'-W TT C C W-3' HpHpPyPy-y-ImImPYPy
73) 5'-W TA T T W-3' HpPYHpHp-y-PypyHpPy
74) 5' -W TA T A W-3' HpPyHpPy-y-HpPyHpPy
75) 5'-W TA T G W-3' HpPyHpIm-y-PyPyHpPy
76) 5' -W TA T C W-3' HpPyHppy-y-ImPyHpPy
77) 5'-W TA A T W-3' HpPyPYHp-y-PYHpHpPy
78) 5'-W TA A A W-3' HpPyPyPy-y-HpHpHpPy
79) 5' -W TA A G W-3' HppyPYIm-y-PYHpHpPy
80) 5' -W TA A C W-3' HpPYPYPy-y-ImHpHpPy
81) 5' -W TA G T W-3' HpPyImHp-y-PyPyHpPy
82) 5'-W TA G A W-3' HpPyImPy-y-HpPyHpPy
83) 5'-W TA G G W-3' HpPYImIm-y-PyPYHpPy
84) 5'-W TA G C W-3' HpPyImPy-y-ImPyHpPy
85) 5'-W TA C T W-3' HpPyPyHp-y-PYImHpPy
86) 5'-W TA C A W-3' Hppypypy_y_Hpl~ppy
87) 5'-W TA C G W-3' HpPyPYIm-y-PyImHpPy
88) 5' -W TA C C W-3' HpPyPyPy-y-ImImHpPy
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/OI714
-26-
TABLE
7:
8-ring
Hairpin
Polyamides
for
recognition
of
6-by
5'-WTSNNW-3'
DNA aromatic amino acid sequence
sequence
89 ) 5' T G T T W-3 ' HpImHpHp-y-PyPyPyPy
-W
90) 5' T G T A W-3' HpImHpPy-y-HpPyPyPy
-W
91) 5'-W T G T G W-3' HpImHpIm-y-PyPyPyPy
92) 5'-W T G T C W-3' HpImHpPy-y-ImPyPyPy
93) 5'-W T G A T W-3' HpImPyHp-y-PyHpPyPy
94) 5'-W T G A A W-3' HpImPyPy-y-HpHpPyPy
95) 5'-W T G A G W-3' HpImPyIm-y-PyHpPyPy
96) 5'-W T G A C W-3' HpImPyPy-y-ImHpPyPy
97) 5'-W T G G T W-3' HpImImHp-y-PyPyPyPy
98) 5'-W T G G A W-3' HpImImPy-y-HpPyPyPy
99) 5'-W T G C T W-3' HpImPyHp-y-PyImPyPy
100) 5' T G C A W-3' HpImPyPy-y-HpImPyPy
-W
101) 5' T G G G W-3' HpIm2mIm-y-PyPyPyPy
-W
102 ) 5' T G G C W-3 ' HpImImPy-y-ImPyPyPy
-W
103) 5'-W T G C G W-3' HpImPyIm-y-PyImPyPy
104) 5'-W T G C C W-3' HpImPyPy-y-ImImPyPy
105) 5'-W T C T T W-3' HpPyHpHp-y-PyPyImPy
106) 5'-W T C T A W-3' HpPyHpPy-y-HpPyImPy
107) 5'-W T C T G W-3' HpPyHpIm-y-PyPyImPy
108) 5' T C T C W-3' HpPyHpPy-y-ImPyImPy
-W
109) 5'-W T C A T W-3' HpPyPyHp-y-PyHpImPy
110) 5' T C A A W-3' HpPyPyPy-y-HpHpImPy
-W
lIl) 5'-W T C A G W-3' HpPyPyIm-y-PyHpImPy
112) 5'-W T C A C W-3' HpPyPyPy-y-ImHpImPy
113) 5' T C G T W-3' HpPyImHp-y-PyPyImPy
-W
114) 5' T C G A W-3' HpPyImPy-y-HpPyImPy
-W
115) 5' T C C T W-3' HpPyPyHp-y-PyImImPy
-W
116) 5' T C C A W-3' HpPyPyPy-y-HpImImPy
-W
117) 5'-W T C G G W-3' HpPyImIm-y-PyPyImPy
118) 5'-W T C G C W-3' HpPyImPy-y-ImPyImPy
119 ) 5 ' T C C G W- 3 ' HpPyPyIm-y-PyImImPy
-W
12 0 5' T C C C W- 3 ' HpPyPyPy-y- ImImImPy
) -W
CA 02281930 1999-08-18
WO 98/37067 PCT/LIS98/01714
-27-
1A13LE
8:
8-ring
Hairpin
Polyamides
for
recognition
of
6-by
5'-WAWNNW-3'
DNA aromatic amino acid sequence
sequence
121 ) 5 A T T T W- 3 ' PyHpHpHp-y- Pypypygp
'
-W
122) 5' A T T A W-3' PyHpHpPy-y-HpPyPyHp
-W
123) 5'-W A T T G W-3' PyHpHpIm-y-PyPyPyHp
124) 5'-W A T T C W-3'
PyHpHpPy-y-ImPyPyHp
125) 5'-W A T A T W-3' PyHpPyHp-y-PyHpPyHp
126) 5'-W A T A A W-3' PyHpPyPy-y-HpHpPyHp
127) 5'-W A T A G W-3' pyHppylm-y-pyHppyHp
128) 5' A T A C W-3' PyHpPyPy-y-ImFipPyHp
-W
129) 5'-W A T G T W-3' PyHpImHp-y-PyPyPyHp
130) 5'-W A T G A W-3' PyHpImPy-y-HpPyPyHp
131) 5' A T G G W-3' PyHpImIm-y-PypypyHp
-W
132) 5'-W A T G C W-3'
PyHpImPy-y-ImPyPyHp
233) 5'-W A T C T W-3' PyHpPyHp-y-PyImPyHp
134) 5'-W A T C A W-3' PyHpPyPy-y-HpImPyHp
135) 5' A T C G W-3' PyHpPyIm-y-PyImPyHp
-W
136) 5'-W A T C C W-3' PyHpPyPy-y-ImImPyHp
137) 5'-W A A T T W-3' PyPyFlpHp-y-PyPyHpHp
138) 5' A A T A W-3' PyPyHpPy-y-HpPyHpHp
-W
139) 5'-W A A T G W-3' PyPyHpIm-y-pypyHpHp
140) 5' A A T C W-3' PyPyHpPy-y-ImPyHpHp
-W
141) 5'-W A A A T W-3' PyPyPyHp-y-PyHpHpHp
142) 5'-W A A A A W-3' PyPyPyPy-y-HpHpHpHp
143) 5'-W A A A G W-3' PyPypylm-y-pyHpHpHp
144) 5' A A A C W-3' PyPyPyPy-y-ImHpHpHp
-W
145) 5'-W A A G T W-3' PypyImHp-y-PyPyHpHp
146) 5'-W A A G A W-3' PyPyImPy-y-HpPyHpHp
147) 5'-W A A G G W-3' PyPyImIm-y-PypyHpHp
14 8 ) 5 A A G C W- 3 ' PyPyImPy-y- ImPyHpI~Ip
'
-W
149) 5' A A C T W-3' pypypyHp_y_pyl~pHp
-W
150) 5' A A C A W-3' PyPyPyPy-y-HpImApHp
-W
151) 5'-W A A C G W-3' PyPyPyIm-y-PyImHpHp
152) 5'-W A A C C W-3' Pypypypy-y-ImImHpHp
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/OI714
-28-
TABLE
9:
8-ring-Hairpin
Polyamides
for
recognition
of
6-by
5'-WASNNW-3'
DNA aromatic amino acid sequence
sequence
153) 5' A GT T W-3' PyImHpHp-y-PyPyPyHp
-W
154) 5' A GT A W-3' PyImHpPy-y-HpPyPyHp
-W
155) 5'-W A GT G W-3' PyImHpIm-y-PyPyPyHp
156) 5'-W A GT C W-3' PyImHpPy-y-ImPyPyHp
157 ) 5' A GA T W-3' PyImPyHp-y-PyHpPyHp
-W
158) 5' A GA A W-3' PyImPyPy-y-HpHpPyHp
-W
159) 5' A GA G W-3' PyImPyIm-y-PyHpPyHp
-W
160) 5' A GA C W-3' PyImPyPy-y-ImHpPyHp
-W
161) 5' A GG T W-3' PyImImHp-y-PyPyPyHp
-W
162) 5' A GG A W-3' PyImImPy-y-HpPyPyHp
-W
163) 5'-W A GC T W-3' PyImPyHp-y-PyImPyHp
164) 5' A GC A W-3' PyImPyPy-y-HpImPyHp
-W
165) 5' A GG G W-3' PyImImIm-y-PyPyPyHp
-W
166) 5' A GG C W-3' PyImImPy-y-ImPyPyHp
-W
167) 5'-W A GC G W-3' PyImPyIm-y-PyImPyHp
16 8 ) 5 A GC C W- 3 ' PyImPyPy-y- ImImPyHp
'
-W
169) 5' A CT T W-3' PyPyHpHp-y-PyPyImHp
-W
170) 5' A CT A W-3' PyPyHpPy-y-HpPyImHp
-W
171) 5' A CT G W-3' PyPyHpIm-y-PyPyImHp
-W
172) 5'-W A CT C W-3' PyPyHpPy-y-ImPyImHp
173 ) 5' A CA T W-3 ' PyPyPyHp-y-PyHpImHp
-W
174) 5' A CA A W-3' PyPyPyPy-y-HpHpImHp
-W
175) 5' A CA G W-3' PyPyPyIm-y-PyHpImHp
-W
176) 5'-W A CA C W-3' PyPyPyPy-y-ImHpImHp
177) 5' A CG T W-3' PyPyImHp-y-PyPyImHp
-W
178) 5' A CG A W-3' PyPyImPy-y-HpPyImHp
-W
179) 5' A CC T W-3' PyPyPyHp-y-PyImImHp
-W
180) 5'-W A CC A W-3' PyPyPyPy-y-HpImImHp
181) 5' A CG G W-3' PyPyImIm-y-PyPyImHp
-W
182) 5'-W A CG C W-3' PyPyImPy-y-ImPyImHp
183) 5' A CC G W-3' PyPyPyIm-y-PyImImHp
-W
184) 5'-W A CC C W-3' PyPyPyPy-y-ImImImHp
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-29-
'FABLE
10:
8-ring
-Hairpin
Polyamides
for
recogmhon
of
6-by
5'-WCWNNW-3'
DNA aromatic amino acid sequence
sequence
185) 5'-W CT T T W-3' PyHpHpHp-y-Pypypylm
186} 5'-W CT T A W-3' PyHpHpPy-y-HpPypyIm
187) 5'-W CT T G W-3' PyHpHpIm-y-PyPyPyIm
18 8 ) 5 ' CT T C W- 3 ' PyHpHpPy-y- ImPyPyIm
-W
189) 5' CT A T W-3' PyHpPyHp-y-PyHpPyIm
-W
190) 5' CT A A W-3' pyHppypy-y-HpHpPyIm
-W
191) 5' CT A G W-3' PyHpPyIm-y-pyHpPyIm
-W
192} 5' CT A C W-3' PyHpPyPy-y-ImHpPyIm
-W
193) 5'-W CT G T W-3' PyHpImHp-y-pypypylm
194) 5'-W CT G A W-3' PYHpImPy-y-HpPyPyIm
195) 5' CT G G W-3' PYHpImIm-y-Pypypylm
-W
196) 5' CT G C W-3' PyHpImPy-y-ImPyPyIm
-W
197) 5'-W CT C T W-3' PyHpPyHp-y-PyImPyIm
198) 5' CT C A W-3' PyHpPyPy-y-HpImPyIm
-W
199) 5'-W CT C G W-3' PyHpPyIm-y-pyImPyIm
200) 5'-W CT C C W-3' PyHpPyPy-y-ImImPyIm
201) 5' CA T T W-3' PyPyHpHp-y-PypyHpIm
-W
202) 5'-W CA T A W-3' PyPyHpPy-y-HpPyHpIm
203} 5'-W CA T G W-3' PyPyHpIm-y-PypyHplm
204) 5'-W CA T C W-3'
PYPYHpPY-Y-ImPyHpIm
205) 5' CA A T W-3' PyPyPyHp-y-PyHpHpIm
-W
206) 5'-W CA A A W-3' Pypypypy-y-HpHpHpIm
207) 5'-W CA A G W-3' PyPyPyIm-y-PYHpHpIm
208) 5' CA A C W-3' PyPypypy-y-ImHpHpIm
-W
209) 5'-W CA G T W-3' PyPyImHp-y-PypyHplm
210) 5' CA G A W-3' PyPyImPy-y-HpPyHpIm
-W
211) 5' CA G G W-3' PyPyImIm-y-PyPyHpIm
-W
212) 5'-W CA G C W-3' PyPyImPy-y-ImPyHpIm
213) 5'-W CA C T W-3' PyPyPyHp-y-pyImHpIm
214) 5' CA C A W-3' Pypypypy-y-HpImHpIm
-W
215) 5' CA C G W-3' PyPypylm-y-PyImHpIm
-W
216) 5' CA C C W-3' pypypypy-y-ImImHpIm
-W
CA 02281930 1999-08-18
WO 981370b7 PCT/US98/01714
-30-
TABLE
11:
8-ring
Hairpin
Polyamides
for
recognition
of
6-by
5'-WCSNNW-3'
DNA aromatic amino acid sequence
sequence
217) 5'-WC G T T W-3' PyImHpHp-y-PyPyPyIm
218) 5'-W~C G T A W-3' PyImHpPy-y-HpPyPyIm
219) 5'-WC G T G W-3' PyImHpIm-y-PyPyPyIm
220) 5'-WC G T C W-3' PyImHpPy-y-ImPyPyIm
221) 5'-WC G A T W-3' PyImPyHp-y-PyHpPyIm
222) 5'-WC G A A W-3' PyImPyPy-y-HpHpPyIm
223) 5'-WC G A G W-3' PyImPyIm-y-PyHpPyIm
224) 5'-WC G A C W-3' PyImPyPy-y-ImHpPyIm
225) 5' C G G T W-3' PyImImHp-y-PyPyPyIm
-W
226) 5'-WC G G A W-3' PyImImPy-y-HpPyPyIm
227) 5'-WC G C T W-3' PyImPyHp-y-PyImPyIm
228) 5' C G C A W-3' PyImPyPy-y-HpImPyIm
-W
229) 5'-WC C T T W-3' PyPyHpHp-y-PyPyImIm
230) 5' C C T A W-3' PyPyHpPy-y-HpPyImIm
-W
231) 5' C C T G W-3' PyPyHpIm-y-PyPyImIm
-W
232) 5' C C T C W-3' PyPyHpPy-y-ImPyImIm
-W
233) 5'-WC C A T W-3' PyPyPyHp-y-PyHpImIm
234) 5'-WC C A A W-3' PyPyPyPy-y-HpHpImIm
235) 5' C C A G W-3' PyPyPyIm-y-PyHpImIm
-W
236) 5'-WC C A C W-3' PyPyPyPy-y-ImHpImIm
237) 5'-WC C G T W-3' PyPyImFip-y-PyPyImIm
238) 5' C C G A W-3' PyPyImPy-y-HpPyImIm
-W
239) 5'-WC C C T W-3' PyPyPyHp-y-PyImImIm
240) 5' C C C A W-3' PyPyPyPy-y-HpImImIm
-W
G9) 5'-WC G G G W-3' PyImImIm-y-PyPyPyIm
G10) 5' C G G C W-3' PyImImPy-y-ImPyPyIm
-W
G11) 5' C G C G W-3' PyImPyIm-y-PyImPyIm
-W
G12) 5'-WC G C C W-3' PyImPyPy-y-ImImPyIm
G13) 5'-WC C G G W-3' PyPyImIm-y-PyPyImIm
G14) 5' C C G C W-3' PyPyImPy-y-ImPyImIm
-W
G15) 5'-WC C C G W-3' PyPyPyIm-y-PyImImIm
G16) 5' C C C C W-3' PyPyPyPy-y-ImImImIm
-W
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-31-
TABLE 12:
8-ring
Hairpin
Polyamides
for
recognition
of
6-by
S'-WGWNNW-3'
with included.
(3-substitutions
DNA aromatic amino acid sequence
sequence
3~i) 5' GT TG W-3' ImHp-~i-Im-y-Pypypypy
-W
S 7~3) 5'-W GT AG W-3' ImHp-~3-Im-y-PyHppyPy
9(3) 5' GT GT W-3' Im-~3-ImHp-y-pypypypy
-W
10(3) 5' GT GA W-3' Im-~3-ImPy-y-HpPyPyPy
-W
I1~3} 5' GT GG W-3' Im-~3-ImIm-y-PyPypypy
-W
12(3) 5' GT GC W-3' Im-(3-ImPy-y-ImPyPyPy
-W
15(3) 5' GT CG W-3' ImHp-(3-Im-y-PyImPyPy
-W
19(3) 5' GA TG W-3' ImPy-~3-Im-y-PyPyHpPy
-W
23(3) 5' GA AG W-3' ImPy-~3-Im-y-PyHpHpPy
-W
253) 5' GA GT W-3' Im-p-ImHp-y-PypyHppy
-W
26(3) 5' GA GA W-3' Im-p-ImPy-y-HpPyHpPy
-W
1S 27(3) 5' GA GG W-3' Im-(3-Imlm-y-PyPyHpPy
-W
28~i) 5' GA GC W-3' Im-(3-ImPy-y-ImPyHpPy
-W
31 5'-W GA GG W-3'
R) ImPy-(3- Im-y-pyImHpPy
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-32-
TABLE
13: 8-ring
Hairpin
Polyamides
for recognition
of 6-by
5'-WGSNNW-3'
with
(3-substitutions
inchzded.
DNA aromatic amino acid sequence
sequence
35(3) 5' G G T G W-3' ImIm-(3-Im-y-PyPyPyPy
-W
393) 5' G G A G W-3' ImIm-~-Im-y-PyHpPyPy
-W
45(3) 5' G C T T W-3' ImPyHpHp-y-Py-(3-ImPy
-W
46(3) 5' G C T A W-3' ImPyIipPy-y-Hp-(3-ImPy
-W
47(3) 5' G C T G W-3' ImPyI-IpIm-y-Py-(3-ImPy
-W
47(32) 5' G C T G W-3' ImPy-~3-Im-y-Py-(3-ImPy
-W
48(3) 5' G C T C W-3' ImPyHpPy-y-Im-(3-ImPy
-W
49(3) 5' G C A T W-3' ImPyPyHp-y-Py-(3-ImPy
-W
50(3) 5' G C A A W-3 T ImPyPyPy-y-Hp-(3-ImPy
-W
513) 5'-W G C A G W-3' ImPyPyIm-y-Py-(3-ImPy
5132) 5' G C A G W-3' ImPy-(3-Im-y-Py-(3-ImPy
-W
i5 523) 5' G C A C W-3' ImPyPyPy-y-Im-(3-ImPy
-W
533) 5' G C G T W-3' ImPyImHp-y-Py-(3-ImPy
-W
53~i2) 5' G C G T W-3' Im-~3-ImHp-y-Py-~3-ImPy
-W
543) 5' G C G A W-3' ImPyImPy-y-Hp-R-ImPy
-W
54(32) 5' G C G A W-3' Im-p-ImPy-y-Hp-(3-ImPy
-W
G3 (3) 5' G G C G W-3' Imlm-~3-Im-y-PyImPyPy
-W
G5(3) 5' G C G G W-3' ImPyImIm-y-Py-(3-ImPy
-W
G5~i2) 5' G C G G W-3' Im-(3-ImIm-y-Py-(3-ImPy
-W
G6~) 5' G C G C W-3' ImPyImPy-y-Im-(3-ImPy
-W
G6(32) 5' G C G C W-3' Im-p-ImPy-y-Im-~3-ImPy
-W
G7 (3) 5' G C C G W-3' ImPy-~3-Im-y-PyImImPy
-W
..__r... _ , , ,
CA 02281930 1999-08-18
WO 98/37067
-33-
PCT/US98/01714
TABL>14: 8-ring
Hairpin Polyamides
for recognition
of 6-by 5'-WTWNNW-3'
with (3-substitutions
includ
d
e
DNA quenc e .
se
aromatic amino acid sequence
59(3) 5' TT T G W-3' HpHp-(3-Im-y-pypypypy
-W
633) 5' TT A G W-3' HpHp-~-Im-
-W -p
y
yHppypy
65(3) 5' TT G T W-3' _ _
-W Hp ~ Imp-Y-PYPYPYPY
663) 5' TT G A W-3' Hp-p-ImPy-y-HpPYPyPy
-W
673) 5' TT G G W-3' Hp-(3-ImIm-y-pypypypY
-W
68(3) 5' TT G C W-3'
-W Hp- ~3- ImPy-y- ImPyPyPy
71(3) 5' TT C G W-3' HpHp-(3-Im-y-PyTmPyPy
-W
75(3) 5' TA T G W-3' Hppy_(3-Im-y-pYpyHppy
-W
79(3) 5' TA A G W-3' HpPy-(3-Im-y-pyHpHpPy
-W
81(3) 5' TA G T W-3' Hp-~i-ImHp-y-PypyHpPy
-W
82(3) 5' TA G A W-3' Hp-(3-ImP
-W Y_Y_HPPYHPPY
83(3) 5' TA G G W-3' Hp-J3-ImIm-y-pypygpPy
-W
843) 5'-W TA G C W-3'
Hp-~3- ImPy-y- ImPyHpPy
87(3) 5' TA C G W-3' HpPy-(3-Im-y-PyImHpPy
-W
CA 02281930 1999-08-18
WO 98137067 PCT/US98/01714
-34-
TABLE 15:
8-ring
Hairpin
Polyamides
for recognition
of 6-by
5'-WTSNNW-3'
with (3-substitutions
included.
DNA aromatic amino acid sequence
sequence
913) 5' T G T G W-3' Hplm-~3-Im-y-PyPyPyPy
-W
95(3) 5' T G A G W-3' HpIm-(3-Im-y-PyHpPyPy
-W
103(3) 5' T G C G W-3' HpIm-(3-Im-y-PyImPyPy
-W
105(3) 5' T C T T W-3' HpPyHpHp-y-Py-~-ImPy
-W
106(3) 5' T C T A W-3' HpPyHpPy-y-Hp-(~-ImPy
-W
107(3) 5' T C T G W-3' HpPyHpIm-y-Py-(3-ImPy
-W
107~i2) 5' T C T G W-3' HpPy-(3-Im-y-Py-(3-ImPy
-W
108(3) 5' T C T C W-3' HpPyHpPy-y-Im-(3-ImPy
-W
109(3) 5' T C A T W-3' HpPyPyHp-y-Py-(3-ImPy
-W
110R) 5' T C A A W-3' HpPyPyPy-y-Hp-p-ImPy
-W
111(3} 5' T C A G W-3' HpPyPyIm-y-Py-p-ImPy
-W
111(32) 5' T C A G W-3' HpPy-(3-Im-y-Py-(3-ImPy
-W
1123) 5' T C A C W-3' HpPyPyPy-y-Im-(3-ImPy
-W
113(3) 5' T C G T W-3' HpPyImHp-y-Py-~3-ImPy
-W
113(32) 5' T C G T W-3' Hp-(3-ImHp-y-Py-(3-ImPy
-W
114(3) 5' T C G A W-3' HpPyImPy-y-Hp-~3-ImPy
-W
114(32) 5' T C G A W-3' Hp-(3-ImPy-y-Hp-(3-ImPy
-W
1173) 5' T C G G W-3' HpPyImIm-y-Py--ImPy
-W
117(32) 5' T C G G W-3' Hp-(3-Imlm-y-Py-(3-ImPy
-W
118(3) 5' T C G C W-3' HpPyImPy-y-Im-~3-ImPy
-W
118(32) 5' T C G C W-3' Hp-(3-ImPy-y-Im-p-ImPy
-W
119(3) 5' T C C G W-3' HpPy-~-Im-y-PyImImPy
-W
..~................~...... ~ . ~ ~ ,.» ,
CA 02281930 1999-08-18
WO 98/37067 PCT/US98101714
-35-
'TABLE 16: 8-ring
Hairpin Polyamides
for recognition
of 6-by 5'-WAWNNW-3'
with (3-substitutions
included.
DNA aromatic amino acid sequence
sequence
123(3) 5' A T TG W-3' pygp_~3_Im_y-pypypyHp
-W
127(3) 5' A T AG W-3' PyHp-~3-Im-y-PyHpPyHp
-W
1293) 5' A T GT W-3' Py-(3-ImHp-y-PyPyPyHp
-W
1303) 5' A T GA W-3' Py-~3-ImPy-y-HpPyPyHp
-W
131(3) 5' A T GG W-3' Py-(3-ImIm-y-Pypypygp
-W
132j3) 5' A T GC W-3' p
-W y-p-ImPy-y-ImPyPyHp
1353) 5' A T CG W-3' PyHp-(3-Im-y-PyImPyHp
-W
139~i} 5' A A TG W-3' PyPy-(3-Im-y-PyPyHpHp
-W
143(3) 5' A A AG W-3' PyPy-~3-Im-y-PyHpHpHp
-W
145(3) 5' A A GT W-3' Py-(3-ImHp-y-PypyHpHp
-W
146(3) 5' A A GA W-3' Py-~-ImPy-y-HpPyHpHp
-W
IS 147p) 5' A A GG W-3' Py-(3-Imlm-y-PyPyHpHp
-W
1480 5' A A GC W-3' Py-p-ImPy-y-ImPyHpHp
-W
151(3) 5' A A CG W-3' PyPy-~3-Im-y-PyImHpHp
-W
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
_3~,_
'TABLE
I 7: 8-ring
Hairpin
Polyamides
for recognition
of 6-by
5'-WASNNW-3'
with (3-substitutions
included.
DNA aromatic amino acid sequence
sequence
155(3) 5' A G T G W-3' Pylm-(3-Im-y-PyPyPyHp
-W
159(3) 5' A G A G W-3' PyIm-(3-Im-y-PyHpPyHp
-W
167~i) 5' A G C G W-3' PyIm-~i-Im-y-PyImPyHp
-W
169~i) 5'-W A C T T W-3' PyPyHpHp-y-Py-(3-ImHp
170~i) 5' A C T A W-3' PyPyHpPy-y-Hp-(3-ImHp
-W
1713) 5' A C T G W-3' PyPyHpIm-y-Py-(3-ImHp
-W
171(32) 5' A C T G W-3' PyPy-p-Im-y-Py-(3-ImHp
-W
172(3) 5' A C T C W-3' PyPyHpPy-y-Im-(3-ImF3p
-W
173(3) 5' A C A T W-3' PyPyPyHp-y-Py-(3-ImHp
-W
1743) 5' A C A A W-3' PyPyPyPy-y-Hp-R-ImHp
-W
1753) 5' A C A G W-3' PyPyPyIm-y-Py-~3-ImHp
-W
17532) 5' A C A G W-3' Pypy-(3-Im-y-Py-(3-ImHp
-W
176(3) 5' A C A C W-3' PyPypyPy-y-Im-(3-ImHp
-W
1770 5' A C G T W-3' PyPyImHp-y-Py-(3-ImHp
-W
177(32) 5' A C G T W-3' Py-(3-ImHp-y-Py-(3-ImHp
-W
178(3) 5' A C G A W-3' PyPyImPy-y-Hp-(3-ImHp
-W
178(32) 5' A C G A W-3' Py-(3-ImPy-y-Hp-/3-ImHp
-W
1813) 5' A C G G W-3' PyPyImIm-y-Py-(3-ImHp
-W
181(32) 5' A C G G W-3' py-(3-Imlm-y-Py-(3-ImHp
-W
182(3) 5' A C G C W-3' PyPyImPy-y-Im-R-ImHp
-W
182(32) 5' A C G C W-3' Py-(3-ImPy-y-Im-(3-ImHp
-W
18332) 5' A C C G W-3' Pypy-~i-Im-y-PyImImHp
-W
~... . .
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-37-
I AI3LP;
I 8: 8-ring
Hairpin
Polyamides
for recognition
of 6-by
5'-WCWNNW-3'
with (3-substitutions
included.
DNA aromatic amino acid sequence
sequence
185(3) 5' C T T TW-3' PyHpHpHp-y-Pypy-(3-Im
-W
186(3) 5''-WC T T AW-3' PyHpHpPy-y-HpPy-(3-Im
1873) 5' C T T GW-3' PyHpHpIm-y-Pypy-(3-Im
-W
187(32) 5' C T T GW-3' p H
-W Y P-~-Im-y-PyPy-(3-Im
188(3) 5' C T T CW-3' pyHpHpPy-y-ImPy-(3-Im
-W
189(3) 5' C T A TW-3' PyHpPyHp-y-PyHp-(3-Im
-W
1903) 5' C T A AW-3' PyHpPyPy-y-HpHp-~i-Im
-W
191(3) 5' C T A GW-3' PyHpPyim-y-PyHp-/3-Im
-W
191(32) 5' C T A GW-3' PyHp-(3-Im-y-PyHp-~3-Im
-W
192(3) 5' C T A CW-3' PyHpPyPy-y-ImHp-J3-Im
-W
193(3) 5' C T G TW-3' PyHpImHp-y-PyPy-~3-Im
-W
1932) 5' C T G TW-3' Py-~i-ImHp-y-Pypy-(3-Im
-W
194(3) 5' C T G AW-3' PyHpImPy-y-HpPy-(3-Im
-W
194(32) 5' C T G AW-3' Py--ImPy-y-HpPy-(3-Im
-W
195p) 5' C T G GW-3' PyHpImIm-y-Pypy-~3-Im
-W
1952) 5' C T G GW-3' Py-(3-ImIm-y-PyPy-~-Im
-W
196(3) 5' C T G CW-3' PyHpImPy-y-ImPy-(3-Im
-W
196(32) 5' C T G CW-3' Py-p-ImPy-y-ImPy-(3-Im
-W
197(3) 5' C T C TW-3' PyHpPyHp-y-PyIm-(3-Im
-W
198(3) 5' C T C AW-3' PyHpPyPy-y-HpIm-(3-Im
-W
199(3) 5' C T C GW-3' PyHpPyIm-y-PyIm-(3-Im
-W
19932) 5' C T C GW-3' PyHp-(3-Im-y-Pylm-p-Im
-W
200(3) 5' C T C CW-3' PyHpPyPy-y-ImIm-(3-Im
-W
201(3) 5' C A T TW-3' PyPyHpHp-y-PyPy-~3-Im
-W
202(3) 5' C A T AW-3' PyPyHpPy-y-HpPy-~3-Im
-W
203~i) 5' C A T GW-3' PyPyHpIm-y-PyPy-~-Im
-W
203~i2) 5' C A T GW-3' p p
-W Y Y-~-Im-y-PyPy-(3-Im
2043) 5' C A T CW-3' PyPyHpPy-y-ImPy-p-Im
-W
205(3) 5' C A A TW-3' PyPyPyHp-y-PyHp-(3-Im
-W
2063) 5' C A A AW-3' PyPypypy-y-HpHp-p-Im
-W
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-3 8-
TABLE 18 (cont}:
8-ring Hairpin
Polyamides
for 6-by 5'-WCWNNW-3'
with (3-substitutions
included.
DNA aromatic amino acid sequence
sequence
207(3) 5' C A A G W-3' PypyPyIm-y-PyHp-(3-Im
-W
207(32) 5' C A A G W-3' PyPy-(3-Im-y-PyHp-(3-Tm
-W
2083) 5' C A A C W-3' PyPypyPy-y-ImHp-(3-Im
-W
209(3) 5' C A G T W-3' PypyImHp-y-PyPy-~-Im
-W
209(32) 5' C A G T W-3' Py-p-ImHp-y-PyPy-(3-Im
-W
210(3) 5' C A G A W-3' PyPyImPy-y-HpPy-p-Im
-W
210(32) 5' C A G A W-3' Py-p-ImPy-y-HpPy-p-Im
-W
211(3) 5' C A G G W-3' PyPyImIm-y-Pypy-(3-Im
-W
211(32) 5' C A G G W-3' Py-(3-Imlm-y-PyPy-R-Im
-W
212(3) 5' C A G C W-3' PyPyImPy-y-ImPy-(3-Im
-W
21232) 5' C A G C W-3' Py-[3-ImPy-y-ImPy-(3-Im
-W
213(3) 5' C A C T W-3' PyPyPyHp-y-Pylm-R-Im
-W
2143) 5' C A C A W-3' PyPyPyPy-y-HpIm-p-Im
-W
2153) 5' C A C G W-3' PyPyPyIm-y-PyIm-~3-Im
-W
215(32) 5' C A C G W-3' PyPy-(3-Im-y-PyIm-~-Im
-W
216(3) 5' C A C C W-3' PyPyPyPy-y-ImIm-~i-Im
-W
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-39-
1A13Lt:
ly: ~-nng
Hairpin
Polyamides
for recognition
of 6-by
5'-WCSNNW-3'
with ~3-substitutions
included
.
DNA aromatic amino acid sequence
sequence
217(3) 5' CG T T W-3' PyImHpHp-y-PyPy-(3-Im
-W
218(3) 5' CG T A W-3' PyImHpPy-y-HpPy-~-Im
-W
219(3) 5' CG T G W-3' PyImHpIm-y-Pypy-(3-Im
-W
219(32) 5' CG T G W-3' Pylm-p-Im-y-PyPy-~i-Im
-W
220(3) 5' CG T C W-3' PyImHpPy-y-ImPy-(3-Im
-W
2210 5' CG A T W-3' PyImPyHp-y-PyHp-~3-Im
-W
222(3) 5' CG A A W-3' PyImPYPy-y-HpHp-~3-Im
-W
223(3) 5' CG A G W-3' PyImPyIm-y-PyHp-p-Im
-W
2232) 5' CG A G W-3' PyIm-~3-Im-y-PyHp-~i-Im
-W
224(3) 5' CG A C W-3' PyImPyPy-y-ImHp-~-Im
-W
2253) 5' CG G T W-3' PyImImHp-Y-Pypy-~3-Im
-W
226(3) 5' CG G A W-3' PyImImPy-Y-HpPy-J3-Im
-W
227(3) 5' CG C T W-3' PyImPyHp-y-PyIm-~3-Im
-W
228(3) 5' CG C A W-3' PyImPyPy-y-HpIm-(3-Im
-W
2293) 5' CC T T W-3' PyPyHpHp-y-Py-(3-ImIm
-W
2303) 5' CC T A W-3' PyPyHpPy-y-Hp-p-ImIm
-W
2313) 5' CC T G W-3' PyPyHpIm-y-Py-~3-ImIm
-W
231(32) 5' CC T G W-3' p p ~~
-W Y Y-t'-Im-y-Py-~3-ImIm
232(3) 5' CC T C W-3' PyPyHpPy-y-Im-~3-ImIm
-W
2333) 5' CC A T W-3' PyPyPyHp-y-Py-(3-ImIm
-W
234(3) 5' CC A A W-3' PyPypypy-y-Hp-R-ImIm
-W
235~i) 5' CC A G W-3' PyPyPyIm-y-Py-p-Imlm
-W
235(32) 5' CC A G W-3' p 'p
-W Y Y-~-Im-y-Py-~3-Imlm
236(3) 5' CC A C W-3' PyPyPyPy-y-Im-~3-ImIm
-W
2370 5' CC G T W-3' PyPyImHp-y-Py-p-ImIm
-W
2372) 5' CC G T W-3' Py-(3-ImHp-Y-Py-~-Imlm
-W
2383) 5' CC G A W-3' PyPyImPy-y-Hp-(3-ImIm
-W
238(32) 5' CC G A W-3' Py-~3-ImPy-y-Hp-~3-ImIm
-W
G9~3) 5' CG G G W-3' PyImImIm-y-pypy-~3-Im
-W
G10(3) 5' CG G C W-3' PyImImPy-Y-ImPy-(3-Im
-W
CA 02281930 1999-08-18
WO 98/37067 PCTIUS98/01714
-40-
TABLE 19 (cont): 8-ring Hairpin Poiyamides for recognition of 6-by 5'-WCSNNW-
3' with (3-substitutions -
included.
DNA sequence aromatic amino acid sequence
611(3) 5' -W C G C G W-3' PyImPyIm-y-PyIm-~3-Im
611(32)5' -W C G C G W-3' Pylm-[3-Im-y-Pylm-/3-Im
G12R) 5' -W C G C C W-3' PyImPyPy-'y-ImIm-~3-Im
613(3) 5' -W C C G G W-3' PyPyImIm-y-Py-~3-Imlm
613(32)5' -W C C G G W-3' Py-(3-ImIm-y-Py-~3-ImIm
G14~3) 5' -W C C G C W-3' PyPyImPy-y-Im-(3-ImIm
G14~2)5' -W C C G C W-3' Py-(3-ImPy-y-Im-(3-Imlm
615(3) 5' -W C C C G W-3' PyPy-(3-Im-y-PyImImim
If the process described above of designing a preferred polyamide molecule
X1X2X3X4-
y-XSX6X~Xg comprising eight aromatic aminoacid residues does not produce a
selective
polyamide that binds to the target identified DNA sequence with subnanomolar
affinity and with
a selectivity over mismatch sequences of greater than a factor of ten, a
polyamide molecule
X 1 X2X3X4X5-y-X6X~XgX9X 1 p having five carboxamide binding pairs can be
designed that is
2o selective for a seven base pair identified target 5'-WNI~I~~1NNW-3'
sequence. The design and
synthesis of the five binding pair polyamide is similar to that of the four
binding pair polyamide
X1X2X3X4-y-XSX6X~Xg described above.
The polyamide design process, shown schematically in Figure 7 provides a
method for
designing a ten carboxamide residue molecule comprising five carboxamide
binding pairs for
selective detection and binding of a target seven base pair 5'- -3' sequence
in the
minor groove of double stranded DNA. The design process identifies an
appropriate polyamide
ligand for recognition of a predetermined seven base pair, 5'-VVI'11~TNNNVV-3'
sequence with
subnanomolar affinity and >10-fold specificity versus mismatch sites. Trauger,
J.W., Baird, E.
3o E. Dervan, P.B. describes the recognition of DNA by designed ligands at
subnanomolar
concentrations. Nature 382, 559-561 (/996).
In order to prepare a polyamide molecule specific for an identified seven base
pair
sequence of double stranded DNA, a user starts the 10-ring hairpin design
process that
implements the minor groove recognition pairing code summarized in Table 2
above. In the
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-41-
. design process a 5'-WNNNNNW-3' sequence was identified. In a preferred
embodiment, the
identified sequence was located within a gene promoter. The identified
sequence was then
defined as S'-WabcdeW-3' in a stepwise process wherein a, b, c, d,and e, were
sequentially and
independently defined as A, G, C, or T. The structure of the polyamide
molecule was then
s correspondingly defined by sequentially chosing antiparallel carboxamide
binding pairs
according to the minor groove pairing code summarized in Table 2 above. Thus,
if a was G,
then X 1 was defined as Im, and X 1 p was defined as Py. If a was C, then X 1
was defined as Py,
and X 1 p was defined as Im. If a was T, then X 1 was def ned as Hp, and X I p
was defined as
Py. If a was A, then X 1 was defined as Py, and X 1 p was defined as Hp.
Similarly, b was defined as A, G, C, or T and corresponding carboxamide
binding pairs
were defined. According to the same rules, if b was G, then X2 was defined as
Im, and X9 was
defined as Py. If b was C, then X2 was defined as Py, and X9 was defined as
Im. Likewise, if b
was T, then X~ was defined as Hp, and X9 was defined as Py. If b was A, then
X2 was defined
~ 5 as Py, and X9 was defined as Hp.
The next step was to define c as A, G, C, or T and then define corresponding
carboxamide binding pairs. Following the same rules, if c was G, then X3 was
defined as Im,
and Xg was defined as Py. If c was C, then X3 was defned as Py, and Xg was
defined as Im.
Similarly, if c was T, then X3 was defined as Hp, and Xg was defined as Py. If
c was A, then
X3 was defined as Py, and Xg was defined as Hp. Similarly, d was defined as A,
G, C, or T and
the corresponding carboxamide binding pair was defined. According to the above
rules, if d was
G, then X4 was defined as Im, and X~ was defined as Py. If d was C, then X4
was defined as
Py, and X~ was defined as Im. If d was T, then X4 was defined as Hp, and X~
was defined as
25 Py. If d was A, then X4 was defined as Py, and X~ was defined as Hp.
Finally, a was defined as
- A, G, C, or T and the corresponding carboxamide binding pair was defined.
According to the
above rules, if a was G, then XS was defined as Im, and X6 was defined as Py.
If a was C, then
XS was defined as Py, and X6 was defined as Im. If a was T, then XS was
defined as Hp, and
X6 was defined as Py. If a was A, then XS was defined as Py, and X6 was
defined as Hp.
With all ten carboxamide residues that participate in the binding pairs now
defined, the
designed polyamide X1X2X3X4X5-y-X6X~XgX9Xlp suitable for binding to the
identified
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-42-
sequence was synthesized using known techniques. Baird, E. E. & Dervan, P. B.
describes~the
solid phase synthesis of polyamides containing imidazole and pyrrole amino
acids: J. Am.
Chem. Soc. 118, 6141-6146 (1996); also see PCT US 97/003332.
The binding affinity of the synthesized polyamide to the identified sequence
was
determined using a quantitative DNase footprint titration method for studying
protein-DNA
interactions described by Brenowitz, M., Senear, D. F., Shea, M. A. & Ackers,
G. K., Methods
Enzymol. 130, 132-181 {1986). If the affinity of the synthesized polyamide at
the target site
was not subnanomolar affinity then substituting at least one (3-alanine
residue for a pyrrole or 3-
1o hydroxypyrrole residue was considered in order to optimize the exact
positions of the binding
pairs of aromatic amino acids. If the affinity of the polyamide at the target
site was
subnanomolar affinity then the sequence specificity of the polyamide versus
mismatch
sequences was determined. If the specificity versus mismatch sites was not >
10-fold specificity
then adding a (3-alanine (shown schematically in Figure 8) was considered, in
order to optimize
the positions of the aromatic amino acids in relationship to the base pairs in
the minor groove.
Specificity of the polyamide molecule for the target identified sequence
versus mismatch
sequence sites of greater than 10-fold was considered a successful result of
design process.
The 1024 polyamide molecules comprising five carboxamide binding pairs that
were
2o designed using this method are useful for binding to the 1024 target S'-
NNMVN-3' core
sequences, and are listed in Tables 20-S 1. A corresponding polyamide molecule
was designed
for each DNA sequence (241-1232) and {G17-G48) using the process outlined
above and shown
schematically in Figure 7.
If the synthesized polyamide molecule did not bind to the target identified
sequence with
subnanomolar affinity or if the synthesized polyamide molecule did not exhibit
a specificity for
the target identified sequence versus mismatch sequence sites of greater than
10-fold, the option
of substituting an aliphatic amino acid residue for one of the carboxamide
residues was
considered. The preferred aliphatic amino acid residue is /3-alanine. At least
one aliphatic
3o amino acid residue such as a (3-alanine residue provided some flexibility
to the central portion of
the polyamide molecule, acting as a "spring" to permit optimization of the
hydrogen bonding
between the carboxamide binding pairs and the nucleotide bases of the double
stranded DNA.
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-43-
In general, it was not found to be advantageous to replace either member of
the terminal
carboxamide binding pair, X1/X10, with (3-alanine. Similarly, ~3-alanine was
not substituted for
members of the binding pair, XS/X6, adjacent to the y hairpin residue. (3-
alanine residues were
not substituted for N-mcthylimidazole residues. The use of (3-alanine in place
of a pyrrole or 3-
hydroxypyrrole amino acid residue provides aromatic/aliphatic pairing (Im/~,
~3/Im, Hp/(3, (i/Hp,
Py/(3, and ~3/Py) and aliphatic/aliphatic pairing (~i/(3) substitution.
The method for selecting which pyrrole amino acid to substitute with (3-
alanine is
schematically illustrated in Figure 8. Selective placement of an aliphatic ~-
alanine (~i) residue
to paired with either a pyrrole (Py), 3-hydroxypyrrole (Hp), or imidazole (Im)
aromatic amino acid
or another (3-alanine residue is found to compensate for sequence composition
effects to improve
recognition and binding of the minor groove of DNA by pyrrole-imidazole
polyamides of the
present invention. If an all-ring polyamide has been found to have an affinity
which is not
subnanomolar, or a specificity versus mismatch sequences which is less than 10-
fold it may be
caused by DNA sequence-composition effects which can be reduced by replacement
of an
aromatic amino acid with an aliphatic (3-alanine residue. In a polyamide
molecule that comprises
five binding pairs it is only beneficial to place (3-alanine in positions X2,
X3, X4, X~, Xg, and
X9. No more than two ~3-alanine residues may be placed within a single hairpin
structure. No
more than a single ~3-residue may be placed within each individual polyamide
subunit, e.g., if X2
2o is replaced with (3-alanine, X3 or X4 cannot be replaced as well.
These rules and others were implemented in the method schematically
illustrated in
Figure 8. This process is suitable for the refinement of the design polyamide
comprising five
binding pairs that has been designed by the method illustrated in Figure 7,
but which lacks
subnanomolar affinity or greater than 10-fold specificity at the identified
target DNA sequence.
As in the basic design method, the designed polyamides are synthesized and the
affinity and
specificity of binding to the target DNA were determined.
As discussed above, for a given 10-ring polyamide molecule there are six
possible
outcomes for the process of substituting a ~3-alanine residue for an aromatic
amino acid residue.
First, there may be no position at which it is possible to add a (3-alanine
residue; in such case, a
better binding affinity or selectivity can be sought in the design and
synthesis of a polyamide
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-44-
with four or six carboxamide binding pairs, described below. Second, the
process may result in
a derivative which contains a single (3-alanine substitution (such derivatives
are numbered
according to the parent numbering scheme such that a single (3-derivative of
compound 5 would
be called 5[3), which is sufficient to produce subnanomolar binding affinity
and >10-fold
specificity, and at which point the process is deemed complete.
Third, the process of Figure 8 may result in a polyamide which contains a
single j3-
alanine substitution which is not sufficient to produce subnanomolar binding
affinity and >IO-
fold specificity, but where there are no additional positions in which it is
possible to substitute a
~3-alanine residue, and in such a case a paired (3-alanine residue should be
added as described in
Figure 9 and text below. Fourth, the process of Figure 7 may result in a
polyamide that contains
a single ~3-alanine substitution that is not sufficient to produce
subnanomolar binding affinity
and >10-fold specificity, but where there is an additional position for ~3-
alanine substitution that
does produce a polyamide with the criterion level of affinity and selectivity.
Tables 52-83 list
polyamide compounds 241(3-12323 and G17~3 -G48~, corresponding to DNA
sequences 241-
1232 and G17 - G48, that contain one or two (3-alanine residues.
A fifth possibility is that substitution at a second position by the method
illustrated in
Figure 9 with a paired ~3-alanine residue is not sufficient to produce a
polyamide having the
2o subnanomolar binding affinity and >10-fold specificity, and a polyamide
with four or six
carboxamide binding pairs, should be designed and synthesized, as described
below. Finally, the
design process may result in a polyamide that has a paired (3-alanine
substitution that is
sufficient to produce subnanomolar binding affinity and >10-fold specificity,
and therefore the.
design process is deemed complete. Tables 52-83 list polyamide compounds 241
(3-1232(3 and
G17~3 -G48~3, corresponding to DNA sequences 241-1232 and G17 - G48, that
contain one or
two (3-alanine residues. In addition, Tables 52-83 list polyamides
corresponding to sequences
(241-1232) and (G17-G48) labeled (241(3p-1232(3p) and (G17(3p-G48(3p) that
contain paired ~3/~
residues added by the process described in Figure 9.
CA 02281930 1999-08-18
WO 98/37067 PCT/IJS98/01714
-45-
TABLE 20:10-ring
Hairpin
Polyamides
for
recognition
of
7-by
5'-WGGWNNW-3'
DNA aromatic amino acid sequence
sequence
241) 5'-W G GT T T W-3' ImImHpHpHp-y-PyPypypypy
S 242) 5'-W G GT T A W-3' ImImHpHpPy-y-HpPypypypy
243} 5'-W G GT T G W-3' ImImHpHpIm-y-PyPyPyPyPy
244) 5'-W G GT T C W-3' ImImHpHpPy-y-ImPyPyPypy
245) 5'-W G GT A T W-3' ImImHpPyHp-y-PyHpPyPyPy
246) 5'-W G GT A A W-3' ImImHpPyPy-y-HpHpPyPyPy
247} 5'-W G GT A G W-3' ImImHpPyIm-y-PyHpPyPyPy
248) 5'-W G GT A C W-3' ImImHpPyPy-y-ImHpPyPyPy
249) 5'-W G GT G T W-3' ImImHpImHp-y-PyPyPypypy
250) 5'-W G GT G A W-3' ImImHpImPy-y-HpPyPyPyPy
251) 5'-W G GT G G W-3' ImImHpImIm-y-pypypypypy
252) 5'-W G GT G C W-3' ImImHpImPy-y-ImPypyPypy
253) 5'-W G GT C T W-3' ImImHpPyHp-y-pyImPyPyPy
254) 5'-W G GT C A W-3' ImImHpPyPy-y-HpImPyPyPy
255) 5'-W G GT C G W-3' ImImHpPyIm-y-PyImPyPyPy
256) 5'-W G GT C C W-3' ImImHpPyPy-y-ImImPyPyPy
257) 5'-W G GA T T W-3' ImImPyHpHp-y-PyPyHpPyPy
258) 5'-W G GA T A W-3' ImImPyHpPy-y-HpPyHpPyPy
259) 5'-W G GA T G W-3' ImImPyHpIm-y-PyPyHpPyPy
260) 5'-W G GA T C W-3' ImImPyHpPy-y-ImPyHpPyPy
261) 5'-W G GA A T W-3' ImImPyPyHp-y-PyHpHpPyPy
262) 5'-W G GA A A W-3' ImImPyPyPy-y-HpHpHpPyPy
263) 5'-W G GA A G W-3' ImZmPyPyIm-y-PyHpHpPyPy
264) 5'-W G GA A C W-3' ImImPyPyPy-y-ImHpHpPyPy
265) 5'-W G GA G T W-3' ImImPyImHp-y-PyPyHpPyPy
266) 5'-W G GA G A W-3' ImImPyimPy-y-HpPyHpPyPy
267) 5'-W G GA G G W-3' ImImPyImIm-y-PyPyHpPyPy
268) 5'-W G GA G C W-3' ImImPyImPy-y-ImPyHpPyPy
269) 5'-W G GA C T W-3' ImImPyPyHp-y-PyImHpPyPy
270) 5'-W G GA C A W-3' ImImPyPyPy-y-HpImHpPyPy
271) 5'-W G GA C G W-3' ImImPyPyIm-y-PyImHpPyPy
272) 5'-W G GA C C W-3' ImImPyPyPy-y-ImImHpPyPy
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-46-
TABLE
21:
10-ring
Hairpin
Polyamides
for
recognition
of
7-by
5'-WGGSNNW-3'
DNA aromatic amino acid sequence
sequence
273) 5' G GG T T W-3' ImImImHpHp-y-PyPyPyPyPy
-W
274) 5' G GG T A W-3' ImImImHpPy-y-HppyPyPyPy
~W
275) 5' G GG T G W-3' ImImImHpIm-y-PyPyPyPyPy
-W
276) 5' G GG T C W-3' ImImImHpPy-y-ImPyPyPyPy
-W
277 ) 5' G GG A T W-3' ImImImPyHp-y-PyHpPyPyPy
-W
278) 5' G GG A A W-3' ImImImPyPy-y-HpHpPypyPy
-W
279) 5' G GG A G W-3' ImImImPyIm-y-PyHppyPyPy
-W
2 8 0 5 ' G GG A C W- 3 ImImImPyPy-y- ImHpPyPypy
) -W '
281) 5' G GG G T W-3' ImImImImHp-y-PyPyPyPyPy
-W
282) 5' G GG G A W-3' ImImImImPy-y-HpPyPyPyPy
-W
283) 5' G GG C T W-3' ImImImPyHp-y-PyImPyPyPy
-W
284) 5' G GG C A W-3' ImImImPypy-y-HpImPyPyPy
-W
285) 5' G GC T T W-3' ImImPyHpHp-y-PyPyImPyPy
-W
286) 5' G GC T A W-3' ImImPyHpPy-y-HpPyImPyPy
-W
287) 5' G GC T G W-3' ImImPyHpIm-y-PyPyImPyPy
-W
288) 5' G GC T C W-3' ImImPyHpPy-y-ImPyImPyPy
-W
289) 5' G GC A T W-3' ImImPyPyHp-y-PyHpImPyPy
-W
290) 5' G GC A A W-3' ImImPyPyPy-y-HpHpImPyPy
-W
291) 5' G GC A G W-3' ImImPyPyIm-y-PyHpImPyPy
-W
292) 5' G GC A C W-3' ImImPyPyPy-y-ImHpImPyPy
-W
293) 5' G GC G T W-3' ImImpyImHp-y-PyPyImPyPy
-W
294) 5' G GC G A W-3' ImImPyImPy-y-HpPyImPyPy
-W
295) 5' G GC C T W-3' ImImPyPyHp-y-PyImImPyPy
-W
296) 5' G GC C A W-3' ImImPyPyPy-y-HpImImPyPy
-W
G17 ) 5' G GG G G W-3 ' ImImImImIm-y-PyPyPyPyPy
-W
G18) 5' G GG G C W-3' ImImImImPy-y-ImPypyPypy
-W
Gl9) 5' G GG C G W-3' ImImImPyIm-y-PyImPyPyPy
-W
G20) 5' G GG C C W-3' ImImImPypy-y-ImImPyPyPy
-W
G21) 5' G GC G G W-3' ImImPyImIm-y-PyPyImPyPy
-W
G22) 5' G GC G C W-3' ImImPyImPy-y-ImPyImPyPy
-W
G23) 5' G GC C G W-3' ImImPyPyIm-y-PyImImPyPy
-W
G24) 5'-W G GC C C W-3' ImImPyPyPy-y-ImImImPypy
CA 02281930 1999-08-18
WO 98/37067 PCT/US98101714
-47-
'/'ABLE
22:
10-ring
Hairpin
Polyamides
for
recognition
of
?-by
5'-WGTWNNW-3'
DNA aromatic amino acid sequence
sequence
297) 5'-W GT T T T W-3' ImHpHpHpHp-y-pypypypypY
298) 5'-W GT T T A W-3' ImHpHpHpPy-y-HpPyPyPyPy
299) 5'-W GT T T G W-3' ImHpHpHpIm-y-pypypypypY
300) 5'-W GT T T C W-3' ImHpHpHpPy-y-ImPYPyPyPy
301) 5'-W GT T A T W-3' ImHpHpPyHp-y-pyHpPyPYPy
302) 5'-W GT T A A W-3' ImHpHpPyPy-y-HpHpPYPyPy
303) 5'-W GT T A G W-3' ImHpHpPyIm-y-PyHpPyPyPy
304) 5'-W GT T A C W-3' ImHpHpPyPy-y-ImHpPyPYPy
305) 5'-W GT T G T W-3' ImHpHpImHp-y-PyPYPyPYPy
3 0 6 5 ' GT T G A W- 3 ImHpHp ImPy-y-HpPyPyPyPy
) -W '
307) 5'-W GT T G G W-3' ImHpHpImIm-y-PyPyPypypy
308) 5'-W GT T G C W-3' ImHpHpImPy-y-ImPyPyPyPy
309) 5'-W GT T C T W-3' ImHpHpPyHp-y-PyImPYPYPy
310) 5'-W GT T C A W-3' ImHpHpPyPy-y-HpImPyPyPy
311) 5' GT T C G W-3' ImHpHpPyim-y-PyImPYPYPy
-W
312 ) 5 ' GT T C C W- 3 ImHpHpPyPy-y- ImImPyPyPy
-W '
313) 5' GT A T T W-3' ImHpPyHpHp-y-PyPyHpPyPy
-W
3 14) 5'-W GT A T A W-3' ImHpPyHpPy-y-HpPyHpPyPy
315) 5' GT A T G W-3' ImHppyHpIm-y-PyPyHpPyPy
-W
316) 5' GT A T C W-3' ImHpPyHpPy-y-ImPyHpPyPy
-W
317) 5' GT A A T W-3' ImHpPyPyHp-y-PyHpHpPyPy
-W
318) 5' GT A A A W-3' ImHpPyPypy-y-HpHpHpPyPy
-W
319) 5' GT A A G W-3' ImHpPYPyIm-y-PyHpHpPyPy
-W
3 2 0 5 ' GT A A C W- 3 ImHpPyPyPy-y- ImHpHpPyPy
) -W '
321) 5' GT A G T W-3' I,~ppYl~p_y_pypyHppypY
-W
322) 5' GT A G A W-3' ImHpPyImPy-y-HpPyHpPyPy
-W
323) 5'-W GT A G G W-3' ImHpPyImIm-y-PypyHpPyPy
324 ) 5 ' GT A G C W-3 ' ImHpPyImPy-y- ImPyHpPyPy
-W
325) 5' GT A C T W-3' ImHpPyPyHp-y-PyImHpPYPy
-W
326) 5' GT A C A W-3' ImHpPyPYPy-y-HpImHpPyPy
-W
327) 5' GT A C G W-3' ImHpPyPYIm-y-PyImHpPyPy
-W
328) 5' GT A C C W-3' ImApPyPyPy-y-ImImHpPyPy
-W
CA 02281930 1999-08-18
WO 98137067 PCT/US98/01714
-48-
TABLE
23:
10-ring
Hairpin
Polyamides
for
recognition
of
7-by
5'-WGTSNNW-3'
DIVA aromatic amino acid sequence
sequence
329) 5' G T G T T W-3' ImHpImHpHp-y-PyPyPyPyPy
-W
330) 5' G T G T A W-3' ImHpImHpPy-y-HpPyPyPyPy
-W
331) 5' G T G T G W-3' ImHpImHpIm-y-PyPyPyPyPy
-W
332) 5'-W G T G T C W-3' ImHpImHpPy-y-ImPyPyPyPy
333) 5'-W G T G A T W-3' ImHpImPyHp-y-PyHpPyPyPy
334) 5'-W G T G A A W-3' ImHpImPyPy-y-HpHpPyPyPy
335) 5'-W G T G A G W-3' ImHpImPyIm-y-PyHpPyPyPy
336) 5' G T G A C W-3' ImHpImPyPy-y-ImHpPyPyPy
-W
337) 5'-W G T G G T W-3' ImHpImImHp-y-PyPyPyPyPy
338) 5'-W G T G G A W-3' ImHpImImPy-y-HpPyPyPyPy
339) 5'-W G T G C T W-3' ImHpImPyHp-y-PyImPyPyPy
340) 5'-W G T G C A W-3' ImHpImPyPy-y-HpImPyPyPy
341) 5'-W G T G G G W-3' ImHpImImIm-y-PyPyPyPyPy
342) 5' G T G G C W-3' ImHpImImPy-y-ImPyPyPyPy
-W
343) 5'-W G T G C G W-3' ImHpImPyIm-y-PyImPyPyPy
344) 5'-W G T G C C W-3' ImHpImPyPy-y-ImImPyPyPy
345) 5' G T C T T W-3' ImHpPyHpHp-y-PyPyImPyPy
-W
346) 5'-W G T C T A W-3' ImHpPyHpPy-y-HpPyImPyPy
347) 5'-W G T C T G W-3' ImHpPyHpIm-y-PyPyImPyPy
348) 5'-W G T C T C W-3' ImHpPyHpPy-y-ImPyImPyPy
349) 5'-W G T C A T W-3' ImHpPyPyHp-y-PyHpImPyPy
350) 5' G T C A A W-3' ImHpPyPyPy-y-HpHpImPyPy
-W
351) 5' G T C A G W-3' ImHpPyPyIm-y-PyHpImPyPy
-W
352) 5'-W G T C A C W-3' ImHpPyPyPy-y-ImHpImPyPy
353) 5'-W G T C G T W-3' ImHpPyImHp-y-PyPyImPyPy
354) 5' G T C G A W-3' ImHpPyImPy-y-HpPyImPyPy
-W
355) 5' G T C C T W-3' ImHpPyPyHp-y-PyImImPyPy
-W
356) 5'-W G T C C A W-3' ImHpPyPyPy-y-HpImImPyPy
357) 5'-W G T C G G W-3' ImHpPyImIm-y-PyPyImPyPy
358) 5'-W G T C G C W-3' ImHpPyImPy-y-ImPyImPyPy
359) 5'-W G T C C G W-3' ImHpPyPyIm-y-PyImImPyPy
3 6 0 5 ' G T C C C W- 3 ImApPyPyPy-y- ImImImPyPy
) -W '
CA 02281930 1999-08-18
WO 98/37067 PCTIUS98/01714
-49-
TABLE
24:
10-ring
Hairpin
Polyamides
for
recognition
of
7-by
5'-WGAWNNW-3'
DNA aromatic amino acid sequence
sequence
361) 5' G A TT T W-3' ImPyHpHpHp-y-PyPyPyHppy
-W
362) 5' G A TT A W-3' ImPyHpHpPy-y-HpPyPyHpPy
-W
363) 5'-W G A TT G W-3' ImPyHpHpIm-y-PyPyPyHpPy
364} 5'-W G A TT C W-3' ImPyHpHpPy-y-ImPyPyHpPy
365) 5' G A TA T W-3' ImPylipPyHp-y-pyHpPyHpPy
-W
366) 5' G A TA A W-3' ImPyHpPyPy-y-HpHpPyHpPy
-W
367) 5'-W G A TA G W-3' ImPyHpPyIm-y-PyHpPyHpPy
368) 5'-W G A TA C W-3' ImPyHpPyPy-y-ImHpPyHpPy
369) 5' G A TG T W-3' ImPyHpImHp-y-PyPypygppy
-W
370) 5' G A TG A W-3' ImPyHpImPy-y-HpPyPyHpPy
-W
371) 5' G A TG G W-3' ImPyHpImIm-y-PyPyPyHpPy
-W
372) 5'-W G A TG C W-3' ImPyHpImPy-y-ImPyPyHpPy
373 ) 5' G A TC T W-3' ImPyHpPyHp-y-PyImPyHpPy
-W
374) 5' G A TC A W-3' ImPyHpPyPy-y-HpImPyHpPy
-W
375) 5' G A TC G W-3' ImPyHpPyIm-y-PyImPyHpPy
-W
37 6 5 ' G A TC C W- 3 ImPyHpPyPy-y- ImImPyHpPy
) -W '
377) 5'-W G A AT T W-3' ImPyPyHpHp-y-PyPyHpHpPy
378) 5' G A AT A W-3' ImPyPyHpPy-y-HpPyHpHpPy
-W
379) 5'-W G A AT G W-3' ImPyPyHpIm-y-PyPyHpHpPy
3 8 0 5 ' G A AT C W- 3 ImPyPyHpPy-y- ImPyHpHpPy
) -W '
3 81 5 ' G A AA T W- 3 ImPyPyPyHp -y- PyHpHpHpPy
) -W '
382) 5'-W G A AA A W-3' ImPyPyPyPy-y-HpHpHpHpPy
3 83 5 ' G A AA G W-3 ' IrriPyPypylm-y-PyHpHpHpPy
) -W
384) 5' G A AA C W-3' ImPyPyPyPy-y-ImllpHpHpPy
-W
385) 5' G A AG T W-3' ImPyPyImHp-y-PyPyHpHpPy
-W
386) 5'-W G A AG A W-3' ImPyPyImpy-y-HpPyHpHpPy
387) 5'-W G A AG G W-3' ImPyPyImIm-y-PyPyHpHpPy
388) 5' G A AG C W-3' ImPyPyImPy-y-ImPyHpHpPy
-W
389) 5'-W G A AC T W-3' ImPyPyPyHp-y-PyImHpHpPy
390) 5' G A AC A W-3' ImPyPyPypy-y-HpImHpHpPy
-W
391) 5'-W G A AC G W-3' ImPyPypyIm-y-PyImHpHpPy
392) 5' G A AC C W-3' ImPyPyPyPy-y-ImImHpHpPy
-W
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-50-
TABLE
25:
10-ring
Hairpin
Polyamides
for
recognition
of
7-by
5'-WGASNNW-3'
DNA aromatic amino acid sequence
sequence
393) 5'-W G AG T T W-3' ImPyImHpHp-y-PyPyPyHpPy
394) 5'-W G AG T A W-3' ImPyImHpPy-y-HpPyPyHpPy
395) 5'-W G AG T G W-3' ImPyImHpIm-y-PyPyPyHpPy
396) 5'-W G AG T C W-3' ImPyImHpPy-y-ImPyPyHpPy
397) 5'-W G AG A T W-3' imPyImPyHp-y-PyHpPyHpPy
398) 5'-W G AG A A W-3' ImPyImPyPy-y-HpHpPyHpPy
399) 5'-W G AG A G W-3' ImPyImPyIm-y-PyHpPyHpPy
400) 5'-W G AG A C W-3' ImPyImPyPy-y-ImHpPyHpPy
401) 5'-W G AG G T W-3' ImPyImImHp-y-PyPyPyHpPy
402) 5'-W G AG G A W-3' ImPyImImPy-y-HpPyPyHpPy
403) 5'-W G AG C T W-3' ImPyImPyHp-y-PyImPyHpPy
404) 5' G AG C A W-3' ImPyImPyPy-y-HpImPyHpPy
-W
405) 5'-W G AG G G W-3' ImPyImImIm-y-PyPyPyHpPy
406) 5' G AG G C W-3' ImPyImImPy-y-ImPyPyHpPy
-W
407) 5'-W G AG C G W-3' ImPyImPyIm-y-PyImPyHpPy
408) 5'-W G AG C C W-3' ImPyImPyPy-y-ImImPyHpPy
409) 5' G AC T T W-3' ImPyPyHpHp-y-PyPyImHpPy
-W
4 10) 5'-W G AC T A W-3' ImPyPyHpPy-y-HpPyImHpPy
411) 5'-W G AC T G W-3' ImPyPyHpIm-y-PyPyImHpPy
412) 5'-W G AC T C W-3' ImPyPyHpPy-y-ImPyImHpPy
413) 5' G AC A T W-3' ImPyPyPyHp-y-PyHpImHpPy
-W
414) 5'-W G AC A A W-3' ImPyPyPyPy-y-HpHpImHpPy
415) 5'-W G AC A G W-3' ImPyPyPyIm-y-PyHpImHpPy
416) 5'-W G AC A C W-3' ImPyPyPyPy-y-ImHpImHpPy
417) 5'-W G AC G T W-3' ImPyPyImAp-y-PyPyImHpPy
418) 5'-W G AC G A W-3' ImPyPyImPy-y-HpPyImHpPy
419) 5'-W G AC C T W-3' ImPyPyPyHp-y-PyImImHpPy
420) 5' G AC C A W-3' ImPyPyPyPy-y-HpimImHpPy
-W
421) 5' G AC G G W-3' ImPyPyImIm-y-PyPyImHpPy
-W
422) 5'-W G AC G C W-3' ImPyPyImPy-y-ImPyImHpPy
423) 5'-W G AC C G W-3' ImPyPyPyIm-y-PyImImHpPy
424) 5'-W G AC C C W-3' ImPyPyPyPy-y-ImImImHpPy
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-51-
TABLE
26:
10-ring
Hairpin
Poiyamides
for
recognition
of
7-by
5'-WGCWNNW-3'
DNA aromatic amino acid sequence
sequence
425) 5'-W G CT T T W-3' ImPyHpHpHp-y-PyPyPyImpy
S 426) 5'-W G CT T A W-3' ImPyHpHpPy-y-HpPyPyImPy
427) 5'-W G CT T G W-3' ImPyHpHpIm-y-PyPyPyImPy
428) 5' -W G CT T C W-3' ImPyHpHpPy-y-ImPyPyImPy
429) 5'-W G CT A T W-3' ImPyHpPyHp-y-PyHpPyImPy
430) 5'-W G CT A A W-3' ImPyHpPyPy-y-HpHpPyImPy
431) 5' -W G CT A G W-3' ImPyHpPyIm-y-PyHpPyImPy
432) 5' -W G CT A C W-3' ImPyHpPyPy-y-ImHpPyImPy
433) 5' -W G CT G T W-3' ImPyHpImHp-y-PyPyPyImpy
434) 5'-W G CT G A W-3' ImPyHpImPy-y-HpPyPyImPy
435) 5'-W G CT G G W-3' ImPyHpImIm-y-PyPyPyImPy
436) 5'-W G CT G C W-3' ImPyHpImpy-y-ImPyPyImPy
437) 5' -W G CT C T W-3' ImPyHpPyHp-y-PyImPyImPy
438) 5' -W G CT C A W-3' ImPyHpPyPy-y-HpImPyImPy
439) 5' -W G CT C G W-3' ImPyHpPyIm-y-PyImPyImPy
440) 5' -W G CT C C W-3' ImPyHpPyPy-y-ImImPyImPy
441) 5' -W G CA T T W-3' ImPyPyHpHp-y-PyPyHpImPy
442) 5'-W G CA T A W-3' ImPyPyHpPy-y-HpPyHpImPy
443 ) 5' -W G CA T G W-3' ImPyPyHpIm-y-PyPyHpImPy
444) 5'-W G CA T C W-3' ImPyPyHpPy-y-ImPyHpImPy
445) 5' -W G CA A T W-3' ImPyPyPyHp-y-PyApHpImPy
446) 5'-W G CA A A W-3' ImPyPyPyPy-y-HpHpHpImPy
447) 5'-W G CA A G W-3' ImpyPyPyIm-y-PyHpHpImPy
4 4 8 5 ' G CA A C W- 3 ImPyPyPypy-y- ImHpHpImPy
) -W '
449) 5' -W G CA G T W-3' ImPyPyImHp-y-PyPyHpImPy
450) 5' -W G CA G A W-3' ImPyPyImPy-y-HpPyHpImPy
4 51 5 ' G CA G G W- 3 ImPyPyImIm-y-PyPyHpImPy
) -W '
452) 5' -W G CA G C W-3' ImPyPyImPy-y-ImPyFipImPy
453) 5' -W G CA C T W-3' ImPyPyPyHp-y-PyImHpImPy
454) 5'-W G CA C A W-3' ImPyPyPyPy-y-HpImHpImPy
455) 5' -W G CA C G W-3' ImPyPyPyIm-y-PyImHpImPy
456) 5'-W G CA C C W-3' ImPyPyPyPy-y-ImImHpImPy
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-52-
TABLE
27:
10-ring
Hairpin
Polyamides
for
recognition
of
7-by
5'-WGCSNNW-3'
DNA aromatic amino acid sequence
sequence
457) 5'-W G C G T T W-3' ImPyImHpHp-y-PyPyPyImPy
458) 5'-W G C G T A W-3' ImPyImHpPy-y-HpPyPyImPy
459) 5' G C G T G W-3' ImPyImHpIm-y-PyPyPyImPy
-W
460) 5'-W G C G T C W-3' ImPyImHpPy-y-ImPyPyImPy
46I) 5'-W G C G A T W-3' ImPyImPyHp-y-PyHpPyImPy
462) 5'-W G C G A A W-3' ImPyImPyPy-y-HpHpPyImPy
463) 5'-W G C G A G W-3' ImPyImPyIm-y-PyHpPyImPy
464) 5'-W G C G A C W-3' ImPyImPyPy-y-ImHpPyImPy
465) 5'-W G C G G T W-3' ImPyImImHp-y-PyPyPyImPy
466) 5'-W G C G G A W-3' ImPyImImPy-y-HpPyPyImPy
467) 5'-W G C G C T W-3' ImPyImPyHp-y-PyImPyImPy
468) 5'-W G C G C A W-3' ImPyImPyPy-y-HpImPyImPy
469) 5'-W G C C T T W-3' ImPyPyHpHp-y-PyPyImImPy
470) 5'-W G C C T A W-3' ImPyPyHpPy-y-HpPyImImPy
471) 5'-W G C C T G W-3' ImPyPyHpIm-y-PyPyImImPy
472) 5'-W G C C T C W-3' ImPyPyHpPy-y-ImPyImImPy
473) 5'-W G C C A T W-3' ImPyPyPyHp-y-PyHpImImPy
474) 5'-W G C C A A W-3' ImPyPyPyPy-y-HpHpImImPy
475) 5'-W G C C A G W-3' ImPyPyPyIm-y-PyHpImImPy
47 6 5' G C C A C W- 3 ImPyPyPyPy-y- ImHpImImPy
) -W '
477) 5'-W G C C G T W-3' ImPyPyImHp-y-PyPyImImPy
478) 5'-W G C C G A W-3' ImPyPyImPy-y-HpPyImImPy
479) 5' G C C C T W-3' Ir~iPyPyPyHp-y-PyImImImPy
-W
480) 5' G C C C A W-3' ImPyPyPyPy-y-HpImImImPy
-W
G25) 5' G C G G G W-3' ImPyImImIm-y-PyPyPyImPy
-W
G26) 5' G C G G C W-3' ImPyImImPy-y-ImPyPyImPy
-W
G27) 5'-W G C G C G W-3' ImPyImPyIm-y-PyImPyImPy
G28) 5' G C G C C W-3' ImPyImPyPy-y-ImImPyImPy
-W
G29) 5' G C C G G W-3' ImPyPyImIm-y-PyPyImImPy
-W
G30) 5'-W G C C G C W-3' ImPyPyImPy-y-ImPyImImPy
G31) 5' G C C C G W-3' ImPyPyPyIm-y-PyImImImPy
-W
G32) 5' G C C C C W-3' ImPyPyPyPy-y-ImImImImPy
-W
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-53-
TABLE 28:
10-ring
Hairpin
Polyamides
for
recognition
of
7-by
5'-WCGWNNW-3'
DNA aromatic amino acid sequence
sequence
481) 5'-W C G T T T W-3' PyImHpHpHp-y-PyPypypylm
482) 5' C G T T A W-3' PyImHpHppy-y-HpPyPyPyIm
=W
483) 5'-W C G T T G W-3' PyImHpHpIm-y-PyPypypylm
484) 5'-W C G T T C W-3' PyImHpHpPy-y-ImPyPyPyIm
485) 5' C G T A T W-3' PyImHpPyHp-y-pyHpPyPyIm
-W
486) 5'-W C G T A A W-3' PyImHpPyPy-y-HpHpPyPyIm
487) 5' C G T A G W-3' PyImHpPyIm-y-PyHpPyPyIm
-W
488) 5'-W C G T A C W-3' PyImHpPyPy-y-ImHpPyPyIm
489) 5'-W C G T G T W-3' PyImHpImHp-y-PyPypypylm
490) 5' C G T G A W-3' PyImHpImPy-y-HpPyPyPyIm
-W
491) 5' C G T G G W-3' PyImHpImIm-y-PyPyPyPyIm
-W
492) 5' C G T G C W-3' PyImHpImPy-y-ImPyPyPyIm
-W
493} 5' C G T C T W-3' PyImHpPyHp-y-PyImPyPyIm
-W
494) 5'-W C G T C A W-3' PyImHpPyPy-y-HpImPyPyIm
495) 5'-W C G T C G W-3' PyImHpPyIm-y-PyImPyPyIm
496) 5' C G T C C W-3' PyImHpPyPy-y-ImImPypyIm
-W
497) 5'-W C G A T T W-3' PyImPyHpHp-y-PyPyHpPyIm
498) 5' C G A T A W-3' PyImPyHpPy-y-HpPyHpPyIm
-W
499) 5' C G A T G W-3' PyImPyHpIm-y-PyPyHpPyIm
-W
500) 5' C G A T C W-3' PyImPyHpPy-y-ImPyHpPyIm
-W
501) 5'-W C G A A T W-3' PyImPyPyHp-y-PyHpHpPyIm
502) 5'-W C G A A A W-3' PyImPyPyPy-y-HpHpHpPyIm
503) 5'-W C G A A G W-3' PyImPyPyIm-y-PyHpHpPyIm
504) 5'-W C G A A C W-3' PyImPyPyPy-y-ImHpHpPyIm
505) 5'-W C G A G T W-3' PyImPyImHp-y-PyPyHpPyIm
506) 5'-W C G A G A W-3' PyImPyImPy-y-HpPyHpPyIm
507) 5'-W C G A G G W-3' PyImPyImIm-y-PyPyHpPyIm
508) 5' C G A G C W-3' PyImPyImPy-y-ImPyHpPyIm
-W
509) 5' C G A C T W-3' PyImPyPyHp-y-PyImHpPyIm
-W
510) 5' C G A C A W-3' PyImPyPyPy-y-HpImHpPyIm
-W
511) 5' C G A C G W-3' PyImPyPyIm-y-PyImHpPyIm
-W
512) 5' C G A C C W-3' PyImPyPyPy-y-ImImHpPyIm
-W
CA 02281930 1999-08-18
WO 98/37067
PCT/US98/OI714
-54-
TABLE
29:
10-ring
Hairpin
Polyanudes
for
recognition
of
7-by
5'-WCGSNNW-3'
DNA aromatic amino acid sequence
sequence
513) 5'-W C G G T TW-3' PyImImHpHp-y-PyPyPyPyIm
514) 5'-W C G G T AW-3' PyImImHpPy-y-HppyPypylm
515) 5' C G G T GW-3' PyImImHpIm-y-pypypypylm
-W
516) 5'-W C G G T CW-3' PyImImHpPy-y-ImPyPyPyIm
517) 5'-W C G G A TW-3' PyImImPyHp-y-PyHpPyPyIm
518) 5' C G G A AW-3' PyImImPyPy-y-HpHpPyPyIm
-W
519) 5' C G G A GW-3' PyImImPyIm-y-PyHpPyPyIm
-W
520) 5'-W C G G A CW-3' PyImImPyPy-y-ImHpPyPyIm
521) 5' C G G G TW-3' PyImImImHp-y-PyPyPyPyIm
-W
522) 5'-W C G G G AW-3' PyImImImPy-y-HpPyPyPyIm
523) 5' C G G C TW-3' PyImImPyHp-y-PyImPyPyIm
-W
524) 5'-W C G G C AW-3' PyImImPyPy-y-HpImPyPyIm
525) 5'-W C G C T TW-3' PyImPyHpHp-y-PyPyImPyIm
526) 5' C G C T AW-3' PyImPyHpPy-y-HpPyImPyIm
-W
527) 5'-W C G C T GW-3' PyImPyHpIm-y-PyPyImPyIm
528) 5' C G C T CW-3' PyImPyHpPy-y-ImPyImPyIm
-W
529) 5' C G C A TW-3' PyImPyPyHp-y-PyHpImPyIm
-W
530) 5'-W C G C A AW-3' PyImPypyPy-y-HpHpImPyIm
531) 5' C G C A GW-3' PyImPyPyIm-y-PyHpImPyIm
-W
532) 5'-W C G C A CW-3' PyImPyPyPy-y-ImHpImPyIm
533) 5'-W C G C G TW-3' PyImPyImHp-y-PyPyImPyIm
534) 5'-W C G C G AW-3' PyImPyImPy-y-HpPyImPyIm
535) 5'-W C G C C TW-3' PyImPyPyAp-y-PyImImPyIm
536) 5'-W C G C C AW-3' PyImPyPyPy-y-HpImImPyIm
G33) 5'-W C G G G GW-3' PyImImImIm-y-PyPyPyPyIm
G34) 5'-W C G G G CW-3' PyImImImPy-y-ImPyPyPyIm
G35) 5' C G G C GW-3' PyImImPyIm-y-PyImPyPyim
-W
G36) 5'-W C G G C CW-3' PyImImPyPy-y-ImImPyPyIm
G37) 5'-W C G C G GW-3' PyImPyImIm-y-PyPyImPyIm
G38) 5' C G C G CW-3' PyImPyImPy-y-ImPyImPyIm
-W
G39) 5' C G C C GW-3' PyImPyPyIm-y-PyImImPyim
-W
G40) 5' C G C C CW-3' PyImPyPyPy-y-ImImImPyim
-W
CA 02281930 1999-08-18
WO 98/37067 PCTIUS98101714
-55-
TABLE
30:
10-ring
Hairpin
Polyamides
for
recognition
of
7-by
5'-WCTWNNW-3'
DNA aromatic amino acid sequence
sequence
537) 5'-W C TT T T W-3' PyHpHpHpHp-y-PyPypypyIm
538) 5'-W C TT T A W-3' PyHpHpHpPy-y-IipPyPyPyIm
539) 5'-W C TT T G W-3' PyHpHpHpIm-y-PyPyPyPyIm
540) 5'-W C TT T C W-3' PyHpHpHpPy-y-ImPyPyPyIm
541) 5'-W C TT A T W-3' PyHpHpPyHp-y-PyHpPyPyIm
542) 5'-W C TT A A W-3' PyHpHpPyPy-y-HpHpPyPyIm
543) 5'-W C TT A G W-3' PyHpHppyIm-y-PyHpPyPyIm
544) 5'-W C TT A C W-3' PyHpHpPyPy-y-ImHpPyPyIm
545) 5'-W C TT G T W-3' PyHpHpImHp-y-PyPyPypylm
546) 5'-W C TT G A W-3' PyHpHpImPy-y-HpPyPyPyIm
547) 5'-W C TT G G W-3' PyHpHpImIm-y-PyPyPypylm
548) 5'-W C TT G C W-3' PyHpHpImPy-y-ImpyPyPyIm
549) 5'-W C TT C T W-3' PyHpHpPyHp-y-PyImpyPyIm
550) 5'-W C TT C A W-3' PyHpHpPyPy-y-HpImPyPyIm
551) 5'-W C TT C G W-3' PyHpHpPyIm-y-pylmpyPyIm
552) 5'-W C TT C C W-3' PyHpHppyPy-y-ImImPyPyIm
553 ) 5' -W C TA T T W-3' PyHpPyHpHp-y-PyPyHpPyIm
554) 5'-W C TA T A W-3' PyHpPyHpPy-y-HpPyHpPyIm
555) 5'-W C TA T G W-3' PyHpPyHpIm-y-PyPyHpPyIm
556) 5'-W C TA T C W-3' PyHpPyHpPy-y-ImPyHppyIm
557) 5'-W C TA A T W-3' PyHpPyPyHp-y-PyHpHpPyIm
558) 5'-W C TA A A W-3' PyHpPyPyPy-y-HpHpHpPyIm
559) 5'-W C TA A G W-3' PyHpPyPyIm-y-PyHpHpPyIm
560) 5'-W C TA A C W-3' PyHpPyPyPy-y-ImHpHpPyIm
561) 5'-W C TA G T W-3' PyHppyImHp-y-PyPyHpPyIm
562) 5'-W C TA G A W-3' PyHpPyImpy-y-HpPyHpPyIm
563) 5'-W C TA G G W-3' PyHpPyImIm-y-PyPyHpPyIm
564) 5' -W C TA G C W-3' PyHpPyImPy-y-ImPyHpPyIm
565) 5'-W C TA C T W-3' PyHpPyPyHp-y-PyImHpPyIm
566) 5' -W C TA C A W-3' PyHpPyPyPy-y-HpImHpPyIm
567) 5'-W C TA C G W-3' PyHpPyPyIm-y-PyImHpPyIm
568) 5' -W C TA C C W-3' PyHpPyPyPy-y-ImImHpPyIm
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-56-
TABLE
31:
10-ring
Hairpin
Polyamides
for
recognition
of
7-by
5'-WCTSNNW-3'
DIVA aromatic amino acid sequence
sequence
569) 5'-W CT G T T W-3' PyHpImHpHp-y-PyPyPyPyIm
570) -5'-W CT G T A W-3' PyIipImHpPy-y-HpPyPyPyIm
571) 5'-W CT G T G W-3' PyHpImHpIm-y-PyPyPyPyIm
572) 5'-W CT G T C W-3' PyHpImHpPy-y-ImPyPyPyIm
573) 5'-W CT G A T W-3' PyHpImPyHp-y-PyHpPyPyIm
574) 5'-W CT G A A W-3' PyHpImPyPy-y-HpHpPyPyIm
575) 5' -W CT G A G W-3' PyHpImPyIm-y-PyHpPyPyIm
576) 5'-W CT G A C W-3' PyHpImPyPy-y-ImHpPyPyIm
577) 5'-W CT G G T W-3' PyHpImImHp-y-PyPyPyPyIm
578) 5'-W CT G G A W-3' PyHpImImPy-y-HpPyPyPyIm
579) 5'-W CT G C T W-3' PyHpImPyHp-y-PyImPyPyIm
580) 5'-W CT G C A W-3' PyHpImPyPy-y-HpImPyPyIm
581) 5'-W CT ~GG G W-3' PyHpImImIm-y-PyPyPyPyIm
582) 5'-W CT G G C W-3' PyHpImImPy-y-ImPyPyPyIm
583) 5'-W CT G C G W-3' PyHpImPyIm-y-PyImPyPyIm
584) 5'-W CT G C C W-3' PyHpImPyPy-y-ImImPyPyIm
585) 5' -W CT C T T W-3' PyHpPyHpHp-y-PyPyImPyIm
586) 5'-W CT C T A W-3' PyHpPyHpPy-y-HpPyImPyIm
587) 5'-W CT C T G W-3' PyHpPyHpIm-y-PyPyImPyIm
588) 5' -W CT C T C W-3' PyHpPyHpPy-y-ImPyImPyIm
589) 5'-W CT C A T W-3' PyHpPyPyHp-y-PyHpImPyIm
590) 5'-W CT C A A W-3' PyHpPyPyPy-y-HpHpImPyIm
591) 5' -W CT C A G W-3' PyHpPyPyIm-y-PyHpImPyIm
592) 5'-W CT C A C W-3' PyHpPyPyPy-y-ImHpImPyIm
593) 5'-W CT C G T W-3' PyHpPyImHp-y-PyPyImPyIm
594) 5' -W CT C G A W-3' PyHpPyImPy-y-HpPyImPyIm
595) 5'-W CT C C T W-3' PyHpPyPyHp-y-PyImImPyIm
596) 5'-W CT C C A W-3' PyHpPyPyPy-y-HpImImPyIm
597) 5'-W CT C G G W-3' PyHpPyImIm-y-PyPyImPyIm
598) 5'-W CT C G C W-3' PyHpPyImPy-y-ImPyImPyIm
599) 5' -W CT C C G W-3' PyHpPyPyIm-y-PyImImPyIm
600) 5'-W CT C C C W-3' PyHpPyPyPy-y-ImImImPyIm
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-5 7-
TABLE
32:
10-ring
Hairpin
Polyamides
for
recognition
of
7-by
5'-WCAWNNW-3'
DNA aromatic amino acid sequence
sequence
601) 5'-W C A T T TW-3' PypyHpHpHp-y-PyPyPyHpIm
602) '5'-W C A T T AW-3' PyPyHpHpPy-y-HpPyPyHpIm
603) 5'-W C A T T GW-3' PypyHpHpIm-y-PyPyPyHpIm
604) 5'-W C A T T CW-3' PyPyHpHppy-y-ImPyPyHpIm
605) 5' C A T A TW-3' PyPyHpPyHp-y-PyHpPyHpIm
-W
606) 5'-W C A T A AW-3' pypyHpPyPy-y-HpHpPyHpIm
607) 5'-W C A T A GW-3' PyPyHpPyIm-y-PyHpPyHpIm
608) 5' C A T A CW-3' PyPyHpPyPy-y-ImHppyHpIm
-W
609) 5' C A T G TW-3' PyPyHpImHp-y-PyPyPyHpIm
-W
610) 5'-W C A T G AW-3'
PyPyHpImPy-y-HpPypyHpIm
611) 5' C A T G GW-3' PyPyHpImIm-y-PypypyHpIm
-W
612) 5' C A T G CW-3' PyPyHpImpy-y-ImPyPyHpIm
-W
613) 5'-W C A T C TW-3' pyPyHpPyHp-y-PyImPyHpIm
614) 5' C A T C AW-3' PyPyHpPyPy-y-HpImPyHpIm
-W
615) 5' C A T C GW-3' PypyHpPyIm-y-PyImPyHpIm
-W
616) 5' C A T C CW-3' PyPyHpPyPy-y-ImImPyHpIm
-W
617) 5' C A A T TW-3' PyPyPyHplip-y-pyPyHpHpIm
-W
618) 5' C A A T AW-3' PyPyPyHpPy-y-HpPyHpHpIm
-W
619) 5' C A A T GW-3' PyPyPyHpIm-y-PypyHpHpIm
-W
620) 5'-W C A A T CW-3' PyPypyHpPy-y-ImPyHpHpIm
621) 5'-W C A A A TW-3' PypypypyHp-y-PyHpHpHpIm
622) 5'-W C A A A AW-3' PyPypypypy-y-HpHpHpHpIm
623) 5'-W C A A A GW-3' PyPyPypylm-y-PyHpHpHpIm
624) 5' C A A A CW-3' pyPyPypypy-y-I~pgpHpIm
-W
625) 5'-W C A A G TW-3' PyPyPyImHp-y-pyPyHpHpIm
626) 5'-W C A A G AW-3' PypypylmPy-y-HpPyHpHpIm
627) 5'-W C A A G GW-3' PyPyPyImIm-y-PyPyHpHpIm
628) 5'-W C A A G CW-3' PyPypyImPy-y-ImPyHpHpIm
629) 5' C A A C TW-3' PyPypypygp-y-pyl~pHpIm
-W
630) 5' C A A C AW-3' pyPypypypy-y-HpImHpHpIm
-W
631) 5' C A A C GW-3' PyPypypyim-y-PyImHpHpIm
-W
632) 5'-W C A A C CW-3' PyPypypypy-y-ImImHpHpIm
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-5 8-
TABLE 10-ring
33: Hairpin
Polyamides
for
recognition
of
7-by
5'-WCASNNW-3'
DNA aromatic amino acid sequence
sequence
633) 5' -W CA G T T W-3' PyPyImHpHp-y-PyPyPyHpIm
634) ~5' CA G T A W-3' PyPyImHpPy-y-HpPyPyHpIm
-W
635) 5' -W CA G T G W-3' PyPyImHpIm-y-PyPyPyHpIm
636) 5'-W CA G T C W-3' PyPyImHpPy-y-ImPyPyHpIm
637) 5'-W CA G A T W-3' PyPyImPyHp-y-PyHpPyHpIm
638) 5'-W CA G A A W-3' PyPyImPyPy-y-HpHpPyHpIm
639) 5' -W CA G A G W-3' PyPyImPyIm-y-PyHpPyHpIm
640) 5' -W CA G A C W-3' PyPyImPyPy-y-ImHpPyHpIm
641) 5' -W CA G G T W-3' PyPyImImHp-y-PyPyPyHpIm
642) 5'-W CA G G A W-3' PyPyImImPy-y-HpPyPyHpIm
643) 5'-W CA G C T W-3' PyPyImPyHp-y-PyImPyHpIm
644) 5' -W CA G C A W-3' PyPyImPyPy-y-HpImPyHpIm
645) 5'-W CA G G G W-3' PyPyImImIm-y-PyPyPyHpIm
646) 5' -W CA G G C W-3' PyPyImImPy-y-ImPyPyHpIm
647) 5'-W CA G C G W-3' PyPyImPyIm-y-PyImPyHpIm
648) 5'-W CA G C C W-3' PyPyImPyPy-y-ImImPyHpIm
649) 5' -W CA C T T W-3' PyPyPyHpFip-y-PyPyImHpIm
650) 5' -W CA C T A W-3' PyPyPyHpPy-y-HpPyImHpIm
651) 5' -W CA C T G W-3' PyPyPyHpIm-y-PyPyImHpIm
652) 5'-W CA C T C W-3' PyPyPyHpPy-y-ImPyimHpim
653) 5'-W CA C A T W-3' PyPyPyPyHp-y-PyHpImHpIm
654) 5' -W CA C A A W-3' PyPyPyPyPy-y-HpHpImHpIm
655) 5'-W CA C A G W-3' ~PyPyPyPyIm-y-PyHpImHpIm
656) 5'-W CA C A C W-3' PyPyPyPyPy-y-ImHpImHpIm
657 5' -W CA C G T W-3' PyPyPyImHp-y-PyPyImHpIm
)
658) 5' -W CA C G A W-3' PyPyPyImPy-y-HpPyImHpIm
659) 5' -W CA C C T W-3' PyPyPyPyHp-y-PyImImHpIm
660) 5' -W CA C C A W-3' PyPyPyPyPy-y-HpImImHpIm
661) 5' -W CA C G G W-3' PyPyPyImIm-y-PyPyImHpIm
662) 5'-W CA C G C W-3' PyPyPyImPy-y-ImPyImHpIm
663) 5'-W CA C C G W-3' PyPyPyPyIm-y-PyImImHpIm
664) 5' -W CA C C C W-3' PyPyPyPyPy-y-ImImImHpIm
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-59-
'TABLE
34:
10-ring
Hairpin
Polyamides
for
recognition
of
7-by
5'-WCCWNNW-3'
DNA aromatic anuno acid sequence
sequence
665) 5'-W C C T T TW-3' PyPyHpHpHp-y-PyPypylmim
666) ~5'-W C C T T AW-3' PyPyHpHpPy-y-HpPyPyImIm
667) 5'-W C C T T GW-3' PyPyHpHpIm-y-PypypylmIm
668) 5' C C T T CW-3' PyPyHpHpPy-y-ImPyPyImIm
-W
669) 5'-W C C T A TW-3' PyPyHpPyHp-y-PyHpPyImIm
670) 5'-W C C T A AW-3' PyPyHpPyPy-y-HpHpPyImIm
671) 5'-W C C T A GW-3' PyPyHpPyIm-y-PyHpPyImIm
672) 5'-W C C T A CW-3' PypyHpPyPy-y-ImHpPyImIm
673) 5'-W C C T G TW-3' PyPyHpImHp-y-PyPypyImlm
674) 5'-W C C T G AW-3'
PyPyHpImPy-y-HpPyPyImIm
675) 5'-W C C T G GW-3' PyPyHpImIm-y-PyPypyImIm
676) 5' C C T G CW-3' PyPyHpImPy-y-ImPyPyImIm
-W
677) 5'-W C C T C TW-3' PyPyHpPyHp-y-PyImPyImIm
678) 5'-W C C T C AW-3' PyPyHpPyPy-y-HpImPyImIm
679) 5'-W C C T C GW-3' PyPyHpPyIm-y-PyImPyImIm
680) 5'-W C C T C CW-3' PyPyHpPyPy-y-ImImPyImIm
681) 5'-W C C A T TW-3' PyPypyHpHp-y-PyPyHpImIm
682) 5' C C A T AW-3' PyPyPyHpPy-y-HpPyHpImIm
-W
683) 5'-W C C A T GW-3' PyPyPyHpIm-y-PyPyHpImIm
684) 5'-W C C A T CW-3' PyPyPyHpPy-y-ImPyHpImIm
685) 5'-W C C A A TW-3' PyPyPyPyHp-y-PyHpHpImIm
2S 686) 5'-W C C A A AW-3' PyPyPyPyPy-y-HpHpHpImIm
687) 5'-W C C A A GW-3' PyPypypylm-y-pyHpHpImIm
688) 5'-W C C A A CW-3' PyPyPyPyPy-y-ImHpHpImIm
689) 5'-W C C A G TW-3' PyPyPyImHp-y-PyPyHpImIm
690) 5'-W C C A G AW-3' PyPyPyImPy-y-HpPyHpImIm
691) 5'-W C C A G GW-3' PyPyPyImIm-y-PyPyHpImIm
692) 5' C C A G CW-3' PyPyPyImPy-y-ImPyHpImIm
-W
693) 5'-W C C A C TW-3' PyPyPyPyHp-y-PyImHpImIm
694) 5'-W C C A C AW-3' PyPyPyPyPy-y-HpImHpImIm
695) 5'-W C C A C GW-3' pyPypypylm-y-pyImHpImIm
696) 5' C C A C CW-3' PyPyPyPypy-y-ImImHpImIm
-W
CA 02281930 1999-08-18
WO 98!37067 PCT/US98/01714
-60-
TABLE
35:
10-ring
Hairpin
Polyamides
for
recognition
of
7-by
5'-WCCSNNW-3'
DNA aromatic amino acid sequence
sequence
697) 5'-W C CG T T W-3' PyPyImHpHp-y-PyPypyImIm
698) ~5' C CG T A W-3' PyPyImHpPy-y-HpPyPyImIm
-W
699) 5' C CG T G W-3' PyPyImHpIm-y-PyPyPyImIm
-W
700) 5' C CG T C W-3' PyPyImHppy-y-ImPyPyImIm
-W
701) 5' C CG A T W-3' PyPyImPyHp-y-PyHpPyImIm
-W
702) 5' C CG A A W-3' PyPyImPyPy-y-HpHpPyImIm
-W
703) 5'-W C CG A G W-3' PyPyImPyIm-y-PyHpPyImIm
704) 5' C CG A C W-3' PyPyImPyPy-y-ImHpPyImIm
-W
705) 5' C CG G T W-3' PyPyImImHp-y-PyPyPyImIm
-W
706) 5' C CG G A W-3' PyPyImImPy-y-HpPyPyImIm
-W
707) 5' C CG C T W-3' PyPyImPyHp-y-PyImPyImIm
-W
708) 5' C CG C A W-3' PyPyImPyPy-y-HpImPyImIm
-W
709) 5' C CC T T W-3' PyPyPyHpHp-y-PyPyImImIm
-W
710) 5' C CC T A W-3' PyPyPyHpPy-y-HpPyImImIm
-W
711) 5' C CC T G W-3' PyPyPyHpIm-y-PyPyImImIm
-W
712) 5' C CC T C W-3' PyPyPyHpPy-y-ImPyImImIm
-W
713) 5' C CC A T W-3' PypyPyPyHp-y-PyHpImImIm
-W
714) 5' C CC A A W-3' PyPyPyPyPy-y-HpHpImImIm
-W
715) 5' C CC A G W-3' PyPyPyPyIm-y-PyHpImImIm
-W
716) 5' C CC A C W-3' PyPyPyPyPy-y-ImHpImImIm
-W
717 ) 5' C CC G T W-3' PyPyPyImHp-y-PyPyImImIm
-W
718 ) 5' C CC G A W-3 ' PyPyPyImPy-y-HpPyImImIm
-W
719) 5' C CC C T W-3' PyPyPyPyHp-y-PyImImImIm
-W
720) 5' C CC C A W-3' PyPyPyPypy-y-HpImImImIm
-W
G41) 5' C CG G G W-3' PyPyImImIm-y-PyPyPyImIm
-W
G42) 5'-W C CG G C W-3' PyPyImImPy-y-ImPyPyImIm
G43) 5' C CG C G W-3' PyPyImPyIm-y-PyImPyImIm
-W
G44) 5' C CG C C W-3' PyPyImPyPy-y-ImImPyImIm
-W
G45) 5' C CC G G W-3' PyPyPyImIm-y-PyPyImImIm
-W
G46) 5' C CC G C W-3' PyPyPyImPy-y-ImPyImImIm
-W
G47) 5'-W C CC C G W-3' PyPyPyPyIm-y-PyImImImIm
G48) 5'-W C CC C C W-3' PyPyPyPyPy-y-ImImImImIm
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/OI714
-61-
TABLE
36:
10-ring
Hairpin
Polyamides
for
recognition
of
7-by
5'-WAGWNNW-3'
DNA aromatic amino acid sequence
sequence
721) 5' -WA G T T T W-3' PyImHpHpHp-y-PyPyPypyHp
722) ~5' -WA G T T A W-3' PyImHpHpPy-y-HpPyPyPyHp
723) 5' -WA G T T G W-3' PyImHpHpIm-y-PyPypypyHp
724) 5' -WA G T T C W-3' PyImHpHpPy-y-ImPyPyPyHp
725) 5' -WA G T A T W-3' PyImHpPyHp-y-PyHpPyPyHp
726) 5' -WA G T A A W-3' PyImHpPyPy-y-HpHpPyPyHp
727) 5' -WA G T A G W-3' PyImHpPyIm-y-PyHpPyPyHp
728) 5' -WA G T A C W-3' PyImHpPyPy-y-ImHppypyI-Ip
729) 5' -WA G T G T W-3' PyImHpImHp-y-PyPyPyPyHp
730) 5' -WA G T G A W-3' PyImHpImPy-y-HpPyPyPyHp
731) 5' -WA G T G G W-3' PyImHpImIm-y-Pypypypygp
732) 5' -WA G T G C W-3' PyImHpImPy-y-ImPyPyPyHp
733) 5' -WA G T C T W-3' PyImHpPyHp-y-PyImPyPyHp
734) 5' -WA G T C A W-3' PyImHpPyPy-y-HpImPyPyHp
735) 5' -WA G T C G W-3' PyImHpPyIm-y-PyImPyPyHp
736) 5' -WA G T C C W-3' PyImHpPyPy-y-ImImPyPyHp
737) 5' -WA G A T T W-3' PyImPyHpHp-y-PyPyHpPyHp
73 8 5' -WA G A T A W-3 PyImPyHpPy-y-HpPyHpPyHp
) '
739) 5' -WA G A T G W-3' PyImPyHpIm-y-PyPyHpPyHp
740) 5' -WA G A T C W-3' PyImPyHpPy-y-ImPyHpPyllp
741) 5' -WA G A A T W-3' PyImPyPyHp-y-PyHpHpPyHp
742) 5' -WA G A A A W-3' PyImPyPyPy-y-HpHpHpPyHp
743) 5' -WA G A A G W-3' PyImPyPyIm-y-PyHpHpPyHp
744) 5' -WA G A A C W-3' PyImPyPyPy-y-ImHpHpPyHp
745) 5' -WA G A G T W-3' PyImPyImHp-y-PyPyHpPyHp
746) 5' -WA G A G A W-3' PyImPyImPy-y-HpPyHpPyHp
747) 5' -WA G A G G W-3' PyImPyImIm-y-PyPyHpPyHp
748) 5' -WA G A G C W-3' PyImPyImPy-y-ImPyHpPyHp
749) 5' -WA G A C T W-3' PyImPyPyHp-y-PyImHpPyHp
750) 5' -WA G A C A W-3' PyImPyPyPy-y-HpImHpPyHp
751) 5' -WA G A C G W-3' PyImPyPyIm-y-PyImHpPyHp
752) 5' -WA G A C C W-3' PyImPyPyPy-y-ImImHpPyHp
CA 02281930 1999-08-18
WO 98137067 PCT/US98/01714
-62-
'TABLE pin
37: Polyamides
10-zing for
Hair recognition
of
7-by
5'-WAGSNNW
3'
DNA aromatic amino acid sequence
sequence
753) 5'-W A G G T T W-3' PyImImHpHp-y-Pypypypygp
754) ~5' A G G T A W-3' PyImImHpPy-y-HpPyPyPyHp
-W
755) 5' A G G T G W-3' PyImImHpIm-y-PypypypyHp
-W
756) 5' -WA G G T C W-3' PyImImHpPy-y-ImPyPyPyHp
757) 5' -WA G G A T W-3' PyImImPyHp-y-PyHpPyPyHp
758) 5' -WA G G A A W-3' PyImImPyPy-y-HpHpPyPyHp
759) 5' -WA G G A G W-3' PyImImPyIm-y-PyHpPyPyHp
760) 5' -WA G G A C W-3' PyImImPyPy-y-ImHpPyPyHp
761) 5' -WA G G G T W-3' PyImImImHp-y-PyPyPyPyHp
762) 5' -WA G G G A W-3' PyImImImPy-y-HpPyPyPyHp
763) 5' -WA G G C T W-3' PyImImPyFip-y-PyImPyPyHp
764) 5' -WA G G C A W-3' PyImImPyPy-y-HpImPyPyHp
765) 5' -WA G C T T W-3' PyImPyApHp-y-PypyImPyHp
766) 5' -WA G C T A W-3' PyImPyHpPy-y-HpPyImPyHp
767) 5' -WA G C T G W-3' PyImPyHpIm-y-PyPyImPyHp
7 6 8 5' -WA G C T C W-3 PyImpyHpPy-y-ImPyImPyHp
) '
769) 5' -WA G C A T W-3' PyImPyPyHp-y-PyHpImPyHp
770) 5' -WA G C A A W-3' PyImPyPyPy-y-HpHpImPyHp
771) 5' -WA G C A G W-3' PyImPyPyIm-y-PyHpImPyHp
772) 5' -WA G C A C W-3' PyImPyPyPy-y-ImHpImPyHp
773) 5' -WA G C G T W-3' PyImPyImHp-y-PypyImPyHp
774) 5' -WA G C G A W-3' PyImPyImPy-y-HpPyImPyHp
775) 5' -WA G C C T W-3' PyImPyPyHp-y-PyImImPyHp
776) 5' -WA G C C A W-3' PyImPyPyPy-y-HpImImPyHp
777) 5' -WA G G G G W-3' PyImImImIm-y-Pypypypygp
778) 5' -WA G G G C W-3' PyImImImPy-y-ImPyPyPyHp
779) 5' -WA G G C G W-3' PyImImPyIm-y-PyImPyPyHp
780) 5' -WA G G C C W-3' PyImImPyPy-y-ImImPyPyHp
781) 5' -WA G C G G W-3' PyImPyImIm-y-PyPyImPyHp
782) 5' -WA G C G C W-3' PyImPyImPy-y-ImPyIrnPyHp
783) 5' -WA G C C G W-3' PyImPyPyIm-y-PyImImPyHp
784) 5' -WA G C C C W-3' PyImPyPyPy-y-ImImImPyHp
r . ,
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-63-
TABLE
38:
10-ring
Hairpin
Polyamides
for
recognition
of
7-by
5'-WATWNNW-3'
-
DNA aromatic amino acid sequence
sequence
785) 5' A T T T TW-3' PyHpHpHpHp-y-pypypypygp
-W
786) '5'-W A T T T AW-3' PyHpHpHpPy-y-HppypypyHp
787) 5'-W A T T T GW-3' PyHpHpHpIm-y-pypypypygp
788) 5' A T T T CW-3' PyHpHpHpPy-y-ImPyPyPyHp
-W
789) 5' A T T A TW-3' PyHpHpPyHp-y-PyHpPyPyHp
-W
790) 5' A T T A AW-3' PyHpHpPyPy-y-HpHpPyPyHp
-W
791) 5' A T T A GW-3' PyHpHpPyIm-y-PyHpPyPyHp
-W
792) 5' A T T A CW-3' PyHpHpPypy-y-I~ppyp~,Hp
-W
793) 5'-W A T T G TW-3'
PyHpHpImHp-y-PyPyPyPyHp
794) 5' A T T G AW-3' PyHpHpImPy-y-HpPyPyPyHp
-W
795) 5'-W A T T G GW-3' PyHpHpImIm-y-pypypypyHp
796) 5'-W A T T G CW-3' PyHpHpImPy-y-ImPyPyPyHp
797) 5' A T T C TW-3' PyHpHpPyHp-y-PyImPyPyHp
-W
798) 5'-W A T T C AW-3' PyHpHpPyPy-y-HpImpyPyHp
799) 5' A T T C GW-3' PyHpHpPyIm-y-PyImPyPyHp
-W
8 00 5' A T T C CW-3 ' PyHpHpPyPy-y- ImImPyPyFip
) -W
801) 5' A T A T TW-3' PyHpPyHpHp-y-PyPyHpPyHp
-W
802) 5'-W A T A T AW-3'
PyHpPyHpPY-Y-HpPYHpPYHP
803) 5'-W A T A T GW-3' PyHpPyHpIm-y-PyPyHpPyHp
804) 5' A T A T CW-3' PyHpPyHpPy-y-ImPyHpPyHp
-W
805) 5' A T A A TW-3' PyHpPyPyHp-y-PyHpHpPyHp
-W
806) 5' A T A A AW-3' PyHpPyPyPy-y-HpHpHpPyHp
-W
807 ) 5' A T A A GW-3' PyHpPyPyIm-y-PyHpHpPyHp
-W
808) 5'-W A T A A CW-3' PyHpPypyPy-y-ImHpHpPYHp
809) 5'-W A T A G TW-3'
PyHpPyImHp-y-PyPyHpPyHp
810) 5' A T A G AW-3' PyHpPyImPy-y-HpPyHpPyHp
-W
811) 5' A T A G GW-3' PyHpPyImIm-y-PypyHpPyHp
-W
812) 5' A T A G CW-3' PyHpPyImPy-y-ImPyHpPyHp
-W
813) 5'-W A T A C TW-3' PyHpPyPyHp-y-PyImHpPyHp
814) 5'-W A T A C AW-3' PyHpPyPyPy-y-HpImHpPyHp
815) 5' A T A C GW-3' PyHpPyPyIm-y-pyImHpPyHp
-W
816) 5' A T A C CW-3' PyHpPyPyPy-y-ImImHpPyHp
-W
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/OI714
-64-
TABLE
39:
i0-ring
Hairpin
Polyamides
for
recognition
of
7-by
5'-WATSNNW-3'
DNA aromatic amino acid sequence
sequence
817 ) 5' -WA T G T TW-3 ' PyHpImHpHp-y-PyPypyPyHp
818) '5' -WA T G T AW-3' PyHpImHppy-y-HpPyPyPyHp
819) 5' -WA T G T GW-3' PyHpImHpIm-y-PypypypyHp
820) 5' -WA T G T CW-3' PyHpImHpPy-y-ImPyPyPyHp
821) 5' -WA T G A TW-3' PyHpImPyHp-y-PyHpPyPyHp
822) 5' -WA T G A AW-3' PyHpImPyPy-y-HpHpPyPyHp
823) 5' -WA T G A GW-3' PyHpImPyIm-y-PyHpPyPyHp
824) 5' -WA T G A CW-3' PyHpImPyPy-y-ImHpPyPyHp
825) 5' -WA T G G TW-3' PyHpImImHp-y-Pypypypygp
826) 5' -WA T G G AW-3' PyHpImImPy-y-HpPyPyPyHp
827) 5' -WA T G C TW-3' PyHpImPyHp-y-PyImPyPyHp
828) 5' -WA T G C AW-3' PyHpImPyPy-y-HpImPyPyHp
829) 5' -WA T G G GW-3' PyHpImImIm-y-PyPyPyPyHp
830) 5' -WA T G G CW-3' PyHpImImPy-y-ImPyPyPyHp
831) 5' -WA T G C GW-3' PyHpImPyIm-y-PyImPyPyHp
832) 5' -WA T G C CW-3' PyHpImPyPy-y-ImImPyPyHp
833) 5' -WA T C T TW-3' PyHpPyHpHp-y-PyPyImPyHp
834) 5' -WA T C T AW-3' PyHpPyHpPy-y-HpPyImPyHp
835) 5' -WA T C T GW-3' PyHpPyHpIm-y-PyPyImPyHp
836) 5' -WA T C T CW-3' PyHpPyHpPy-y-ImPyImPyHp
837) 5' -WA T C A TW-3' PyHpPyPyHp-y-PyHpImPyHp
838) 5' -WA T C A AW-3' PyHpPyPyPy-y-HpHpImPyHp
839) 5' -WA T C A GW-3' ~ PyHpPyPyIm-y-PyHpImPyHp
840) 5' -WA T C A CW-3' PyHpPyPyPy-y-ImHpImPyHp
841) 5' -WA T C G TW-3' PyHpPyImHp-y-PyPyImPyHp
842) 5' -WA T C G AW-3' PyHpPyImPy-y-HpPyImPyHp
843) 5' -WA T C C TW-3' PyHpPyPyHp-y-PyImImPyHp
844) 5' -WA T C C AW-3' PyHpPyPyPy-y-HpImImPyHp
845) 5' -WA T C G GW-3' PyHpPyImIm-y-PyPyImPyHp
846) 5' -WA T C G CW-3' PyHpPyImPy-y-ImPyImPyHp
847) 5' -WA T C C GW-3' PyHpPyPyIm-y-PyImImPyHp
848) 5' -WA T C C CW-3' PyHpPyPyPy-y-ImImImPyHp
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/OI714
-65-
TABLE
40:
10-ring
Hairpin
Yolyamides
for
recognition
of
7-by
5'-WAAWNNW-3'
DNA aromatic amino acid sequence
sequence
' 849) 5' -WA A T TT W-3' PyPyHpHpHp-y-PypypyHpHp
S 850) 'S' -WA A T TA W-3' PyPyHpHpPy-y-HpPyPyHpHp
851) 5' -WA A T TG W-3' PyPyHpI-iplm-y-PYPypyHpHp
852) 5' -WA A T TC W-3' PyPyHpHpPy-y-ImPyPyHpHp
853) 5' -WA A T AT W-3' PyPyHpPyHp-y-PyHpPyHpHp
854) 5' -WA A T AA W-3' PyPyHpPyPy-y-HpHpPyHpHp
855) 5' -WA A T AG W-3' PyPyHpPyIm-y-PyHpPyHpHp
856) 5' -WA A T AC W-3' PyPyHpPyPy-y-I~pPyHpHp
857) 5' -WA A T GT W-3'
PYPYHPImHp-y-PyPyPyHpHp
858) 5' -WA A T GA W-3' PyPyHpImPy-y-HpPyPyHpHp
859) 5' -WA A T GG W-3' PyPyHpImIm-y-PypypyHpHp
?5 860) 5' -WA A T GC W-3'
PyPyHpImPy-y-ImPyPyHpHp
861) 5' -WA A ~TCT W-3' PyPyHpPyHp-y-PyImPyHpHp
862) 5' -WA A T CA W-3' PyPyHpPyPy-y-HpImPyHpHp
863) 5' -WA A T CG W-3' PyPyHpPyIm-y-PyImPyHpHp
864) 5' -WA A T CC W-3' PyPyHpPyPy-y-ImImPyHpHp
865) 5' -WA A A TT W-3' PyPyPyHpHp-y-PypyHpHpHp
866) 5' -WA A A TA W-3' PyPypygppy-y-HpPyHpHpHp
867) 5' -WA A A TG W-3' Pypypygplm-y-PyPyHpHpHp
868) 5' -WA A A TC W-3' PyPyPyHpPy-y-ImPyHpHpHp
869) 5' -WA A A AT W-3' PyPyPyPyHp-y-PyHpHpHpHp
870) 5' -WA A A AA W-3' PyPyPypyPy-y-HpHpHpHpHp
871) 5' -WA A A AG W-3' Pypypypylm-y-PyHpHpHpHp
872) 5' -WA A A AC W-3' Pypypypypy-y-I~pHpHpHp
873) 5' -WA A A GT W-3'
PyPyPyImHp-y-PyPyHpHpHp
874 ) 5' -WA A A GA W-3 ' PyPyPyImPy-y-HpPyHpHpHp
875) 5' -WA A A GG W-3' PyPyPyImIm-y-PyPyHpHpHp
876) 5' -WA A A GC W-3'
PyPyPyImPy-y-ImPyHpHpHp
877) 5' -WA A A CT W-3' Pypypypygp-y-pyl~pHpHp
878) 5' -WA A A CA W-3' PyPyPyPypy-y-HpI~pHpHp
879) 5' -WA A A CG W-3' PyPyPyPyIm-y-PyImHpHpHp
880) 5' -WA A A CC W-3' PyPyPyPyPy-y-ImImHpHpHp
CA 02281930 1999-08-18
WO 98/37067 PCT/CTS98/01714
-66-
TABLE
41:
10-ring
Haitpin
Polyamides
for
recognition
of
7-by
5'-WAASNNW-3'
DNA aromatic amino acid sequence
sequence
881) 5' -WA A G T T W-3' PyPyImHpHp-y-PyPyPyHpHp
882) ~5' -WA A G T A W-3' PyPyImHpPy-y-HpPyPyHpHp
883) 5' -WA A G T G W-3' PyPyImHpIm-y-PyPyPyHpHp
884) 5' -WA A G T C W-3' PyPyImHpPy-y-ImPyPyHpHp
885) 5' -WA A G A T W-3' PyPyImPyHp-y-PyHpPyHpHp
886) 5' -WA A G A A W-3' PyPyImPyPy-y-HpHpPyHpHp
887) 5' -WA A G A G W-3' PyPyImPyIm-y-PyHpPyHpHp
888) 5' -WA A G A C W-3' PyPyImPyPy-y-ImHpPyHpHp
889) 5' -WA A G G T W-3' PyPyImImHp-y-PyPyPyHpHp
890) 5' -WA A G G A W-3' PyPyImImPy-y-HpPyPyHpHp
891} 5' -WA A G C T W-3' PyPyImPyHp-y-PyImPyHpHp
892) 5' -WA A G C A W-3' PyPyImPyPy-y-HpImPyHpHp
893) 5' -WA A G G G W-3' PyPyImImIm-y-PyPyPyHpHp
894) 5' -WA A G G C W-3' PyPyImImPy-y-ImPyPyHpHp
895) 5' -WA A G C G W-3' PyPyImPyIm-y-PyImPyHpHp
896) 5' -WA A G C C W-3' PyPyImPyPy-y-ImImPyHpHp
897) 5' -WA A C T T W-3' PyPyPyHpHp-y-PyPyImHpHp
898) 5' -WA A C T A W-3' PyPyPyHpPy-y-HpPyImHpHp
899) 5' -WA A C T G W-3' PyPyPyHpIm-y-PyPyImHpHp
900) 5' -WA A C T C W-3' PyPyPyHpPy-y-ImPyImHpHp
901) 5' -WA A C A T W-3' PyPyPyPyHp-y-PyHpImHpHp
902} 5' -WA A C A A W-3' PyPyPyPyPy-y-HpHpImHpHp
903) 5' -WA A C A G W-3' PyPyPyPyIm-y-PyHpImHpHp
904) 5' -WA A C A C W-3' PyPyPyPyPy-y-ImHpImHpHp
905) 5' -WA A C G T W-3' PyPyPyImHp-y-PyPyImHpHp
906) 5' -WA A C G A W-3' PyPyPyImPy-y-HpPyImHpHp
907) 5' -WA A C C T W-3' PyPyPyPyHp-y-PyImImHpHp
908} 5' -WA A C C A W-3' PyPyPyPyPy-y-HpImImFipHp
909) 5' -WA A C G G W-3' PyPyPyImIm-y-PyPyImHpHp
910) 5' -WA A C G C W-3' PyPyPyImPy-y-ImPyImHpHp
911) 5' -WA A C C G W-3' PyPyPyPyIm-y-PyImImHpHp
912) 5' -WA A C C C W-3' PyPyPyPyPy-y-ImImImHpHp
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-67-
TABLE
42:
10-ring
Hairpin
Polyamides
for
recognition
of
?-by
5'-WACWNNW-3'
DNA aromatic amino acid sequence
sequence
913 ) 5' -WA C T T T W-3' PyPyHpHpHp-y-PyPyPyImHp
914 ) '5' -WA C T T A W-3 PyPyHpHpPy-Y-HpPyPyImHp
'
915) 5' -WA C T T G W-3' PYPYHpgpIm-Y-PYPYPyImHp
916) 5' -WA C T T C W-3' PyPyHpHpPy-y-ImPyPyImHp
917) 5' -WA C T A T W-3' PyPyHpPyHp-Y-PyHpPyImHp
918) 5' -WA C T A A W-3' PyPyHpPyPy-y-HpHpPyImHp
919) 5' -WA C T A G W-3' PyPyHpPyIm-y-PyHpPyImHp
92 0 5' -WA C T A C W- 3 PyPyHpPyPy-Y- ImHppyImHp
) '
921) 5' -WA C T G T W-3' pypygpl~p-Y-p~,pypyl~p
922) 5' -WA C T G A W-3' PyPyHpImPy-y-HpPyPyImHp
923) 5' -WA C T G G W-3' PypyHpImIm-y-PyPyPyImHp
924} 5' -WA C T G C W-3' PyPyHpImPy-y-ImPyPyImHp
925) 5' -WA C T C T W-3' PyPyHpPyHp-y-PyImPyImHp
926) 5' -WA C T C A W-3' PyPyHpPyPy-Y-HpImPyImHp
927 ) 5' -WA C T C G W-3' PyPyHpPyim-y-PyImPyImHp
928) 5' -WA C T C C W-3' PypyHppypy-y-ImImPyImHp
929) 5' -WA C A T T W-3' PyPyPyHpHp-y-PyPyHpImHp
930) 5' -WA C A T A W-3' PypyPyHpPy-y-HpPyHpImHp
931) 5' -WA C A T G W-3' PyPyPyHpIm-y-PyPyHpImHp
932) 5' -WA C A T C W-3' PyPyPyHpPy-y-ImPyHpImHp
933) 5' -WA C A A T W-3' PypypypyHp-y-PyHpHpImHp
934) 5' -WA C A A A W-3' PyPyPyPyPy-y-HpHpHpImHp
935) 5' -WA C A A G W-3' PyPyPyPyIm-y-PyHpHpImHp
93 6 5' -WA C A A C W-3 PyPyPyPyPy-y- ImHpHpImHp
) '
937) 5' -WA C A G T W-3' PyPypyImHp-y-PyPYHpImHp
938} 5' -WA C A G A W-3' PyPyPyImPy-y-HpPyHpImHp
939) 5' -WA C A G G W-3' PyPyPyImIm-y-PyPyHpImHp
940) 5' -WA C A G C W-3' PyPypyImPy-y-ImPyHpImHp
941) 5' -WA C A C T W-3' PyPyPyPyHp-Y-PyImI3pImHp
942 ) 5' -WA C A C A W-3 PyPyPyPyPy-y-HpImHpImHp
'
943 ) 5' -WA C A C G W-3 PyPypypylm-y-pyImHpImHp
'
944) 5' -WA C A C C W-3' pypypypypy-Y-ImImHpImHp
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-68-
'TABLE 10-ring
43: Hairpin
Polyamides
for
recognition
of
7-by
5'-WACSNNW-3'
DNA aromatic amino acid sequence
sequence
945) 5' A C G TT W-3' PyPyImHpHp-y-pypypylmHp
-W
946) ~5'-W A C G TA W-3' PyPyImHpPy-y-HpPyPyImHp
947) 5'-W A C G TG W-3' PyPyImHpIm-y-PyPyPyImHp
948) 5' A C G TC W-3' PyPyImHpPy-y-ImPyPyImHp
-W
949) 5'-W A C G AT W-3' PyPyImPyHp-y-pyHpPyImHp
950) 5'-W A C G AA W-3' PyPyImPyPy-y-HpHpPyImHp
951) 5' A C G AG W-3' PyPyImPyIm-y-PyHpPyImHp
-W
952) 5' A C G AC W-3' PyPyImPyPy-y-ImHpPyImHp
-W
953) 5'-W A C G GT W-3' PyPyImImHp-y-PyPyPyImHp
954) 5' A C G GA W-3' PyPyImImPy-y-HpPyPyImHp
-W
955) 5' A C G CT W-3' PyPyImPyHp-y-PyImPyImHp
-W
956) 5' A C G CA W-3' PyPyImPyPy-y-HpImPyImHp
-W
957) 5'-W A C ~CTT W-3' PyPyPyHpHp-y-PyPyImImHp
958) 5'-W A C C TA W-3' PyPyPyHpPy-y-HpPyImImHp
959) 5' A C C TG W-3' PyPyPyHpIm-y-PyPyImImHp
-W
960) 5' A C C TC W-3' PyPyPyHpPy-y-ImPyImImHp
-W
961) 5' A C C AT W-3' PyPyPyPyHp-y-PyHpImImHp
-W
962) 5'-W A C C AA W-3' PyPyPyPyPy-y-HpHpImImHp
963) 5'-W A C C AG W-3' PyPyPyPyIm-y-PyHpImImHp
964) 5' A C C AC W-3' PyPyPyPyPy-y-ImHpImImHp
-W
965) 5' A C C GT W-3' PyPyPyImHp-y-PypyImImHp
-W
966) 5' A C C GA W-3' PyPyPyImPy-y-HpPyImImHp
-W
967) 5' A C C CT W-3' PyPyPyPyHp-y-PyImImImHp
-W
968) 5' A C C CA W-3' PyPyPyPyPy-y-HpImImImHp
-W
969) 5'-W A C G GG W-3' PyPyImImIm-y-PyPyPyImHp
970) 5'-W A C G GC W-3' PyPyImImPy-y-ImPyPyImHp
971) 5' A C G CG W-3' PyPyImPyIm-y-PyImPyImHp
-W
972) 5' A C G CC W-3' PyPyImPyPy-y-ImImPyImHp
-W
973) 5'-W A C C GG W-3' PyPyPyImIm-y-PyPyImImHp
974) 5'-W A C C GC W-3' PyPyPyImPy-y-ImPyImImHp
975) 5'-W A C C CG W-3' PyPyPyPyIm-y-PyImImImHp
976) 5'-W A C C CC W-3' PyPypypypy-y-ImImImImHp
CA 02281930 1999-08-18
WO 98137067 PCT/US98101714
-69-
TABLE 44:
10-ring
Hairpin
Poiyamides
for
recognition
of
7-by
5'-WTGWNNW-3'
DNA aromatic amino acid sequence
sequence
977 ) 5' -WT G T TT W-3 ' HpImHpHpHp-y-PyPYPYPyPy
978) ~5' -WT G T TA W-3' HpImHpHpPy-y-HpPyPyPYPy
979) 5' -WT G T TG W-3' HpImHpHpIm-y-PYPyPyPypy
980) 5' -WT G T TC W-3' HpImHpHpPy-y-ImPyPyPyPy
981) 5' -WT G T AT W-3' HpImHpPyHp-y-PYHpPYPyPy
982) 5' -WT G T AA W-3' HpImHppyPy-y-HpHpPyPYPy
983) 5' -WT G T AG W-3' HpImHpPyIm-y-PyHpPyPYPy
984) 5' -WT G T AC W-3' HpImHpPyPy-y-ImHpPYPYpy
985) 5' -WT G T GT W-3' HpImHpImHp-y-PYpyPYpypY
986) 5' -WT G T GA W-3' HpImHpImPy-y-HpPYPyPyPy
987) 5' -WT G T GG W-3' HpImHpImIm-y-PyPYPyPYPy
IS 988) 5' -WT G T GC W-3' HpImHpImPy-y-ImPyPYPyPy
989) 5' -WT G T CT W-3' HpImHpPyHp-y-PYImPyPyPy
990) 5' -WT G T CA W-3' HpImHpPyPy-y-HpImPyPyPy
991) 5' -WT G T CG W-3' HpImHpPyIm-y-PyImPyPyPy
992) 5' -WT G T CC W-3' HpImHpPYPy-y-ImImPyPYPy
993) 5' -WT G A TT W-3' HpImPyHpHp-y-pypyHpPyPy
994) 5' W HpImPyHpPy-y-HpPyHpPyPy
T
G
A
T
A
W-3'
995) 5' -WT G A TG W-3' HpImPyl3plm-y-PyPyHpPypy
996) 5' -WT G A TC W-3' HpImPyHpPy-y-ImPyHpPyPy
997) 5' -WT G A AT W-3' HpImPYPyHp-y-PyHpHpPyPy
998) 5' -WT G A AA W-3' HpImPYPyPy-y-HpHpHpPyPy
999) 5' -WT G A AG W-3' HpImPyPyIm-y-PyHpHpPyPy
1000) 5' -WT G A AC W-3' HpImPyPyPy-y-ImHpHpPYPy
1001) 5' -WT G A GT W-3' Hpln,pyl~p-y_pypYHppypy
1002) 5' -WT G A GA W-3' HpImPyImPy-y-HpPyHpPyPy
1003 5' -WT G A GG W-3 ' HpImPYImIm-y-PyPyHpPyPy
)
1004) 5' -WT G A GC W-3' HpImPyImPy-y-ImPyHpPyPy
1005) 5' -WT G A CT W-3' HpImPyPyHp-y-PYImHpPyPy
1006) 5' -WT G A CA W-3' HpImPYPYPy-y-HpImHpPyPy
1007) 5' -WT G A CG W-3' HpImPyPyIm-y-PyImHpPypy
1008) 5' -WT G A CC W-3' HpImPyPyPy-y-ImImHpPyPy
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-70-
TABLE
45:
10-ring
Hairpin
Polyamides
for
recognition
of
7-by
5'-WTGSNNW-3'
DNA aromatic amino acid sequence
sequence
1009) 5' -W T GG T T W-3' HpImImHpHp-y-PyPyPyPyPy
1010) 'S'-W T GG T A W-3' HpImImHpPy-y-HpPyPyPyPy
1011) 5' -W T GG T G W-3' HpImImHpIm-y-PyPyPyPyPy
1012) 5' -W T GG T C W-3' HpImImHpPy-y-ImPyPyPyPy
1013) 5' -W T GG A T W-3' HpImImPyHp-y-PyHpPyPyPy
1014) 5' -W T GG A A W-3' HpImImPyPy-y-HpHpPyPyPy
1015) 5' -W T GG A G W-3' HpImImPyIm-y-PyHpPyPyPy
1016) 5' -W T GG A C W-3' HpImImPyPy-y-ImHpPyPyPy
1017) 5' -W T GG G T W-3' HpImImImHp-y-PyPyPyPyPy
1018) 5' -W T GG G A W-3' HpImImImPy-~/-HpPyPyPyPy
1019) 5' -W T GG C T W-3' HpImImPyHp-y-PyImPyPyPy
1020) 5' -W T GG C A W-3' HpImImPyPy-y-HpImPyPyPy
1021) 5' -W T GC T T W-3' HpImPyHpHp-y-PyPyImPyPy
1022) 5' -W T GC T A W-3' HpImPyHpPy-y-HpPyImPyPy
1023 5' -W T GC T G W-3 ' HpImPyHpIm-y-PyPyImPyPy
)
1024) 5' -W T GC T C W-3' HpImPyHpPy-y-ImPyImPyPy
1025) 5' -W T GC A T W-3' HpImPyPyHp-y-PyHpImPyPy
1026) 5' -W T GC A A W-3' HpImPyPyPy-y-HpHpImPyPy
1027) 5' -W T GC A G W-3' HpImPyPyIrn-y-PyHpImPyPy
1028) 5' -W T GC A C W-3' HpImPyPyPy-y-ImHpImPyPy
1029) 5' -W T GC G T W-3' HpImPyImHp-y-PyPyImPyPy
1030) 5' -W T GC G A W-3' HpImPyImPy-y-HpPyImPyPy
1031) 5' -W T GC C T W-3' HpImPyPyHp-y-PyImImPyPy
1032) 5' -W T GC C A W-3' HpImPyPyPy-y-HpImImPyPy
1033) 5' -W T GG G G W-3' HpImImImIm-y-PyPyPyPyPy
1034) 5' -W T GG G C W-3' HpImImImPy-y-ImPyPyPyPy
1035) 5' -W T GG C G W-3' HpImImPyIm-y-PyImPyPyPy
1036) 5' -W T GG C C W-3' HpImImPyPy-y-ImImPyPyPy
1037 5' -W T GC G G W-3 ' HpImPyImIm-y-PyPyImPyPy
)
1038) 5' -W T GC G C W-3' HpImPyImPy-y-ImPyImPyPy
1039) 5' -W T GC C G W-3' HpImPyPyIm-y-PyImImPyPy
104 0 5' -W T GC C C W-3 ' HpImPyPyPy-y-ImImImPyPy
)
CA 02281930 1999-08-18
WO 98/3?067 PCT/US98/01714
_71_
TABLE
46:
10-ring
Hairpin
Polyamides
for
recognition
of
7-by
5'-WTTWNNW-3'
DNA aromatic amino acid sequence
sequence
1041) 5' -WT T T T T W-3' HpHpHpHpHp-y-PyPyPypypy
1042) '5'-W T T T T A W-3' HpHpHpHpPy-y-HpPyPyPypy
1043) 5' -WT T T T G W-3' HpHpHpHpIm-y-PyPyPyPyPy
1044) 5' -WT T T T C W-3' HpHpHpHpPy-y-ImPyPyPyPy
1045) 5' -WT T T A T W-3' HpHpHpPyHp-y-PyHpPyPyPy
1046) 5' -WT T T A A W-3' HpHpHpPyPy-y-HpHpPyPyPy
1047) 5' -WT T T A G W-3' HpHpHpPyIm-y-PyHpPyPyPy
1048) 5' -WT T T A C W-3' HpHpHpPyPy-y-ImHpPyPyPy
1049) 5' -WT T T G T W-3' HpHpHpImHp-y-Pypypypypy
1050) 5' -WT T T G A W-3' HpHpHpImPy-y-HpPyPyPyPy
1051) 5' -WT T T G G W-3' HpHpHpImIm-y-PyPypypypy
1052) 5' -WT T T G C W-3' HpHpHpImPy-y-ImPyPyPyPy
1053) 5' -WT T T C T W-3' HpHpHpPyHp-y-PyImPyPyPy
1054) 5' -WT T T C A W-3' HpHpHpPyPy-y-HpImPyPyPy
1055) 5' -WT T T C G W-3' HpHpHpPyIm-y-PyImPyPyPy
1056) 5' -WT T T C C W-3' HpHpHpPyPy-y-ImTmPyPyPy
1057) 5' -WT T A T T W-3' HpHpPyHpHp-y-PypyHpPyPy
1058) 5' -WT T A T A W-3' HpHpPyHpPy-y-HpPyHpPyPy
1059) 5' -WT T A T G W-3' HpHpPyHpIm-y-PyPyHpPyPy
1060) 5' -WT T A T C W-3' HpHpPyHpPy-y-ImPyHpPyPy
1061) 5' -WT T A A T W-3' HpHpPyPyHp-y-pyHpHpPyPy
1062) 5' -WT T A A A W-3' HpHpPyPyPy-y-HpHpHpPyPy
1063) 5' -WT T A A G W-3' HpHpPyPyIm-y-PyHpHpPyPy
1064) 5' -WT T A A C W-3' HpHpPyPyPy-y-ImHpHpPyPy
1065) 5' -WT T A G T W-3' HpHpPyImHp-y-PyPyHpPyPy
1066) 5' -WT T A G A W-3' HpHpPyImPy-y-HpPyHpPyPy
1067) 5' -WT T A G G W-3' HpHpPyImIm-y-PyPyHpPyPy
1068) 5' -WT T A G C W-3' HpHpPyImPy-y-ImPyHpPyPy
1069) 5' -WT T A C T W-3' HpHpPyPyHp-y-PyImHpPyPy
1070) 5' -WT T A C A W-3' HpHpPyPyPy-y-HpImHpPyPy
1071} 5' -WT T A C G W-3' HpApPyPyIm-y-PyImHpPyPy
1072) 5' -WT T A C C W-3' HpApPyPyPy-y-ImImHpPyPy
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-72-
TABLE
47:
10-ring
Hairpin
Polyamides
for
recognition
of
7-by
5'-WTTSNNW-3'
DNA aromatic amino acid sequence
sequence
1073) 5'-W T T G TT W-3' HpHpImHpHp-y-PyPyPyPYPy
1074) -5'-WT T G TA W-3'
HpHpImHpPy-y-HpPyPyPYPy
1075) 5' T T G TG W-3' HpHpImHpIm-y-Pypypypypy
-W
1076) 5'-W T T G TC W-3'
HpHpImHpPy-y-ImPyPyPyPy
1077) 5'-W T T G AT W-3' HpHpImPYHp-y-pygppyPyPy
1078) 5'-W T T G AA W-3' HpHpImPyPy-y-HpHpPYPyPy
1079) 5' T T G AG W-3' HpHpImPyIm-y-PYHpPyPyPy
-W
1080) 5' T T G AC W-3' HpHpImPyPy-y-ImHpPYPYPy
-W
1081) 5' T T G GT W-3' HpHpImImHp-y-pypypypypy
-W
1082) 5' T T G GA W-3' HpHpImImPy-y-HpPyPyPyPy
-W
1083) 5'-W T T G CT W-3'
HpHpImPYHp-y-PyImPyPyPy
1084) 5'-W T T G CA W-3' HpHpImPyPy-y-HpImPyPyPy
1085) 5' T T G GG W-3' HpHpImImIm-y-pypypypypy
-W
1086) 5' T T G GC W-3' HpHpImImPy-y-ImPyPyPYPy
-W
1087) 5'-W T T G CG W-3' HpHpImPYIm-y-PyImPyPyPy
1088) 5' T T G CC W-3' HpHpImPyPy-y-ImImPyPYPy
-W
1089) 5'-W T T C TT W-3' HpHpPyHpHp-y-PypyImPYPy
1090) 5' T T C TA W-3' HpHpPYHpPy-y-HpPYImPyPy
-W
1091) 5' T T C TG W-3' HpHpPyHpIm-y-PypyImPyPy
-W
1092) 5'-W T T C TC W-3' HpHpPyHpPy-y-ImPyImPyPy
1093) 5'-W T T C AT W-3' HpHpPyPyHp-y-PyHpImPYPy
1094) 5'-W T T C AA W-3' HpHpPyPyPy-y-HpHpImPyPy
1095) 5' T T C AG W-3' ' HpHpPyPyIm-y-PYHpImPypy
-W
1096) 5'-W T T C AC W-3' HpHpPYPYPy-y-ImHpImPYPY
1097) 5'-W T T C GT W-3' HpgppYl~p_y_pypylmpypy
1098) 5' T T C GA W-3' HpHpPyImPy-y-HpPyImPyPy
-W
1099) 5' T T C CT W-3' HpHpPyPyHp-y-PyImImPyPy
-W
1100) 5' T T C CA W-3' HpHpPyPyPy-y-HpImImPYPy
-W
1101) 5' T T C GG W-3' HpHpPyImIm-y-PyPyImPyPy
-W
1102) 5'-W T T C GC W-3' HpHpPyImPy-y-ImPyImPyPy
1103) 5'-W T T C CG W-3' HpHpPyPyIm-y-PyImImPyPy
1104) 5'-W T T C CC W-3' HpHpPyPyPy-y-ImImImPyPy
. ,
CA 02281930 1999-08-18
WO 98/37067
PCTIUS98/01714
-73-
TABLE
48:
10-ring
Hairpin
Polyamides
for
recognition
of
7-by
5'-WTAWNNW-3'
DNA aromatic amino acid sequence
sequence
1105) 5' -WT A T T T W-3' HpPyHpHpHp-y-PyPyPyHpPy
S 1106) ~5'-WT A T T A W-3' HpPyHpHpPy-y-HpPyPyHpPy
1107) 5' -WT A T T G W-3' HpPyHpHpIm-y-PypyPyHpPy
1108) 5' -WT A T T C W-3' HpPyHpHpPy-y-ImPyPyHpPy
1109) 5' -WT A T A T W-3' HpPyHpPyHp-y-PyHpPyHpPy
1110) 5' -WT A T A A W-3' HpPyHpPyPy-y-HpHpPyHpPy
1111) 5' -WT A T A G W-3' HpPyHpPyIm-y-PyHpPyHpPy
1112) 5' -WT A T A C W-3' HpPyHpPyPy-y-ImHpPyHpPy
1113) 5' -WT A T G T W-3' HpPyHpImHp-y-PyPyPyHpPy
1114) 5' -WT A T G A W-3' HpPyHpImPy-y-HpPyPyHpPy
1115) 5' -WT A T G G W-3' HpPyHpImIm-y-PyPyPyHpPy
1116) 5' -WT A T G C W-3' HpPyHpImPy-y-ImPyPyHppy
1117) 5' -WT A T C T W-3' HpPyHpPyHp-y-PyImPyHpPy
1118) 5' -WT A T C A W-3' HpPyHpPyPy-y-HpImPyHpPy
1119) 5' -WT A T C G W-3' HpPyHpPyIm-y-PyImPyHpPy
1120) 5' -WT A T C C W-3' HpPyHpPyPy-y-ImImPyHpPy
1121) 5' -WT A A T T W-3' HpPyPyHpHp-y-PyPyHpHpPy
1122) 5' -WT A A T A W-3' HpPyPyHpPy-y-HpPyHpHpPy
1123) 5' -WT A A T G W-3' HpPyPyHpIm-y-PyPyHpHpPy
1124) 5' -WT A A T C W-3' HpPyPyHpPy-y-ImPyHpHpPy
1125) 5' -WT A A A T W-3' HpPyPyPyHp-y-PyHpHpHpPy
1126) 5' -WT A A A A W-3' HpPyPyPyPy-y-HpHpHpHpPy
1127) 5' -WT A A A G W-3' HpPyPyPyIm-y-PyHpHpHpPy
1128) 5' -WT A A A C W-3' HpPyPyPyPy-y-ImHpHpHpPy
1129) 5' -WT A A G T W-3' HpPyPyImHp-y-PyPyHpHpPy
1130) 5' -WT A A G A W-3' HpPyPyImPy-y-HpPyHpHpPy
1131) 5' -WT A A G G W-3' HpPyPyImIm-y-PyPyHpHpPy
1132) 5' -WT A A G C W-3' HpPyPyImPy-y-ImPyHpHpPy
1133) 5' -WT A A C T W-3' HpPyPyPyHp-y-PyImHpHpPy
1134) 5' -WT A A C A W-3' HpPyPyPyPy-y-HpImHpHpPy
1135) 5' -WT A A C G W-3' HpPyPyPyIm-y-PyImHpHpPy
1136) 5' -WT A A C C W-3' HpPyPyPyPy-y-ImImHpHpPy
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-74-
TABLE
49:
10-ring
Hairpin
Polyamides
for
recognition
of
7-by
5'-WTASNNW-3'
DNA aromatic amino acid sequence
sequence
1137 ) 5' -WT A G T T W-3 HpPyImHpHp-y-PyPypyHpPy
'
S 1138) ~5'-WT A G T A W-3' HpPyImHpPy-y-HpPyPyHpPy
1139) 5' -WT A G T G W-3' HpPyImHpIm-y-PyPyPyHpPy
1140) 5' -WT A G T C W-3' HpPyImHpPy-y-ImPypyHpPy
1141) 5' -WT A G A T W-3' HpPyImPyHp-y-PyHpPyHpPy
1142) 5' -WT A G A A W-3' HpPyImPyPy-y-HpHpPyHpPy
1143) 5' -WT A G A G W-3' HpPyImPyIm-y-PyHpPyHpPy
1144) 5' -WT A G A C W-3' HpPyImPyPy-y-ImHpPyI-IpPy
1145) 5' -WT A G G T W-3' HpPyImImHp-y-PyPyPyHpPy
1146) 5' -WT A G G A W-3' HpPyImImPy-y-HpPyPyHpPy
1147) 5' -WT A G C T W-3' HpPyImPyHp-y-PyImPyI-IpPy
1148) 5' -WT A G C A W-3' HpPyImPyPy-y-HpImPyHpPy
1149) 5' -WT A G G G W-3' HpPyImImIm-y-PyPyPyHpPy
1150) 5' -WT A G G C W-3' HpPyImImPy-y-ImPyPyHpPy
1151) 5' -WT A G C G W-3' HpPyImPyIm-y-PyImPyHpPy
1152) 5' -WT A G C C W-3' HpPyImPyPy-y-ImImPyHpPy
1153) 5' -WT A C T T W-3' HpPyPyHpHp-y-PyPyImHppy
1154) 5' -WT A C T A W-3' HpPyPyHpPy-y-HpPyImHpPy
1155) 5' -WT A C T G W-3' HpPyPyHpIm-y-PyPyImHpPy
1156 ) 5' -WT A C T C W-3 HppyPyHpPy-y-ImPyImHpPy
'
1157) 5' -WT A C A T W-3' HpPyPyPyHp-y-PyHpImHpPy
1158) 5' -WT A C A A W-3' HpPyPyPyPy-y-HpHpImHpPy
1159) 5' -WT A C A G W-3' HpPyPyPyIm-y-PyHpImHpPy
1160) 5' -WT A C A C W-3' HpPyPyPyPy-y-ImHpImHpPy
1161) 5' -WT A C G T W-3' HppyPyImHp-y-PyPyImHpPy
1162) 5' -WT A C G A W-3' HpPyPyImPy-y-HpPyImHpPy
1163) 5' -WT A C C T W-3' HpPyPyPyHp-y-PyImImHpPy
1164 ) 5' -WT A C C A W-3 HpPyPyPyPy-y-HpImImHpPy
'
1165) 5' -WT A C G G W-3' HpPyPyImIm-y-PyPyImHpPy
1166 ) 5' -WT A C G C W-3 HpPyPyImPy-y-ImPyImHpPy
'
1167) 5' -WT A C C G W-3' HpPyPyPyIm-y-PyImImHpPy
1168) 5' -WT A C C C W-3' HpPyPyPyPy-y-ImImImHpPy
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-75-
l
Al3LH
50:
10-ring
Hairpin
Polyamides
for
recognition
of
7-by
5'-WTCWNNW-3'
DNA aromatic amino acid sequence
sequence
1169) 5'-W T C TT T W-3' HpPyHpHpHp-y-PypypylmPy
1170) ~5'-W T C TT A W-3' HpPyHpHpPy-y-HpPyPyImPy
1171) 5'-W T C TT G W-3' HpPyHpHpIm-y-Pypypylmpy
1172) 5'-W T C TT C W-3' HpPyHpHpPy-y-ImPyPyImPy
1173) 5'-W T C TA T W-3'
HPPYHPPYHP-Y-PYHPPYImPy
1174) 5'-W T C TA A W-3' HpPyHpPyPy-y-HpHpPyImPy
1175) 5'-W T C TA G W-3' HpPyHpPyIm-y-PyHpPyImPy
1176) 5'-W T C TA C W-3' HpPyHpPypy-y-ImHppyImPy
1177) 5'-W T C TG T W-3' HppyHpl~p_Y-pypypylmPy
1178) 5'-W T C TG A W-3' HpPyHpImPy-y-HpPyPyImPy
1179) 5'-W T C TG G W-3' HpPyHpImIm-y-PyPyPyImPy
1180) 5'-W T C TG C W-3' HpPyHpImPy-y-ImPyPyImPy
1181) 5'-W T C TC T W-3' HpPyHpPyHp-y-PyImPyImPy
1182) 5'-W T C TC A W-3' HpPyHpPypy-y-HpImPyImPy
1183) 5'-W T C TC G W-3' HpPyHpPyIm-y-PyImPyImPy
1184) 5'-W T C TC C W-3' HpPyHpPyPy-y-ImImPyImPy
1185) 5'-W T C AT T W-3' HpPyPyHpHp-y-PyPyHpImPy
1186) 5'-W T C AT A W-3' HpPyPyHpPy-y-HpPyHpImPy
1187) 5'-W T C AT G W-3' HpPyPyHpIm-y-PyPyHpImPy
1188) 5'-W T C AT C W-3' HpPyPyHpPy-y-ImPyHpImPy
1189) 5'-W T C AA T W-3' HpPyPyPyHp-y-PyHpHpImPy
1190) 5'-W T C AA A W-3' HpPyPyPyPy-y-HpHpHpImPy
1191) 5'-W T C AA G W-3' ~ HpPyPyPyIm-y-PyHpHpImPy
1192) 5'-W T C AA C W-3' HpPyPyPyPy-y-ImHpHpImPy
1193) 5'-W T C AG T W-3' HpPyPyImHp-y-PyPyHpImPy
1194) 5'-W T C AG A W-3' HpPyPyImPy-y-HpPyHpImPy
1195) 5'-W T C AG G W-3' HpPyPyImIm-y-PyPyHpImPy
1196) 5'-W T C AG C W-3' HpPyPyImPy-y-ImPyHpImPy
1197) 5'-W T C AC T W-3' HpPyPyPyHp-y-PyImHpImPy
1198) 5'-W T C AC A W-3' HpPyPyPyPy-y-HpImHpImPy
1199) 5'-W T C AC G W-3' HpPyPyPyIm-y-PyImHpImPy
1200) 5'-W T C AC C W-3' HpPyPyPyPy-y-ImImHpImPy
CA 02281930 1999-08-18
WO 98/37067 PCTlUS98/01714
-76-
TABLE
51:
l0~ring
Hairpin
Polyamides
for
recognition
of
7-by
5'-WTCSNNW-3'
DNA aromatic amino acid sequence
sequence
1201) 5' -W T CG T T W-3' HpPyImHpHp-y-PyPyPyImPy
1202) ~5'-W T CG T A W-3' HpPyImHpPy-y-HpPyPyImPy
1203) 5' -W T CG T G W-3' HpPyImHpIm-y-PyPyPyImPy
1204) 5' -W T CG T C W-3' HpPyImHpPy-y-ImPyPyImPy
1205) 5' -W T CG A T W-3' HpPyImPyHp-y-PyHpPyImPy
1206) 5' -W T CG A A W-3' HpPyImPyPy-y-HpHpPyImPy
1207) 5' -W T CG A G W-3' HpPyImPyIm-y-PyHpPyImPy
1208) 5' -W T CG A C W-3' HpPyImPyPy-y-ImHpPyImPy
1209) 5' -W T CG G T W-3' HpPyImImHp-y-PyPyPyImPy
1210) 5' -W T CG G A W-3' HpPyImImPy-y-HpPyPyImPy
1211) 5' -W T CG C T W-3' HpPyImPyHp-y-PyImPyImPy
1212) 5' -W T CG C A W-3' HpPyImPyPy-y-HpImPyImPy
1213) 5' -W T CC T T W-3' HpPyPyHpHp-y-PyPyImImPy
1214) 5' -W T CC T A W-3' HpPyPyHpPy-y-HpPyImImPy
1215) 5' -W T CC T G W-3' HpPyPyHpIm-y-PyPyImImPy
1216 5' -W T CC T C W-3 ' HpPyPyHpPy-y- ImPyImImPy
)
1217 5' -W T CC A T W-3 ' HpPyPyPyHp-y-PyHpImImPy
)
1218) 5' -W T CC A A W-3' HpPyPyPyPy-y-HpHpImImPy
1219) 5' -W T CC A G W-3' HpPyPyPyIm-y-PyHpImImPy
1220) 5' -W T CC A C W-3' HpPyPyPyPy-y-ImHpImImPy
1221) 5' -W T CC G T W-3' HpPyPyImHp-y-PyPyImImPy
1222 5' -W T CC G A W-3' HpPyPyImPy-y-HpPyImImPy
)
1223 5' -W T CC C T W-3 ' HpPyPyPyHp-y-PyImImImPy
)
1224) 5' -W T CC C A W-3' HpPyPyPyPy-y-HpImImImPy
1225) 5' -W T CG G G W-3' HpPyImImIm-y-PyPyPyImPy
1226) 5' -W T CG G C W-3' HpPyImImPy-y-ImPyPyImPy
1227) 5' -W T CG C G W-3' HpPyImPyIm-y-PyImPyImPy
1228) 5' -W T CG C C W-3' HpPyImPyPy-y-ImImPyImPy
1229) 5' -W T CC G G W-3' HpPyPyImIm-y-PyPyImImPy
1230) 5' -W T CC G C W-3' HpPyPyImPy-y-ImPyImImPy
1231) 5' -W T CC C G W-3' HpPyPyPyIm-y-PyImImImPy
1232 5' -W T CC C C W-3 ' HpPyPyPyPy-y-ImImImImPy
)
CA 02281930 1999-08-18
WO 98/37067 PCT/US98101714
_77_
TABLE 52 :
10-ring
Hairpin
Yolyamides
for
recognition
of
7-by
5'-WGGWNNW-3'
with
(3
substitutions.
DNA aromatic amino acid sequence
sequence
243(3) 5' G G T TG W-3' ImIm-~-HpIm-y-PYpypypypY
-W
243~3p) '5' G G T TG W-3' ImIm-[3-HpIm-y-PYPy-~3-pypy
-W
247(3) 5' G G T AG W-3' Imlm-J3-PyIm-y-PyHpPyPyPy
-W
247~p) 5' G G T AG W-3' ImIm-~-PyIm-y-PYHp-(3-PyPy
-W
249(3) 5' G G T GT W-3' ImIm-(3-ImHp-y-Pypypypypy
-W
249(3p) 5' G G T GT W-3' ImIm-~3-ImHp-y-Pypy-~3-pypY
-W
2503) 5' G G T GA W-3' ImIm-~i-ImPy-y-HpPyPyPyPy
-W
250(3p) 5' G G T GA W-3' ImIm-(3-ImPy-y-HpPy-~i-PypY
-W
2513) 5' G G T GG W-3' ImIm-(3-ImIm-y-pypypypypy
-W
251(3p) 5' G G T GG W-3' Imlm-(3-Imlm-y-PyPy-(3-PyPy
-W
252(3) 5' G G T GC W-3' Imlm-/3-ImPy-y-ImPyPyPyPy
-W
252(3p) 5' G G T GC W-3' Imam-(3-ImPy-y-ImPy-(3-Pypy
-W
255(3) 5' G G T CG W-3' ImIm-~-Pylm-y-pyImPyPyPy
-W
255~ip) 5' G G T CG W-3' ImIm-(3-PYIm-y-PyIm-a-PyPy
-W
2593) 5' G G A TG W-3' ImIm-(3-HpIm-y-PyPyHpPyPy
-W
259~3p) 5' G G A TG W-3' ImIm-(3-HpIm-y-PyPy-(3-PyPy
-W
263(3) 5' G G A AG W-3' ImIm-p-PyIm-y-PyHpHpPyPy
-W
263(3p) 5' G G A AG W-3' ImIm-(3-PyIm-y-PyHp-~3-PyPy
-W
2653) 5' G G A GT W-3' ImIm-(3-ImHp-y-PypyHppypy
-W
265(3p) 5' G G A GT W-3' Imlm-(3-ImHp-y-PyPy-p-PyPy
-W
266(3) 5' G G A GA W-3' ImIm-(3-ImPy-y-HpPyHpPyPy
-W
266~3p) 5' G G A GA W-3' Imlm-~3-ImPy-y-HpPy-(3-PyPy
-W
267(3) 5' G G A GG W-3' ImIm-(3-ImIm-y-PyPyHpPyPy
-W
267(3p) 5' G G A GG W-3' ImIm-/3-ImIm-y-Pypy-~-pypy
-W
2683) 5' G G A GC W-3' Imlm-~3-ImPy-y-ImpyHpPyPy
-W
268~3p) 5' G G A GC W-3' ImIm-(3-ImPy-y-ImPy-~3-PyPy
-W
271(3) 5' G G A CG W-3' ImIm-~3-PyIm-y-PyImHpPyPy
-W
271(3p) 5' G G A CG W-3' Imlm-(3-PyIm-y-PyIm-j3-PyPy
-W
CA 02281930 1999-08-18
WO 98I370b7 PCT/US98/01714
_78_
TABLE
53: 10-ring
Hairpin
Polyamides
for recognition
of 7-by
5'-WGGSNNW-3'
with
(3 substitutions.
DNA aromatic amino acid sequence
sequence
273(3) 5' G G G TT W-3' ImImIm-p-Hp-y-PyPyPyPyPy
-W
273~3p) ~ G G G TT W-3' ImImIm-(3-Hp-y-Py-(3-PyPyPy
5'
-W
274(3) 5' G G G TA W-3' ImImIm-(3-Py-y-HpPyPyPyPy
-W
274~3p) 5' G G G TA W-3' ImImIm-~3-Py-y-Hp-(3-PyPyPy
-W
275(3) 5' G G G TG W-3' ImImIm-~3-Im-y-PyPyPyPyPy
-W
275~3p) 5' G G G TG W-3' ImImIm-~3-Im-y-Py-(3-PyPyPy
-W
276(3) 5' G G G TC W-3' ImImIm-(3-Py-y-ImPyPyPyPy
-W
276(3p) 5' G G G TC W-3' ImImIm-(3-Py-y-Im-(3-PyPyPy
-W
277(3) 5'-W G G G AT W-3' ImImIm-(3-Hp-y-PyHpPyPyPy
277~3p) 5' G G G AT W-3' ImImIm-(3-Hp-y-Py-~3-PyPyPy
-W
2783) 5' G G G AA W-3' ImImIm-(3-Py-y-HpHpPyPyPy
-W
278(3p) 5' G G G AA W-3' ImImIm-~-Py-y-Hp-/3-PyPyPy
-W
279(3) 5' G G G AG W-3' ImImIm-(3-Im-y-PyHpPyPyPy
-W
279~3p) 5' G G G AG W-3' ImImIm-~-Im-y-Py-[3-PyPyPy
-W
280(3) 5' G G G AC W-3' ImImIm-(3-Py-y-ImHpPyPyPy
-W
280(3p) 5' G G G AC W-3' ImImIm-(3-Py-y-Im-~3-PyPyPy
-W
283(3) 5' G G G CT W-3' ImImIm-p-Hp-y-PyImPyPyPy
-W
284(3) 5' G G G CA W-3' ImImIm-(3-Py-y-HpImPyPyPy
-W
285(3) 5' G G C TT W-3' ImImPylipHp-y-Py-p-ImPyPy
-W
285(3p) 5' G G C TT W-3' ImImPy-(3-Hp-y-Py-(3-ImPyPy
-W
286(3) 5' G G C TA W-3' ImImPyHpPy-y-Hp-~i-ImPyPy
-W
286~3p) 5' G G C TA W-3' ImImPy-(3-Py-y-Hp-(3-ImPyPy
-W
287~i) 5' G G C TG W-3' ImIm-~3-HpIm-y-Py-(3-ImPyPy
-W
288(3) 5' G G C TC W-3' ImImPyHpPy-y-Im-(3-ImPyPy
-W
288~ip) 5' G G C TC W-3' ImImPy-(3-Py-y-Im-(3-ImPyPy
-W
289(3) 5' G G C AT W-3' ImImPyPyHp-y-Py-p-ImPyPy
-W
289(3p) 5' G G C AT W-3' ImImPy-/3-Hp-y-Py-(3-ImPyPy
-W
290(3) 5' G G C AA W-3' ImImPyPyPy-y-Hp-~-ImPyPy
-W
290~ip) 5' G G C AA W-3' ImImPy-(3-Py-y-Hp-(3-ImPyPy
-W
CA 02281930 1999-08-18
WO 98137067
_79_
PCT/US98/01714
TABLE 53 (cont.): ecogmrion of 7-by 5'-WGGSNNW-3'
10-ring Hairpin with ~3 substitutions
Polyamides for
r
.
DNA aromatic amino acid sequence
sequence
291(3) 5'-W GG C A G W-3' ImIm-(3-PyIm-y-py-(3-ImPyPy
292(3) 5' GG C A C W-3' TmImPyPyPy-y-Im-(3-ImPyPy
-W
292(3p) ~ GG C A C W-3' ImImPy-(3-Py-y-Im-~i-ImPyPy
5'
-W
293(3) 5' GG C G T W-3' Imam-(3-ImHp-y-Py-(3-ImPyPy
-W
294(3) 5' GG C G A W-3' ImIm-(3-ImPy-y-Hp-(3-ImPyPy
-W
295x) 5'-W GG C C T W-3' ImImPyPyHp-y-pylmlm-(3-Py
2963) 5' GG C C A W-3' ImImPyPypy-y-HpImIm-p-Py
-W
619(3) 5' GG G C G W-3' ImImIm-(3-Im-y-PyImPyPyPy
-W
G20(3) 5' GG G C C W-3' ImImIm-(3-Py-y-ImImPypyPy
-W
G21(3) 5' GG C G G W-3' Imlm-/3-Imlm-y-Py-(3-ImPyPy
-W
G22(3) 5' GG C G C W-3' ImIm-(3-Impy-y-Im-~3-ImPyPy
-W
G23~3) 5' GG C C G W-3' Imlm-(3-Pylm-y-PyImIm-(3-Py
-W
G24(3) 5' GG C C C W-3' ImImPyPyPy-y-ImImIm-(3-Py
-W
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-80-
TABLE :
54 10-ring
Hairpin
Polyamides
for
recognition
of
7-by
5'-WGTWNNW-3'
with
(3
substitutions.
DNA aromatic amino acid sequence
sequence
299(3) 5' G T T T G W-3' ImHp-(3-HpIm-y-PyPyPyPyPy
-W
299~3p) 5' G T T T G W-3' ImHp-J3-HpIm-y-PyPy-(3-PyPy
-W
303(3) ' G T T A G W-3' ImHp-(3-PyIm-y-PyHpPyPyPy
5'
-W
303~3p) 5' G T T A G W-3' ImHp-(3-PyIm-y-PyHp-(3-PyPy
-W
305(3) 5' G T T G T W-3' ImHp-(3-ImHp-y-PyPyPyPyPy
-W
305(3p) 5' G T T G T W-3' ImHp-(3-ImHp-y-PyPy-(3-PyPy
-W
306(3) 5' G T T G A W-3' ImHp-~3-ImPy-y-HpPyPyPyPy
-W
306(3p) 5' G T T G A W-3' ImHp-~3-ImPy-y-HpPy-(3-PyPy
-W
3073) 5' G T T G G W-3' ImHp-(3-ImIm-y-PyPyPyPyPy
-W
307~p) 5' G T T G G W-3' ImHp-J3-ImIm-y-PyPy-~3-PyPy
-W
3083) 5' G T T G C W-3' ImHp-(3-ImPy-y-ImPyPyPyPy
-W
308~3p) 5' G T T G C W-3' ImHp-(3-ImPy-y-ImPy-p-PyPy
-W
3113) 5' G T T C G W-3' ImHp-~3-PyIm-y-PyImPyPyPy
-W
311(3p) 5' G T T C G W-3' ImHp-(3-Pylm-y-Pylm-~i-PyPy
-W
3153) 5' G T A T G W-3' ImHp-p-HpIm-y-PyPyHpPyPy
-W
315(3p) 5' G T A T G W-3' ImHp-p-HpIm-y-PyPy-(3-PyPy
-W
3193) 5' G T A A G W-3' ImHp-(3-Pylm-y-PyHpHpPyPy
-W
319(3p) 5' G T A A G W-3' ImHp-~3-PyIm-y-PyHp-(3-PyPy
-W
321~i) 5' G T A G T W-3' ImHp-(3-ImHp-y-PyPyApPyPy
-W
321(3p) 5' G T A G T W-3' ImHp-(3-ImHp-y-PyPy-(3-PyPy
-W
322(3) 5' G T A G A W-3' ImHp-~i-ImPy-y-HpPyHpPyPy
-W
322(3p) 5' G T A G A W-3' ImHp-~3-ImPy-y-HpPy-(3-PyPy
-W
323(3) 5' G T A G G W-3' ImHp-~3-Imlm-y-PyPyHpPyPy
-W
323(3p) 5' G T A G G W-3' ImHp-~3-ImIm-y-PyPy-(3-PyPy
-W
324(3) 5' G T A G C W-3' ImHp-(3-ImPy-y-ImPyHpPyPy
-W
324~p) 5' G T A G C W-3' ImHp-(3-ImPy-y-ImPy--PyPy
-W
327(3) 5' G T A C G W-3' ImHp-(3-PyIm-y-PyImHpPyPy
-W
327(3p) 5' G T A C G W-3' ImHp-(3-PyIm-y-Pylm-(3-PyPy
-W
CA 02281930 1999-08-18
WO 98/37067 PCT/LTS98101714
-81-
'TABLE
55: 10-ring
Hairpin
Polyamides
for recognition
of 7-by
5'-WGTSNNW-3'
with ~3
substitutions.
DNA aromatic amino acid sequence
sequence
3293) 5' G T G T T W-3' Im-(3-ImHpHp-y-PyPyPYPYPy
-W
329(3P) '5'-WG T G T T W-3' Im-(3-ImHpHp-y-Pypypy-p-py
3303) 5' G T G T A W-3' Im-J3-ImHpPy-y-Hppypypypy
-W
330(3p 5' G T G T A W-3' Im-(3-ImHpPy-Y-HpPYPy-~3-py
-W
3313) 5' G T G T G W-3' Im-(3-ImHpIm-y-PyPyPYPyPy
-W
331(3p) 5' G T G T G W-3' Im-(3-ImHpIm-y-PyPYPy-~3-Py
-W
332J3) 5' G T G T C W-3' Im-a-ImHpPy-y-ImPyPyPYPy
-W
332(3p) 5' G T G T C W-3' Im-~-ImHpPy-y-ImPYPy-/3-Py
-W
333(3) 5' G T G A T W-3' Im-(3-ImPyHp-Y-PYHpPyPyPy
-W
333~ip) 5' G T G A T W-3' Im-~3-ImPYHp-y-PyHpPy-(3-Py
-W
334(3) 5' G T G A A W-3' Im-~3-ImPyPy-y-HpHpPYPYPy
-W
334(3p) 5' G T G A A W-3' Im-(3-ImPyPy-y-HpHpPy-p-Py
-W
335~i) 5' G T G A G W-3' Im-(3-ImPyIm-y-PyHpPYPYPy
-W
335pp) 5' G T G A G W-3' Im-p-ImPyIm-Y-PyHpPy-(3-Py
-W
3363) 5' G T G A C W-3' Im-p-ImPyPy-y-ImHpPYPYPy
-W
336(3p) 5' G T G A C W-3' Im-(3-ImPyPy-y-ImHppy-p-Py
-W
337(3) 5' G T G G T W-3' Im-(3-ImImHp-y-PyPypypypy
-W
337(3p) 5' G T G G T W-3' Im-~3-ImImHp-y-PYPyPy-(3-Py
-W
338(3) 5' G T G G A W-3' Im-(3-ImImPy-y-HpPYPYPYPy
-W
338~3p) 5' G T G G A W-3' Im-(3-ImImPy-y-HpPyPy-(3-Py
-W
339(3) 5' G T G C T W-3' Im-~-ImPyHp-y-PYImPyPyPy
-W
339~p) 5' G T G C T W-3' Im-~3-ImPYHp-y-PyImPy-p-Py
-W
3403) 5' G T G C A W-3' ~ Im-p-ImPyPy-y-HpImPyPyPy
-W
340(3p) 5' G T G C A W-3' Im-p-ImPyPy-Y-HpImPy-~3-Py
-W
3413) 5' G T G G G W-3' Im-p-ImImIm-y-PyPyPyPyPy
-W
341(3p) 5' G T G G G W-3' Im-~3-ImImIm-y-PypyPy-(3-PY
-W
342(3) 5' G T G G C W-3' Im-(3-ImImPy-y-ImPyPYPyPy
-W
342(3p) 5' G T G G C W-3' Im-(3-ImImPy-y-ImPyPy-(3-Py
-W
343(3) 5' G T G C G W-3' Im-(3-ImPyIm-y-PyImPyPypy
-W
CA 02281930 1999-08-18
WO 98/37067 PCT/US98101714
-82-
TABLE 55 Polyamides
(cont.): for
10-ring recognition
Hairpin of
7-by
5'-WGTS1VNW-3'
with
J3
substitutions.
DNA aromatic amino acid sequence
sequence
343(3p) 5' G T GC G W-3' Im-(3-ImPyIm-y-PyImPy-(3-Py
-W
344(3) 5' G T GC C W-3' Im-(3-ImPyPy-y-ImImPyPyPy
-W
344(3p) '5' G T GC C W-3' Im-p-ImPyPy-y-ImImPy-(3-Py
-W
345(3) 5' G T CT T W-3' ImHpPyI~IpHp-y-Py-~3-ImPyPy
-W
345~3p) 5' G T CT T W-3' ImHpPy-~3-Hp-y-Py-(3-ImPyPy
-W
346(3) 5' G T CT A W-3' ImHpPyHpPy-y-Hp-(3-ImPyPy
-W
346(3p) 5' G T CT A W-3' ImHpPy-~3-Py-y-Hp-(3-ImPyPy
-W
3473} 5' G T CT G W-3' ImHp-(3-HpIm-y-Py-p-ImPyPy
-W
3483) 5' G T CT C W-3' ImHpPyHpPy-y-Im-(3-ImPyPy
-W
348(3p) 5' G T CT C W-3' ImHpPy-(3-Py-y-Im-~3-ImPyPy
-W
349(3) 5' G T CA T W-3' ImHpPypyHp-y-Py-~-ImPyPy
-W
349(3p) 5' G T CA T W-3 T ImHpPyPyHp-y-Py--ImPyPy
-W
350(3) 5' G T CA A W-3' ImHpPyPyPy-y-Hp-~3-ImPyPy
-W
350~3p) 5' G T CA A W-3' ImHpPy-(3-Py-y-Hp-~i-ImPyPy
-W
351(3} 5' G T CA G W-3' ImHp-~3-PyIm-y-Py-(3-ImPyPy
-W
3523) 5' G T CA C W-3' ImHpPyPyPy-y-Im-~3-ImPyPy
-W
352(3p) 5' G T CA C W-3' ImHpPy-(3-Py-y-Im-(3-ImPypy
-W
3533) 5' G T CG T W-3' ImHp-(3-ImHp-y-Py-(3-ImPyPy
-W
354(3) 5' G T CG A W-3' ImHp-~-Impy-y-Hp--ImPypy
-W
3553) 5' G T CC T W-3' ImHpPypyHp-y-PyImIm-(3-Py
-W
355~3p) 5' G T CC T W-3' Im-(3-PyPyHp-y-PyImIm-[3-Py
-W
3563) 5' G T CC A W-3' ImHppyPyPy-y-HpImIm-p-Py
-W
356~3p) 5' G T CC A W-3' Im-~3-PyPyPy-y-HpImIm-(3-Py
-W
357(3) 5' G T CG G W-3' ImHp-(3-ImIm-y-Py-p-ImPyPy
-W
358(3) 5' G T CG C W-3' ImHp-(i-ImPy-y-Im-(3-ImPyPy
-W
359(3) 5' G T CC G W-3' ImHp-/3-Pylm-y-PyImIm-(i-Py
-W
360(3) 5' G T CC C W-3' ImHpPyPyPy-y-ImImIm-~3-Py
-W
360~ip) 5' G T CC C W-3' Im-p-PyPyPy-y-ImImIm-p-Py
-W
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
_g3_
TABLE 56: l0-ring
Hairpin
Polyamides
for
recognition
of
7-by
5'-WGAWNNW-3'
with
~3
substitutions.
DNA aromatic amino acid sequence
sequence
363(3) 5' G A T T G W-3' ImPy-~-HpIm-y-Pypypygppy
-W
363~3p) 5' G A T T G W-3' ImPy-(3-HpIm-y-Pypy-(3-Hppy
-W
3673) ' G A T A G W-3' ImPy-(3-PyIm-y-pyHpPYHpPy
S'
-W
367pp) 5' G A T A G W-3' ImPy-p-PyIm-y-PYHp-(3-HpPy
-W
369(3) 5' G A T G T W-3' ImPy-~3-ImHp-y-PyPYPYHpPy
-W
369(3p) 5' G A T G T W-3' ImPy-~3-ImHp-y-pypy-(3-HpPy
-W
370(3) 5' G A T G A W-3' ImPy-(3-ImPy-y-HpPYPYHpPy
-W
370~p) 5' G A T G A W-3' ImPy-(3-ImPy-y-HpPy-~3-HpPy
-W
371~i) 5' G A T G G W-3' ImPy-p-ImIm-y-PyPypyHpPy
-W
371(3p) 5' G A T G G W-3' ImPy-(3-ImIm-y-Pypy-~-HpPy
-W
372(3) 5' G A T G C W-3'
-W ImPy- (3 - ImPy-y- ImPYPyHpPy
372(3p) 5' G A T G C W-3' ImPy-p-ImPy-y-ImPy-~3-HpPy
-W
375(3) 5' G A T C G W-3' ImPy-(3-Pylm-y-PyImPYHpPy
-W
375~3p) 5' G A T C G W-3' ImPy-(3-PyIm-y-pylm-(3-HpPy
-W
379(3) 5' G A A T G W-3' ImPy-~-HpIm-y-PYPYHpHpPy
-W
379(3p) 5' G A A T G W-3' ImPy-p-HpIm-y-PyPy-(3-HpPy
-W
383(3) 5' G A A A G W-3' ImPy-~3-PyIm-y-PYHpHpHpPy
-W
383(3p) 5' G A A A G W-3' ImPy-~3-PYIm-y-pyHp-(3-HpPy
-W
385(3) 5' G A A G T W-3' ImPy-~3-ImHp-y-PyPYHpHpPy
-W
385(3p) 5' G A A G T W-3' ImPy-(3-ImHp-y-Pypy-~3-HppY
-W
386(3) 5' G A A G A W-3'
-W ImPy-(3-ImPy-y-HpPyHpHpPy
386(3p) 5' G A A G A W-3' ImPy-~3-ImPy-y-HpPy-(3-HpPy
-W
387(3) 5' G A A G G W-3' ImPy-(3-Imlm-y-PyPYHpHpPy
-W
387(3p) 5'-WG A A G G W-3'
ImPy-(3-ImIm-y-PyPy-(3-HpPy
3883) 5' G A A G C W-3' ImP
-W y-~3-ImPy-y-ImPyHpHpPy
388(3p) 5' G A A G C W-3' ImPy-~3-ImPy-y-ImPy-/3-HpPy
-W
391~i) 5'-WG A A C G W-3' ImPy-~-PyIm-y-PyImHpHpPy
391(3p) 5' G A A C G W-3' ImPy-(3-Pylm-y-PyIm-~-HpPy
-W
CA 02281930 1999-08-18
WO 98137067 PCTICTS98/01714
-84-
TABLE
57: 10-ring
Hairpin
Polyamides
for recognition
of 7-by
5'-WGASNNW-3'
with
(3 substitutions.
DNA aromatic amino acid sequence
sequence
393) 5' G A G TT W-3' Im--ImHpHp-y-PyPyPyHpPy
-W
394(3p) 5'-W G A G TA W-3' Im--ImHpPy-y-Hppypy--py
395(3) ~ G A G TG W-3' Im--ImHpIm-y-PyPyPyHpPy
5'
-W
395~3p) 5'-W G A G TG W-3' Im--ImHpIm-y-PyPyPy--Py
396) 5'-W G A G TC W-3' Im--ImHpPy-y-ImPyPyHpPy
396p) 5' G A G TC W-3' Im--ImHpPy-y-ImPyPy--Py
-W
397) 5' G A G AT W-3' Im--ImPyHp-y-PyHpPyHpPy
-W
397~p) 5' G A G AT W-3' Im-~i-ImpyHp-y-PyHpPy--Py
-W
398) 5' G A G AA W-3' Im--ImPyPy-y-HpHpPyHpPy
-W
398p) 5'-W G A G AA W-3' Im--ImPyPy-y-HpHpPy--Py
399(3) 5' G A G AG W-3' Im--ImPyIm-y-PyI-ippyHpPy
-W
399~3p) 5' G A G AG W-3' Im-(3-ImPyIm-y-PyHpPy--Py
-W
400(3) 5' G A G AC W-3' Im--ImpyPy-y-ImHpPyHpPy
-W
400(3p) 5'-W G A G AC W-3' Im-~-ImpyPy-y-ImHppy-p-Py
401(3) 5' G A G GT W-3' Im--ImImHp-y-PypyPyHpPy
-W
401p) 5'-W G A G GT W-3' Im--ImImHp-y-PyPypy--py
402) 5' G A G GA W-3' Im--ImImPy-y-HppyPyHpPy
-W
402p) 5'-W G A G GA W-3' Im--ImImPy-y-HpPyPy--Py
403 ) 5'-W G A G CT W-3' Im--ImPyHp-y-PyImPyHpPy
403(3p) 5' G A G CT W-3' Im--ImPyHp-y-PyImPy--Py
-W
404) 5'-W G A G CA W-3' Im--ImPyPy-y-HpImPyHpPy
404~3p) 5'-W G A G CA W-3' Im--ImPyPy-y-HpImPy--Py
405(3) 5' G A G GG W-3' Im--ImImIm-y-PyPyPyHpPy
-W
405p) 5'-W G A G GG W-3' 'Im--ImImIm-y-PyPyPy--Py
406(3) 5' G A G GC W-3' Im-(3-ImImPy-y-ImPyPyHpPy
-W
406~ip) 5' G A G GC W-3' Im--ImImPy-y-ImPyPy--Py
-W
407(3) 5'-W G A G CG W-3' Im--ImPyIm-y-PyImPyHpPy
407(3p) 5'-W G A G CG W-3' Im--ImPyIm-y-PyImPy--Py
408) 5' G A G CC W-3' Im-(3-ImPyPy-y-ImImPyHpPy
-W
408(3p) 5' G A G CC W-3' Im--ImPyPy-y-ImImPy-(3-Py
-W
CA 02281930 1999-08-18
WO 98137067 PCT/US98/01714
-85-
1 AliLlr S / (cont):
10-ring Hairpin
Polyamides for
recognition of
7-by 5'-WGASNNW-3'
with (3 substitutions.
D NA aromatic amino acid sequence
sequence
4093) 5'-W G AC T T W-3' ImPyPyHpHp-y-py-(3-I~pPy
409(3p) 5' G AC T T W-3' ImPyPy-~3-Hp-y-Py-(3-ImHpPy
-W
4103) 'S' G AC T A W-3' ImPyPyHpPy-y-Hp-(3-ImHpPy
-W
410(3p) 5' G AC T A W-3' ImPyPy-(3-Py-y-Hp-(3-ImHpPy
-W
411(3) 5' G AC T G W-3' ImPy-~i-HpIm-y-Py-(3-ImHpPy
-W
412(3) 5'-W G AC T C W-3' ImPYPyHpPy-y-Im-(3-ImHpPy
412pp) 5'-W G AC T C W-3' ImPYPy-~-py-y-Im-~-ImHpPy
413(3) 5' G AC A T W-3' ImPYPyPyHp-y-py-(3-I~ppy
-W
413~3p) 5' G AC A T W-3' ImPyPy-~3-Hp-y-Py-(~_ImHppy
-W
414(3) 5' G AC A A W-3' Impypypypy_y-Hp-~-I~ppy
-W
414(3p) 5' G AC A A W-3' ImPyPy-(3-Py-y-Hp-(3-I~ppY
-W
415(3) 5' G AC A G W-3' ImPy-~3-Pylm-y-Py-(3-ImHpPy
-W
416(3) 5' G AC A C W-3' ImPypypypy-y-Im-/3-ImHpPy
-W
416(3p) 5' G AC A C W-3' ImPyPy-(3-Py-y-Im-(3-ImHpPy
-W
417(3) 5' G AC G T W-3' ImPy-(3-ImHp-y-Py-(3-ImHpPy
-W
4183) 5' G AC G A W-3' ImPy-~3-ImPy-y-Hp-~3-ImHppy
-W
419(3) 5' G AC C T W-3' Im-~-PyPyHp-y-PyImIm-(3-Py
-W
419(3p) 5' G AC C T W-3' ImPYPYPyHp-y-PyImIm-(3-Py
-W
4200 5' G AC C A W-3' Im-p-Pypypy-y-HpImIm-(3-Py
-W
420(3p) 5' G AC C A W-3' ImPYPyPypy-y-HpImIm-~3-Py
-W
421(3) 5' G AC G G W-3' ImPy-~3-Imlm-y-Py-~3-ImHpPy
-W
422(3) 5' G AC G C W-3' ImPy-y-ImPy-y-Im-(3-ImHpPy
-W
423(3) 5' G AC C G W-3' ImPy-(3-Pylm-y-PyImIm-~3-Py
-W
424(3) 5' G AC C C W-3' ImPyPyPyPy-y-ImImIm-(3-Py
-W
424(3p) 5' G AC C C W-3' Im-(3-PyPyPy-y-ImImIm-~i-Py
-W
CA 02281930 1999-08-18
WO 98137067 PCT/US98/01714
-86-
TABLE 58:
10-ring
Hairpin
Polyamides
for recognition
of 7-by
5'-WGCWNNW-3'
with p
substitutions.
DNA aromatic amino acid sequence
sequence
425(3) 5' G CT T T W-3' ImPyHpHpHp-y-PyPy-(3-ImPy
-W
425(3p) ' G CT T T W-3' ImPy-~3-HpHp-y-PyPy-(3-ImPy
5'
-W
426x) 5' G CT T A W-3' ImPyHpHpPy-y-HpPy-(3-ImPy
-W
426(3p) 5' G CT T A W-3' ImPy-J3-HpPy-y-HpPy-(3-ImPy
-W
427(3) 5' G CT T G W-3' ImPy-~3-Hp lm-y-PyPy-(3-Impy
-W
428(3) 5' G CT T C W-3' ImPyHpHpPy-y-ImPy-~3-ImPy
-W
428(3p) 5' G CT T C W-3' Impy-(3-HpPy-y-ImPy-(3-Impy
-W
429(3) 5' G CT A T W-3' ImPyHpPyHp-y-PyHp-(3-ImPy
-W
429(3p) 5' G CT A T W-3' ImPy-(3-PyHp-y-PyHp-(3-ImPy
-W
4303) 5' G CT A A W-3' ImPyHpPyPy-y-HpHp-(3-ImPy
-W
430(3p) 5' G CT A A W-3' ImPy-(3-PyPy-y-HpHp-(3-ImPy
-W
431(3) 5' G CT A G W-3' ImPy-~i-Pylm-y-PyHp-(3-ImPy
-W
432(3) 5' G CT A C W-3' ImPyHpPyPy-y-ImHp-~i-ImPy
-W
432(3p) 5' G CT A C W-3' ImPy-(3-PyPy-y-ImHp-(3-ImPy
-W
433(3) 5' G CT G T W-3' ImPy-(3-ImHp-y-Pypy-(3-ImPy
-W
434(3) 5' G CT G A W-3' ImPy-(3-ImPy-y-HpPy-a-ImPy
-W
435~i) 5' G CT G G W-3' ImPy-(3-ImIm-y-PyPy-~i-ImPy
-W
436(3) 5' G CT G C W-3' ImPy-(3-ImPy-y-ImPy-(3-ImPy
-W
437(3) 5' G CT C T W-3' ImPyHpPyHp-y-Pylm-(3-ImPy
-W
437(3p) 5' G CT C T W-3' ImPy-(3-PyHp-y-PyIm-(3-ImPy
-W
438~i) 5' G CT C A W-3' ImPylipPyPy-y-Hplm-(3-ImPy
-W
438(3p) 5' G CT C A W-3' ImPy-(3-PyPy-y-Hplm-~i-ImPy
-W
439(3) 5'-W G CT C G W-3' Impy-(3-PyIm-y-PyIm-~i-ImPy
4403) 5' G CT C C W-3' ImPyHpPyPy-y-ImIm-ji-ImPy
-W
440(3p) 5' G CT C C W-3' ImPy-(3-PyPy-y-Imlm-(3-ImPy
-W
441(3) 5' G CA T T W-3' ImPyPyHpHp-y-PyPy-~i-ImPy
-W
441~p) 5' G CA T T W-3' ImPy-(3-HpHp-y-PyPy-/3-ImPy
-W
442(3} 5' G CA T A W-3' ImPyPyHpPy-y-HpPy-~3-ImPy
-W
442(3p) 5' G CA T A W-3' ImPy-~3-HpPy-y-HpPy-(3-ImPy
-W
443(3) 5' G CA T G W-3' ImPy-(3-Hplm-y-PyPy-(3-ImPy
-W
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-87_
TABLE 58 (cont):
10-ring Hairpin
Polyamides for
recognition of
7-by 5'-WGCWNNW-3'
with (3 substitutions.
DNA aromatic amino acid sequence
sequence
444(3) 5' G C A T CW-3' ImPyPyHpPy-y-ImPy-~3-ImPy
-W
444~3p) 5' G C A T CW-3' ImPy-(3-HpPy-y-ImPy-(3-Impy
-W
445(3) ' G C A A TW-3' ImPyPyPyHp-y-PyHp-(3-ImPy
5'
-W
445(3p) 5' G C A A TW-3' ImPy-(3-PyHp-y-PyHp-R-ImPy
-W
446(3) 5' G C A A AW-3' ImPyPyPyPy-y-HpHp-(3-ImPy
-W
446~3p) 5' G C A A AW-3' ImPy-(3-pypy-y-HpHp-a-ImPy
-W
447(3) 5' G C A A GW-3' ImPy-(3-Pylm-y-PyHp-(3-ImPy
-W
4483) 5' G C A A CW-3' ImPyPypypy-y-ImHp-(3-ImPy
-W
448(3p) 5'-W G C A A CW-3' ImPy-(3-PyPy-y-ImHp-~i-ImPy
449(3) 5'-W G C A G TW-3' ImPy-~3-ImHp-y-PyPy-(3-ImPy
450(3) 5' G C A G AW-3' ImPy-~-ImPy-y-Hppy-(3-Impy
-W
4513) 5' G C A G GW-3' ImPy-(3-ImIm-y-PyPy-(3-ImPy
-W
4523) 5' G C A G CW-3' ImPy-J3-ImPy-y-ImPy-~i-ImPy
-W
4533) 5' G C A C TW-3' ImPyPyPyHp-y-Pylm-(3-ImPy
-W
453~3p) 5' G C A C TW-3' ImPy-(3-PyHp-y-Pylm-p-ImPy
-W
4540 5' G C A C AW-3' ImPyPyPyPy-y-HpIm-~3-ImPy
-W
454(3p) 5' G C A C AW-3' ImPy-~3-PyPy-y-Hplm-(3-ImPy
-W
455(3) 5' G C A C GW-3' ImPy-(3-PyIm-y-PyIm-(3-ImPy
-W
4563) 5' G C A C CW-3' ImpyPyPypy-y-Imam-(3-ImPy
-W
456(3p) 5' G C A C CW-3' ImPy-(3-PyPy-y-Imlm-(3-ImPy
-W
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
_88_
TABLE 59:
10-ring
Hairpin
Polyamides
for recognition
of 7-by
5'-WGCSNNW-3'
with
substitutions.
DNA aromatic amino acid sequence
sequence
457) 5' G C GT T W-3' Im--ImHpHp-y-PyPy--ImPy
-W
458(3) ~ G C GT A W-3' Im--ImHpPy-y-HpPy--ImPy
5'
-W
4593) 5' G C GT G W-3' Im--ImHpIm-y-PyPy--ImPy
-W
460(3) 5' G C GT C W-3' Im--ImHpPy-y-ImPy--ImPy
-W
461) 5' G C GA T W-3' Im--ImPyHp-y-PyHp--ImPy
-W
462(3) 5' G C GA A W-3' Im--ImPyPy-y-HpHp--ImPy
-W
463) 5' G C GA G W-3' Im--ImPyIm-y-PyHp--ImPy
-W
4643) 5' G C GA C W-3' Im--ImPyPy-y-ImHp--ImPy
-W
465(3) 5' G C GG T W-3' Im--ImImHp-y-PyPy--ImPy
-W
466(3) 5' G C GG A W-3' Im-(3-ImImPy-y-HpPy--ImPy
-W
467(3) 5' G C GG T W-3' Im--ImPyHp-y-PyIm--ImPy
-W
468(3) 5' G C GC A W-3' Im--ImPyPy-y-HpIm--ImPy
-W
469) 5'-W G C CT T W-3' ImPyPyHpHp-y-Py-~-ImImPy
469~3p) 5'-W G C CT T W-3' ImPyPy--Hp-y-Py--ImImPy
470) 5' G C CT A W-3' ImPyPyHpPy-y-Hp--ImImPy
-W
470p) 5' G C CT A W-3' ImPyPy--Py-y-Hp--ImImPy
-W
4710 5' G C CT G W-3' ImPy--Hplm-y-Py--ImImPy
-W
472(3) 5' G C CT C W-3' ImPyPyHpPy-y-Im--ImImPy
-W
472(3p) 5' G C CT C W-3' ImPyPy--Py-y-Im--ImImPy
-W
473(3) 5' G C CA T W-3' ImPyPyPyHp-y-Py--ImImPy
-W
473p) 5'-W G C CA T W-3' ImPyPy--Hp-y-Py--ImImPy
474~i) 5' G C CA A W-3' ImPyPyPyPy-y-Hp--ImImPy
-W
474pp) 5'-W G C CA A W-3' ImPyPy--Py-y-Hp--ImImPy
4753) 5' G C CA G W-3' ImPy--Pylm-y-Py--ImImPy
-W
476(3) 5' G C CA C W-3' ImPyPyPyPy-y-Im--ImImPy
-W
476(3p) 5' G C CA C W-3' ImPyPy--Py-y-Im--ImImPy
-W
4773) 5' G C CG T W-3' ImPy--ImHp-y-Py--ImImPy
-W
478(3) 5' G C CG A W-3' ImPy--ImPy-y-Hp--ImImPy
-W
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-89-
TABLE 59 (cont):
10-ring Hairpin
Polyamides for
recognition of
7-by 5'-WGCSNNW-3'
with ~i substihrtions.
DNA aromatic amino acid sequence
sequence
G25(3) 5' GC G G W-3' Im-(3-ImImIm-y-PyPy-~3-ImPy
-W G
G26(3) 5' GC G C W-3' Im-(3-ImImPy-y-ImPy-p-ImPy
-W G
G27~3) ~5' GC C G W-3' Im-(3-ImPyIm-y-Pylm-(3-ImPy
-W G
G28(3) 5' GC C C W-3' Im-~3-ImPyPy-y-ImIm-~i-ImPy
-W G
G29(3) 5'-W GC G G W-3' ImPy-~3-Imlm-y-Py-(3-ImImPy
C
G30(3) 5' GC G C W-3' ImPy-(3-ImPy-y-Im-~3-ImImPy
-W C
G31(3) 5' GC C G W-3' ImPy-(3-Pylm-y-PyImImImPy
-W C
CA 02281930 1999-08-18
WO 9S/37067 PCT/US98101714
-90-
TABLE 60: 10-ring
Hairpin
Polyamides
for
recognition
of
7-by
S'-WCGWNNW-3'
with
(3
substitutions.
DNA aromatic amino acid sequence
sequence
4810 5' C G T T T W-3' PyImHpHpHp-y-PyPy-(3-PyIm
-W
481(3p) '5' C G T T T W-3' PyIm-(3-HpHp-y-PyPy-(3-PyIm
-W
4823) 5' C G T T A W-3' PyImHpHpPy-y-HpPy-(3-PyIm
-W
482~3P) 5' C G T T A W-3' Pylm-/3-Hppy-y-Hppy-~3-pylm
-W
4833) 5' C G T T G W-3' PyIm-~3-HpIm-y-Pypy-p-Pylm
-W
484(3) 5' C G T T C W-3' PyImHpHppy-y-ImPy-/3-PyIm
-W
484(3p} 5'-WC G T T C W-3' Pylm-(3-HpPy-y-ImPy-(3-PyIm
4853) 5' C G T A T W-3' PyImHpPyHp-y-PyHp-[3-PyIm
-W
485(3p) 5' C G T A T W-3' PyIm-(3-PyHp-y-PyHp-(3-PyIm
-W
486(3) 5' C G T A A W-3' PyImHpPyPy-y-HpHp-(3-pylm
-W
486(3p) 5' C G T A A W-3' PyIm-~3-Pypy-Y-HpHp-(3-pylm
-W
4873) 5' C G T A G W-3' PyIm-J3-Pylm-y-PyHp-(3-Pylm
-W
488J3) 5' C G T A C W-3' PyImHpPyPy-y-ImHp-~3-Pylm
-W
488(3p) 5' C G T A C W-3' PyIm-(3-PyPy-y-ImHp-(3-PyIm
-W
489(3} 5' C G T G T W-3' PyIm-~-ImHp-Y-Pypy-~3-pylm
-W
490(3) 5' C G T G A W-3' Pylm-(3-Impy-y-HpPy-(3-PyIm
-W
491(3) 5' C G T G G W-3' PyIm-~-ImIm-y-pyPy-(3-pyIm
-W
492(3) 5' C G T G C W-3' PyIm-[3-ImPy-y-Impy-~3-PyIm
-W
493x) 5' C G T C T W-3' PyImHpPyHp-y-PyIm-p-PyIm
-W
493(3p) 5' C G T C T W-3' Pylm-(3-PyHp-y-PyIm-(3-PyIm
-W
4943) 5' C G T C A W-3' PyImHpPyPy-y-HpIm-~3-PyIm
-W
494(3p) 5' C G T C A W-3' PyIm-J3-PyPy-y-HpIm-(3-PyIm
-W
495(3) 5' C G T C G W-3' PyIm-(3-PyIm-y-PyIm-(3-PyIm
-W
496(3) 5' C G T C C W-3' PyImHpPyPy-y-Imlm-~i-PyIm
-W
496(3p) 5' C G T C C W-3' PyIm-~3-PyPy-y-ImIm-~3-PyIm
-W
4973) 5' C G A T T W-3' PyImPyHpHp-y-Pypy-(3-pyIm
-W
497(3p) 5' C G A T T W-3' PyIm-~3-HpHp-y-PyPy-(3-pyIm
-W
498(3) 5' C G A T A W-3' PyImPyHpPy-y-HpPy-p-PyIm
-W
498(3p) 5' C G A T A W-3' Pylm-~i-HpPy-y-HpPy-(3-PyIm
-W
CA 02281930 1999-08-18
WO 98/37067 PCT/US9810I714
-91-
TABLE 60 (cont):
10-ring Hairpin
Polyamides for
recognition of
7-by 5'-WCGWNNW-3'
with (3 substitutions.
DNA aromatic amino acid sequence
sequence
499(3) 5' C G A T GW-3' Pylm-(3-Hplm-y-Pypy-(3-pylm
-W
500(3) 5' C G A T CW-3' PyImPyHpPy-y-ImPy-(3-pylm
-W
500(3p) ~ C G A T CW-3' PyIm-(3-HpPy-y-ImPy-~_pyln~
5'
-W
501~i) 5' C G A A TW-3' PyImPyPyHp-y-PyHp-(3-PyIm
-W
501(3p) 5' C G A A TW-3' PyIm-(3-PyHp-y-PyHp-(3-PyIm
-W
5023) 5' C G A A AW-3' PyImPyPyPy-y-HpHp-~3-Pylm
-W
502~3p) 5' C G A A AW-3' PyIm-(3-Pypy-y-HpHp-~-PyIm
-W
5030 5' C G A A GW-3' PyIm-(3-PyIm-y-PyHp-~3-Pylm
-W
504 ) 5' C G A A CW-3'
-W PyImPyPyPy-y-ImHp-(3-PyIm
504(3p) 5' C G A A CW-3' Pyim-(3-PyPy-y-ImHp-~3-pylm
-W
505(3) 5' C G A G TW-3'
-W Pylm-(3-ImHp-y-PyPy-(3-PyIm
5063) 5' C G A G AW-3' PyIm-p-ImPy-y-HpPy-p-pyIm
-W
507(3) 5' C G A G GW-3' PyIm-(3-Imlm-y-Pypy-(3-pylm
-W
50B(3} 5' C G A G CW-3' PyIm-~i-ImPy-y-ImPy-(3-PyIm
-W
5093) 5' C G A C TW-3' PyImPyPyHp-y-PyIm-(3-PyIm
-W
509~p) 5'-W C G A C TW-3' PyIm-(3-PyHp-y-pylm-(3-PyIm
5100 5' C G A C AW-3' PyImPyPyPy-y-Hplm-~3-Pylm
-W
510(3p} 5' C G A C AW-3' PyIm-~3-PyPy-y-HpIm-(3-PyIm
-W
511~i) 5' C G A C GW-3' PyIm-(3-PyIm-y-PyIm-(3-PyIm
-W
5123) 5' C G A C CW-3' PyImPyPyPy-y-ImIm-~3-PyIm
-W
5I2~3p) 5' C G A C CW-3' PyIm-~3-PyPy-y-ImIm-(3-PyIm
-W
CA 02281930 1999-08-18
WO 98/37067 PCTIUS98/01714
-92-
TABLE 61:
10-ring
Hairpin
Polyamides
for recognition
of 7-by
5'-WCGSNNW-3'
with (3
substitutions.
DNA aromatic amino acid sequence
sequence
513(3) 5' C G GT T W-3' PyImIm-(3-Hp-y-PyPy-(3-PyIm
-W
514(3) -5' C G GT A W-3' PyImIm-~i-Py-y-HpPy-(3-Pylm
-W
515(3) 5' C G GT G W-3' PyImIm-(3-Im-y-PyPy-(3-Pylm
-W
516(3) 5' C G GT C W-3' PyImIm-(3-Py-y-ImPy-(3-Pylm
-W
517(3) 5' C G GA T W-3' PyImIm-(3-Hp-y-PyHp-~3-Pylm
-W
518(3) 5' C G GA A W-3' PyImIm-(3-Py-y-HpHp-(3-PyIm
-W
5193) 5' C G GA G W-3' PyImIm-(3-Im-y-PyHp-(3-PyIm
-W
520(3) 5' C G GA C W-3' PyImIm-~3-Py-y-ImHp-~3-PyIm
-W
521~i) 5' C G GG T W-3' PyImImImHp-y-PyPy-(3-PyIm
-W
522(3) 5' C G GG A W-3' PyImImImPy-y-HpPy-~3-PyIm
-W
523(3) 5' C G GC T W-3' PyImIm-~-Hp-y-PyIm-~3-PyIm
-W
524(3) 5' C G GC A W-3' PyImIm-~3-Py-y-HpIm-(3-PyIm
-W
5250 5' C G CT T W-3' PyImPyHpHp-y-Py-~3-ImPyIm
-W
525(3p) 5' C G CT T W-3' PyImPy-(3-Hp-y-Py-(3-ImPyIm
-W
526(3) 5' C G CT A W-3' PyImPyHpPy-y-Hp-~3-ImPyIm
-W
526(3p) 5' C G CT A W-3' PyImPy-(3-Py-y-Hp-p-ImPyIm
-W
5273) 5' C G CT G W-3' Pylm-(3-Hplm-y-Py-p-ImPyIm
-W
528(3) 5' C G CT C W-3' PyImPyHpPy-y-Im-(3-ImPyIm
-W
528(3p) 5' C G CT C W-3' PyImPy-(3-Py-y-Im-(3-ImPyIm
-W
529(3) 5' C G CA T W-3' PyImPyPyHp-y-Py-(3-ImPyIm
-W
529(3p) 5' C G CA T W-3' PyImPy-(3-Hp-y-Py-~3-ImPyIm
-W
530(3) 5' C G CA A W-3' PyImPyPyPy-y-Hp-(3-ImPyIm
-W
530(3p) 5' C G CA A W-3' PyImPy-~3-Py-y-Hp-~3-ImPyIm
-W
531(3) 5' C G CA G W-3' PyIm-(3-Pylm-y-Py-[3-ImPyIm
-W
532(3) 5'-W C G CA C W-3' PyImPyPyPy-y-Im-p-ImPyIm
532(3p) 5' C G CA C W-3' PyImPy-~3-Py-y-Im-p-ImPyIm
-W
533(3) 5' C G CG T W-3' Pylm-p-ImHp-y-Py-p-ImPyIm
-W
5343) 5' C G CG A W-3' Pylm-~3-ImPy-y-Hp-(3-ImPyIm
-W
CA 02281930 1999-08-18
WO 98137067 PCT/US98/01714
-93-
TABLE 61 (cont):
10-ring Hairpin
Polyamides for
recognition of
7-by 5'-WCGSNNW-3'
with p substitutions
.
DNA aromatic amino acid sequence
sequence
5353) 5' C G C C TW-3' PyImPyPyHp-y-PyImIm-p-Im
-W
536(3) ~5' C G C C AW-3' PyImPyPyPy-y-HpImIm-(3-Im
-W
G33(3) 5' C G G G GW-3' PyImImImIm-y-PyPy-(3-PyIm
-W
G34(3) 5' C G G G CW-3' PyImImImPy-y-ImPy-(3-PyIm
-W
G35~3) 5' C G G C GW-3' PyImIm-~-Im-y-Pylm-(3-PyIm
-W
G36(3) 5' C G G C CW-3' PyImIm-~3-Py-y-ImIm-(3-PyIm
-W
G37(3) 5'-W C G C G GW-3' Pylm-(3-ImIm-y-Py-(3-ImPyIm
G38(3) 5' C G C G CW-3' PyIm-~3-ImPy-y-Im-(3-ImPyIm
-W
G39(3) 5' C G C C GW-3' PyIm-(3-PyIm-y-PyImIm-~i-Im
-W
G40(3) 5' C G C C CW-3' PyImPyPyPy-y-ImImIm-(3-Im
-W
CA 02281930 1999-08-18
WO 98/37067. PCT/US98/01714
-94-
TABLE 62:
I 0-ring
Hairpin
Polyamides
for recognition
of 7-by
5'-WCTWNNW-3'
with ~3
substitutions.
DNA aromatic amino acid sequence
sequence
537(3) 5' C T TT T W-3' PyHpHpHpHp-y-PyPy-(3-Pylm
-W
537(3p) 'S' C T TT T W-3' PyHp-(3-HpHp-y-PyPy-(3-PyIm
-w
538~i) 5' C T TT A W-3' PyHpHpHpPy-y-HpPy-(3-PyIm
-W
538(3p) 5' C T TT A W-3' PyHp-(3-HpPy-y-HpPy-~3-Pylm
-W
539(3) 5' C T TT G W-3' PyHp-~3-HpIm-y-PyPy-(3-PyIm
-W
540~i) 5' C T TT C W-3' PyHpHpHpPy-y-ImPy-(3-PyIm
-W
540(3p) 5' C T TT C W-3' PyAp-(3-HpPy-y-ImPy-~3-PyIm
-W
541R) 5' C T TA T W-3' PyHpHpPyHp-y-PyHp-(3-PyIm
-W
541(3p) 5' C T TA T W-3' PyHp-(3-PyHp-y-PyHp-(3-PyIm
-W
5420 5' C T TA A W-3' PyHpHpPyPy-y-HpHp-(3-PyIm
-W
542(3p) 5' C T TA A W-3' PyHp-p-PyPy-y-HpHp-(3-PyIm
-W
543~i) 5' C T TA G W-3' PyHp-~i-PyIm-y-PyHp-~-PyIm
-W
544(3) 5' C T TA C W-3' PyHpHpPyPy-y-ImHp-(3-Pylm
-W ~
544(3p) 5' C T TA C W-3' PyHp-(3-PyPy-y-ImHp-~3-Pylm
-W
545(3) 5' C T TG T W-3' PyHp-(3-ImI-Ip-y-PyPy-(3-PyIm
-W
5463) 5' C T TG A W-3' PyHp-(3-ImPy-y-HpPy-~-PyIm
-W
547(3) 5' C T TG G W-3' PyHp-(3-Imlm-y-PyPy-(3-Pylm
-W
548(3) 5' C T TG C W-3' PyHp-(3-ImPy-y-ImPy-(3-PyIm
-W
549(3) 5' C T TC T W-3' PyHpHpPyHp-y-PyIm-~3-Pylm
-W
549(3p) 5' C T TC T W-3' PyHp-~3-PyHp-y-PyIm-~3-PyIm
-W
550(3) 5' C T TC A W-3' PyHpHpPyPy-y-HpIm-[3-PyIm
-W
550~3p) 5' C T TC A W-3' PyHp-[3-PyPy-y-HpIm-(3-PyIm
-W
5513) 5' C T TC G W-3' PyHp-~i-Pylm-y-PyIm-~3-Pylm
-W
5523) 5' C T TC C W-3' PyHpHpPyPy-y-ImIm-(3-PyIm
-W
552(3p) 5' C T TC C W-3' PyHp-(3-PyPy-y-Imlm-(3-PyIm
-W
553(3) 5' C T AT T W-3' PyHpPyHpHp-y-PyPy-~i-PyIm
-W
553(3p) 5' C T AT T W-3' PyHp-~i-HpHp-y-PyPy-~i-PyIm
-W
554(3) 5' C T AT A W-3' PyHpPyHpPy-y-HpPy-(3-PyIm
-W
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-95-
TABLE 62
(cont):
10-ring
Hairpin
Polyamides
for recognition
of 7-by
5'-WCTWNNW-3'
with p
substitutions.
DNA aromatic amino acid sequence
sequence
554(3p) 5' C TA T A W-3' PyHp-(3-HpPy-y-HpPy-~i-Pylm
-W
555(3) ~ C TA T G W-3' PyHp-(i-Hplm-y-PyPy-p-pyIm
5'
-W
5563) 5' C TA T C W-3' PyHpPyHpPy-Y-ImPy-~3-PyIm
-W
556(3p) 5' C TA T C W-3' PyHp-(3-HpPy-y-ImPy-(3-PyIm
-W
557(3) 5' C TA A T W-3' PyHpPyPyHp-Y-PyHp-(3-PyIm
-W
557~3p) 5' C TA A T W-3' PyHp-(3-PyHp-y-PyHp-(3-Pylm
-W
5580 5' C TA A A W-3' PyHpPyPyPy-Y-HpHp-/3-PyIm
-W
558~ip) 5' C TA A A W-3' PyHp-(3-PyPy-y-HpHp-(3-PyIm
-W
559(3) 5' C TA A G W-3' PyHp-~-PyIm-y-PyHp-(3-PyIm
-W
5603) 5' C TA A C W-3' PyHpPyPyPy-y-ImHp-(3-PYIm
-W
560(3p) 5' C TA A C W-3' PyHp-(3-PyPy-y-ImHp-(3-Pylm
-W
5613) 5' C TA G T W-3' PyHp-(3-ImHp-y-PYPy-(3-pylm
-W
562~i) 5' C TA G A W-3 T PyHp-(3-ImPy-y-HpPy-(3-PyIm
-W
563(3) 5' C TA G G W-3' PyHp-(3-ImIm-y-PyPy-(3-PyIm
-W
564~i) 5' C TA G C W-3' PyHp-~3-ImPy-y-ImPy-~3-PyIm
-W
565(3) 5' C TA C T W-3' PyHpPyPyHp-y-PyIm-(3-PyIm
-W
565~3p) 5' C TA C T W-3' PyHp-(3-PyHp-Y-PyIm-(3-PyIm
-W
5663) 5' C TA C A W-3' PyHppyPyPy-Y-HpIm-(3-PyIm
-W
566(3p) 5' C TA C A W-3' PyHp-~i-PyPy-y-Hplm-(3-PyIm
-W
567(3) 5' C TA C G W-3' PyHp-(3-PyIm-y-PyIm-(3-PyIm
-W
5683) 5'-W C TA C C W-3' PyHpPyPyPy-y-ImIm-(3-PyIm
568pp) 5' C TA C C W-3' PyHp-yPYPY-y-Imlm-(3-Pylm
-W
CA 02281930 1999-08-18
WO 98/37067 PCT/US98101714
-96-
TABLE
63: 10-ring
Hairpin
Polyamides
for recognition
of 7-by
5'-WCTSNNW-3'
with
~3 substitutions.
DNA aromatic amino acid sequence
sequence
5693) 5' C T GT T W-3' Py-(3-ImHpHp-y-PyPy-(3-PyIm
-W
570(3) 'S' C T GT A W-3' Py-(3-ImHpPy-y-HpPy-~i-PyIm
-W
571(3) 5' C T GT G W-3' Py-~i-ImHpIm-y-PyPy-(3-Pylm
-W
572(3) 5' C T GT C W-3' Py-(3-ImHpPy-y-ImPy-(3-Pylm
-W
5733) 5' C T GA T W-3' Py-(3-ImPyHp-y-PyHp-(3-PyIm
-W
574(3) 5' C T GA A W-3' Py-(3-ImPyPy-y-HpHp-(3-PyIm
-W
5753) 5' C T GA G W-3' Py-(3-ImPyIm-y-PyHp-(3-PyIm
-W
576(3) 5' C T GA C W-3' Py-(3-ImPyPy-y-ImHp-(3-PyIm
-W
577(3) 5' C T GG T W-3' Py-~3-ImImHp-y-PyPy-(3-PyIm
-W
578(3) 5' C T GG A W-3' Py-(3-ImImPy-y-HpPy-(3-PyIm
-W
579(3) 5' C T GC T W-3' Py-(3-ImPyHp-y-PyIm-~-PyIm
-W
5803) 5' C T GC A W-3' Py-(3-ImPyPy-y-Hplm-(3-PyIm
-W
581(3) 5' C T GG G W-3' Py-~3-ImImIm-y-PyPy-(3-Pylm
-W
5823) 5' C T GG C W-3' Py-(3-ImImPy-y-ImPy-p-PyIm
-W
583(3) 5' C T GC G W-3' Py-(3-ImPyIm-y-PyIm-p-PyIm
-W
584(3) 5' C T GC C W-3' Py-(3-ImPyPy-y-ImIm-~-PyIm
-W
5853) 5' C T CT T W-3' PyHpPyHpHp-y-Py-(3-ImPyIm
-W
585~3p) 5' C T CT T W-3' PyHpPy-/3-Hp-y-Py-(3-ImPyIm
-W
586(3) 5' C T CT A W-3' PyHpPyHpPy-y-Hp-p-ImPyIm
-W
586(3p) 5' C T CT A W-3' PyHpPy-(3-Py-y-Hp-(3-ImPyIm
-W
587(3) 5' C T CT G W-3' PyHp-p-HpIm-y-Py-(3-ImPyIm
-W
5883) 5' C T CT C W-3' PyHpPyHpPy-y-Im-a-ImPyim
-W
588(3p} 5' C T CT C W-3' PyHpPy-(3-Py-y-Im-(3-ImPyIm
-W
589(3) 5' C T CA T W-3' PyHpPyPyAp-y-Py-~3-ImPyIm
-W
589(3p) 5' C T CA T W-3' PyHpPy-(3-Hp-y-Py-~3-ImPyIm
-W
590(3) 5' C T CA A W-3' PyHpPyPyPy-y-Hp-(3-ImPyIm
-W
590(3p) 5' C T CA A W-3' PyHpPy-~3-Py-y-Hp-~-ImPyIm
-W
591(3) 5' C T CA G W-3' PyHp-(3-PyIm-y-Py-(3-ImPyIm
-W
CA 02281930 1999-08-18
WO 98/37067 PCT/US98101714
_97_
TABLE 63 (cont): in
10-ring Hairp Polyamides
for
recognition
of
7-by
5'-WCTSNNW-3'
with
(3
substitutions.
DNA aromatic amino acid sequence
sequence
592(3) 5' C TC A C W-3' PyHpPyPyPy-y-Im-~3-ImPyIm
-W
592(3p) 5' C TC A C W-3' PyHpPy-(3-Py-y-Im-~i-ImPyIm
- -W
593R) 'S'-WC TC G T W-3'
PYHP-~-I~P-y-PY-~-ImPYIm
594(3) 5' C TC G A W-3' PyHp-(3-ImPy-y-Hp-~3-ImPYIm
-W
595~i) 5' C TC C T W-3' PyHpPyPyHp-y-PyImIm-(3-Im
-W
595(3p) 5' C TC C T W-3' Py-~3-PypyHp-y-PyImIm-~-Im
-W
596(3) 5' C TC C A W-3' PyHpPyPyPy-y-HpImIm-(3-Im
-W
596(3p) 5' C TC C A W-3' Py-~3-Pypypy-y-HpImIm-~3-Im
-W
5973) 5' C TC G G W-3' PyHp-p-ImIm-y-Py-(3-ImPyIm
-W
598(3) 5' C TC G C W-3' P H
-W Y p-~3-ImPy-y-Im-(3-ImPyIm
599(3) 5' C TC C G W-3' PyHp-~i-Pylm-y-pylmIm-~3-Im
-W
600R) 5'-W C TC C C W-3' PyHpPyPYPy-y-ImImIm-(3-Im
600(3p) 5' C TC C C W-3' Py-(3-PyPyPy-y-ImImIm-~-Im
-W
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-98-
TABLE 64:
10-ring
Hairpin
Polyamides
for recognition
of 7-by
S'-WCAWNNW-3'
with p
substitutions.
DNA aromatic amino acid sequence
sequence
6013) 5' C AT T T W-3' PyPyHpHpHp-y-PyPy-/3-HpIm
-W
601(3p) '5' C AT T T W-3' PyPy-R-HpHp-y-PyPy-(3-HpIm
-W
6023) 5' C AT T A W-3' PyPyHpHpPy-y-HpPy-(3-HpIm
-W
602(3p) 5' C AT T A W-3 ' PyPy-(3-HpPy-y-HpPy-~i-Hplm
-W
603(3) 5' C AT T G W-3' PyPy-~3-HpIm-y-PyPy-~i-Hplm
-W
6040 5' C AT T C W-3' PyPyHpHpPy-y-ImPy-(3-HpIm
-W
604~3p) 5' C AT T C W-3' PyPy-R-HpPy-y-ImPy-(3-Hplm
-W
6053) 5' C AT A T W-3' PyPyHpPyHp-y-PyHp-~i-HpIm
-W
605~3p) 5' C AT A T W-3' PyPy-(3-PyHp-y-PyHp-J3-Hplm
-W
6063) 5' C AT A A W-3' PyPyHpPyPy-y-HpHp-(3-HpIm
-W
606(3p) 5' C AT A A W-3' PyPy-(3-PyPy-y-HpHp-(3-Hplm
-W
607(3) 5' C AT A G W-3' PyPy-(3-Pylm-y-PyHp-(3-Hplm
-W
608~i) 5' C AT A C W-3' PyPyHpPyPy-y-ImHp-(3-HpIm
-W
608(3p) 5' C AT A C W-3' PyPy-(3-PyPy-y-ImHp-(3-HpIm
-W
609(3) 5' C AT G T W-3' PyPy-(3-ImHp-y-PyPy-(3-HpIm
-W
610(3) 5' C AT G A W-3' PyPy-(3-ImPy-y-HpPy-~i-HpIm
-W
611(3) 5' C AT G G W-3' PyPy-(3-ImIm-y-PyPy-(3-HpIm
-W
612(3) 5' C AT G C W-3' PyPy-(3-ImPy-y-ImPy-(3-HpIm
-W
613(3) 5' C AT C T W-3' PyPyHpPyHp-y-PyIm-[3-HpIm
-W
613~p) 5' C AT C T W-3' PyPy-p-PyHp-y-PyIm-(3-HpIm
-W
6143) 5' C AT C A W-3 ' PyPyHpPyPy-y-HpIm-~3-HpIm
-W
614~3p) 5' C AT C A W-3' PyPy-j3-PyPy-y-HpIm-(3-HpIm
-W
615(3) 5' C AT C G W-3' PyPy-(3-PyIm-y-PyIm-~i-HpIm
-W
6163) 5' C AT C C W-3' PyPyHpPyPy-y-ImIm-(3-HpIm
-W
616~3p) 5' C AT C C W-3' PyPy-~i-PyPy-y-ImIm-~-HpIm
-W
6I7~3) 5' C AA T T W-3' PyPyPyHpHp-y-PyPy-(3-HpIm
-W
617~p) 5' C AA T T W-3' PyPy-(3-HpHp-y-PyPy-~i-HpIm
-W
6180 5' C AA T A W-3' PyPyPyHpPy-y-HpPy-p-HpIm
-W
618(3p) 5' C AA T A W-3' PyPy-~-HpPy-y-HpPy-(3-HpIm
-W
CA 02281930 1999-08-18
WO 98/37067 PCT/US98I01714
_9c~_
. TABLE 64 (cont):
10-ring Hairpin
Polyamides for
recognition of
7-by 5'-WCAWNNW-3'
with substitutions.
DNA aromatic amino acid sequence
sequence
619(3) 5' C A A T G W-3' Pypy--Hplm-y-pypy_-Hplm
-W
620) 5' C A A T C W-3' PyPyPyHpPy-~-ImPy--HpIm
-W
620~ip) ~ C A A T C W-3' Pypy--HpPy-y-ImPy-(3-Hplm
5'
-W
6Z1) 5'-W C A A A T W-3' PyPyPyPyHp-r-PyHp--HpIm
621(3p) 5' C A A A T W-3' PyPy-(3-PyHp-y-PyHp-(3-HpIm
-W
622(3) 5'-W C A A A A W-3' PyPyPyPyPy-y-HpHp--Hplm
622p) 5' C A A A A W-3' PyPy--Pypy-y-Hpgp-(3-HpIm
-W
623) 5' C A A A G W-3' PyPy--Pylm-y-PyHp--HpIm
-W
6243) 5' C A A A C W-3' PyPyPyPyPy-'y-ImHp--Hplm
-W
624p) 5' C A A A C W-3' PyPy--pypy-~-ImHp_-Hplm
-W
625) 5' C A A G T W-3' PyPy--ImHp-y-PyPy--HpIm
-W
626) 5' C A A G A W-3' PyPy--ImPy-y-HpPy--HpIm
-W
IS 627(3) 5' C A A G G W-3' PyPy--ImIm-y-PyPy--Hplm
-W
6283) 5' C A A G C W-3' PyPy--ImPy-y-ImPy--HpIm
-W
6293) 5'-W C A A C T W-3' PyPyPyPyHp-y-PyIm--HpIm
629p) 5'-W C A A C T W-3' PyPy--PyHp-y-PyIm--HpIm
630(3) 5' C A A C A W-3' PyPyPyPyPy-y-HpIm--HpIm
-W
630p) 5'-W C A A C A W-3' PyPy--PyPy-y-HpIm--HpIm
631) 5'-W C A A C G W-3' PyPy--PyIm-y-PyIm--HpIm
632(3) 5' C A A C C W-3' PyPyPyPyPy-y-Imlm--HpIm
-W
632p) 5'-W C A A C C W-3' PyPy--PyPy-y-ImIm--HpIm
CA 02281930 1999-08-18
WO 98137067 PCT/US98/01714
-100-
TABLE 65:
10-ring
Hairpin
Polyamides
for recognition
of 7-by
5'-WCASNNW-3'
with (3
substitutions.
DNA aromatic amino acid sequence
sequence
633~i) 5' C A G TT W-3' Py-(3-ImHpHp-y-PyPy-(3-HpIm
-W
6343) ' C A G TA W-3' Py-(3-ImHppy-y-Hppy-/3-Hpim
5'
-W
635~i) 5' C A G TG W-3' Py-~3-ImHpIm-y-PyPy-(3-Hplm
-W
636(3) 5' C A G TC W-3' Py-(3-ImHpPy-y-ImPy-(3-HpIm
-W
637(3) 5' C A G AT W-3' Py-(3-ImPyHp-y-PyHp-(3-HpIm
-W
638(3) 5' C A G AA W-3' Py-(3-ImPyPy-y-HpHp-(3-Hplm
-W
6393) 5' C A G AG W-3' Py-~i-ImPyIm-y-PyHp-~3-HpIm
-W
640(3) 5' C A G AC W-3' Py-(3-ImPyPy-y-ImHp-(3-HpIm
-W
641(3) 5' C A G GT W-3' Py-(3-ImImHp-y-PyPy-(3-HpIm
-W
6423) 5' C A G GA W-3' Py-(3-ImImPy-y-HpPy-~3-HpIm
-W
643(3) 5' C A G CT W-3' Py-(3-ImPyHp-y-PyIm-~3-Hplm
-W
644(3) 5' C A G CA W-3' Py-(3-ImPyPy-y-HpIm-(3-HpIm
-W
645(3) 5' C A G GG W-3' Py-(3-ImImIm-y-PyPy-(3-Hplm
-W
6463) 5' C A G GC W-3' Py-(3-ImImPy-y-ImPy-(3-HpIm
-W
647(3) 5' C A G CG W-3' Py-(3-ImPyIm-y-Pylm-(3-Hplm
-W
6483) 5' C A G CC W-3' Py-(3-ImPyPy-y-Imlm-(3-Hplm
-W
6493) 5'-W C A C TT W-3' PyPyPyHpHp-y-Py-(3-ImHpIm
649(3p) 5' C A C TT W-3' PyPyPy-(3-Hp-y-Py-~i-ImHpIm
-W
6503) 5' C A C TA W-3' PyPyPyHpPy-y-Hp-(3-ImHpIm
-W
650(3p) 5' C A C TA W-3' PyPyPy-(3-Py-y-Hp-~i-ImHpIm
-W
651(3) 5' C A C TG W-3' PyPy-(3-HpIm-y-Py-(3-ImHpIm
-W
652~i) 5' C A C TC W-3' PyPyPyHpPy-y-Im-~3-ImHpIm
-W
652(3p) 5' C A C TC W-3' PyPyPy-(3-Py-y-Im-(3-ImHpIm
-W
653(3) 5' C A C AT W-3' PyPyPyPyHp-y-Py-(3-ImHpIm
-W
653(3p) 5' C A C AT W-3' PyPyPy-(3-Hp-y-Py-p-ImHpIm
-W
654(3) 5' C A C AA W-3' PyPyPyPyPy-y-Hp-(3-ImHpIm
-W
654(3p) 5' C A C AA W-3' PyPyPy-(3-Py-y-Hp-(3-ImHpIm
-W
655(3) 5' C A C AG W-3' PyPy-(3-PyIm-y-Py-(3-ImHpIm
-W
CA 02281930 1999-08-18
WO 98/37067
PCT/US98101714
-101-
. TABLE 65 (cont):
10-ring Hairpin
Polyamides for
recognition of
7-by 5'-WCASNNW-3'
with p substitutions.
DNA aromatic amino acid sequence
sequence
656(3) 5' C A C A C W-3' PyPyPyPyPy-y-Im-(3-ImHpIm
-W
656(3p) 5' C A C A C W-3' PyPyPy-(3-Py-y-Im-(3-ImHpIm
-W
6573) '5' C A C G T W-3' PyPy-(3-ImHp-y-Py-p-ImHpIm
-W
658(3p) 5' C A C G A W-3' PyPy-~-ImPy-y-Hp-~_ImHpIm
-W
6590 5' C A C C T W-3' PyPyPyPyHp-y-PyImIm-(3-Im
-W
659(3p) 5' C A C C T W-3' Py-(3-PyPyHp-r-PyImIm-(3-Im
-W
660(3) 5' C A C C A W-3' PyPyPyPyPy-y-HpImIm-~-Im
-W
660(3p) 5' C A C C A W-3' Py-/3-PyPyPy-y-HpImIm-(3-Im
-W
6613) 5' C A C G G W-3' PyPy-/3-ImIm-y-Py-(3-ImHpIm
-W
662(3) 5' C A C G C W-3' PyPy-(3-ImPy-y-Im-j3-ImHpIm
-W
6633} 5' C A C C G W-3' PyPy-(3-pylm-y-PyImIm-(i-Im
-W
664(3} 5' C A C C C W-3' PyPyPyPyPy-y-ImImIm-(3-Im
-W
664~3p) 5' C A C C C W-3' Py-p-Pypypy-y-ImImIm-(3-Im
-W
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-102-
TABLE 66:
10-ring
Hairpin
Polyamides
for recognition
of 7-by
S'-WCCWNNW-3'
with ~
substitutions.
DNA aromatic amino acid sequence
sequence
665(3) 5' C C TT T W-3' PyPyHpHpHp-y-PyPy-(3-ImIm
-W
665(3p) '5' C C TT T W-3' PyPy-(3-HpHp-y-PyPy-~3-ImIm
-W
666(3) 5' C C TT A W-3' PyPyHpHpPy-y-HpPy-~-ImIm
-W
666(3p) 5' C C TT A W-3' PyPy-(3-HpPy-y-HpPy-p-ImIm
-W
667(3) 5' C C TT G W-3' PyPy-(3-HpIm-y-PyPy-(3-ImIm
-W
668(3) 5' C C TT C W-3' PyPyHpHpPy-y-ImPy-~3-Imlm
-W
668(3p) 5' C C TT C W-3' PyPy-(3-HpPy-y-ImPy-(3-ImIm
-W
669(3) 5' C C TA T W-3' PyPyHpPyHp-y-PyHp-(3-ImIm
-W
669(3p) 5' C C TA T W-3' PyPy-[3-PyAp-y-PyHp-(3-ImIm
-W
670(3) 5' C C TA A W-3' PyPylipPyPy-y-HpHp-(3-ImIm
-W
670~3p) 5' C C TA A W-3' PyPy-(3-PyPy-y-HpHp-(3-ImIm
-W
671(3) 5' C C TA G W-3' PyPy-(3-PyIm-y-PyHp-(3-ImIm
-W
672(3) 5' C C TA C W-3' PyPyHpPyPy-y-ImHp-(3-ImIm
-W
672(3p) 5' C C TA C W-3' PyPy-[3-PyPy-y-ImHp-~3-ImIm
-W
673(3) 5' C C TG T W-3' PyPy-(3-ImHp-y-PyPy-(3-Imlm
-W
674(3) 5' C C TG A W-3' PyPy-~-ImPy-y-HpPy-(3-ImIm
-W
6753) 5' C C TG G W-3' PyPy-~3-ImIm-y-PyPy-(3-ImIm
-W
676(3) 5' C C TG C W-3' PyPy-p-ImPy-y-ImPy-(3-ImIm
-W
677(3) 5' C C TC T W-3' PyPyHpPyHp-y-PyIm-(3-ImIm
-W
677(3p) 5' C C TC T W-3' PyPy-(3-PyHp-y-PyIm-/3-ImIm
-W
678(3) 5'-W C C TC A W-3' PyPyHpPyPy-y-Hplm-(3-ImIm
678(3p) 5' C C TC A W-3' PyPy-p-PyPy-y-Hplm-~i-ImIm
-W
679p) 5' C C TC G W-3' PyPy-p-PyIm-y-Pylm-(3-ImIm
-W
680(3) 5' C C TC C W-3' PyPyHpPyPy-y-Imlm-~i-Imlm
-W
680~3p) 5' C C TC C W-3' PyPy-(3-PyPy-y-Imlm-(3-Imlm
-W
681R) 5' C C AT T W-3' PyPyPyHpHp-y-PyPy-~3-ImIm
-W
681~p) 5' C C AT T W-3' PyPy-(1-HpHp-y-PyPy-~-ImIm
-W
682(3) 5' C C AT A W-3' PyPyPyHpPy-y-HpPy-~3-ImIm
-W
682(3p) 5' C C AT A W-3' PyPy-~i-HpPy-y-HpPy-(3-ImIm
-W
CA 02281930 1999-08-18
WO 98/37067 PCT/U598I01714
-103-
TABLE 66: 10-ring
Hairpin Polyamides
for recognition
of 7-by 5'-WCCWNNW-3'
with p substitutions.
DNA aromatic amino acid sequence
sequence
683(3) 5' C C A TG W-3' Pypy-(3-HpIm-y-PyPy-~-ImIm
-W
684(3) '5'-WC C A TC W-3' PyPyPyHpPy-y-ImPy-~3-ImIm
684(3p) 5' C C A TC W-3' PyPy-~i-HpPy-y-ImPy-(3-ImIm
-W
6853) 5' C C A AT W-3' PyPyPyPyHp-y-PyHp-(3-ImIm
-W
685(3p) 5' C C A AT W-3' PyPy-(3-PyHp-y-PyHp-p-ImIm
-W
686(3) 5' C C A AA W-3' PyPyPyPyPy-y-HpHp-(3-ImIm
-W
686(3p) 5' C C A AA W-3' PyPy-~3-PyPy-y-HpHp-~-ImIm
-W
687(3) 5' C C A AG W-3' PyPy-p-PyIm-y-PyHp-(3-ImIm
-W
6883) 5' C C A AC W-3' PyPyPyPyPy-y-ImHp-(3-ImIm
-W
688~3p) 5' C C A AC W-3' PyPy-(3-pypy-y-I~p_~_ImIm
-W
689(3) 5' C C A GT W-3' PyPy-j3-ImHp-y-PyPy-/3-ImIm
-W
690(3) 5' C C A GA W-3' PyPy-(3-ImPy-y-HpPy-(3-ImIm
-W
691(3) 5' C C A GG W-3' PyPy-(3-ImIm-y-PyPy-(3-ImIm
-W
6923) 5' C C A GC W-3' PyPy-(3-ImPy-y-ImPy-(3-Imlm
-W
693(3) 5' C C A CT W-3' PyPyPyPyHp-y-PyIm-(3-ImIm
-W
693~ip) 5' C C A CT W-3' Pypy-(3-PyHp-y-Pylm-(3-ImIm
-W
694(3) 5' C C A CA W-3' PyPyPyPyPy-y-Hplm-/3-ImIm
-W
694(3p) 5' C C A CA W-3' PyPy-~i-PyPy-y-Hplm-[3-Imlm
-W
695(3) 5' C C A CG W-3' PyPy-(3-PyIm-y-Pylm-~3-ImIm
-W
696(3) 5' C C A CC W-3' PyPyPyPyPy-y-ImIm-p-ImIm
-W
696~ip) 5' C C A CC W-3' PyPy-(3-PyPy-y-ImIm-(3-Imlm
-W
CA 02281930 1999-08-18
WO 98/37067
PCT/US98/01714
-104-
TABLE
67: 10-ring
Hairpin
Polyamides
for recognition
of 7-by
5'-WCCSNNW-3'
with
(3 substitutions.
DNA aromatic amino acid sequence
sequence
697(3) 5' C C G T TW-3' Py-~3-ImHpHp-y-PyPy-~3-ImIm
-W
698(3) '5' C C G T AW-3' Py-~3-ImHpPy-y-HpPy-(3-ImIm
-W
6993) 5' C C G T GW-3' Py-~i-ImHpIm-y-PyPy-p-Imlm
-W
700(3) 5' C C G T CW-3' Py-~3-ImHpPy-y-ImPy-(3-ImIm
-W
701(3) 5' C C G A TW-3' Py-[3-ImPyHp-y-PyHp-(3-ImIm
-W
702(3) 5' C C G A AW-3' Py-(3-ImPyPy-y-HpHp-p-ImIm -
-W
703(3) 5' C C G A GW-3' Py-~i-ImPyIm-y-PyHp-p-Imlm
-W
7043? 5'-W C C G A CW-3' p
y-p-ImPyPy-y-ImHp-(3-ImIm
705(3) 5' C C G G TW-3' p
-W y-(3-ImImHp-y-PyPy-(3- ImIm
706(3) 5' C C G G AW-3' Py-~-ImImPy-y-HpPy-(3-ImIm
-W
707(3) 5' C C G C TW-3' Py-(3-ImPyHp-y-PyIm-R-ImIm
-W
708(3) 5' C C G C AW-3' Py-(3-ImPyPy-y-Hplm-~i-Imlm
-W
709~i) 5' C C C T TW-3' PyPypyHpHp-y-Py-(3-ImImIm
-W
709~ip) 5' C C C T TW-3' PyPyPy-(3-Hp-y-Py-(3-ImImIm
-W
710(3) 5'-W C C C T AW-3' PyPyPyHpPy-y-Hp-~i-ImImIm
710(3p) 5' C C C T AW-3' PyPyPy-~3-Py-y-Hp-~i-ImImIm
-W
7113) 5'-W C C C T GW-3' PyPy-(3-HpIm-y-Py-(3-ImImIm
7123) 5' C C C T CW-3' PyPyPyHpPy-y-Im-(3-ImImIm
-W
712(3p) 5' C C C T CW-3' PyPyPy-~i-Py-y-Im-~3-ImImIm
-W
713(3) 5' C C C A TW-3' PyPyPyPyHp-y-Py-(3-ImImIm
-W
713~3p) 5' C C C A TW-3' PyPyPy-(3-Hp-y-Py-(3-ImImIm
-W
714(3) 5' C C C A AW-3' PyPyPyPyPy-y-Hp-(3-ImImIm
-W
714(3p) 5' C C C A AW-3' PyPyPy-(3-Py-y-Hp-~i-ImImIm
-W
715(3) 5' C C C A GW-3' PyPy-~3-Pylm-y-Py-(3-ImImIm
-W
716(3) 5' C C C A CW-3' PyPypypypy-y-Im-(3-ImImIm
-W
716(3p) 5' C C C A CW-3' PyPyPy-(3-Py-y-Im-~i-ImImIm
-W
717(3) 5' C C C G TW-3' PyPy-(3-ImHp-y-Py-(3-ImImIm
-W
718)3) 5' C C C G AW-3' PyPy-p-ImPy-y-Hp-(3-ImImIm
-W
CA 02281930 1999-08-18
WO 98!37067 PCT/US98/01714
-105-
TABLE 67 (cont):
10-ring Hairpin
Polyamides for
recognition of
7-by 5'-WCCSNNW-3'
with ~3 substitutions.
DNA sequence aromatic
amino acid sequence
G4l~i) 5' C C G G G W-3' Py-(~-ImImIm-y-PyPy-(3-ImIm
-W
G42~3) 5' C C G G C W-3' Py-(3-ImImPy-y-ImPy-(3-ImIm
-W
G43(3) '5' C C G C G W-3' Py-[3-ImPyIm-y-Pylm-p-Imlm
-W
G44(3) 5' C C G C C W-3' Py-(3-ImPyPy-y-ImIm-(3-ImIm
-W
645(3) 5' C C C G G W-3' PyPy-p-ImIm-y-Py-(3-ImImIm
-W
G46~3) 5' C C C G C W-3' PyPy-(3-ImPy-y-Im-~3-ImImIm
-W
G47(3) 5'-W C C C C G W-3' PyPy-(3-Pylm-y-PyImImImIm
CA 02281930 1999-08-18
WO 98/37067 PCT/US98101714
-106-
TABLE 68:
10-ring
Hairpin
Polyamides
for recognition
of 7-by
5'-WAGWNNW-3'
with ~3
substitutions.
DNA aromatic amino acid sequence
sequence
7230 5'-W A G TT G W-3' Pylm-(3-HpIm-y-PyPyPyPyHp
723(3p) '5'-W A G TT G W-3' PyIm-~3-HpIm-y-PyPy-(3-PyHp
727(3) 5'-W A G TA G W-3' PyIm-(3-Pylm-y-PyHpPyPyHp
727~3p) 5'-W A G TA G W-3' PyIm-(3-PyIm-y-PyHp-(3-PyHp
729(3) 5'-W A G TG T W-3' Pylm-~3-ImHp-y-PyPyPyPyHp
729(3p) 5'-W A G TG T W-3' PyIm-(3-ImHp-y-PyPy-(3-PyHp
730(3) 5'-W A G TG A W-3' PyIm-[3-ImPy-y-HpPyPyPyHp
730(3p) 5'-W A G TG A W-3' PyIm-~i-ImPy-y-HpPy-~-PyHp
7313) 5'-W A G TG G W-3' PyIm-(3-ImIm-y-PyPyPyPyHp
731(3p) 5'-W A G TG G W-3' PyIm-~i-Imlm-y-PyPy-(3-PyHp
732(3) 5'-W A G TG C W-3' PyIm-(3-ImPy-y-ImPyPyPyHp
732(3p) 5'-W A G TG C W-3' PyIm-(3-ImPy-y-ImPy-J3-PyHp
735(3) 5'-W A G TC G W-3' Pyim-~-PyIm-y-PyImPyPyHp
735(3p) 5'-W A G TC G W-3' Pylm-(3-Pylm-y-Pylm-(3-PyHp
739(3) 5'-W A G AT G W-3' PyIm-p-HpIm-y-PyPyHpPyIip
739~p) 5'-W A G AT G W-3' PyIm-~3-HpIm-y-PyPy-~3-PyHp
743(3) 5'-W A G AA G W-3' PyIm-(3-PyIm-y-PyHpHpPyHp
743~ip) 5'-W A G AA G W-3' PyIm-(3-Pylm-y-PyHp-p-PyHp
745(3) 5'-W A G AG T W-3' PyIm-(3-ImHp-y-PyPyHpPyHp
745(3p) 5'-W A G AG T W-3' PyIm-~i-ImHp-y-PyPy-(3-PyHp
7463) 5'-W A G AG A W-3' PyIm-(3-ImPy-y-HpPyHpPyHp
746(3p) 5'-W A G AG A W-3' PyIm-(3-ImPy-y-HpPy-~3-PyHp
747(3) 5'-W A G AG G W-3' PyIm-~i-ImIm-y-PyPyHpPyHp
747~3p) 5'-W A G AG G W-3' PyIm-p-ImIm-y-PyPy-(3-PyHp
748(3) 5'-W A G AG C W-3' PyIm-p-ImPy-y-ImPyHpPyHp
748(3p) 5'-W A G AG C W-3' Pylm-(3-ImPy-y-ImPy-~3-PyHp
751(3) 5'-W A G AC G W-3' PyIm-(3-PyIm-y-PyImHpPyHp
751(3p) 5'-W A G AC G W-3' PyIm-(3-PyIm-y-Pylm-~i-PyHp
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-107-
TABLE :
69 10-ring
Hairpin
Polyamides
for
recognition
of
7-by
5'-WAGSNNW-3'
with
(3
substitutions.
DNA aromatic amino acid sequence
sequence
753(3) 5' A G G T TW-3' PyImIm-(3-Hp-y-pypypypyHp
-W
753~3P) '5'-WA G G T TW-3' PyIrttIm-J3-Hp-y-py-(3-pypyHp
754(3) 5' A G G T AW-3' PyImIm-~3-Py-y-HpPyPyPyHp
-W
754~3p) 5' A G G T AW-3' PyImIm-(3-Py-y-Hp-~-PypyHp
-W
755(3) 5' A G G T GW-3' PyImIm-(3-Im-y-PyPypypyHp
-W
755pp) 5' A G G T GW-3' PyImIm-(3-Im-y-Py-~3-pypyHp
-W
7563) 5' A G G T CW-3' PyImIm-~3-py-y-ImPyPyPyHp
-W
756(3p) 5' A G G T CW-3' PyImIm-(3-Py-y-Im-(3-PyPyHp
-W
757(3) 5' A G G A TW-3' PyImIm-~3-Hp-y-PyHpPyPyHp
-W
757~3P) 5' A G G A TW-3' PyImIm-(3-Hp-y-Py-(3-pypyHp
-W
7583) 5' A G G A AW-3' PyImIm-(3-Py-y-HpHpPyPyHp
-W
758(3p) 5' A G G A AW-3' PyImIm-(3-Py-y-Hp-(3-PyPyHp
-W
759(3) 5' A G G A GW-3' PyImIm-p-Im-y-PyHpPyPyHp
-W
759~3p) 5' A G G A GW-3' PyImIm-~3-Im-y-Py-~-pypygp
-W
760(3) 5' A G G A CW-3' PyImIm-(3-Py-y-ImHpPyPyHp
-W
760~p) 5' A G G A CW-3' PyImIm-(3-Py-y-Im-~-PyPyHp
-W
763(3) 5' A G G C TW-3' PyImIm-(3-Hp-y-PyImPyPyHp
-W
7643) 5' A G G C AW-3' Pylmim-(3-Py-y-HpImPyPyHp
-W
765(3) 5' A G C T TW-3' PyImPyHpHp-y-Py-~3-ImPyHp
-W
765pp) 5' A G C T TW-3' PyImPy-(3-Hp-y-py-(3-ImPyHp
-W
7663) 5' A G C T AW-3' PyImPyHpPy-y-Hp-(3-ImPyHp
-W
766(3p) 5' A G C T AW-3' PyImPy-(3-Py-y-Hp-(3-ImPyHp
-W
7673) 5' A G C T GW-3' PyIm-(3-HpIm-y-Py-(3-ImPyAp
-W
768(3) 5' A G C T CW-3' PyImPyHpPy-y-Im-~3-ImPyHp
-W
768~ip) 5' A G C T CW-3' PyImPy-(3-Py-y-Im-~-ImPyHp
-W
769(3) 5' A G C A TW-3' PyImPyPyHp-y-Py-p-ImPyHp
-W
769(3p) 5' A G C A TW-3' PyImPy-~i-Hp-y-py-(3-ImPyHp
-W
770(3) 5' A G C A AW-3' PyImPyPyPy-y-Hp-(3-ImPyHp
-W
CA 02281930 1999-08-18
WO 98137067 PCT/US98/01714
-108-
lAIiLL by (cont):
IU-ring Hairpin
Polyamides
for recognition
of 7-by 5'-WAGSNNW-3'
with (3 substitutions.
DNA aromatic amino acid sequence
sequence
770~3p) 5'-WA G C A A W-3' PyImPy-(3-Py-y-Hp-(3-ImPyHp
771(3) .5'-WA G C A G W-3' PyIm-~3-PyIm-y-Py-(3-ImPyHp
772(3) 5'-WA G C A C W-3' PyImPyPyPy-y-Im-(3-ImPyHp
772(3p) 5'-WA G C A C W-3' PyImPy-(3-Py-y-Im-~3-ImPyHp
7733) 5'-WA G C G T W-3' PyIm-(3-ImHp-y-Py-~-ImPyHp
7743) 5'-WA G C G A W-3' Pylm-(3-ImPy-y-Hp-(3-ImPyHp
775(3) 5'-WA G C C T W-3' PyImPyPyHp-y-PyImIm-/3-Hp
776~i) 5'-WA G C C A W-3' PyImPyPyPy-y-HpImIm-~3-Hp
7793) 5'-WA G G C G W-3' PyImIm-(3-Im-y-PyImPyPyHp
780(3) 5'-WA G G C C W-3' PyImIm-~3-Py-y-ImImPyPyHp
781(3) 5'-WA G C G G W-3' PyIm-~-ImIm-y-Py-~i-ImPyHp
782(3) 5'-WA G C G C W-3' Pylm-/3-ImPy-'y-Im-~-ImPyHp
783(3) 5'-WA G C C G W-3' Pylm-(3-Pylm-y-PyImIm-(3-Hp
784(3) 5'-WA G C C C W-3' PyImPyPyPy-y-ImImIm-a-Hp
CA 02281930 1999-08-18
WO 98/37067 PCT/US98101714
- I 09-
TABLE 70:
10-ring
Hairpin
Polyamides
for recognition
of 7-by
5'-WATWNNW-3'
with (3
substitutions.
DNA aromatic amino acid sequence
sequence
7873) 5'-WA T T T G W-3' PyHp_R_Hplm-y-PypyPypyHp
787(3p) . -WA T T T G W-3' PyHp-~3-HpIm-y-PyPy-(3-PyHp
5'
791(3) 5'-WA T T A G W-3' PyHp-(3-PyIm-y-PyHpPyPyHp
791(~p) 5'-WA T T A G W-3' PyHp-(3-PyIm-y-PyHp-p-PyHp
793(3) 5'-WA T T G T W-3' PyHp-~i-ImHp-y-PyPyPyPyHp
793~P) 5'-WA T T G T W-3' pyHp-~_I~p_y_pypy-~j-pyHp
7943) 5'-WA T T G A W-3' PyHp-p-ImPy-y-HpPyPyPyHp
794(3p) 5'-WA T T G A W-3' PyHp-~-ImPy-y-HpPy-~3-PyHp
795(3) 5'-WA T T G G W-3' PyHp-~3-Imlm-y-PypypypyHp
795~3P) 5'-WA T T G G W-3' PyHp-~-ImPy-y-ImPyPyPyHp
796(3p) 5'-WA T T G C W-3' Pylip-p-ImPy-y-ImPy-/3-PyHp
799(3) 5'-WA T T C G W-3' PyHp-p-pyIm-y-PyImPyPyHp
799(3p) 5'-WA T T C G W-3' PyHp-(3-Pylm-y-PyIm-p-PyHp
803~i) 5'-WA T A T G W-3' PyHp-/3-HpIm-y-PypyHpPyHp
803(3p) 5'-WA T A T G W-3' PyHp-~3-HpIm-y-PyPy-~3-PyHp
8073) 5'-WA T A A G W-3' PyHp-~-PyIm-y-PyHpHpPyHp
807(3p) 5'-WA T A A G W-3' PyHp-(3-PyIm-y-PyHp-~3-PyHp
8093) 5'-WA T A G T W-3' PyHp-(3-ImHp-y-PYPYHpPyHp
809(3p) 5'-WA T A G T W-3' PyHp-(3-ImHp-y-PYPy-p-PyHp
810(3) 5'-WA T A G A W-3 ' PyHp-(3-ImPy-y-HpPyHpPyHp
810~3p) 5'-WA T A G A W-3' PyHp-~-ImPy-y-HpPy-(3-PyHp
811~i) 5'-WA T A G G W-3' PyHp-[3-ImIm-y-pypyHpPyHp
811~3P) 5'-WA T A G G W-3' PyHp-/3-ImIm-y-PyPy-(3-PyHp
812~i) 5'-WA T A G C W-3' p H
Y P-p-ImPy-y-ImPyHpPyHp
812~ip) 5'-WA T A G C W-3' PyHp-(3-Impy-y-Impy-p-PyHp
815(3) 5'-WA T A C G W-3' PyHp-(3-pylm-y-PyImHpPyHp
815~3p) 5'-WA T A C G W-3' PyHp-p-PyIm-y-Pylm-~i-PyHp
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-110-
TABLE 71:
I 0-ring
Hairpin
Polyamides
for recognition
of 7-by
S'-WATSNNW-3'
with p
substitutions.
DNA aromatic amino acid sequence
sequence
817~i) 5'-W A T GT T W-3' Py-J3-ImHpHp-y-PyPyPyPyHp
817(3p) ' -W A T GT T W-3' py-(3-I~pgp_y_pypypy_p-Hp
S'
8183) 5'-W A T GT A W-3 Py-(3-ImHpPy-y-HpPyPyPyHp
818(3p) 5'-W A T GT A W-3' Py-(3-ImHpPy-y-HpPyPy-~3-Hp
8193) 5'-W A T GT G W-3' Py-(3-ImHpIm-y-PyPyPyPyHp
819~3p) 5'-W A T GT G W-3' Py-/3-ImHpIm-y-PyPyPy-(3-Hp
820(3) 5'-W A T GT C W-3' Py-~3-ImHppy-y-ImPyPyPyHp
820(3p) 5'-W A T GT C W-3' py-(3-ImHpPy-y-ImPyPy-~3-Hp
821(3) 5'-W A T GA T W-3' Py-(3-ImPyHp-y-PyHpPyPyHp
821(3p) 5'-W A T GA T W-3' Py-/3-ImPyHp-y-PyHpPy-(3-Hp
822(3} 5'-W A T GA A W-3' Py-(3-ImPyPy-y-HpHppyPyHp
822(3p) 5'-W A T GA A W-3' Py-(3-ImPyPy-y-HpHpPy-~3-Hp
823(3) 5'-W A T GA G W-3' Py-p-ImPyIm-y-PyHpPyPyHp
823(3p) 5'-W A T GA G W-3' Py-/3-ImPyIm-y-PyHpPy-~i-Hp
824(3) 5'-W A T GA C W-3' Py-(3-ImPyPy-y-ImHpPyPyHp
824(3p} 5'-W A T GA C W-3' Py-(3-ImPyPy-y-ImHpPy-(3-Hp
825(3) 5'-W A T GG T W-3' Py-(3-ImImHp-y-PypyPyPyHp
825~3p} 5'-W A T GG T W-3' Py-(3-ImImHp-y-PyPyPy-(3-Hp
826(3) 5'-W A T GG A W-3' Py-~3-ImImPy-y-HpPyPyPyHp
826(3p) 5'-W A T GG A W-3' Py-(3-ImImPy-y-HpPyPy-p-Hp
8273) 5'-W A T GC T W-3' Py-p-ImPyHp-y-PyImPyPyHp
827(3p) 5'-W A T GC T W-3' Py-~3-ImPyHp-y-PyImPy-p-Hp
8283) 5'-W A T GC A W-3' Py-p-ImPyPy-y-HpImPyPyHp
828(3p} 5'-W A T GC A W-3' Py-p-ImPyPy-y-HpImPy-~3-Hp
8290 5'-W A T GG G W-3' Py-(3-ImImIm-y-PypyPyPyHp
829~p) 5'-W A T GG G W-3' Py-(3-ImImIm-y-PyPyPy-(3-Hp
830(3) 5'-W A T GG C W-3' Py-j3-ImImPy-y-ImPyPyPyHp
830(3p) 5'-W A T GG C W-3' Py-(3-ImImPy-y-ImPyPy-(3-Hp
831(3) 5'-W A T GC G W-3' Py-(3-ImPyIm-y-PyImPyPyHp
831(3p) 5'-W A T GC G W-3' Py-(3-ImPyIm-y-PyImPy-~3-Hp
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-111-
TABLE 71:
I 0-ring
Hairpin
Polyamides
for recognition
of 7-by
5'-WATSNNW-3'
with p
substitutions.
DNA aromatic amino acid sequence
sequence
8323) 5'-W A TG C C W-3' Py-~-ImPyPy-y-ImImPyPyHp
832~3p) ' -W A TG C C W-3' Py-~-ImPyPy-y-ImImPy-~3-Hp
5'
833(3) 5'-W A TC T T W-3' PyHpPyHpHp-y-Py-~3-ImPyHp
833~p) 5'-W A TC T T W-3' PyHpPy-(3-Hp-y-Py-(3-ImPyHp
8340 5'-W A TC T A W-3' PyHpPyHpPy-y-Hp-(3-ImPyHp
834~3p) 5'-W A TC T A W-3' PyHpPy-~3-Py-y-Hp-(3-ImPyHp
8353) 5'-W A TC T G W-3' PyHp-(3-HpIm-y-Py-(3-ImPyHp
836~i) 5'-W A TC T C W-3' PyHpPyHpPy-y-Im-(3-ImPyHp
836(3p) 5'-W A TC T C W-3' PyHpPy-~3-py-y-Im-(3-ImPyHp
837(3) 5'-W A TC A T W-3' PyHpPyPyHp-y-Py-(3-ImPyHp
837~3p) 5'-W A TC A T W-3' PyHpPy-(3-Hp-y-Py-(3-ImPyHp
8383) 5'-W A TC A A W-3' PyHpPyPyPy-y-Hp-(3-ImPyHp
838(3p) 5'-W A TC A A W-3' PyHpPy-~3-Py-y-Hp-(3-ImPyHp
839(3) 5'-W A TC A G W-3' PyHp-~3-PyIm-y-Py-(3-ImPyHp
$40(3) 5'-W A TC A C W-3' PyHpPyPyPy-y-Im-p-ImPyHp
840~p) 5'-W A TC A C W-3' PyHpPy-~i-Py-y-Im-~3-ImPyHp
841(3) 5'-W A TC G T W-3' PyHp-(3-ImHp-y-Py-(3-ImPyHp
842(3) 5'-W A TC G A W-3' PyHp-~-ImPy-y-Hp-~-ImPyHp
8430 5'-W A TC C T W-3' PyHpPyPyHp-y-PyImIm-(3-Hp
843(3p) 5'-W A TC C T W-3' py-(3-pypygp-y-pylmIm-~3-Hp
8443) 5'-W A TC C A W-3' PyHppyPyPy-y-HpImIm-(3-Hp
844(3p) 5'-W A TC C A W-3' py-p-pypypy-y-HpImIm-(3-Hp
845 ) 5'-W A TC G G W-3'
PyHp-(3-ImIm-y-Py-(3-ImPyHp
8463) 5'-W A TC G C W-3' PyHp-(3-ImPy-y-Im-(3-ImPyHp
8473) 5'-W A TC C G W-3' PyHp-(3-PyIm-y-PyImIm-(3-Hp
- 8483) 5'-W A TC C C W-3' PyHpPyPyPy-y-ImImIm-~3-Hp
848(3p) 5'-W A TC C C W-3' Py-(3-PyPyPy-y-ImImIm-(3-Hp
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-112-
TABLE 72:
10-ring
Hairpin
Polyamides
for recognition
of 7-by
5'-WAAWNNW-3'
with ~3
substitutions.
DNA aromatic amino acid sequence
sequence
851(3) 5' -WA AT T G W-3' PyPy-~3-Hp lm-y-PyPyPyHpHp
851~3p) ' -WA AT T G W-3' PyPy-J3-Hplm-y-PyPy-~3-HpHp
5'
8553) 5' -WA AT A G W-3' PyPy-~3-Pylm-y-PyHppyHpHp
855(3p) 5' -WA AT A G W-3' Pypy-p-PyIm-y-PyHp-~3-HpHp
857(3) 5' -WA AT G T W-3' PyPy-~3-ImHp-y-PyPyPyHpHp
857(3p) 5' -WA AT G T W-3' PyPy-~-ImHp-y-PyPy-(3-HpHp
858(3) 5' -WA AT G A W-3' PyPy-(3-ImPy-y-HpPyPyHpHp
858(3p) 5' -WA AT G A W-3' PyPy-(3-ImPy-y-Hppy-(3-HpHp
8593) 5' -WA AT G G W-3' Pypy-(3-Imlm-y-PyPyPyHpHp
859~3p) 5' -WA AT G G W-3' PyPy-(3-Imlm-y-Pypy-~-HpHp
8603) 5' -WA AT G C W-3' PyPy-(3-ImPy-y-ImPyPyHpHp
860(3p) 5' -WA AT G C W-3' PyPy-[3-ImPy-y-ImPy-(3-HpHp
8633) 5' -WA AT C G W-3' PyPy-(3-PyIm-y-PyImPyHpHp
863(3p) 5' -WA AT C G W-3' PyPy-(3-Pylm-y-PyIm-(3-HpHp
8673) 5' -WA AA T G W-3' PyPy-(3-HpIm-y-PyPyHpHpHp
867(3p) 5' -WA AA T G W-3' PyPy-(3-Hplm-y-PyPy-(3-HpHp
871(3) 5' -WA AA A G W-3' PyPy-(3-PyIm-y-PyHpHpHpHp
871~3p) 5' -WA AA A G W-3' PyPy-p-PyIm-y-PyHp-(3-HpAp
8733) 5' -WA AA G T W-3' PyPy-(3-ImHp-y-PyPyHpHpHp
873(3p) 5' -WA AA G T W-3' PyPy-(3-ImHp-y-PyPy-(3-HpHp
874(3) 5' -WA AA G A W-3' PyPy-p-ImPy-y-HpPyHpHpHp
874~p) 5' -WA AA G A W-3' PyPy-(i-ImPy-y-HpPy-(3-HpHp
875(3) 5' -WA AA G G W-3' PyPy-p-ImIm-y-PyPyHpHpHp
875(3p) 5' -WA AA G G W-3' PyPy-~3-Imlm-y-PyPy-~i-HpHp
876(3) 5' -WA AA G C W-3' Pypy-(3-ImPy-y-ImPyHpHpHp
876~ip) 5' -WA AA G C W-3' PyPy-~i-ImPy-y-ImPy-(3-HpHp
8793) 5' -WA AA C G W-3' PyPy-~i-PyIm-y-PyImHpHpHp
879(3p) 5' -WA AA C G W-3' PyPy-(3-PyIm-y-PyIm-(3-HpHp
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-113-
TABLE
73: 10-ring
Hairpin
Polyamides
for recognition
of 7-by
5'-WAASNNW-3'
with
substitutions.
DNA aromatic amino acid sequence
sequence
' 881) 5' A A GT T W-3' Py--IrnHpHp-y-PyPyPyHpHp
-W
881p) '5' A A GT T W-3' py__I~pHp-y-pyPypy--Hp
-W
882) 5' A A GT A W-3' Py--ImHpPy-y-HpPyPyHpHp
-W
882P) 5' A A GT A W-3' py--I~ppy_y-Hppypy--Hp
-W
883) 5' A A GT G W-3' Py--ImHpIm-y-PyPypyHpHp
-W
883(3p) 5'-W A A GT G W-3' Py--ImHpIm-y-PyPyPy--Hp
884) 5'-W A A GT C W-3' p
y--ImHpPy-y-ImPyPyHpHp
884(3p) 5' A A GT C W-3' p
-W y--ImHppy-y-ImPyPy--Hp
8853) 5' A A GA T W-3'
-W Py--ImPyHp-y-PyHpPyHpHp
885p) 5' A A GA T W-3' Py--ImPyHp-y-PyHpPy--Hp
-W
886(3) 5' A A GA A W-3'
-W Py--ImPyPy-y-HpHpPyHpHp
886p) 5'-W A A GA A W-3'
Py--ImPyPy-y-HpHpPy--Hp
887) 5' A A GA G W-3' Py--ImPyIm-y-PyHpPyHpHp
-W
887(3p) 5' A A GA G W-3' Py--ImPyIm-y-PyHpPy--Hp
-W
888) 5' A A GA C W-3' Py--ImPyPy-y-ImHpPyI-IpHp
-W
888~iP) 5' A A GA C W-3' Py--ImPyPy-y-ImHpPy--Hp
-W
889) 5'-W A A GG T W-3'
Py--ImImHp-y-PyPyPyHpHp
889p) 5'-W A A GG T W-3'
Py--ImImHp-y-PyPyPy--Hp
890(3) 5'-W A A GG A W-3'
Py--ImImPy-y-HpPyPyHpHp
890p) 5'-W A A GG A W-3'
Py--ImImPy-y-HpPyPy--Hp
891) 5' A A GC T W-3' Py--ImPyHp-y-PyTmPyHpHp
-W
891p) 5' A A GC T W-3' Py--ImPyHp-y-PyImPy--Hp
-W
892) 5'-W A A GC A W-3'
Py--ImPyPy-y-HpImPyHpHp
892p) 5'-W A A GC A W-3'
Py--ImPyPy-y-HpImPy--HP
893(3) 5' A A GG G W-3' Py--ImImIm-y-PyPyPyHpHp
-W
893p) 5' A A GG G W-3' Py--ImImIm-y-PyPyPy--Hp
-W
894) 5' A A GG C W-3' Py--ImImPy-y-ImPyPyHpHp
-W
894p) 5'-W A A GG C W-3'
Py--ImImPy-y-ImPyPy--Hp
895(3) 5' A A GC G W-3' Py--ImPyIm-y-PyImPyHpHp
-W
895p) 5'-W A A GC G W-3' Py--ImPyIm-y-PyImPy--Hp
CA 02281930 1999-08-18
WO 98/37067
PCT/US98/01714
-114-
TABLE 73 (cont); Polyamides
10-ring Hairpin for
recognition
of
7-by
5'-WAASNNW-3'
with
(3
substitutions.
DNA aromatic amino acid sequence
sequence
896(3) 5'-W A AG C C W-3' Py-p-ImPyPy-y-ImImPyHpHp
896(3p) 5'-W A AG C C W-3' Py-p-ImPyPy-y-ImImPy-(3-Hp
8973) ~ -W A AC T T W-3' PyPyPyHpHp-y-Py-~i-ImHpHp
5'
897(3p) 5'-W A AC T T W-3' pypypy_R_Hp_y_py_~_I~pHp
898(3) 5'-W A AC T A W-3' PyPyPyHpPy-y-Hp-(3-ImHpHp
898~3p) 5'-W A AC T A W-3' PyPyPy-(3-py-y-Hp_(3-ImApHp
899(3) 5'-W A AC T G W-3' PyPy-(3-HpIm-y-Py-(3-ImHpHp
900(3) 5'-W A AC T C W-3' PyPyPyHpPy-y-Im-~3-ImHpHp
900(3p) 5'-W A AC T C W-3' PyPyPy-(3-Py-y-Im-(3-ImHpHp
901(3) 5'-W A AC A T W-3' PyPyPyPyHp-y-Py-(3-ImHpHp
901(3p) 5'-W A AC A T W-3' PyPyPy-(3-Hp-y-py_~3-ImHpHp
902(3) 5'-W A AC A A W-3' PyPyPypypy-y-Hp_~-ImHpHp
902~3p) 5'-W A AC A A W-3' pypypy_~_py_y_Hp-~-I~pHp
903~i) 5'-W A AC A G W-3' PyPy-(3-pylm_y_py_~_I~pHp
904(3) 5'-W A AC A C W-3' PyPyPyPyPy-y-Im-~3-ImHpHp
904(3p) 5'-W A AC A C W-3' PyPyPy-~3-Py-y-Im-(3-ImHpHp
905(3) 5'-W A AC G T W-3' PyPy-(3-ImHp-y-Py-p-ImHpHp
9063) 5'-W A AC G A W-3' PyPy-(3-ImPy-y-Hp-(3-ImHpHp
9073) 5'-W A AC C T W-3' PyPypypyHp-y-PyImIm-p-Hp
907(3p) 5'-W A AC C T W-3' Py-(3-PyPyHp-y-PyImIm-(3-Hp
908(3) 5'-W A AC C A W-3' PyPyPyPyPy-y-HpImIm-(3-Hp
908~3p) 5'-W A AC C A W-3' Py-(3-PyPyPy-y-HpImIm-p-Hp
9093) 5'-W A AC G G W-3' PyPy-(3-Imlm-y-Py-(3-ImHpHp
910(3) 5'-W A AC G C W-3' PyPy-(3-ImPy-y-Im-(3-ImHpHp
9113) 5'-W A AC C G W-3' PyPy-~3-PyIm-y-PyImIm-(3-Hp
912(3) 5'-W A AC C C W-3' PyPyPyPyPy-y-ImImIm-(3-Hp
912~3p) 5'-W A AC C C W-3' Py-(3-pypypy-y-ImImIm-p-Hp
CA 02281930 1999-08-18
WO 98/37067 PCT/US98101714
-115-
' TABLE
74: 30-ring
Hairpin
Polyamides
for recognition
of 7-by
5'-WACWNNW-3'
with
~3 substitutions
.
DNA aromatic amino acid sequence
sequence
913(3) 5' -WA C T TT W-3' PyPyHpHpHp-y-PyPy-(3-ImFip
913(3p) .5'-WA C T TT W-3' PyPy-(3-HpHp-y-Pypy-(3-ImHp
914(3) 5' -WA C T TA W-3' PyPyHpHpPy-y-HpPy-(3-ImHp
914(3p) 5' -WA C T TA W-3' pyPy-p-HpPy-y-HpPy-j3-ImHp
9153) 5' -WA C T TG W-3' PyPy-(3-HpIm-y-PyPy-(3-ImHp
916(3) 5' -WA C T TC W-3' PyPyHpHpPy-Y-ImPy-(3-ImHp
916(3p) 5' -WA C T TC W-3' PyPy-(3-HpPy-y-ImPy-(3-ImHp
9173) 5' -WA C T AT W-3' PyPyHpPyHp-y-PyHp-~3-ImHp
9I7(3p) 5' -WA C T AT W-3' PyPyHpPyHp-y-PyHp-(3-ImHp
918~i) 5' -WA C T AA W-3' PyPyHpPyPy-y-HpHp-(3-ImHp
918~3p) 5' -WA C T AA W-3' PyPy-(3-PyPy-y-HpHp-(3-ImHp
9193) 5' -WA C T AG W-3' PyPy-p-pylm-y-PyHp-~i-ImHp
920(3) 5' -WA C .TAC W-3' PyPyHpPyPy-Y-ImHp-(3-ImHp
920(3p) 5' -WA C T AC W-3' PyPy-(3-PyPy-y-ImIip-(3-ImHp
921(3) 5' -WA C T GT W-3' pypy-~-Imp-y_pypy-a_I~p
922(3) 5' -WA C T GA W-3' PyPy-~3-ImPy-y-HpPy-(3-ImHp
923(3) 5' -WA C T GG W-3' PyPy-(3-Imlm-y-PyPy-(3-ImHp
924(3) 5' -WA C T GC W-3' PyPy-~3-ImPy-y-ImPy-(3-ImHp
925(3) 5' -WA C T CT W-3' PyPyHpPyHp-y-PyIm-~3-ImHp
925~3p) 5' -WA C T CT W-3' PyPy-(1-PyHp-Y-pylm-(3-ImHp
9260 5' -WA C T CA W-3' PyPyHpPyPy-y-HpIm-(3-ImHp
926(3p) 5' -WA C T CA W-3' PyPy-(3-PyPy-Y-Hplm-~3-ImHp
927(3) 5' -WA C T CG W-3' PyPy-(3-PyIm-y-PyIm-(3-ImHp
928(3) 5' -WA C T CC W-3' PyPyHpPyPy-y-ImIm-[3-ImHp
928~3p) 5' -WA C T CC W-3' PyPy-(3-pypy-y-Imlm-~3-ImHp
929(3) 5' -WA C A TT W-3' PyPyPyHpHp-y-PyPy-/3-ImHp
' 30 929~3p) 5' -WA C A TT W-3' pypy-(3-gpgp_y_pypy_~_I~p
9303) 5' -WA C A TA W-3' PyPyPyHpPy-Y-HpPy-(3-ImHp
930~3p) 5' -WA C A TA W-3' pypy-(3-Hppy-y-HpPy-p-ImHp
9313) 5' -WA C A TG W-3' Pypy-(3-Hplm-Y_pypy_p-I~p
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-11G-
TABLE 74 (cont):
10-ring Hairpin
Polyamides
for recognition
of 7-by 5'-WACWNNW-3'
with p substitutions.
DNA aromatic amino acid sequence
sequence
932(3) 5'-W A CA T C W-3' PyPyPyHpPy-y-ImPy-(3-ImHp
932(3p) '5'-W A CA T C W-3' PyPy-(3-HpPy-y-ImPy-[3-ImHp
9333) 5'-W A CA A T W-3' PyPyPyPyHp-y-PyHp-(3-ImHp
933(3p) 5'-W A CA A T W-3' PyPy-(3-PyHp-y-PyHp-(3-ImHp
934(3) 5'-W A CA A A W-3' PyPyPyPyPy-y-HpHp-(3-ImHp
934(3p) 5'-W A CA A A W-3' PyPy-(3-PyPy-y-HpHp-(3-ImHp
1(? 935~i) 5'-W A CA A G W-3' PyPy-(3-PyIm-y-PyHp-p-ImHp
936(3) 5'-W A CA A C W-3' PyPypypypy-y-I~p-~-I~p
936(3p) 5'-W A CA A C W-3' PyPy-(3-PyPy-y-ImHp-(i-ImHp
937(3) 5'-W A CA G T W-3' PyPy-(3-ImHp-y-PyPy-p-ImHp
938(3) 5'-W A CA G A W-3' PyPy-(3-ImPy-y-HpPy-~3-ImHp
9393) 5'-W A CA G G W-3' PyPy-~3-Imlm-y-PyPy-(3-ImHp
940(3) 5'-W A CA G C W-3' PyPy-(3-ImPy-y-ImPy-(3-ImHp
941(3) 5'-W A CA C T W-3' PyPyPyPyHp-y-PyIm-(3-ImAp
941~p) 5'-W A CA C T W-3' PyPy-(3-PyHp-y-Pylm-(i-ImFip
942(3) 5'-W A CA C A W-3' PyPyPyPyPy-y-HpIm-(3-ImHp
942(3p) 5'-W A CA C A W-3' PyPy-(3-PyPy-y-HpIm-~3-ImHp
943(3) 5'-W A CA C G W-3' PyPy-(3-PyIm-y-PyIm-~-ImHp
9443) 5'-W A CA C C W-3' PyPyPyPyPy-y-ImIm-(3-ImHp
944(3p) 5'-W A CA C C W-3' PyPy-(3-Pypy-y-ImIm-(3-ImHp
CA 02281930 1999-08-18
WO 98137067 PCT/US98/01714
-117-
TABLE
75: 10-ring
Hairpin
Polyamides
for recognition
of 7-by
5'-WACSNNW-3'
with
(3 substitutions.
D1~1A aromatic amino acid sequence
sequence
9453) 5' -WA C GT T W-3' Py-(3-ImHpHp-Y-Pypy-(3-Imp
9463) '5'-WA C GT A W-3' py_~3_I~ppy_y-Hppy_~-I~p
9473) 5' -WA C GT G W-3' Py-(3-ImHpIm-y-Pypy-a-ImHp
948(3) 5' -WA C GT C W-3' Py-(3-ImHpPy-y-ImPy-~3-ImHp
949(3) 5' -WA C GA T W-3' Py-(3-ImPyHp-y-pyHp-/3-ImHp
950(3) 5' -WA C GA A W-3' Py-~3-ImPyPy-y-HpHp-~-ImHp
9513) 5' -WA C GA G W-3' Py-J3-ImPyIm-y-PyHp-[3-ImHp
952(3) 5' -WA C GA C W-3' Py-(3-ImPyPy-Y-ImHp-(3-ImHp
9533) 5' -WA C GG T W-3' Py-(3-ImImHp-y-PyPy-p-I~p
954(3) 5' -WA C GG A W-3' Py-(3-ImImPy-y-Hppy-(3-ImHp
9553) 5' -WA C GC T W-3' Py-(3-ImPyHp-y-Pylm-(3-ImHp
9563) 5' -WA C GC A W-3' Py-(3-ImPyPy-y-Hplm-(3-ImHp
9573) 5' -WA C CT T W-3' PyPypyHpHp-y-Py-(3-ImImHp
957(3p) 5' -WA C CT T W-3' PyPyPy-~3-Hp-Y-Py-~3-ImImHp
958(3) 5' -WA C CT A W-3' PyPyPyHpPy-y-Hp-(3-ImImHp
958~3p) 5' -WA C CT A W-3' PyPypy-~3-py-y-Hp-~-ImImHp
959p) 5' -WA C CT G W-3' PyPy-j3-HpIm-y-Py-(3-ImImHp
960(3) 5' -WA C CT C W-3' PyPyPyHpPy-y-Im-~-ImImHp
960pp) 5' -WA C CT C W-3' Pypypy-(3-py-y-Im_~-ImImHp
961~i) 5' -WA C CA T W-3' PyPyPyPyHp-y-Py-~3-ImImHp
961(3p) 5' -WA C CA T W-3' PyPyPy-/3-Hp-y-Py-(3-ImImHp
9623) 5' -WA C CA A W-3' pypypypypy_y_Hp_~-ImImHp
962~3p) 5' -WA C CA A W-3' pypypy-(3-py-y-Hp-~-ImImHp
9633) 5' -WA C CA G W-3' PyPy-(3-pylm-y-Py-(3-ImImHp
964) 5' -WA C CA C W-3' PyPyPyPyPy-y-Im-~3-ImImHp
964(3p) 5' -WA C CA C W-3' PyPypy-(3-Py-y-Im_~3-ImImHp
965(3) 5' -WA C CG T W-3' PyPy-~3_ImHp-y-Py-~i-ImImHp
966(3) 5' -WA C CG A W-3' Pypy-~-Impy-y-Hp-~3-ImImHp
969(3) 5' -WA C GG G W-3' Py-(3-ImImIm-y-Pypy-~3-I~p
970~i) 5' -WA C GG C W-3'
Py-(3-ImImPy-y-ImPy-~3-ImHp
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-118-
TABLE 75 (cont):
10-ring Hairpin
Polyamides
for recognition
of 7-by 5'-WACSNNW-3'
with (3 substitutions.
DNA sequence aromatic amino acid sequence
9713) 5' -W A C G W-3' Py-(3-ImPyIm-y-PyIm-~-ImHp
C G
972(3) 5' -W A C C W-3' Py-(3-ImPyPy-y-ImIm-(3-ImHp
C G
973(3) ' 5' -W G G W-3' PyPy-(3-Imlm-y-Py-~-ImImHp
A C C
974(3) 5' -W A G C W-3' PyPy-~-ImPy-y-Im-(3-ImImHp
C C
9753) 5' -W A C G W-3' PyPy-(3-PyIm-y-PyImImImHp
C C
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-119-
TABLE 76:
10-ring
Hairpin
Polyamides
for recognition
of 7-by
5'-WTGWNNW-3'
with (3
substitutions.
DNA aromatic amino acid sequence
sequence
979(3) 5' -WT G T T GW-3' Hplm-(3-HpIm-y-PyPyPyPyPy
979(3p) ~ -WT G T T GW-3' HpIm-~3-HpIm-y-PyPy-(3-PyPy
5'
9833) 5' -WT G T A GW-3' HpIm-/3-PyIm-y-PyHpPypyPy
983(3p) 5' -WT G T A GW-3' Hplm-~3-PyIm-y-PyHp-(3-PyPy
985(3) 5' -WT G T G TW-3' HpIm-p-ImHp-y-PyPyPyPyPy
985(3p) 5' -WT G T G TW-3' HpIm-(3-ImHp-y-PyPy-~i-PyPy
9863) 5' -WT G T G AW-3' HpIm-~3-ImPy-y-HpPypypypy
986~3p) 5' -WT G T G AW-3' HpIm-(3-ImPy-~y-HpPy-~3-PyPy
987(3) 5' -WT G T G GW-3' Hplm-p-Imlm-y-PyPyPyPyPy
987(3p) 5' -WT G T G GW-3' HpIm-(3-Imlm-y-PyPy-p-PyPy
988(3) 5' -WT G T G CW-3' HpIm-(3-ImPy-y-ImPyPYPyPy
IS 988(3p) 5' -WT G T G CW-3' Hplm-~-ImPy-y-ImPy-p-Pypy
9913) 5' -WT G T C GW-3' Hplm-~i-Pylm-y-PyImPypyPy
991(3p) 5' -WT G T C GW-3' Hplm-(3-Pylm-y-Pylm-~3-PyPy
9953) 5' -WT G A T GW-3' Hplm-(3-HpIm-y-PyPyHpPyPy
995~p) 5' -WT G A T GW-3' HpIm-(3-HpIm-y-PyPy-(3-PyPy
999(3) 5' -WT G A A GW-3' HpIm-(3-Pylm-y-PyHpHpPyPy
999~3p) 5' -WT G A A GW-3' HpIm-(3-PyIm-y-PyHp-~3-PyPy
1001(3) 5' -WT G A G TW-3' HpIm-(3-ImHp-y-PyPyHpPyPy
1001~3p) 5' -WT G A G TW-3' HpIm-p-ImHp-y-PyPy-(3-PyPy
1002(3) 5' -WT G A G AW-3' Hplm-(3-ImPy-y-HpPyHpPyPy
1002~3p) 5' -WT G A G AW-3' HpIm-(3-ImPy-y-HpPy-(3-PyPy
1003(3) 5' -WT G A G GW-3' HpIm-~3-Imlm-y-PyPyHpPyPy
1003~3p) 5' -WT G A G GW-3' HpIm-~3-ImIm-y-PyPy-(3-PyPY
10043) 5' -WT G A G CW-3' HpIm-(3-ImPy-y-ImPyHpPyPy
- 1004~ip) 5' -WT G A G CW-3' Hplm-~3-ImPy-y-ImPy-(3-PyPy
10073) 5' -WT G A C GW-3' HpIm-(3-PyIm-y-PyImHpPyPy
1007(3p) 5' -WT G A C GW-3' Hplm-(3-PyIm-y-Pylm-(3-PyPy
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-120-
TABLE 77:
10-ring
Hairpin
Polyamides
for recognition
of 7-by
5'-WTGSNNW-3'
with substitutions.
DNA sequence aromatic amino acid sequence
1009(3) 5'-W T GG T T W-3' HpImIm--Hp-y-PyPyPyPyPy
1009p)' 5'-W T GG T T W-3' HpImIm--Hp-y-Py--PyPyPy
1010(3) 5'-W T GG T A W-3' HpImIm--Py-y-HpPyPyPyPy
1010(3p) 5'-W T GG T A W-3' HpImIm--Py-y-Hp--PyPyPy
10113) 5'-W T GG T G W-3' HpImIm--Im-y-PyPyPyPyPy
1011(3p) 5'-W T GG T G W-3' HpImIm--Im-y-Py--PyPyPy
1012(3) 5'-W T GG T C W-3' HpImIm--Py-y-ImPyPyPyPy
1012~p) 5'-W T GG T C W-3' HpImIm--Py-y-Im--PyPyPy
1013(3) 5'-W T GG A T W-3' HpImIm--Hp-y-PyHpPyPyPy
1013p) 5'-W T GG A T W-3' HpImIm--Hp-y-Py--PyPyPy
1014(3) 5'-W T GG A A W-3' HpImIm--Py-y-HpHpPyPyPy
1014p) 5'-W T GG A A W-3' HpImIm--Py-y-Hp--PyPyPy
10153) 5'-W T GG A G W-3' HpImIm--Im-y-PyHpPyPyPy
1015(3p) 5'-W T GG A G W-3' HpImIm--Im-y-Py-(3-PyPyPy
10163) 5'-W T GG A C W-3' HpImIm--Py-y-ImHpPyPyPy
1016(3p) 5'-W T GG A C W-3' HpImIm-(3-Py-y-Im--PyPyPy
1019(3) 5'-W T GG C T W-3' HpImIm--Hp-y-PyImPyPyPy
10203) 5'-W T GG C A W-3' HpImIm--Py-y-HpImPyPyPy
1021(3) 5'-W T GC T T W-3' HpImPyHpHp-y-Py--ImPyPy
1021(3p) 5'-W T GC T T W-3' HpImPy--Hp-y-Py--ImPyPy
1022(3) 5'-W T GC T A W-3' HpImPyHpPy-y-Hp--ImPyPy
1022(3p) 5'-W T GC T A W-3' HpImPy-(3-Py-y-Hp--ImPyPy
1023) 5'-W T GC T G W-3' HpIm--Hplm-y-Py--ImPyPy
10243) 5'-W T GC T C W-3' HpImPyHpPy-y-Im-/3-ImPyPy
1024p) 5'-W T GC T C W-3' HpImPy--Py-y-Im--ImPyPy
1025(3) 5'-W T GC A T W-3' HpImPyPyHp-y-Py-(i-ImPyPy
1025(3p) 5'-W T GC A T W-3' HpImPy--Hp-y-Py--ImPyPy
1026(3) 5'-W T GC A A W-3' HpImPyPyPy-y-Hp--ImPyPy
1026~p) 5'-W T GC A A W-3' HpImPy--Py-y-Hp--ImPyPy
10273) 5'-W T GC A G W-3' HpIm--PyIm-y-Py--ImPyPy
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-121-
TABLE 77 (cont): Polyamides
10-ring Hairpin for
recognition
of
7-by
5'-WTGSNNW-3'
with
p
substitutions.
DNA aromatic amino acid sequence
sequence
1028(3) 5' -WT G C A C W-3' HpImPyPyPy-y-Im-~3-ImPyP
1028(3p)' 5' -WT G C A C W-3' HpImPy-(3-Py-y-Im-~i-ImPyPy
1029(3) 5' -WT G G G T W-3' HpIm-(3-ImHp-y-py-(3-ImPypy
1030(3) 5' -WT G C G A W-3' Hplm-~-ImPy-y-Hp-(3-ImPyPy
1031(3) 5' -WT G C C T W-3' HpImPyPyHp-y-PyImIm-~i-Py
1031(3p) 5' -WT G C C T W-3' HpImPy-p-Hp-y-PyImIm-(3-Py
10323) 5' -WT G C C A W-3' HpImPyPyPy-y-HpImIm-(3-Py
1032~3p) 5' -WT G C C A W-3' HpImPy-(3-Py-y-HpImIm-(3-Py
1035(3) 5' -WT G G C G W-3' HpImIm-(3-Im-y-PyImPyPyPy
1036) 5' -WT G G C C W-3' HpImIm-~3-Py-y-ImImPyPyPy
1037(3) 5' -WT G C G G W-3' HpIm-(3-ImIm-y-Py-(3-ImPyPy
1038(3) 5' -WT G C G C W-3' Hplm-(3-ImPy-y-Im-(3-ImPyPy
1039~i) 5' -WT G C C G W-3' Hplm-(3-Pylm-y-pylmlm-(3-Py
1040(3) 5' -WT G C C C W-3' HpImPyPyPy-y-ImImIm-~3-Py
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-122-
TABLE 78:
10-ring
Hairpin
Polyamides
for recognition
of 7-by
5'-WTTWIVNW-3'
with p
substitutions.
DNA sequence aromatic amino acid sequence
10433) 5'-WT T T T G W-3' HpHp-(3-Hplm-y-PyPyPyPyPy
1043(3p)' 5'-WT T T T G W-3 HpHp-(3-HpIm-y-PyPy-(3-PyPy
T
10473) 5'-WT T T A G W-3' HpHp-(3-PyIm-y-PyHpPyPyPy
1047(3p) 5'-WT T T A G W-3' HpHp-~i-Pylm-y-PyHp-(3-PyPy
1049(3) 5'-WT T T G T W-3' HpHp-~i-ImHp-y-PyPyPyPyPy
1049~3p) 5'-WT T T G T W-3' HpHp-p-ImHp-y-PyPy-(3-PyPy
1050(3) 5'-WT T T G A W-3' HpHp-(3-ImPy-y-HpPyPyPyPy
1050(3p) 5'-WT T T G A W-3' HpHp-(3-ImPy-y-HpPy-p-PyPy
1051(3) 5'-WT T T G G W-3' HpHp-(3-Imlm-y-PyPyPyPyPy
1051(3p) 5'-WT T T G G W-3' HpHp-(i-ImIm-y-PyPy-(3-PyPy
1052(3) 5'-WT T T G C W-3' HpHp-(3-ImPy-y-ImPyPyPyPy
1052(3p) 5'-WT T T G C W-3' HpHp-(3-ImPy-y-ImPy-(3-PyPy
1055(3) 5'-WT T T C G W-3' HpHp-(3-Pylm-y-PyImPyPyPy
1055~3p) 5'-WT T T C G W-3' HpHp-~3-PyIm-y-PyIm-p-PyPy
1059~i) 5'-WT T A T G W-3' HpHp-(3-HpIm-y-PyPyHpPyPy
1059(3p) 5'-WT T A T G W-3' HpHp-~3-HpIm-y-PyPy-R-PyPy
1063(3) 5'-WT T A A G W-3' HpHp-~3-Pylm-y-PyHpHpPyPy
1063~3p) 5'-WT T A A G W-3' HpHp--PyIm-y-PyHp-(3-PyPy
1065(3) 5'-WT T A G T W-3' HpHp-(3-ImHp-y-PyPyHpPyPy
1065(3p) 5'-WT T A G T W-3' HpHp-~-ImHp-y-PyPy-p-PyPy
1066~i) 5'-WT T A G A W-3' HpHp-p-ImPy-y-HpPyHpPyPy
1066(3p) 5'-WT T A G A W-3' HpHp-J3-ImPy-y-HpPy-/3-PyPy
1067(3) 5'-WT T A G G W-3' ~ HpHp-(3-Imlm-y-PyPyHpPyPy
1067(3p) 5'-WT T A G G W-3' HpHp-(3-ImIm-y-PyPy-(3-PyPy
1068(3) 5'-WT T A G C W-3' HpHp-(3-ImPy-y-ImPyHpPyPy
1068(3p) 5'-WT T A G C W-3' HpHp-~3-ImPy-y-ImPy-(3-PyPy
1071(3) 5'-WT T A C G W-3' HpHp-(3-PyIm-y-PyImHpPyPy
1071~ip) 5'-WT T A C G W-3' HpHp-~3-PyIm-y-PyIm-p-PyPy
n
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-I23-
TABLE 79:
10-ring
Hairpin
Polyamides
for recognition
of 7-by
5'-WTTSNNW-3'
with ~i
substitutions
DNA aromatic amino acid sequence
sequence
1073R) 5' -WT T G T TW-3' Hp-~3-I,~pgp-y-pypypypypy
1073~3p)' 5' -WT T G T TW-3' Hp-(3-ImHpAp-y-PyPYPy-(3-py
1074(3) 5' -WT T G T AW-3' Hp-(3-ImHpPy-y-HppypypypY
1074(3p) 5' -WT T G T AW-3' Hp-(3-ImHpPy-y-HpPYPy-~3_py
1075(3) 5' -WT T G T GW-3' Hp-~3-ImHpIm-y-PyPYPyPyPy
1075(3p) 5' -WT T G T GW-3' Hp-p-ImHpIm-y-PyPYPy-(3-Py
10763) 5' -WT T G T CW-3' Hp-(3-ImHpPy-y-ImPyPyPyPy
1076(3p) 5' -WT T G T CW-3' Hp-(3-ImHpPy-y-ImPyPy-~-Py
1077(3) 5' -WT T G A TW-3' Hp-(3-ImPyHp-y-PyHpPyPyPy
1077(3p) 5' -WT T G A TW-3' Hp-(3-ImPyHp-y-PYHpPy-(3-Py
1078(3) 5' -WT T G A AW-3' Hp-(3-ImPyPy-y-HpHpPyPyPy
I5 1078~3p) 5' -WT T G A AW-3' Hp-~3-ImPyPy-y-HpHpPy-p-Py
1079(3) 5' -WT T G A GW-3' Hp-(3-ImPyIm-y-PyHpPyPyPy
1079~3p) 5' -WT T G A GW-3' Hp-(3-ImPyIm-y-PYHpPy-~-Py
1080(3) 5' -WT T G A CW-3' Hp-~3-ImPyPy-y-ImHpPyPYPy
1080(3p} 5' -WT T G A CW-3' Hp-(3-ImPyPy-y-ImHpPy-/3-Py
1081(3) 5' -WT T G G TW-3' Hp-(3-ImImHp-y-PyPypypypY
1081(3p) 5' -WT T G G TW-3' Hp-(3-ImImHp-y-PYPypy-(3-py
10820 5' -WT T G G AW-3' Hp-(3-ImImPy-y-HpPypyPyPy
1082~p) 5' -WT T G G AW-3' Hp-~-ImImPy-y-HpPYPy-~3-Py
1083(3) 5' -WT T G C TW-3' Hp-(3-ImPyHp-y-PyImPyPyPy
1083~3p) 5' -WT T G C TW-3' Hp-(3-ImPyHp-y-PyImPy-~-Py
10843) 5' -WT T G C AW-3' Hp-~i-ImPyPy-y-HpImPYPyPy
1084(3p) 5' -WT T G C AW-3' Hp-~3-ImPyPy-y-HpImPy-~3-Py
10850 5' -WT T G G GW-3' Hp-(3-ImImIm-y-PYPypypypy
- 1085(3p) 5' -WT T G G GW-3' Hp-J3-ImImIm-y-PyPyPy-~3-Py
10863) 5' -WT T G G CW-3' Hp-~i-ImImPy-y-ImPyPyPyPy
1086(3p) 5' -WT T G G CW-3' Hp-(3-ImImPy-y-ImPyPy-~i-Py
1087) 5' -WT T G C GW-3' Hp-~3-ImPYIm-y-PyImPyPyPy
1087(3p) 5' -WT T G C GW-3' Hp-(3-ImPYIm-y-PyImPy-/3-Py
CA 02281930 1999-08-18
WO 98/370b7 PCT/US98/01714
-124-
TABLE 79
(cont):
10-ring
Hairpin
Polyamides
for recognition
of 7-by
5'-WTTSNNW-3'
with (3
substitutions
DNA aromatic amino acid sequence
sequence
1088(3) 5'-W T T G CC W-3' Hp-p-ImPyPy-y-ImImPyPyPy
1088(3p)' 5'-W T T G CC W-3' Hp-(3-ImPyPy-y-ImImPy-(3-Py
1089(3) 5'-W T T C TT W-3' HpHpPyHpHp-y-Py-(3-ImPyPy
1089(3p) 5'-W T T C TT W-3' HpHpPy-p-Hp-y-Py-(3-ImPyPy
1090(3) 5'-W T T C TA W-3' HpHpPyHpPy-y-Hp-(3-ImPyPy
1090(3p) 5'-W T T C TA W-3' HpHpPy-(3-Py-y-Hp-(3-ImPyPy
1091~i) 5'-W T T C TG W-3' HpHp-(3-HpIm-y-Py-~i-ImPyPy
10923) 5'-W T T C TC W-3' HpHpPyApPy-y-Im-(3-ImPyPy
1092(3p) 5'-W T T C TC W-3' HpHpPy-(3-Py-y-Im-(3-ImPyPy
10933) 5'-W T T C AT W-3' HpHpPyPyHp-y-Py-~3-ImPyPy
1093(3p) 5'-W T T C AT W-3' HpHpPy-~i-Hp-y-Py-/3-ImPyPy
10943) 5'-W T T C AA W-3' HpHpPyPyPy-y-Hp-(3-ImPyPy
1094(3p) 5'-W T T C AA W-3' HpHpPy-~3-Py-y-Hp-~i-ImPyPy
10953) 5'-W T T C AG W-3' HpHp-(3-Pylm-y-Py-(3-ImPyPy
10963) 5'-W T T C AC W-3' HpHpPyPyPy-y-Im-/3-ImPyPy
1096(3p) 5'-W T T C AC W-3' HpHpPy-(3-Py-y-Im-(i-ImPyPy
1097(3) 5'-W T T C GT W-3' HpHp-(3-ImHp-y-Py-[3-ImPyPy
1098(3) 5'-W T T C GA W-3' HpHp-~3-ImPy-y-Hp-p-ImPyPy
1099) 5'-W T T C CT W-3' HpHpPyPyHp-y-PyimIm-~3-Py
1099(3p) 5'-W T T C CT W-3' Hp-(3-PyPyHp-y-PyImIm-(3-Py
1100(3) 5'-W T T C CA W-3 HpHpPyPyPy-y-HpImIm-p-Py
'
1100~ip) 5'-W T T C CA W-3' Hp-~i-PyPyPy-y-HpImIm-~-Py
1101(3) 5'-W T T C GG W-3' HpHp-(3-ImIm-y-Py-(3-ImPyPy
1102(3) 5'-W T T C GC W-3' HpHp-(3-ImPy-y-Im-~i-ImPyPy
1103(3) 5'-W T T C CG W-3' HpHp-(3-PyIm-y-PyImIm-(3-Py
CA 02281930 1999-08-18
WO 98/37067 PCTIUS98/01714
-12S-
TABLE 80:
10-ring
Hairpin
Polyamides
for recognition
of 7-by
S'-WTAWNNW-3'
with (3
substitutions
DNA aromatic amino acid sequence
sequence
11073) 5'-W T A TT G W-3' HpPy-(3-HpIm-y-PypypyHppy
S I107(3p)' S'-W T A TT G W-3' HpPy-p-Hplm-y-Pypy-(3-HpPy
1111(3) 5'-W T A TA G W-3' HpPy-~3-Pylm-y-PyHpPyHpPy
1111~p) 5'-W T A TA G W-3' HpPy-~3-PyIm-y-PyHp-(3-HpPy
11133) 5'-W T A TG T W-3' HpPy-(3-ImHp-y-Pypypygppy
1113(3p) 5'-W T A TG T W-3' HpPy-p_ImHp_y_p~,p~,_~_HppY
11143) 5'-W T A TG A W-3' HpPy-p-ImPy-y-HpPYPyHpPy
1114(3p) 5'-W T A TG A W-3' HpPy-(3-ImPy-y-HpPy-(3-HpPy
1115(3) 5'-W T A TG G W-3' HpPy-(3-Imlm-y-Pypypygppy
1115(3p) 5'-W T A TG G W-3' HpPy-(3-ImIm-y-PyPy-(3-HpPy
1116(3) 5'-W T A TG C W-3' HpPy-~3-ImPy-y-ImPyPyHpPy
1S 1116~3p) 5'-W T A TG C W-3' HpPy-R-ImPy-y-ImPy-J3-HpPy
11193) 5'-W T A TC G W-3' HpPy-~i-PYim-y-PyImPyHpPy
1119(3p) 5'-W T A TC G W-3' HpPy-(3-PyIm-y-PyIm-(3-HpPy
11233) 5'-W T A AT G W-3' HpPy-(3-HpIm-y-PyPyHpHpPy
1123(3P) 5'-W T A AT G W-3' HpPy-p-HpIm-y-PyPy-(3-HpPY
1127(3) 5'-W T A AA G W-3' HpPy-(3-PYIm-y-PyHpHpHpPy
1127(3p) 5'-W T A AA G W-3' HpPy-(3-Pylm-y-PyHp-(3-HpPy
1129(3) 5'-W T A AG T W-3' HpPy-(3-ImHp-y-PyPyHpHpPy
1129(3p) 5'-W T A AG T W-3' Hppy-(3_I~p_y_p~,py_a-Hppy
1130(3) 5'-W T A AG A W-3' HpPy-~3-ImPy-y-HpPyHpHpPy
1130(3p) 5'-W T A AG A W-3' HpPy-~3-ImPy-y-HpPy-(3-HpPy
1131(3) 5'-W T A AG G W-3' HpPy-(3-ImIm-y-PyPyI-IpHppy
1131~p) 5'-W T A AG G W-3' HpPy-(3-ImIm-y-Pypy-(3-Hppy
1132(3) 5'-W T A AG C W-3' HpPy-(3-ImPy-y-ImPyHpHpPy
1132(3p) 5'-W T A AG C W-3' HpPy-~i-ImPy-y-ImPy-p-HpPy
1135~i) 5'-W T A AC G W-3' Hppy_~_pylm_y_pYImHpHppy
1135~p) 5'-W T A AC G W-3' HpPy-(3-PyIm-y-PYIm-~i-HpPy
CA 02281930 1999-08-18
WO 98/37067 PCT/US98I01714
-126-
TABLE 81: in
10-ring Polyamides
Hairp for
recognition
of
7-by
5'-WTASNNW-3'
with
(3
substitutions
DNA aromatic amino acid sequence
sequence
1137(3) 5' -W T A GT T W-3' Hp-(3-ImHpHp-y-PyPyPyHpPy
1137(3p) 5' -W T A GT T W-3' Hp-(3-ImHpHp-y-PyPyPy-~3-Py
1138(3) 5' -W T A GT A W-3' Hp-(3-ImHpPy-y-HpPyPyHpPy
1138~ip) 5' -W T A GT A W-3' Hp-p-ImHpPy-y-HpPyPy-(3-Py
1139(3) 5' -W T A GT G W-3' Hp-~3-ImHpIm-y-PyPyPyHpPy
1139(3p) 5' -W T A GT G W-3' Hp-~3-ImHpIm-y-PyPyPy-(3-Py
11403) 5' -W T A GT C W-3' Hp-~3-ImHpPy-y-ImPyPyHpPy
1140(3p) 5' -W T A GT C W-3' Hp-(3-ImHpPy-y-ImPyPy-(3-Py
1141(3) 5' -W T A GA T W-3' Hp-~3-ImPyHp-y-PyHpPyHpPy
1141(3p) 5' -W T A GA T W-3' Hp-(3-ImPyHp-y-PyHpPy-(3-Py
1142(3) 5' -W T A GA A W-3' Hp-(3-ImPyPy-y-HpHpPyHpPy
1142~ip) 5' -W T A GA A W-3' Hp-(3-ImPyPy-y-HpHpPy-(3-Py
11433) 5' -W T A GA G W-3' Hp-(3-ImPyIm-y-PyHpPyHpPy
1143(3p) 5' -W T A GA G W-3' Hp-(3-ImPyIm-y-PyHpPy-~3-Py
11443) 5' -W T A GA C W-3' Hp-(3-ImPyPy-y-ImHpPyHpPy
1144(3p) 5' -W T A GA C W-3' Hp-~-ImPyPy-y-ImHpPy-~3-Py
11453) 5' -W T A GG T W-3' Hp-~-ImImHp-y-PyPyPyHpPy
1145~3p) 5' -W T A GG T W-3' Hp-p-ImImHp-y-PyPyPy-(3-Py
1146(3) 5' -W T A GG A W-3' Hp-(3-ImImPy-y-HpPyPyHpPy
1146(3p) 5' -W T A GG A W-3' Hp-~-ImImPy-y-HpPyPy-(3-Py
1147(3) 5' -W T A GC T W-3' Hp-~3-ImPyHp-y-PyImPyHpPy
1147~ip) 5' -W T A GC T W-3' Hp-(3-ImPyHp-y-PyImPy-(3-Py
1148(3) 5' -W T A GC A W-3' ~ Hp-~i-ImPyPy-y-HpImPyHpPy
1148(3p) 5' -W T A GC A W-3' Hp-p-ImPyPy-y-HpImPy-~i-Py
11493) 5' -W T A GG G W-3' Hp-(3-ImImIm-y-PyPyPyHpPy
1149(3p) 5' -W T A GG G W-3' Hp-~i-ImImIm-y-PyPyPy-(3-Py
1150(3) 5' -W T A GG C W-3' Hp-(3-ImImPy-y-ImPyPyHpPy
1150(3p) 5' -W T A GG C W-3' Hp-~3-ImImPy-y-ImPyPy-~i-Py
1151(3) 5' -W T A GC G W-3' Hp-p-ImPyIm-y-PyImPyHpPy
1151~3p) 5' -W T A GC G W-3' Hp-(3-ImPyIm-y-PyImPy-~-Py
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-127-
TABLE 81
(cont):
10-ring
Hairpin
Polyamides
for recognition
of 7-by
5'-WTASNNW-3'
with (3
substitutions
DNA aromatic amino acid sequence
sequence
1152(3) 5' -WT A G C CW-3' Hp-(3-ImPyPy-y-ImImPyHpPy
1152(3p). 5' -WT A G C CW-3' Hp-(3-ImPyPy-y-ImImPy-~3-Py
1153(3) 5' -WT A C T TW-3' HpPyPyHpHp-y-Py-(3-ImHpPy
1153(3p) 5' -WT A C T TW-3' HpPyPy-(3-Hp-y-Py-(3-ImHpPy
1154(3) 5' -WT A C T AW-3' HpPyPyHpPy-y-Hp-~3-ImHpPy
1154~ip) 5' -WT A C T AW-3' HpPyPy-p-py-y-Hp_p_I~ppy
11553) 5' -WT A C T GW-3' HpPy-(3-HpIm-y-Py-~3-ImHpPy
1156(3) 5' -WT A C T CW-3' HpPyPyHpPy-y-Im-(3-ImHpPy
1156(3p) 5' -WT A C T CW-3' HpPyPy-(3-Py-y-Im-~i-ImApPy
11573) 5' -WT A C A TW-3' HpPyPyPyHp-y-Py-(3-ImHpPy
1157(3p) 5' -WT A C A TW-3' HpPyPy-(3-Hp-y-Py-~3-ImHppy
IS 1158~i) 5' -WT A C A AW-3' HpPyPyPyPy-y-Hp-(3-ImHpPy
1158(3p) 5' -WT A C A AW-3' HpPypy-(3-Py-y-Hp-/3-ImHpPy
1159(3) 5' -WT A C A GW-3' HpPy-(i-PyIm-y-Py-(3-ImHpPy
11603) 5' -WT A C A CW-3' HpPyPyPyPy-y-Im-(3-ImHpPy
1160(3p) 5' -WT A C A CW-3' HpPyPy-(3-Py-y-Im-(3-ImHpPy
1161) 5' -WT A C G TW-3' Hppy-~3-I~p_y-py-~_I~ppy
1162(3) 5' -WT A C G AW-3' HpPy-(3-ImPy-y-Hp-~-ImHpPy
1163(3) 5' -WT A C C TW-3' HpPyPyPyHp-y-PyImIm-(3-Py
1163(3p) 5' -WT A C C TW-3' Hp-(3-PyPyHp-y-PyImIm-(3-Py
1164(3) 5' -WT A C C AW-3' HpPyPyPyPy-y-HpImIm-p-Py
1164(3p) 5' -WT A C C AW-3' Hp-~3-PyPyPy-y-HpImIm-(3-Py
1165~i) 5' -WT A C G GW-3' HpPy-(3-ImIm-y-Py-(3-ImHpPy
1166(3) 5' -WT A C G CW-3' HpPy-(3-ImPy-y-Im-~3-ImHpPy
1167(3) 5' -WT A C C GW-3' HpPy-(3-PyIm-y-PyImIm-(3-Py
CA 02281930 1999-08-18
WO 98137067 PCT/US98I01714
-128-
TABLE 82:
10-ring
Hairpin
Polyamides
for recognition
of ?-by
5'-WTCWNNW-3'
with R
substitutions
DNA sequence aromatic amino acid sequence
11703) 5'-W T CT T A W-3' HpPyHpHpPy-y-HpPy-p-ImPy
S 1170(3p)' S'-W T CT T A W-3' HpPy-~3-HpPy-y-HpPy-(3-ImPy
1171~i) 5'-W T CT T G W-3' HpPy-(3-HpIm-y-PyPy-~i-ImPy
1I72~i) 5'-W T CT T C W-3' HpPyHpHpPy-y-ImPy-(3-ImPy
1172(3p) 5'-W T CT T C W-3' HpPy-(3-HpPy-y-ImPy-(3-ImPy
1173(3) 5'-W T CT A T W-3' HpPyHpPyHp-y-PyHp-(3-ImPy
1173(3p) 5'-W T CT A T W-3' HpPy-~3-PyHp-y-PyHp-(3-ImPy
1174(3) 5'-W T CT A A W-3' HpPyHpPyPy-y-HpHp-(3-ImPy
1I74(3p) 5'-W T CT A A W-3' HpPy-~3-PyPy-y-HpHp-(3-ImPy
1175(3) 5'-W T CT A G W-3' HpPy-(3-PyIm-y-PyHp-(3-ImPy
1176J3) 5'-W T CT A C W-3' HpPyHpPyPy-y-ImHp-p-ImPy
1176(3p) 5'-W T CT A C W-3' HpPy-(3-PyPy-y-ImHp-(3-ImPy
1177(3) 5'-W T CT G T W-3' HpPy-(3-ImHp-y-PyPy-(3-ImPy
1178(3) 5'-W T CT G A W-3' HpPy-[3-ImPy-y-HpPy-[3-ImPy
11793) 5'-W T CT G G W-3' HpPy-(3-Imlm-y-PyPy-(3-ImPy
1180(3) 5'-W T CT G C W-3' HpPy-(3-ImPy-y-ImPy-(3-ImPy
1181(3) 5'-W T CT C T W-3' HpPyHpPyHp-y-PyIm-p-ImBy
1181~3p) 5'-W T CT C T W-3' HpPy-(3-PyHp-y-PyIm-p-ImPy
1182(3) 5'-W T CT C A W-3' HpPyHpPyPy-y-HpIm-[3-ImPy
1182~3p) 5'-W T CT C A W-3' HpPy-(3-PyPy-y-HpIm-p-ImPy
1183(3) 5'-W T CT C G W-3' HpPy-p-Pylm-y-PyIm-(3-ImPy
1184(3) 5'-W T CT C C W-3' HpPyHpPyPy-y-Imlm-(3-ImPy
1184~3p) 5'-W T CT C C W-3' ~ HpPy-j3-PyPy-y-Imlm-(3-ImPy
1185(3) 5'-W T CA T T W-3' HpPyPyHpHp-y-PyPy-(3-ImPy
1185~3p) 5'-W T CA T T W-3' HpPy-(3-HpHp-y-PyPy-~3-ImPy
1186(3) 5'-W T CA T A W-3' HpPyPyHpPy-y-HpPy-p-ImPy
1186(3p) 5'-W T CA T A W-3' HpPy-(3-HpPy-y-HpPy-(3-ImPy
11873) 5'-W T CA T G W-3' HpPy-p-HpIm-y-PyPy-(3-ImPy
CA 02281930 1999-08-18
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-129-
TABLE 82 (cont):
10-ring Hairpin
Polyamides for
recognition of
7-by 5'-WTCWNNW-3'
with substitutions
DNA sequence aromatic amino acid sequence
1188) 5'-WT C A T CW-3' HpPyPyHpPy-y-ImPy--ImPy
1188p)~ 5'-WT C A T CW-3' HpPy--HpPy-y-ImPy--Impy
1189) 5'-WT C A A TW-3' HpPyPyPyHp-y-PyHp--ImPy
1189p) 5'-WT C A A TW-3' HpPy--pyHp-y-pyHp--ImPy
1190(3) 5'-WT C A A AW-3' HpPyPyPyPy-y-HpHp--ImPy
1190p) 5'-WT C A A AW-3' HpPy--PyPy-y-HpHp--ImPy
1191) 5'-WT C A A GW-3' HpPy--pyIm-y-PyHp--ImPy
1192) 5'-WT C A A CW-3' HppypyPyPy-y-ImHp--ImPy
1192p) 5'-WT C A A CW-3' HpPy--pypy-y-ImHp--ImPy
1193(3) 5'-WT C A G TW-3' HpPy--ImHp-y-PyPy--ImPy
1194) 5'-WT C A G AW-3' HpPy--ImPy-y-HpPy--ImPy
IS 11953) 5'-WT C A G GW-3' HpPy--Imlm-y-PyPy--ImPy
1196) 5'-WT C A G CW-3' HpPy--ImPy-y-ImPy--ImPy
1197(3) 5'-WT C A C TW-3' HpPyPyPyHp-y-PyIm--ImPy
1197p) 5'-WT C A C TW-3' HpPy--PyHp-y-Pylm--ImPy
1198) 5'-WT C A C AW-3' HpPyPyPyPy-y-HpIm--ImPy
1198p) 5'-WT C A C AW-3' HpPy--PyPy-y-Hplm--ImPy
1199) 5'-WT C A C GW-3' HpPy--PyIm-y-PyIm--ImPy
1200) 5'-WT C A C CW-3' HpPyPyPyPy-y-ImIm--ImPy
1200p) 5'-WT C A C CW-3' HpPy--pypy-y-ImIm--ImPy
CA 02281930 1999-08-18
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-130-
TABLE 83:
10-ring
Hairpin
Polyamides
for recognition
of 7-by
S'-WTCSNNW-3'
with ~i
substitutions
DNA aromatic amino acid sequence
sequence
1201(3) 5' -W TC G T T W-3' Hp-(3-ImHpHp-y-PyPy-J3-ImPy
1202(3) 5''-W TC G T A W-3' Hp-(3-ImHpPy-y-HpPy-(3-ImPy
12033) 5' -W TC G T G W-3' Hp-~3-ImHpIm-y-PyPy-/3-ImPy
1204(3) 5' -W TC G T C W-3' Hp-(3-ImHpPy-y-ImPy-(3-ImPy
1205(3) 5' -W TC G A T W-3' Hp-(3-ImPyHp-y-PyHp-~i-ImPy
1206(3) 5' -W TC G A A W-3' Hp-(3-ImPyPy-y-HpHp-(3-ImPy
1207(3) 5' -W TC G A G W-3' Hp-(3-ImPyIm-y-PyHp-~3-ImPy
1208~i) 5' -W TC G A C W-3' Hp-(3-ImPyPy-y-ImHp-(3-ImPy
12093) 5' -W TC G G T W-3' Hp-(3-ImImHp-y-PyPy-(3-ImPy
1210(3) 5' -W TC G G A W-3' Hp-~3-ImImPy-y-HpPy-R-ImPy
1211(3) 5' -W TC G C T W-3' Hp-(3-ImPyHp-y-Pylm-p-ImPy
12123) 5' -W TC G C A W-3' Hp-~3-ImPyPy-y-Hplm-(3-ImPy
12133) 5' -W TC C T T W-3' HpPyPyHpHp-y-Py-p-ImImPy
1213(3p) 5' -W TC C T T W-3' HpPyPy-~i-Hp-y-Py-(3-ImImPy
12143) 5' -W TC C T A W-3' HpPyPyHpPy-y-Hp-~-ImImPy
1214(3p) 5' -W TC C T A W-3' HpPyPy-(3-Py-y-Hp-(3-ImImPy
12153) 5' -W TC C T G W-3' HpPy-(3-HpIm-y-Py-(3-ImImPy
1216(3) 5' -W TC C T C W-3' HpPyPyHpPy-y-Im-~3-ImImPy
1216(3p) 5' -W TC C T C W-3' HpPyPy-~3-Py-y-Im-~3-ImImPy
1217(3) 5' -W TC C A T W-3' HpPyPyPyHp-y-Py-~3-ImImPy
1217~3p) 5' -W TC C A T W-3' HpPyPy-(3-Hp-y-Py-p-ImImPy
1218(3) 5' -W TC C A A W-3' HpPyPyPyPy-y-Hp-[3-ImImPy
1218(3p) 5' -W TC C A A W-3' HpPyP-(3-Py-y-Hp-~-ImImPy
12193) 5' -W TC C A G W-3' HpPy-[3-PyIm-y-Py-(3-ImImPy
1220(3) 5' -W TC C A C W-3' HpPyPyPyPy-y-Im-R-ImImPy
1220~3p) 5' -W TC C A C W-3' HpPyPy-~i-Py-y-Im-~3-ImImPy
1221(3) 5' -W TC C G T W-3' HpPy-p-ImHp-y-Py-(3-ImImPy
1222(3) 5' -W TC C G A W-3' HpPy-~3-ImPy-y-Hp-(3-ImImPy
1225(3) 5' -W TC G G G W-3' Hp-(3-ImImIm-y-PyPy-(3-ImPy
CA 02281930 1999-08-18
WO 98137067
PCT/US98/01714
-131-
TABLE 83 (cont): 10-ring Hairpin Polyamides for recognition of 7-by 5'-WTCSNNW-
3' with (3 substitutions
DNA sequence aromatic amino acid sequence
1226(3) 5' -W T C G G C W-3' Hp-~3-ImImPy-y-ImPy-(3-ImPy
12273) 5' -W T C G C G W-3' Hp-(3-ImPyIm-y-Pyim-(3-ImPy
12280 5' -W T C G C C W-3' Hp-(3-ImPyPy-y-Imlm-y-ImPy
1229(3) 5' -W T C C G G W-3' H p
P Yrj-ImIm-y-Py-(3-ImImPy
1230~i) 5' -W T C C G C W-3' HpPy-(3-ImPy-y-Im-~i-ImImPy
1231(3) 5' -W T C C C G W-3' HpPy-(3-pyIm-y-PyImImImPy
If the process described above of designing a preferred polyamide molecule
comprising
four or five carboxamide binding pairs does not produce a selective polyamide
that binds to the
target identified DNA sequence with subnanomolar affinity and with a
selectivity over mismatch
sequences of greater than a factor of ten, a polyamide molecule
X1X2X3X4XSX6-Y-X7X8X9X1OX11X12 having six carboxamide binding pairs can be
designed that is selective for an eight base pair identified target 5'-
WNTI~JNNNW-3' sequence.
The design and synthesis of six binding pair polyamides is essentially the
same as that of the
2o four and five binding pair polyamides described above.
The polyamide design process for six carboxamide binding pair polyamides is
shown
schematically in Figure 10 A and the upper half of l OB. The method for
chosing the residues
that can be replaced by a (3-alanine residue is shown schematically in the
lower half of Figure 10
B and in Figure 11. The 1024 possible 12-ring hairpins which target the 1024
5'-GNNNNN-3'
core sequences are listed in Tables 84-I 15. Each DNA sequence entry can be
correlated to its
corresponding polyamide recognition sequence using the process outlined in
this figure. The
1024 possible I2-ring hairpins which target the 1024 5'-CNNNNN-3' core
sequences are listed
in Tables 116-147. Each DNA sequence entry can be correlated to its
corresponding polyamide
3o recognition sequence using the process outlined in this figure.
Figure 11 shows a process for replacement of aromatic amino acid residues with
aliphatic
(3-aIanine 'spring' residues in order to enhance the DNA binding properties of
12-ring hairpin
polyamides. Selective placement of an aliphatic (3-alanine (/3) residue paired
side-by-side with
either a pyrrole (Py) or imidazoIe (Im) aromatic amino acid or another (3-
alanine residue is found
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-132-
to compensate for sequence composition effects for recognition of the minor
groove of DNA by
hairpin pyrrole-imidazole polyamides. If an all-ring polyamide has been found
to have an
affinity which is not subnanomolar, or a specificity versus mismatch sequences
which is less
than 10-fold it may be caused by DNA sequence-composition effects which can be
tuned out by
replacement of an aromatic amino acid with an aliphatic j3-alanine spring.
Rules have been
determined to help determine the exact placement of the (3-spring residues.
For example, within
the 12-ring template, it is only beneficial to place ~3-alanine within
positions X2, X3, X4, XS,
Xg, X9, and X10 X11,. No more than two (3-alanine residues may be placed
within a single
hairpin structure. No more than a single (3-residue may be placed within each
individual
to poiyamide subunit. Tables 148-1079 list derivatives of sequences (1233-
2224) labeled (1223(3-
2224[3) which contain two (3-alanine residues assigned according to the
process outlined in
Figure 11A & B.
CA 02281930 1999-08-18
WO 98/37067 , PCT/US98/01714
-133-
1 AtiLl; 12-ring
84: Hairpin
Polyamides
for
recognition
of
8-by
5'-WGGGWNNW-3'
DNA aromatic amino acid sequence
sequence
1233) 5'-W GG G T T T W-3' ImImImHpHpHp-y-PYPYPYPYPYpy
1234) 5'~-W GG G T T A W-3' ImImImHpHpPy-y-HpPyPYPyPyPy
1235) 5'-W GG G T T G W-3' ImImImHpHpIm-y-Pypypypypypy
1236) 5'-W GG G T T C W-3' ImTmImHpHppy-y-ImpyPYPypypy
1237) 5'-W GG G T A T W-3' ImImImHpPYHp-y-PyHpPyPyPyPy
1238) 5' GG G T A A W-3' ImImImHpPyPy-y-HpHpPyPYPYPy
-W
1239) 5'-W GG G T A G W-3' ImImImHpPyIm-y-PyHpPYpypypY
1240) 5'-W GG G T A C W-3' ImImImHpPyPy-y-ImHpPYPYPYPy
1241) 5'-W GG G T G T W-3' ImImImHpImHp-y-pypypypypypy
1242} 5'-W GG G T G A W-3' ImImImHpImPy-y-HpPyPyPyPyPy
1243) 5'-W GG G T G G W-3' ImImImHpImIm-y-PyPYPyPyPYPy
1244) 5' GG G T G C W-3' ImImImHpImPy-y-ImPyPYPyPyPy
-W
1245) 5' GG G T C T W-3' ImImImHpPyHp-y-PyImPyPyPyPy
-W
1246) 5'-W GG G T C A W-3' ImImImHpPYPy-y-HpImPYPYPYPy
1247) 5'-W GG G T C G W-3' ImImImHpPyIm-y-pyImPyPyPYPy
1248) 5'-W GG G T C C W-3' ImImImHpPYPy-y-ImImPyPYPyPy
1249) 5'-W GG G A T T W-3' ImImImPyHpHp-y-PYPyHpPyPyPy
1250) 5'-W GG G A T A W-3' ImImImPyHpPy-y-HpPyHpPyPyPy
1251) 5'-W GG G A T G W-3' TmImImPyHpIm-y-PypyHpPyPyPy
1252) 5'-W GG G A T C W-3' ImImImPyHpPy-y-ImPyHpPyPyPy
1253) 5'-W GG G A A T W-3' ImImImPyPyHp-y-PyHpHpPYPyPy
1254) 5'-W GG G A A A W-3' ImImImPyPyPy-y-HpHpHppyPyPy
1255) 5'-W GG G A A G W-3' ImImImPyPyIm-y-PyHpHpPYPyPy
1256) 5'-W GG G A A C W-3' ImImImPyPYPy-y-ImHpHpPYPyPy
1257) 5'-W GG G A G T W-3' ImImImPyImHp-y-PyPyHpPyPYPy
1258) 5'-W GG G A G A W-3' ImImImPyImPy-y-HpPyHpPyPyPy
1259) 5'-W GG G A G G W-3' ImImImPyImIm-y-P
P
H
P
P
p
y
y
p
y
y
y
12 60 5' GG G A G C W-3 ImImImPyImPy-y- ImPYHpPyPyPy
) -W '
1261) 5'-W GG G A C T W-3' ImImImPyPyHp-y-PyImHpPYPYPY
1262) 5'-W GG G A C A W-3' ImImImPyPypy-y-HpImHpPyPyPy
1263) 5'-W GG G A C G W-3' ImImImPyPyIm-y-PyImHpPypypy
1264) 5'-W GG G A C C W-3' ImImImPyPYPy-y-ImImHpPyPYPy
CA 02281930 1999-08-18
WO 98137067 - PCT/US98101714
-134-
TABLE
85:
12-ring
Hairpin
Polyamides
for
recognition
of
8-by
5'-WGGGSNNW-3'
'
DNA aromatic amino acid sequence
sequence
1265) 5' -W GG G G T T W-3' ImImImImHpHp-y-PyPyPyPyPyPy
1266) 5' -W GG G G T A W-3' ImImImImHpPy-y-HpPyPyPyPyPy
S 1267) 5'~-W GG G G T G W-3' ImImImImHpIm-y-PyPyPyPyPyPy
1268} 5' -W GG G G T C W-3' ImImImImHpPy-y-ImPyPyPyPyPy
1269) 5' -W GG G G A T W-3' ImImImImPyHp-y-PyHpPyPyPyPy
1270) 5' -W GG G G A A W-3' ImImImImPyPy-y-HpHpPyPyPyPy
1271) 5' -W GG G G A G W-3' ImImImImPyIm-y-PyHpPyPyPyPy
1272) 5' -W GG G G A C W-3' ImImImImPyPy-y-ImHpPypyPyPy
1273} 5' -W GG G G G T W-3' ImImImImImHp-y-PyPypypypypy
1274) 5' -W GG G G G A W-3' ImImImImImPy-y-HpPyPyPyPyPy
1275) 5' -W GG G G C T W-3' ImImImImPyHp-y-PyImPyPyPyPy
1276) 5' -W GG G G C A W-3' ImImImImPyPy-y-HpImPyPyPyPy
1277) 5' -W GG G C T T W-3' ImImImPyHpHp-y-PyPyImPyPyPy
1278} 5' -W GG G C T A W-3' ImImImPyHpPy-y-HpPyImPyPyPy
1279) 5' -W GG G C T G W-3' ImImImPyHpIm-y-PyPyImPyPyPy
1280) 5' -W GG G C T C W-3' ImImImPyHpPy-y-ImPyImPyPyPy
1281) 5' -W GG G C A T W-3' ImImImPypyHp-y-PyHpImPyPyPy
1282) 5' -W GG G C A A W-3' ImImImPyPyPy-y-HpHpImPyPyPy
1283) 5' -W GG G C A G W-3' ImImImPyPyIm-y-PyHpImPyPyPy
1284) 5' -W GG G C A C W-3' ImImImPyPyPy-y-ImHpImPyPyPy
1285) 5' -W GG G C G T W-3' ImImImPyImHp-y-PyPyImPyPyPy
12 86 5' -W GG G C G A W-3 ImImImPyImPy-y-HpPyImPyPyPy
) '
1287) 5' -W GG G C C T W-3' ImImImPyPyHp-y-PyImImPyPyPy
1288) 5' -W GG G C C A W-3' ImImImPyPyPy-y-HpImImPyPyPy
G4 9 5' -W GG G G G G W-3 ImImImImImIm-y-PyPyPyPyPyPy
) '
G50) 5' -W GG G G G C W-3' ImImImImImPy-y-ImPyPyPyPyPy
G51) 5' -W GG G G C G W-3' ImImImImPyIm-y-PyImPyPyPyPy
G52) 5' -W GG G G C C W-3' ImImImImPyPy-y-ImImPyPyPyPy
G53) 5' -W GG G C G G W-3' ImImImPyImIm-y-PyPyImPyPyPy
G54 ) 5' -W GG G C G C W-3 ImImImPyImPy-y-ImPyImPyPyPy
'
G55) 5' -W GG G C C G W-3' ImImImPyPyIm-y-PyImImPyPyPy
G56) 5' -W GG G C C C W-3' ImImImPypyPy-y-ImImImPyPyPy
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-135-
TABLE
86:
12-ring
Hairpin
Polyamides
for
recognition
of
8-by
5'-WGGTWNNW-3'
DNA aromatic amino acid sequence
sequence
1289) 5' -WG G T T TT W-3' ImImHpHpHpHp-y-PyPyPyPyPypy
1290) 5' '-WG G T T TA W-3' ImImHpHpHpPy-y-HpPyPyPyPyPy
1291) 5' -WG G T T TG W-3' ImImHpHpHpIm-y-PyPyPyPyPyPy
1292) 5' -WG G T T TC W-3' ImImHpApHpPy-y-ImPyPyPyPyPy
1293) 5' -WG G T T AT W-3' ImImHpHpPyHp-y-PyHpPyPyPyPy
12 94 5' -WG G T T AA W-3 ImImHpHpPyPy-y-HpHpPyPyPyPy
) '
1295) 5' -WG G T T AG W-3' ImImHpHpPyIm-y-PyHpPyPyPyPy
1296) 5' -WG G T T AC W-3' ImImHpHpPyPy-y-ImHppyPyPyPy
1297) 5' -WG G T T GT W-3' ImImHpHpImHp-y-PyPyPyPyPyPy
1298) 5' -WG G T T GA W-3' ImImHpHpImPy-y-HpPypyPyPyPy
1299) 5' -WG G T T GG W-3' ImImHpHpImIm-y-PyPyPyPypypy
1300) 5' -WG G T T GC W-3' ImImHpHpImPy-y-ImpyPyPyPypy
1301) 5' -WG G T T CT W-3' ImImHpHpPyHp-y-PyImPyPyPyPy
1302) 5' -WG G T T CA W-3' ImImHpHpPyPy-y-HpImPyPyPyPy
1303) 5' -WG G T T CG W-3' ImImHpHppylm-y-PyImPyPyPyPy
1304) 5' -WG G T T CC W-3' ImImHpHpPyPy-y-ImImPypyPyPy
1305) 5' -WG G T A TT W-3' ImImHpPyHpHp-y-PyPyHpPyPyPy
1306) 5' -WG G T A TA W-3' ImImHpPyHpPy-y-HpPyHpPyPyPy
1307) 5' -WG G T A TG W-3' ImImHpPyHpIm-y-PyPyHpPyPyPy
1308) 5' -WG G T A TC W-3' ImImHpPyHpPy-y-ImPyHpPyPyPy
1309) 5' -WG G T A AT W-3' ImImHpPyPyHp-y-PyHpHpPyPyPy
1310 5' -WG G T A AA W-3 ImImHpPyPyPy-y-HpHpHpPyPyPy
) '
1311) 5' -WG G T A AG W-3' ImImHpPyPyIm-y-PyHpHpPyPyPy
1312) 5' -WG G T A AC W-3' ImImHpPyPyPy-y-ImHpHpPyPyPy
1313) 5' -WG G T A GT W-3' ImImHpPyImHp-y-PyPyHpPyPyPy
a 1314) 5' -WG G T A GA W-3' ImImHpPyImPy-y-HpPyHpPyPyPy
1315) 5' -WG G T A GG W-3' ImImHpPyImIm-y-PyPyHpPyPyPy
1316) 5' -WG G T A GC W-3' ImImHpPyImPy-y-ImPyHpPyPyPy
1317) 5' -WG G T A CT W-3' ImImHpPyPyHp-y-pyImHpPyPyPy
1318) 5' -WG G T A CA W-3' ImImHpPyPyPy-y-HpImHppyPyPy
1319) 5' -WG G T A CG W-3' ImImHpPyPyIm-y-PyImHpPyPyPy
1320) 5' -WG G T A CC W-3' ImImHpPyPyPy-y-ImImHpPyPyPy
CA 02281930 1999-08-18
WO 38/37067 PCT/US98/01714
-136-
TABLE
87:
12-ring
Hairpin
Polyamides
for
recognition
of
8-by
5'-WGGTSNNW-3'
DNA aromatic amino acid sequence
sequence
1321) 5' -W G GT G T T W-3' ImImHpImHpHp-y-PyPyPyPyPyPy
1322) 5' -W G GT G T A W-3' ImImHpImHpPy-y_Hppypypypypy
1323) 5' -W G GT G T G W-3' ImImHpImHpIm-y-PyPyPyPyPyPy
1324) 5' -W G GT G T C W-3' ImImHpImHpPy-y-ImPyPyPyPyPy
1325) 5' -W G GT G A T W-3' ImImHpImPyHp-y-PyHpPyPyPyPy
1326) 5' -W G GT G A A W-3' ImImHpImPyPy-y-HpHpPyPyPyPy
1327) 5' -W G GT G A G W-3' ImImHpImPyIm-y-PyHpPyPyPyPy
1328) 5' -W G GT G A C W-3' ImImHpImPyPy-y-ImHpPyPyPyPy
1329) 5' -W G GT G G T W-3' ImImHpImImHp-y-PyPyPyPyPyPy
1330) 5' -W G GT G G A W-3' ImImHpImImPy-y-HpPyPyPyPyPy
1331) 5' -W G GT G C T W-3' ImImHpImPyHp-y-PyImPyPyPyPy
1332) 5' -W G GT G C A W-3' ImImHpImPyPy-y-HpImPyPyPyPy
1333) 5' -W G GT G G G W-3' ImImApImImIm-y-PyPyPyPyPyPy
1334) 5' -W G GT G G C W-3' ImImHpImImPy-y-ImPyPyPyPyPy
1335) 5' -W G GT G C G W-3' ImImHpImPyIm-y-PyImPyPyPyPy
1336) 5' -W G GT G C C W-3' ImImHpImPyPy-y-ImImPyPyPyPy
1337) 5' -W G GT C T T W-3' ImImHpPyHpHp-y-PyPyImPyPyPy
1338) 5' -W G GT C T A W-3' ImImHpPyHpPy-y-HpPyImPyPyPy
1339) 5' -W G GT C T G W-3' ImImHpPyHpIm-y-PyPyImPyPyPy
1340) 5' -W G GT C T C W-3' ImImHpPyHpPy-y-ImPyImPyPyPy
1341) 5' -W G GT C A T W-3' ImImHpPyPyHp-y-PyHpImPyPyPy
1342) 5' -W G GT C A A W-3' ImImHpPyPyPy-y-HpHpImPyPypy
1343) 5' -W G GT C A G W-3' ImImHpPyPyIm-y-PyHpImPyPyPy
1344) 5' -W G GT C A C W-3' ImImHpPyPyPy-y-ImHpImPyPyPy
1345) 5' -W G GT C G T W-3' ImImHpPyImHp-y-PyPyImPyPyPy
1346) 5' -W G GT C G A W-3' ImImHpPyImPy-y-HpPyImPyPyPy
1347) 5' -W G GT C C T W-3' ImImHpPyPyHp-y-PyImImPyPyPy
1348) 5' -W G GT C C A W-3' ImImHpPyPyPy-y-HpImImPyPyPy
1349) 5' -W G GT C G G W-3' ImImHpPyImIm-y-PyPyimPyPyPy
1350) 5' -W G GT C G C W-3' ImImHpPyImPy-y-ImPyImPyPyPy
1351) 5' -W G GT C C G W-3' ImImHpPyPyIm-y-PyImImpyPyPy
1352) 5' -W G GT C C C W-3' ImImHpPyPyPy-y-ImImImPyPyPy
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-137-
lAt3Ll;
~i8:
12-ring
Hairpin
Polyamides
for
recognition
of
8-by
5'-WGGAWNNW-3'
DNA aromatic amino acid sequence
sequence
1353) 5'-W G G A T TT W-3' ImImPyHpHpHp-y-PyPyPyHpPyPy
1354) 5' G G A T TA W-3' ImImPyHpHpPy-y-HpPyPyHpPyPy
-W
1355) 5' G G A T TG W-3' ImImPyHpHpIm-y-PyPyPyHpPyPy
-W
1356) 5' G G A T TC W-3' ImImPyHpHpPy-y-ImPyPyHpPyPy
-W
1357 5' G G A T AT W-3 ImImPyHpPyHp-y-PyHpPyHpPyPy
) -W '
1358) 5' G G A T AA W-3' ImImPyHpPyPy-y-HpHpPyHppyPy
-W
1359) 5' G G A T AG W-3' ImImPyHpPyIm-y-PyHpPyHpPyPy
-W
1360) 5'-W G G A T AC W-3' ImImPyHpPyPy-y-ImHpPyHpPyPy
1361) 5' G G A T GT W-3' ImImPyHpImHp-y-pypypyHpPyPy
-W
1362) 5' G G A T GA W-3' ImImPyHpImPy-y-HpPyPyHpPyPy
-W
1363) 5'-W G G A T GG W-3' ImImPyHpImIm-y-PyPyPyHpPyPy
IS 1364) 5'-W G G A T GC W-3' ImImPyHpImPy-y-ImPyPyHpPyPy
1365) 5' G G A T CT W-3' ImImPyHpPyHp-y-PyImPyHpPyPy
-W
1366) 5' G G A T CA W-3' ImImPyHpPyPy-y-HpImPyHpPyPy
-W
1367) 5'-W G G A T CG W-3' imImPyHpPyIm-y-PyImPyHpPyPy
1368) 5'-W G G A T CC W-3' ImImPyHpPyPy-y-ImImPyHpPyPy
1369) 5' G G A A TT W-3' ImImPyPyHpHp-y-PyPyHpHpPyPy
-W
1370) 5'-W G G A A TA W-3' ImImPyPyHpPy-y-HpPyHpHpPyPy
1371) 5' G G A A TG W-3' ImImPyPyHpIm-y-PyPyHpHpPyPy
-W
1372) 5' G G A A TC W-3' ImImPyPyHpPy-y-ImPyHpHpPyPy
-W
1373) 5'-W G G A A AT W-3' ImImPyPyPyHp-y-PyHpHpHpPyPy
1374) 5'-W G G A A AA W-3' ImImPyPypypy-y-HpHpHpHpPyPy
1375) 5' G G A A AG W-3' ImImPyPypyIm-y-PyHpHpHpPyPy
-W
1376) 5' G G A A AC W-3' ImImPyPyPyPy-y-ImHpHpHpPyPy
-W
1377) 5'-W G G A A GT W-3' ImImPyPyImHp-y-PyPyHpHpPyPy
1378) 5' G G A A GA W-3' ImImPyPyImPy-y-HpPyHpHpPyPy
-W
1379) 5' G G A A GG W-3' ImImPyPyImIm-y-PyPyHpHpPyPy
-W
13 8 5' G G A A GC W- 3 ImImPyPyImPy-y- ImPyHpHpPyPy
0 ) -W '
1381) 5' G G A A CT W-3' ImImPyPyPyHp-y-PyImApHpPyPy
-W
1382) 5' G G A A CA W-3' ImImPypypypy-y_HpI~pHppyPy
-W
1383} 5' G G A A CG W-3' ImImPyPyPyIm-y-PyImHpHpPyPy
-W
1384) 5'-W G G A A CC W-3' ImImPyPyPyPy-y-ImImHpHpPyPy
CA 02281930 1999-08-18
WO 98137067 PCT/US98/01714
-138-
TABLE
89:
12-ring
Hairpin
Polyamides
for
recognition
of
8-by
5'-WGGASNNW-3'
DNA aromatic amino acid sequence
sequence
1385} 5' -WG G A G TT W-3' ImImPyImHpHp-y-PyPypyHpPyPy
1386) 5' -WG G A G TA W-3' ImImPyImHpPy-y-HpPyPyHpPyPy
1387} 5' -WG G A G TG W-3' ImImPyImHpIm-y-PyPyPyHpPyPy
1388) 5' -WG G A G TC W-3' ImImPyImHpPy-y-ImPyPyHpPyPy
1389) 5' -WG G A G AT W-3' Im3mPyImPyHp-y-PyHpPyHpPyPy
1390} 5' -WG G A G AA W-3' ImImPyImPyPy-y-HpHpPyHpPyPy
1391) 5' -WG G A G AG W-3' ImImPyImPyIm-y-PyHpPyHpPyPy
1392) 5' -WG G A G AC W-3' ImImPyImPyPy-y-ImHpPyHpPyPy
1393) 5' -WG G A G GT W-3' ImImPyImImHp-y-PyPyPyHpPyPy
13 94 5' -WG G A G GA W-3 ' ImImPyImImPy-y-HpPyPyHppyPy
)
1395) 5' -WG G A G CT w-3' ImImPyImPyHp-y-PyImPyHpPyPy
1396) 5' -WG G A G CA W-3' ImImPyImPyPy-y-HpImPyHpPyPy
1397) 5' -WG G A G GG W-3' ImImPyImImIm-y-PyPyPyHppyPy
13 9 5' -WG G A G GC W-3 ' ImImPyImImPy-y- ImPyPyHpPyPy
8 )
1399) 5' -WG G A G CG W-3' ImImPyImPyIm-y-PyImPyHpPyPy
1400) 5' -WG G A G CC W-3' ImImPyImPyPy-y-ImImPyHpPyPy
1401) 5' -WG G A C TT W-3' ImImPyPyHpHp-y-PyPyImHpPyPy
1402) 5' -WG G A C TA W-3' ImImPyPyHpPy-y-HpPyImHpPyPy
1403 5' -WG G A C TG W-3' ImImPyPyHpIm-y-PyPyImHpPyPy
)
1404) 5' -WG G A C TC W-3' ImImPyPyHpPy-y-ImPyImHpPyPy
1405) 5' -WG G A C AT W-3' ImImPyPyPyHp-y-PyHpImHpPyPy
1406) 5' -WG G A C AA W-3' ImImPyPyPyPy-y-HpHpImHpPyPy
1407) 5' -WG G A C AG W-3' ImImPyPyPyIm-y-PyHpImHpPyPy
1408} 5' -WG G A C AC W-3' ImImPyPyPyPy-y-ImHpImHpPyPy
1409} 5' -WG G A C GT W-3' ImImPyPyImHp-y-PypyImHpPyPy
1410 5' -WG G A C GA W-3 ' ImImPyPyImPy-y-HpPyImHpPyPy
)
1411) 5' -WG G A C CT W-3' ImImPyPyPyHp-y-PyImImHpPyPy
1412 5' -WG G A C CA W- 3 ImImPyPyPyPy-y-HpImImHpPypy
) '
1413) 5' -WG G A C GG W-3' ImImPyPyImIm-y-PyPyImHpPyPy
1414) 5' -WG G A C GC W-3' ImImPyPyImPy-y-ImPyImHpPypy
1415) 5' -WG G A C CG W-3' ImImPyPyPyIm-y-PyImImHpPyPy
1416) 5' -WG G A C CC W-3' ImImPyPyPyPy-y-ImImImFippyPy
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-139-
TABLE
90:
12-ring
Hairpin
Polyamides
for
recognition
of
8-by
5'-WGGCWNNW-3'
DNA aromatic amino acid sequence
sequence
1417) 5' -W GG C T T T W-3' ImImPyHpHpHp-y-PyPyPyImPyPy
1418 5' -W GG C T T A W-3 ImImPyHpHpPy-y-HpPyPyImPyPy
) '
1419) 5' -W GG C T T G W-3' ImImPyHpHpIm-y-PyPyPyImPyPy
1420) 5' -W GG C T T C W-3' ImImPyHpHpPy-y-ImPyPyImPyPy
1421) 5' -W GG C T A T W-3' ImImPyHpPyHp-y-PyHpPyImPyPy
1422) 5' -W GG C T A A W-3' ImImPyHpPyPy-y-HpHpPyImPyPy
1423) 5' -W GG C T A G W-3' ImImPyHpPyIm-y-PyHpPyImPyPy
1424) 5' -W GG C T A C W-3' ImImPyHpPyPy-y-ImHpPyImPyPy
1425) 5' -W GG C T G T W-3' ImImPyHpImHp-y-PyPyPyImPyPy
1426) 5' -W GG C T G A W-3' ImImPyHpImPy-y-HpPyPyImPyPy
1427) 5' -W GG C T G G W-3' ImImPyHpImIm-y-PyPyPyImPyPy
1428) 5' -W GG C T G C W-3' ImImPyHpImPy-y-ImPyPyImPyPy
1429) 5' -W GG C T C T W-3' ImImPyHpPyHp-y-PyImPyImPyPy
1430) 5' -W GG C T C A W-3' ImImPyHpPyPy-y-HpImPyImPyPy
143I) 5' -W GG C T C G W-3' ImImPyHpPyIm-y-PyImPyImPyPy
1432) 5' -W GG C T C C W-3' ImImPyHpPyPy-y-ImImPyImPyPy
1433) 5' -W GG C A T T W-3' ImImPyPyHpHp-y-PyPyHpImPyPy
1434) 5' -W GG C A T A W-3' ImImPyPyHpPy-y-HpPyHpImPyPy
1435) 5' -W GG C A T G W-3' ImImPyPyHpIm-y-PyPyHpImPyPy
1436) 5' -W GG C A T C W-3' ImImPyPyHpPy-y-ImPyHpImPyPy
1437) 5' -W GG C A A T W-3' ImImpyPyPyHp-y-PyHpHpImPyPy
1438) 5' -W GG C A A A W-3' ImImPyPyPyPy-y-HpHpHpImPyPy
1439) 5' -W GG C A A G W-3' ImImPyPyPyIm-y-PyHpHpImPyPy
1440) 5' -W GG C A A C W-3' ImImPyPyPyPy-y-ImHpHpImPyPy
1441) 5' -W GG C A G T W-3' ImImPyPyImHp-y-PyPyHpImPyPy
1442) 5' -W GG C A G A W-3' ImImPyPyImPy-y-HpPyHpImPyPy
1443) 5' -W GG C A G G W-3' ImImPyPyImIm-y-PyPyHpImPyPy
1444) 5' -W GG C A G C W-3' ImImPyPyimPy-
y -ImPyHpImPyPy
1445) 5' -W GG C A C T W-3' ImImPyPyPyHp-y-PyImHpImPyPy
1446) 5' -W GG C A C A W-3' ImImPyPyPyPy-y-HpImHpImPyPy
1447) 5' -W GG C A C G W-3' ImImPyPyPyIm-y-PyImHpImPyPy
1448) 5' -W GG C A C C W-3' ImImPyPyPyPy-y-ImImHpImPyPy
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-140-
TABLE
91:
12-ring
Hairpin
Polyamides
for
recognition
of 8-by
5'-WGGCSNNW-3'
DNA aromatic amino acid sequence
sequence
1449) 5' GG C G T T W-3' ImImPyImHpHp-y-PyPyPyImPyPy
-W
1450) 5' GG C G T A W-3' ImImPyImHpPy-y-HpPyPyImPyPy
-W
1451) 5' GG C G T G W-3' ImImPyImHpIm-y-PyPyPyImPyPy
-W
1452) 5' GG C G T C W-3' ImImPyImHpPy-y-ImPyPyImPyPy
-W
1453) 5' GG C G A T W-3' ImImPyImPyHp-y-PyHpPyImPyPy
-W
1454) 5'-W GG C G A A W-3' ImImPyImPyPy-y-HpHpPyImPyPy
1455) 5' GG C G A G W-3' ImImPyImPyIm-y-PyHpPyImPyPy
-W
1456) 5' GG C G A C W-3' ImImPyImPyPy-y-ImHpPyImPyPy
-W
1457) 5'-W GG C G G T W-3' ImImPyImImHp-y-PyPyPyImPyPy
1458) 5' GG C G G A W-3' ImImPyImImPy-y-HpPyPyImPyPy
-W
1459) 5' GG C G C T W-3' ImImPyImPyHp-y-PyImPyImPyPy
-W
1460) 5' GG C G C A W-3' ImImPyImPyPy-y-HpImPyImPyPy
-W
1461) 5' GG C C T T W-3' ImImPyPyHpHp-y-PyPyImImPyPy
-W
1462) 5' GG C C T A W-3' ImImPyPyHpPy-y-HpPyImImPyPy
-W
1463 5' GG C C T G W-3' ImImPyPyHpIm-y-PyPyImImPyPy
) -W
1464) 5' GG C C T C W-3' ImImPyPyHpPy-y-ImPyImImPyPy
-W
1465) 5' GG C C A T W-3' ImImPyPyPyHp-y-PyHpImImPyPy
-W
1466) 5' GG C C A A W-3' ImImPyPyPyPy-y-HpHpImImPyPy
-W
1467) 5'-W GG C C A G W-3' ImImPyPyPyIm-y-PyHpImImPyPy
1468) 5' GG C C A C W-3' ImImPyPyPyPy-y-ImHpImImPyPy
-W
1469) 5' GG C C G T W-3' ImImPyPyImHp-y-PyPyImImPyPy
-W
1470) 5' GG C C G A W-3' ImImPyPyImPy-y-HpPyImImPyPy
-W
1471) 5' GG C C C T W-3' ImImPyPyPyHp-y-PyImImImPyPy
-W
1472) 5' GG C C C A W-3' ImImPyPyPyPy-y-HpImImImPyPy
-W
G57) 5' GG C G G G W-3' ImImPyImImIm-y-PyPyPyImPyPy
-W
G58) 5' GG C G G C W-3' ImImPyImImPy-y-ImPyPyImPyPy
-W
G59) 5' GG C G C G W-3' ImImPyImPyIm-y-PyImPyImPyPy
-W
G60) 5' GG C G C C W-3' ImImPyImPyPy-y-ImImPyImPyPy
-W
G61) 5' GG C C G G W-3' ImImPyPyImIm-y-PyPyImImPyPy
-W
G62) 5' GG C C G C W-3' ImImPyPyImPy-y-ImPyImImPyPy
-W
G63) 5' GG C C C G W-3' ImImPyPyPyIm-y-PyImImImPyPy
-W
G64) 5' GG C C C C W-3' ImImPyPyPyPy-y-ImImImImPyPy
-W
CA 02281930 1999-08-18
WO 98!37067 PCT/US98/01714
-141-
TABLE
92:
12-ring
Hairpin
Polyamides
for
recognition
of
8-by
5'-WGCGWNNW-3'
DNA aromatic amino acid sequence
sequence
1473) 5' -W G C GT T T W-3' ImPyImHpHpHp-y-PyPyPyPyImPy
.
1474) 5' -W G C GT T A W-3' ImPyImHpHpPy-y-HppypyPyImPy
1475) 5' -W G C GT T G W-3' ImPyImHpHpIm-y-PyPypypylmpy
1476) 5' -W G C GT T C W-3' ImPyImHpHpPy-y-ImPyPyPyImPy
1477) 5' -W G C GT A T W-3' ImPyImHpPyHp-y-PyHpPyPyImPy
1478) 5' -W G C GT A A W-3' ImPyImHpPyPy-y-HpHpPyPyImPy
1479) 5' -W G C GT A G W-3' ImPyImHpPyIm-y-PyHpPyPyImPy
1480) 5' -W G C GT A C W-3' ImPyImHpPyPy-y-ImHpPyPyImPy
1481} 5' -W G C GT G T W-3' ImPyImHpImHp-y-PyPyPypyImPy
1482) 5' -W G C GT G A W-3' ImPyImHpImPy-y-HpPyPypyImPy
1483) 5' -W G C GT G G W-3' ImPyImHpImIm-y-PypyPyPyImPy
1484) 5' -W G C GT G C W-3' ImPyImfipImPy-y-ImPyPyPyImPy
1485) 5' -W G C GT C T W-3' ImPyImHpPyHp-y-PyImPyPyImPy
1486 5' -W G C GT C A W-3' ImpyImHpPyPy-y-HpImPyPyImPy
)
1487) 5' -W G C GT C G W-3' ImPyImHpPyIm-y-PyImpyPyImPy
1488) 5' -W G C GT C C W-3' ImPyImHpPyPy-y-ImimPyPyImPy
1489) 5' -W G C GA T T W-3' ImPyImPyHpHp-y-PyPyHpPyImPy
1490) 5' -W G C GA T A W-3' ImPyImPyHpPy-y-HpPyHpPyImPy
1491) 5' -W G C GA T G W-3' ImPyImPyHpIm-y-PyPyHpPyImPy
1492) 5' -W G C GA T C W-3' ImPyImPyHpPy-y-ImPyHpPyImPy
1493) 5' -W G C GA A T W-3' ImPyImPyPyHp-y-pyHpHpPyImPy
1494) 5' -W G C GA A A W-3' ImPyImPyPypy-y-HpHpHpPyImPy
1495) 5' -W G C GA A G W-3' ImPyImpypylm-y-PyHpHpPyImPy
1496) 5' -W G C GA A C W-3' ImPyImPyPyPy-y-ImHpHppyImPy
1497) 5' -W G C GA G T W-3' ImpyImPyImHp-y-PypyHpPyImPy
1498) 5' -W G C GA G A W-3' ImPyImPyImpy-y-HpPyHpPyImPy
1499) 5' -W G C GA G G W-3' ImPyImPyImIm-y-PyPyHpPyImPy
1490) 5' -W G C GA G C W-3' ImPyImPyImpy-y-ImPyHpPyImPy
1501) 5' -W G C GA C T w-3' ImPyImPyPyHp-y-PyImHpPyImPy
1502) 5' -W G C GA C A W-3' ImPyImPyPyPy-y-HpImHpPyImPy
_ 1503) 5' -W G C GA C G W-3' ImPyImPyPyIm-y-PyImHpPyImPy
1504) 5' -W G C GA C C W-3' ImPyImPyPyPy-y-ImImHpPyImPy
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-142-
TABLE
93:
I2-ring
Hairpin
Polyamides
for
recognition
of
8-by
5'-WGCGSNNW-3'
DNA aromatic amino acid sequence
sequence
1505) 5' -WG C G G T T W-3' ImPyImImHpHp-y-PyPyPyPyImPy
1506) 5' -WG C G G T A W-3' ImPyImImHpPy-y-HpPyPyPyImPy
1507) 5' -WG C G G T G W-3' ImPyImImHpIm-y-PyPyPyPyImPy
1508) 5' -WG C G G T C W-3' ImPyImImHpPy-y-ImPyPyPyImPy
1509) 5' -WG C G G A T W-3' ImPyImImPyHp-y-PyHpPyPyImPy
1510) 5' -WG C G G A A W-3' ImPyImImPyPy-y-HpHpPyPyImPy
1511) 5' -WG C G G A G W-3' ImPyImImPyIm-y-PyHpPyPyImPy
1512) 5' -WG C G G A C W-3' ImPyImImPyPy-y-ImHpPyPyImPy
1513) 5' -WG C G G G T W-3' ImPyImImImHp-y-PyPyPyPyImPy
1514 5' -WG C G G G A W-3 ImPyImImImPy-y-HpPyPyPyImPy
) '
1515) 5' -WG C G G C T W-3' ImPyImImPyHp-y-PyImPyPyImPy
IS 1516) 5' -WG C G G C A W-3' ImPyImImPyPy-y-HpImPyPyImPy
1517) 5' -WG C G C T T W-3' ImPyImPyHpHp-y-PyPyImPyImPy
1518) 5' -WG C G C T A W-3' ImPyImPyHpPy-y-HpPyImPyImPy
1519) 5' -WG C G C T G W-3' ImPyImPyHpIm-y-PyPyImPyImPy
1520) 5' -WG C G C T C W-3' ImPyImPyHpPy-y-ImPyImPyImPy
1521) 5' -WG C G C A T W-3' ImPyImPyPyHp-y-PyHpImPyImPy
1522) 5' -WG C G C A A W-3' ImPyImPyPyPy-y-HpHpImPyImPy
1523) 5' -WG C G C A G W-3' ImPyImPyPyIm-y-PyHpImPyImPy
1524) 5' -WG C G C A C W-3' ImPyImPyPyPy-y-ImHpImPyImPy
1525) 5' -WG C G C G T W-3' ImPyImPyImHp-y-PyPyImPyImPy
1526) 5' -WG C G C G A W-3' ImPyImPyImPy-y-HpPyImPyImPy
1527) 5' -WG C G C C T W-3' ImPyImPyPyHp-y-PyImImPyImPy
1528) 5' -WG C G C C A W-3' ImPyImPyPyPy-y-HpImImPyImPy
G65) 5' -WG C G G G G W-3' ImPyImImIrnIm-y-PyPyPyPyImPy
G66) 5' -WG C G G G C W-3' ImPyImImImPy-y-ImPyPyPyImPy
G67 ) 5' -WG C G G C G W-3 ImPyImImPyIm-y-PyImPyPyImPy
'
G68) 5' -WG C G G C C W-3' ImPyImImPyPy-y-ImImPyPyImPy
G69) 5' -WG C G C G G W-3' ImPyimPyImIm-y-PyPyImPyImPy
G70) 5' -WG C G C G C W-3' ImPyImPyImPy-y-ImPyImPyImPy
G71) 5' -WG C G C C G W-3' ImPyImPyPyIm-y-PyImImPyImPy
G72) 5' -WG C G C C C W-3' ImPyImPyPyPy-y-ImImImPyImPy
CA 02281930 1999-08-18
WO 98137067 , PCT/US98/01714
-143-
1A13L1;
94:
12-ring
Hairpin
Polyamides
for
recognition
of
8-by
5'-WGCTWNNW-3'
DNA aromatic amino acid sequence
sequence
1529) 5'-W G C TT T T W-3' ImPyHpHpHpHp-y-PypypypylmPy
1530) 5''-W G C TT T A W-3' ImPyHpHpHpPy-y-HppyPyPyImPy
1531) 5' G C TT T G W-3' ImPyHpHpHpIm-y-PypypypylmPy
-W
1532) 5' G C TT T C W-3' ImPyHpHpHpPy-y-ImPyPyPyImPy
-W
1533 5' G C TT A T W-3 ImPyHpHpPyHp-y-PyHpPyPyImPy
) -W '
1534) 5'-W G C TT A A W-3' ImpyHpHpPyPy-y-HpHpPyPyImPy
1535) 5' G C TT A G W-3' ImPyHpHpPyIm-y-PyHpPyPyImPy
-W
1536) 5'-W G C TT A C W-3' ImPyHpHpPyPy-y-ImHpPyPyImPy
1537) 5'-W G C TT G T W-3' ImPyHpHpImHp-y-PyPyPyPyImPy
1538) 5' G C TT G A W-3 ImPyHpHpImPy-y-HpPyPyPyImPy
-W T
1539) 5'-W G C TT G G W-3' ImPyHpHpImIm-y-pypypypylmPy
1540) 5' G C TT G C W-3' ImPyHpHpImPy-y-ImPyPyPyImPy
-W
154I) 5' G C TT C T W-3' ImPyHpHpPyHp-y-pyImPyPyImPy
-W
1542) 5'-W G C TT C A W-3' ImPyHpHpPyPy-y-HpImPyPyImPy
1543) 5' G C TT C G W-3' ImPyHpHpPyIm-y-PyImPyPyImPy
-W
1544) 5'-W G C TT C C W-3' ImPyHpHpPyPy-y-ImImPypyImPy
1545) 5' G C TA T T W-3' ImPyHpPyHpHp-y-PyPyHpPyImPy
-W
1546) 5'-W G C TA T A W-3' ImPyHpPyHpPy-y-HpPyHpPyImPy
1547 5' G C TA T G W-3 ImPyHpPyHpim-y-PyPyHppyImPy
) -W '
154 B 5' G C TA T C W-3 ImPyHpPyHpPy-y- ImPyHpPyImPy
) -W '
1549) 5' G C TA A T W-3' ImpyHppyPyHp-y-PyHpHpPyImPy
-W
1550 5' G C TA A A W-3 ImPyHpPyPyPy-y-HpHpHpPyImPy
) -W '
1551) 5' G C TA A G W-3' ImPyHpPypyIm-y-PyHpHpPyImPy
-W
1552) 5' G C TA A C W-3' ImPyHpPyPyPy-y-ImHpHpPyImPy
-W
1553) 5' G C TA G T W-3' ImPyHpPyImHp-y-PyPyHpPyImPy
-W
1554) 5'-W G C TA G A W-3' ImPyHpPyImPy-y-HpPyHpPyImPy
1555) 5'-W G C TA G G W-3' ImPyHpPyImIm-y-PyPyHpPyImPy
1556) 5'-W G C TA G C W-3' ImPyHpPyImPy-y-ImPyHpPyImPy
1557) 5'-W G C TA C T W-3' ImPyHpPyPyHp-y-PyImHpPyImPy
1558) 5' G C TA C A W-3' ImPyHpPyPyPy-y-HpImHpPyTmPy
-W
1559) 5' G C TA C G W-3' ImPyHpPyPyIm-y-PyImHpPyImPy
-W
1560) 5' G C TA C C W-3' ImPyHpPyPyPy-y-ImImHpPyImPy
-W
CA 02281930 1999-08-18
WO 98/37067 PCT/C1S98/01714
-144-
TABLE 95: 12-ring Hairpin Polyamides for recognition of 8-by 5'-WGCTSNNW-3'
DNA sequence aromatic amino acid sequence
1561) 5'-W G C T G T T W-3' ImPyHpImHpHp-y-PyPyPyPyImPy
1562) 5'-W G C T G T A W-3' ImPyHpImHpPy-y-HpPyPyPyImPy
1563) 5'-W G C T G T G W-3' ImPyHpImHpIm-y-PyPyPyPyImPy
1564) 5'-W G C T G T C W-3' ImPyHpImHpPy-y-ImPyPyPyImPy
1565) 5' -W G C T G A T W-3' ImPyHpImPyHp-y-PyHpPyPyImPy
1566) 5'-W G C T G A A W-3' ImPyHpImPyPy-y-HpHpPyPyImPy
1567) 5'-W G C T G A G W-3' ImPyHpImPyIm-y-PyHpPyPyImPy
1568) 5' -W G C T G A C W-3' ImPyHpImPyPy-y-ImHpPyPyImPy
1569) 5'-W G C T G G T W-3' ImPyHpImImHp-y-PyPyPyPyImPy
1570) 5'-W G C T G G A W-3' ImPyHpImImPy-y-HpPyPyPyImPy
1571) 5'-W G C T G C T W-3' ImPyHpImPyHp-y-PyImPyPyImPy
1572) 5'-W G C T G C A W-3' ImPyHpImPyPy-y-HpImPyPyImPy
1573) 5'-W G C T G G G W-3' ImPyHpImImIm-y-PyPyPyPyImPy
1574) 5' -W G C T G G C. W-3' ImPyHpImImPy-y-ImPyPyPyImPy
1575) 5'-W G C T G C G W-3' ImPyHpImPyIm-y-PyImPyPyImPy
1576) 5'-W G C T G C C W-3' ImPyHpImPyPy-y-ImImPyPyImPy
1577) 5' -WG C TC T T W-3' ImPyHpPyHpHp-y-PyPyImPyImPy
1578) 5' -WG C TC T A W-3' ImPyHpPyHpPy-y-HpPyImPyImPy
1579) 5' -WG C TC T G W-3' ImPyHpPyHpIm-y-PyPyImPyImPy
1580) 5' -WG C TC T C W-3' ImPyHpPyHpPy-y-ImPyImPyImPy
1581) 5' -WG C TC A T W-3' ImPyHpPyPyHp-y-PyHpImPyImPy
1582) 5' -WG C TC A A W-3' ImPyHpPyPyPy-y-HpHpImPyImPy
1583) 5' -WG C TC A G W-3' ImPyHpPyPyIm-y-PyHpImPyImPy
1584) 5' -WG C TC A C W-3' ImPyHpPyPyPy-y-ImHpImPyImPy
1585) 5' -WG C TC G T W-3' ImPyHpPyImHp-y-PyPyImPyImPy
1586) 5' -WG C TC G A W-3' ImPyHpPyImPy-y-HpPyImPyImPy
1587) 5' -WG C TC C T W-3' ImPyHpPyPyHp-y-PyImImPyImPy
1588) 5' -WG C TC C A W-3' ImPyHpPyPyPy-y-HpImImPyImPy
1589) 5' -WG C TC G G W-3' ImPyHpPyImIm-y-PyPyImPyImPy
1590) 5' -WG C TC G C W-3' ImPyHpPyImPy-y-ImPyImPyImPy
1591) 5' -WG C TC C G W-3' ImPyHpPyPyIm-y-PyImImPyImPy
1592) 5' -WG C TC C C W-3' ImPyHpPyPyPy-y-ImImImPyImPy
CA 02281930 1999-08-18
WO 98/37067 PCTlUS98/01714
-145-
TABLE
96:
12-ring
Hairpin
Polyamides
for
recognition
of
8-by
5'-WGCAWNNW-3'
DNA aromatic amino acid sequence
sequence
1593) 5'-W G C A TT T W-3' ImPyPyHpHpHp-y-pypypyHpImPy
1594) 5''-W G C A TT A W-3' ImPyPyHpHpPy-y-HpPyPyHpImPy
1595) 5' -W G C A TT G W-3' ImPyPyHpHpIm-y-PypypygplmPy
1596) 5' -W G C A TT C W-3' ImPyPyHpHpPy-y-ImPyPyHpImPy
1597) 5' -W G C A TA T W-3' ImPyPyHpPyHp-y-PyHpPyHpImPy
1598) 5' -W G C A TA A W-3' ImPyPyHpPyPy-y-HpHpPyHpImPy
1599) 5' -W G C A TA G W-3' ImPyPyHpPyIm-y-PyHpPyHpImPy
1600) 5' -W G C A TA C W-3' ImPyPyHpPyPy-y-ImHpPyHpImPy
1601) 5' -W G C A TG T W-3' ImPyPyHpImAp-y-PyPyPyHpImPy
1602) 5' -W G C A TG A W-3' ImPyPyHpImPy-y-HpPyPyHpImPy
1603) 5' -W G C A TG G W-3' ImPyPyHpImIm-y-PyPyPyHpImPy
1604) 5' -W G C A TG C W-3' ImPyPyHpImPy-y-ImPyPyHpImPy
1605) 5' -W G C A TC T W-3' ImPyPyHpPyHp-y-PyImPyHpImPy
1606) 5' -W G C A TC A W-3' ImPyPyHpPyPy-y-HpImPyHpImPy
1607) 5' -W G C A TC G W-3' ImPyPyHpPyIm-y-PyImPyHpImPy
1608) 5' -W G C A TC C W-3' ImPyPyHpPyPy-y-ImImPyHpImPy
1609) 5' -W G C A AT T W-3' ImPyPyPyHpHp-y-PyPyHpHpImPy
1610) 5' -W G C A AT A W-3' ImPyPyPyHpPy-y-HpPyHpHpimPy
1611) 5' -W G C A AT G W-3' ImPyPyPyHpIm-y-PyPyHpHpImPy
1612) 5' -W G C A AT C W-3' ImPyPyPyHpPy-y-ImPyHpHpImPy
1613) 5' -W G C A AA T W-3' ImPyPyPyPyHp-y-PyHpHpHpImPy
1614) 5' -W G C A AA A W-3' ImPyPyPyPyPy-y-HpHpHpFipImPy
1615) 5' -W G C A AA G W-3' ImPyPyPyPyIm-y-PyHpHpHpImPy
1616 5' -W G C A AA C W-3' ImPyPyPyPyPy-y-ImHpHpHpImPy
)
1617) 5' -W G C A AG T W-3' ImPyPyPyImHp-y-PypyHpHpImPy
1618) 5' -W G C A AG A W-3' ImPyPyPyImPy-y-HpPyHpHpImPy
1619) 5' -W G C A AG G W-3' ImPyPyPyImIm-y-PyPyFipHpImPy
1620) 5' -W G C A AG C W-3' ImPyPyPyImPy-y-ImPyHpHpImPy
1621) 5' -W G C A AC T W-3' ImPyPyPyPyHp-y-pyImHpHpImPy
1622) 5' -W G C A AC A W-3' ImPyPyPypypy-y-HpI~pHpImPy
1623) 5' -W G C A AC G W-3' ImPyPyPyPyIm-y-PyImHpHpImPy
1624) 5' -W G C A AC C W-3' ImPyPyPypyPy-y-ImImHpHpImPy
CA 02281930 1999-08-18
WO 18/37067 PCT/US98/01714
-146-
TABLE
97:
12-ring
Hairpin
PoIyamides
for
recognition
of
8-by
5'-WGCASNNW-3'
DNA aromatic amino acid sequence
sequence
1625) 5' -W G CA G T T W-3' ImPyPyImHpHp-y-PyPyPyHpImPy
1626) 5' ~-WG CA G T A W-3' ImPyPyImHpPy-y-HpPyPyHpItaPy
1627) 5' -W G CA G T G W-3' ImPyPyImHpIm-y-PyPyPyHpImPy
1628) 5' -W G CA G T C W-3' ImPyPyImHpPy-y-ImPyPyHpImPy
1629) 5' -W G CA G A T W-3' ImPyPyImPyHp-y-PyHpPyHpImPy
1630) 5' -W G CA G A A W-3' ImPyPyImPyPy-y-HpHpPyHpImPy
1631) 5' -W G CA G A G W-3' ImPyPyImPyIm-y-PyHpPyHpImPy
1632) 5' -W G CA G A C W-3' ImPyPyImPyPy-y-ImHpPyHpImPy
1633} 5' -W G CA G G T W-3' ImPyPyImImHp-y-PyPyPyHpImPy
1634) 5' -W G CA G G A W-3' ImPyPyImImPy-y-HpPyPyHpImPy
1635) 5' -W G CA G C T W-3' ImPyPyImPyHp-y-PyImPyHpImPy
1636) 5' -W G CA G C A W-3' ImPyPyImPyPy-y-HpImPyHpImPy
1637) 5' -W G CA G G G W-3' ImPyPyImImIm-y-PyPyPyHpImPy
1638} 5' -W G CA G G C W-3' ImPyPyImImPy-y-ImPyPyHpImPy
1639) 5' -W G CA G C G W-3' ImPyPyImPyIm-y-PyImPyHpImPy
1640) 5' -W G CA G C C W-3' ImPyPyImPyPy-y-ImImPyHpImPy
1641) 5' -W G CA C T T W-3' ImPyPyPyHpHp-y-PyPyImHpImPy
1642) 5' -W G CA C T A W-3' ImPyPyPyHpPy-y-HpPyImHpImPy
1643) 5' -W G CA C T G W-3' ImPyPyPyHpIm-y-PyPyImHp3mPy
1644) 5' -W G CA C T C W-3' ImPyPyPyHpPy-y-ImPyImHpImPy
1645) 5' -W G CA C A T W-3' ImPyPyPyPyHp-y-PyHpImHpImPy
1646) 5' -W G CA C A A W-3' ImPyPyPyPyPy-y-HpHpImHpImPy
1647) 5' -W G CA C A G W-3' ImPyPyPyPyIm-y-PyHpImHpImPy
1648) 5' -W G CA C A C W-3' ImPyPyPyPyPy-y-ImHpImHpImPy
1649) 5' -W G CA C G T W-3' ImPyPyPyImHp-y-PyPyImHpImPy
1650) 5' -W G CA C G A W-3' ImPyPyPyImPy-y-HpPyImHpImPy
1651) 5' -W G CA C C T W-3' ImPyPyPyPyHp-y-PyImImHpImPy
1652) 5' -W G CA C C A W-3' ImPyPyPyPyPy-y-HpImImHpImPy
1653) 5' -W G CA C G G W-3' ImPyPyPyImim-y-PyPyImHpImPy
1654) 5' -W G CA C G C W-3' ImPyPyPyImPy-y-ImPyImHpImPy
1655) 5' -W G CA C C G W-3' ImPyPyPyPyIm-y-PyImImHpImPy
1656) 5' -W G CA C C C W-3' ImPyPyPyPyPy-y-ImImImHpImPy
CA 02281930 1999-08-18
WO 98137067 PCT/US98/01714
-147-
1'A13LE
98:
12-ring
Hairpin
Polyamides
for
recognition
of
8-by
5'-WGCCWNNW-3'
DNA aromatic amino acid sequence
sequence
1657) 5' -WG C CT T T W-3' ImPyPyHpHpHp-y-PyPypyImImPy
1658) 5' -WG C CT T A W-3' ImPyPyHpHpPy-y-HpPyPyImImPy
1659) 5' -WG C CT T G W-3' ImPyPyHpHpIm-y-PyPyPyImImPy
1660) 5' -WG C CT T C W-3' ImPyPyHpHpPy-y-ImPyPyImImPy
1661) 5' -WG C CT A T W-3' ImPyPyHpPyHp-y-PyHpPyImImPy
1662) 5' -WG C CT A A W-3' ImPyPyHpPyPy-y-HpHpPyImImPy
1663) 5' -WG C CT A G W-3' ImPypyHpPyIm-y-PyHpPyImImPy
1664) 5' -WG C CT A C W-3' ImPyPyHpPyPy-y-ImHppyImImPy
1665) 5' -WG C CT G T W-3' ImPyPyHpImHp-y-PyPyPyImImPy
1666) 5' -WG C CT G A W-3' ImPyPyHpImPy-y-HpPyPyImImPy
1667) 5' -WG C CT G G W-3' ImPyPyHpImIm-y-PyPyPyImImpy
1668) 5' -WG C CT G C W-3' ImPyPyHpImPy-y-ImPyPyImImPy
1669) 5' -WG C CT C T W-3' ImPyPyHpPyHp-y-PyImPyImImPy
1670) 5' -WG C CT C A W-3' ImPyPyHpPyPy-y-HpImPyImImPy
1671) 5' -WG C CT C G W-3' ImPyPyHpPyIm-y-PyImPyImImPy
1672) 5' -WG C CT C C W-3' ImPyPyHpPyPy-y-ImImPyImImPy
1673) 5' -WG C CA T T W-3' ImPyPyPyHpHp-y-PyPyHpImImPy
1674) 5' -WG C CA T A W-3' ImPyPyPyHpPy-y-HpPyHpImImPy
1675) 5' -WG C CA T G W-3' ImPyPyPyHpIm-y-PyPyHpImImPy
1676) 5' -WG C CA T C W-3' ImPyPyPyHpPy-y-ImPyHpImImPy
1677) 5' -WG C CA A T W-3' ImPyPyPyPyHp-y-PyHpHpImImPy
1678) 5' -WG C CA A A W-3' ImPyPyPypypy-y-HpHpHpImImPy
1679) 5' -WG C CA A G W-3' ImPyPyPyPyIm-y-PyApHpImImPy
1680) 5' -WG C CA A C W-3' ImPyPyPyPyPy-y-ImHpHpImImPy
1681) 5' -WG C CA G T W-3' ImPyPyPyImHp-y-pypyHpImImPy
1682) 5' -WG C CA G A W-3' ImPyPyPyImPy-y-HpPyHpImImPy
1683 ) 5' -WG C CA G G W-3' ImPyPyPyImIm-y-pypyHpImImPy
1684) 5' -WG C CA G C W-3' mPyPyPyImPy-y-ImPyHpImImPy
I
1685) 5' -WG C CA C T W-3' ImPyPyPyPyHp-y-PyImHpImImPy
1686) 5' -WG C CA C A W-3' ImPyPyPyPyPy-y-HpImHpImImPy
1687) 5' -WG C CA C G W-3' ImPyPyPyPyIm-y-PyImHpImImPy
1688) 5' -WG C CA C C W-3' ImPyPyPyPyPy-y-ImImIipImImPy
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-148-
TABLE
99:
12-ring
Hairpin
Polyamides
for
recognition
of
8-by
5'-WGCCSNNW-3'
DNA aromatic amino acid sequence
sequence
1689) 5' -WG C C G T T W-3' ImPyPyImHpHp-y-PyPyPyImImPy
1690) 5' -WG C C G T A W-3' ImPyPyImHpPy-y-HpPyPyImImPy
1691) 5' -WG C C G T G W-3' ImPyPyImHpIm-y-PyPyPyImImPy
1692) 5' -WG C C G T C W-3' ImPyPyImHpPy-y-ImPyPyImImPy
1693) 5' -WG C C G A T W-3' ImPyPyImPyHp-y-PyHpPyImImPy
1694) 5' -WG C C G A A W-3' ImPyPyImPyPy-y-HpHpPyImImPy
16 9 5 5' -WG C C G A G W-3 ImPyPyImPyIm-y-PyHpPyImImPy
) '
1696) 5' -WG C C G A C W-3' ImPyPyImPyPy-y-ImHpPyImImPy
1697) 5' -WG C C G G T W-3' ImPyPyImImHp-y-PyPyPyImImPy
1698) 5' -WG C C G G A W-3' ImPyPyImImPy-y-HpPyPyImImPy
1699) 5' -WG C C G C T W-3' ImPyPyImPyHp-y-PyImPyImImPy
1700) 5' -WG C C G C A W-3' ImPyPyImPyPy-y-HpImPyImImPy
1701) 5' -WG C C C T T W-3' ImPyPyPyHpHp-y-PyPyImImImPy
1702) 5' -WG C C C T A W-3' ImPyPyPyHpPy-y-HpPyImImImPy
1703) 5' -WG C C C T G W-3' ImPyPyPyHpIm-y-PyPyImImImPy
1704) 5' -WG C C C T C W-3' ImPyPyPyHpPy-y-ImPyImImImPy
1705) 5' -WG C C C A T W-3' ImPyPyPyPyHp-y-PyHpImImImPy
1706) 5' -WG C C C A A W-3' ImPyPyPyPyPy-y-HpHpImImImPy
1707) 5' -WG C C C A G W-3' ImPyPyPyPyIm-y-PyHpImImImPy
1708) 5' -WG C C C A C W-3' ImPyPyPyPyPy-y-ImHpImImImPy
1709) 5' -WG C C C G T W-3' ImPyPyPyImHp-y-PyPyImImImPy
1710 ) 5' -WG C C C G A W-3 ImPyPyPyImPy-y-HpPyImImImPy
'
1711) 5' -WG C C C C T W-3' ImPyPyPyPyHp-y-PyImImImImPy
1712) 5' -WG C C C C A W-3' ImPyPyPyPyPy-y-HpImImImImPy
G73) 5' -WG C C G G G W-3' ImPyPyImImIm-y-PyPyPyImImPy
G74 ) 5' -WG C C G G C W- 3 ImPyPyImImPy-y- ImPyPyImImPy
'
G75) 5' -WG C C G C G W-3' ImPyPyImPyIm-y-PyImPyImImPy
G7 6 ) 5' -WG C C G C C W- 3 ImPyPyImPyPy-y-ImImPyImImPy
'
G77) 5' -WG C C C G G W-3' ImPyPyPyImIm-y-PyPyImImImPy
G7 8 ) 5' -WG C C C G C W- 3 ImPyPyPyImPy-y- ImPyImImImPy
'
G7 9 ) 5' -WG C C C C G W- 3 ImPyPyPyPyIm-y-PyImImImImPy
'
G80) 5' -WG C C C C C W-3' ImPyPyPyPyPy-y-ImImImImImPy
CA 02281930 1999-08-18
WO 98/37067 PCTIUS98/Oi714
-149-
TABLE
100:
12-ring
Hairpin
Polyamides
for recognition
of 8-by
5'-WGAGWNNW-3'
DNA aromatic amino acid sequence
sequence
1713) 5' -WG A G T T TW-3' ImPyImHpHpHp-y-PyPypypyHppy
1714) 5' -WG A G T T AW-3' ImPyImHpHpPy-y-HpPyPyPyHpPy
1715) 5' -WG A G T T GW-3' ImPyImHpHpIm-y-PyPyPyPyHpPy
1716) 5' -WG A G T T CW-3' ImPyImHpHpPy-y-ImPyPyPyHpPy
1717) 5' -WG A G T A TW-3' ImPyImHpPyHp-y-PyHpPyPyHpPy
1718) 5' -WG A G T A AW-3' ImPyImHpPyPy-y-HpHpPyPyHpPy
1719) 5' -WG A G T A GW-3' ImPyImHpPyIm-y-PyHpPyPyHpPy
17 2 0 5' -WG A G T A CW-3 ImPyImHpPyPy-y- ImHpPyPyFipPy
) '
1721) 5' -WG A G T G TW-3' ImPyImHpImHp-y-PyPyPyPyHpPy
1722) 5' -WG A G T G AW-3' ImPyImHpImPy-y-HpPyPyPyHpPy
1723) 5' -WG A G T G GW-3' ImPyImHpImIm-y-PyPyPyPyHpPy
1724) 5' -WG A G T G CW-3' ImPyImHpImPy-y-ImPyPypyHpPy
1725) 5' -WG A G T C TW-3' ImPyImHpPyHp-y-PyImPyPyHpPy
1726) 5' -WG A G T C AW-3' ImPyImHpPyPy-y-HpImPyPyHpPy
1727) 5' -WG A G T C GW-3' ImPyImHpPyIm-y-PyImPyPyHpPy
1728) 5' -WG A G T C CW-3' ImPyImHpPyPy-y-ImImPyPyHpPy
1729) 5' -WG A G A T TW-3' ImPyImPyHpHp-y-PyPyHpPyHpPy
1730) 5' -WG A G A T AW-3' ImPyImPyHpPy-y-HpPyHpPyHpPy
1731) 5' -WG A G A T GW-3' ImPyImPyHpIm-y-PyPyHpPyHpPy
1732) 5' -WG A G A T CW-3' ImPyImPyHpPy-y-ImPyHpPyHpPy
1733) 5' -WG A G A A TW-3' ImPyImPyPyHp-y-PyHpHpPyHpPy
1734) 5' -WG A G A A AW-3' ImPyImPyPyPy-y-HpHpHpPyHpPy
1735) 5' -WG A G A A GW-3' ImPyImPyPyIm-y-PyHpHpPyHpPy
1736) 5' -WG A G A A CW-3' ImPyImPyPyPy-y-ImHpHpPyHpPy
1737) 5' -WG A G A G TW-3' ImPyImPyImHp-y-PyPyHpPyHpPy
1738) 5' -WG A G A G AW-3' ImPyImPyImPy-y-HpPyHpPyHpPy
1739) 5' -WG A G A G GW-3' ImPyImPyImIm-y-PyPyHpPyHpPy
1740) 5' -WG A G A G CW-3' ImPyImPyImPy-y-ImPyHpPyHpPy
1741) 5' -WG A G A C TW-3' ImPyImPyPyAp-y-PyImHpPyHpPy
1742) 5' -WG A G A C AW-3' ImPyImPyPyPy-y-HpImHpPyHpPy
1743) 5' -WG A G A C GW-3' ImPyImPyPyIm-y-PyImHpPyHpPy
1744) 5' -WG A G A C CW-3' ImPyImPyPyPy-y-ImImHpPyHpPy
CA 02281930 1999-08-18
WO 98/37067 PCT/L1S98/01714
-150-
TABLE
101:
12-ring
Hairpin
Polyamides
for recognition
of 8-by
5'-WGAGSNNW-3'
DNA aromatic amino acid sequence
sequence
1745) 5'-W G A GG T T W-3' ImpyImImHpHp-y-PyPypypyHpPy
1746) 5''-W G A GG T A W-3' ImPyImImHpPy-y-HpPyPyPyHpPy
1747) 5'-W G A GG T G W-3' ImPyImImHpIm-y-PyPyPypyHpPy
1748) 5'-W G A GG T C W-3' ImPyImImHpPy-y-ImPyPyPyHppy
1749) 5'-W G A GG A T W-3' ImPyImImPyHp-y-PyHpPyPyHpPy
1750) 5'-W G A GG A A W-3' ImPyImImPyPy-y-HpHpPyPyHpPy
1751) 5'-W G A GG A G W-3' ImPyImImPyIm-y-PyHpPyPyHpPy
1752) 5'-W G A GG A C W-3' ImPyImImPyPy-y-ImHpPyPyHpPy
1753} 5'-W G A GG G T W-3' ImPyImImImHp-y-PyPyPyPyHpPy
1754) 5'-W G A GG G A W-3' ImPyImImImPy-y-HpPyPyPyHpPy
1755} 5'-W G A GG C T W-3' ImPyImImPyHp-y-PyImPyPyHpPy
1756) 5'-W G A GG C A W-3' ImPyImImPyPy-y-HpImPyPyHpPy
1757) 5'-W G A GC T T W-3' ImPyImPyHpHp-y-PyPyImPyFipPy
1758) 5'-W G A GC T A W-3' ImPyImPyHpPy-y-HpPyImPyHpPy
1759) 5'-W G A GC T G W-3' ImPyImPyHpIm-y-PyPyImPyHpPy
1760) 5'-W G A GC T C W-3' ImPyImPyHpPy-y-ImPyImPyHpPy
1761} 5'-W G A GC A T W-3' ImPyImPyPyHp-y-PyHpImPyHpPy
1762) 5'-W G A GC A A W-3' ImPyImPyPyPy-y-HpHpImPyHpPy
1763) 5'-W G A GC A G W-3' ImPyImPyPyIm-y-PyHpImpyHpPy
1764) 5'-W G A GC A C W-3' ImPyImPyPyPy-y-ImHpImPyHpPy
1765) 5'-W G A GC G T W-3' ImPyImPyImHp-y-PyPyImPyHpPy
1766) 5'-W G A GC G A W-3' ImPyImPyImPy-y-HpPyImPyHpPy
1767) 5'-W G A GC C T W-3' ImpyImPyPyHp-y-PyImImPyHpPy
1768) 5'-W G A GC C A W-3' ImPyImPyPyPy-y-HpImImPyHpPy
1769) 5'-W G A GG G G W-3' ImPyImImImIm-y-PyPyPyPyHpPy
1770) 5'-W G A GG G C W-3' ImPyImImImPy-y-ImPyPyPyHpPy
1771) 5'-W G A GG C G W-3' ImPyImImPyIm-y-PyImPyPyHpPy
1772) 5'-W G A GG C C W-3' ImPyImImPyPy-y-ImImPyPyHpPy
1773) 5'-W G A GC G G W-3' ImPyImPyImIm-y-PyPyImPyHpPy
1774) 5'-W G A GC G C W-3' ImPyImPyImPy-y-ImPyImPyHppy
1775) 5'-W G A GC C G W-3' ImPyImPyPyIm-y-PyImImPyHpPy
1776) 5'-W G A GC C C W-3' ImPyImPyPyPy-y-ImImImPyHpPy
CA 02281930 1999-08-18
WO 98/37067 , PCT/US98/01714
-151-
TABLE
102:
12-ring
Hairpin
Polyamides
for recognition
of 8-by
5'-WGATWNNW-3'
DNA aromatic amino acid sequence
sequence
1777) 5'-W G A T TT T W-3' ImPyHpHpHpHp-y-PyPyPyPyHpPy
1778) 5'~-W G A T TT A W-3' ImPyHpHpHppy-y-HpPyPyPyHpPy
1779) 5' G A T TT G W-3' ImPyHpHpHpIm-y-PyPyPyPyHpPy
-W
1780) 5'-W G A T TT C W-3' ImPyHpHpHpPy-y-ImPyPyPyHpPy
1781) 5'-W G A T TA T W-3' ImPyHpHpPyHp-y-PyHpPyPyHpPy
1782) 5'-W G A T TA A W-3' ImPyHpHpPypy-y-HpHppypyHpPy
1783 ) 5'-W G A T TA G W-3 ImPyHpHpPyIm-y-PyApPyPyHpPy
'
1784) 5'-W G A T TA C W-3' ImPyHpHpPypy-y-I~ppypygppy
1785) 5'-W G A T TG T W-3' ImPyHpHpImHp-y-pypypypyHppy
1786) 5'-W G A T TG A W-3' ImPyHpHpImPy-y-HpPyPyPyHpPy
1787) 5'-W G A T TG G W-3' ImPyHpHpImIm-y-PyPypypygpPy
1788) 5'-W G A T TG C W-3' ImpyHpHpImPy-y-ImPyPypyHppy
1789) 5'-W G A T TC T W-3' ImPyHpHpPyHp-y-PyImPyPyHpPy
1790) 5'-W G A T TC A W-3' ImPyHpHpPyPy-y-HpImPyPyHpPy
1791) 5'-W G A T TC G W-3' ImPyHpHpPyIm-y-pyImPyPyHpPy
1792) 5'-W G A T TC C W-3' ImPyHpHpPyPy-y-ImImPyPyHpPy
1793) 5'-W G A T AT T W-3' ImPyHpPyHpHp-y-PypyHpPyHpPy
1794) 5'-W G A T AT A W-3' ImPyHpPyHpPy-y-HpPyHpPyHpPy
1795) 5'-W G A T AT G W-3' ImPyHpPyHpIm-y-PyPyHpPyHpPy
1796) 5'-W G A T AT C W-3' ImPyHpPyHpPy-y-ImPyHpPyHpPy
1797) 5'-W G A T AA T W-3' ImPyHpPyPyHp-y-PyHpHpPyHpPy
1798) 5'-W G A T AA A W-3' ImPyHpPyPyPy-y-HpHpHpPyHpPy
1799) 5'-W G A T AA G W-3' ImPylipPypyIm-y-PyHpHpPyHpPy
1800) 5'-W G A T AA C W-3' ImPyHpPyPyPy-y-ImHpHppyHpPy
1801) 5'-W G A T AG T W-3' ImPyHpPyImHp-y-pyPyHppyHpPy
1802) 5'-W G A T AG A W-3' ImPyHpPyImPy-y-HpPyHpPyHpPy
1803) 5'-W G A T AG G W-3' ImPyHpPyImIm-y-PyPyHpPyHpPy
1804) 5'-W G A T AG C W-3' ImPyHpPyImPy-y-ImPyHpPyHpPy
1805) 5'-W G A T AC T W-3' ImPyHpPyPyHp-y-PyImHpPyHpPy
1806) 5'-W G A T AC A W-3' ImPyHpPyPyPy-y-HpImHpPyHpPy
_ 1807) 5'-W G A T AC G W-3' ImPyHpPyPyIm-y-PyImHpPyHpPy
1808) 5'-W G A T AC C W-3' ImPyHpPyPyPy-y-ImImHpPyHpPy
CA 02281930 1999-08-18
WO 98137067 PCT/US98/01714
-152-
TABLE
103:
12-ring
Hairpin
Polyamides
for
recognition
of
8-by
5'-WGATSNNW-3'
DNA aromatic amino acid sequence
sequence
1809) 5' -WG A T G TT W-3' ImPyHpImHpHp-y-PyPyPyPyHpPy
1810) 5' -WG A T G TA W-3' ImPyHpImHpPy-y-HpPyPyPyHpPy
1811) 5' -WG A T G TG W-3' ImPyHpImHpIm-y-PyPyPyPyHpPy
1812) 5' -WG A T G TC W-3' ImPyHpImHpPy-y-ImPyPyPyHpPy
1813) 5' -WG A T G AT W-3' ImPyHpImPyHp-y-PyHpPyPyHpPy
1814) 5' -WG A T G AA W-3' ImPyHpImPyPy-y-HpHpPyPyHpPy
1815) 5' -WG A T G AG W-3' ImPyHpImPyIm-y-PyF-IpPyPyHpPy
1816) 5' -WG A T G AC W-3' ImPyHpImPyPy-y-ImHpPyPyHpPy
1817) 5' -WG A T G GT W-3' ImPyHpImImHp-y-PyPyPyPyHpPy
1818) 5' -WG A T G GA W-3' ImPyHpImImPy-y-HpPyPyPyHpPy
1819) 5' -WG A T G CT W-3' ImPyHpImPyHp-y-PyImPyPyHpPy
1820) 5' -WG A T G GA W-3' ImPyHpImPyPy-y-HpImPyPyHpPy
1821) 5' -WG A T G GG W-3' ImPyHpImImIm-y-PyPyPyPyHpPy
1822) 5' -WG A T G GC W-3' ImPyHpImImPy-y-ImPyPyPyHpPy
1823) 5' -WG A T G CG W-3' ImPyHpImPyIm-y-PyImPyPyHpPy
1824) 5' -WG A T G CC W-3' ImPyHpImPyPy-y-ImImPyPyHpPy
1825) 5' -WG A T C TT W-3' ImPyHpPyHpHp-y-PyPyImPyHpPy
1826) 5' -WG A T C TA W-3' ImPyHpPyHpPy-y-HpPyImPyHpPy
1827) 5' -WG A T C TG W-3' ImPyHpPyHpIm-y-PyPyImPyHpPy
1828) 5' -WG A T C TC W-3' ImPyHpPyHpPy-y-ImPyImPyHpPy
1829) 5' -WG A T C AT W-3' ImPyHpPyPyHp-y-PyHpImPyHpPy
1830) 5' -WG A T C AA W-3' ImPyHpPyPyPy-y-HpHpImPyHpPy
1831) 5' -WG A T C AG W-3' ImPyHpPyPyIm-y-PyHpImPyHpPy
1832) 5' -WG A T C AC W-3' ImPyHpPyPyPy-y-ImHpImPyHpPy
1833) 5' -WG A T C GT W-3' ImPyHpPyImHp-y-PyPyImPyHpPy
1834) 5' -WG A T C GA W-3' ImPyHpPyImPy-y-HpPyImPyHpPy
1835) 5' -WG A T C CT W-3' ImPyHpPyPyHp-y-PyImImPyHpPy
1836) 5' -WG A T C CA W-3' ImPyHpPyPyPy-y-HpImImPyHpPy
1837) 5' -WG A T C GG W-3' ImPyHpPyImIm-y-PyPyImPyHpPy
1838) 5' -WG A T C GC W-3' ImPyHpPyImPy-y-ImPyImPyHpPy
183 9 5' -WG A T C CG W-3' ImPyHpPyPyIm-y-PyImImPyHpPy
)
1840) 5' -WG A T C CC W-3' ImPyHpPyPyPy-y-ImImImPyHpPy
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-153-
TABLE
104:
12-ring
Hairpin
Polyamides
for recognition
of 8-by
5'-WGAAWNNW-3'
DNA aromatic amino acid sequence
sequence
184I) 5'-W G A AT T T W-3' ImPyPyHpHpHp-y-PypypyHpHpPy
1842) 5'-W G A AT T A W-3' ImPyPyHpHpPy-y-HpPyPyHpHpPy
1843) 5'-W G A AT T G W-3' ImPyPyHpHpIm-y-PyPypyHpHpPy
1844) 5'-W G A AT T C W-3' ImPyPyHpHpPy-y-ImPyPyHpHpPy
1845) 5'-W G A AT A T W-3' ImPyPyHpPyHp-y-PyHpPyHpHpPy
1846) 5'-W G A AT A A W-3' ImPyPyHpPyPy-y-HpHpPyHpHpPy
1847 ) 5'-W G A AT A G W-3 ImPyPyHpPyIm-y-PyHpPyHpHpPy
'
1848) 5'-W G A AT A C W-3' ImPyPyHpPyPy-y-ImHpPyHpHpPy
1849) 5'-W G A AT G T W-3' ImPyPyHpImHp-y-PypypyHpHpPy
1850) 5'-W G A AT G A W-3' ImPyPyHpImPy-y-HpPyPyHpHpPy
1851) 5'-W G A AT G G W-3' ImPyPyHpImIm-y-PyPyPyHpHppy
1852) 5'-W G A AT G C W-3' ImPypyHpImPy-y-ImPyPyHpHpPy
1853) 5'-W G A AT C T W-3' ImPyPyHpPyHp-y-PyImPyHpHpPy
1854) 5'-W G A AT C A W-3' ImPyPyHpPyPy-y-HpImPyHpHpPy
1855) 5'-W G A AT C G W-3' ImPyPyHpPyIm-y-PyImPyHpHpPy
1856) 5'-W G A AT C C W-3' ImPyPyHpPyPy-y-ImImPyHpHpPy
1857 ) 5'-W G A AA T T W-3' ImPyPyPyHpHp-y-PyPyHpHpHpPy
1858) 5'-W G A AA T A W-3' ImPyPyPyHpPy-y-HpPyHpHpHpPy
1869) 5'-W G A AA T G W-3' ImPyPyPyHpIm-y-PyPyHpHpHpPy
1860) 5'-W G A AA T C W-3' ImPyPyPyApPy-y-ImPyHpHpHpPy
1861) 5'-W G A AA A T W-3' ImPyPyPypyHp-y-PyHpHpHpHpPy
1862 ) 5'-W G A AA A A W-3 ImPyPyPyPyPy-y-HpHpHpHpHpPy
'
1863) 5'-W G A AA A G W-3' ImPyPyPyPyIm-y-PyHpHpHpHpPy
1864) 5'-W G A AA A C W-3' ImPyPyPyPyPy-y-ImHpHpHpHpPy
1865) 5'-W G A AA G T W-3' ImPyPyPyImHp-y-pyPyHpHpHpPy
1866) 5'-W G A AA G A W-3' ImPyPypyImPy-y-HpPyHpHpHpPy
1867) 5'-W G A AA G G W-3' ImPyPyPyImIm-y-PyPyHpHpHpPy
1868) 5'-W G A AA G C W-3' ImPyPyPyImPy-y-ImPyHpHpHpPy
1869) 5'-W G A AA C T W-3' ImPyPyPypyHp-y-PyImHpHpHpPy
1870) 5'-W G A AA C A W-3' ImPyPyPypypy-y-HpI,~pHpgpPy
_ 1871) 5'-W G A AA C G W-3' ImPyPypypyIm-y-PyImHpHpHpPy
1872) 5'-W G A AA C C W-3' ImPyPyPypypy-y-ImImHpHpHpPy
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-154-
TABLE 105:
12-ring
I airpin
Polyamides
for recognition
of 8-by
5'-WGAASNNW-3'
DNA sequence aromatic amino acid sequence
1873) 5'-W G A GT T W-3' ImPyPyImHpHp-y-PyPypygpgppy
A
1874) 5'-W G A GT A W-3' ImPyPyImHpPy-y-HpPyPyHpHpPy
A
1875) 5' -W G GT G W-3' ImPyPyImHpIm-y-PyPyPyHpHpPy
A A
1876) 5' -W G GT C W-3' ImPyPyImHpPy-y-ImPyPyHpHpPy
A A
1877) 5'-W G A GA T W-3' ImPyPyImPyHp-y-PyHpPyHpHpPy
A
1878) 5'-W G A GA A W-3' ImPyPyImPyPy-y-HpHpPyHpHpPy
A
1879) 5'-W G AA G A G W-3' ImPyPyImPyIm-y-pyHpPyHpHppy
1880) 5'-W G AA G A C W-3' ImPyPyImPypy-y-ImHppyHpHpPy
1881) 5'-W G AA G G T W-3' ImPyPyImImHp-y-PyPyPyHpHpPy
1882) 5'-W G AA G G A W-3' ImPyPyImImPy-y-HpPyPyHpHpPy
1883) 5'-W G AA G C T W-3' ImPyPyImPyHp-y-PyImPyHpHpPy
1884) 5'-W G AA G C A W-3' ImPyPyImPyPy-y-HpImpyHpHpPy
1885) 5'-W G A A G G G W-3' ImPyPyImImIm-y-PyPyPyHpHpPy
1886) 5' -W G A A G G C W-3' ImPyPyImImPy-y-ImpyPyHpHpPy
1887) 5'-W G A A G C G W-3' ImPyPyImPyIm-y-PyImPyHpHpPy
1888) 5'-W G A A G C C W-3' ImPyPyImPypy-y-ImImPyHpHpPy
1889) 5'-W G A A CT T W-3' ImPyPyPyHpHp-y-PyPyImHpHpPy
1890) 5'-W G A A CT A W-3' ImPyPyPyHpPy-y-HpPyImHpHpPy
1891) 5'-W G A A CT G W-3' ImPyPyPyHpIm-y-PyPyImHpHpPy
1892) 5'-W G A A CT C W-3' ImPyPyPyHpPy-y-ImPyImHpHpPy
1893) 5'-W G A A CA T W-3' ImPyPyPypyHp-y-PyHpImHpHpPy
1894) 5'-W G A A CA A W-3' ImPyPyPyPyPy-y-HpHpImHpHpPy
1895) 5'-W G A A CA G W-3' ImPyPyPyPyIm-y-PyHpImHpHpPy
1896) 5'-W G A A CA C W-3' ImPyPyPyPyPy-y-ImHpImHpHpPy
1897) 5'-W G A A CG T W-3' ImPyPyPyImHp-y-PyPyImHpHpPy
1898) 5'-W G A A CG A W-3' ImPyPyPyImPy-y-HpPyImHpHpPy
1899) 5'-W G A A CC T W-3' ImPyPyPyPyHp-y-PyImImHpHpPy
1900) 5'-W G A A CC A W-3' ImPyPyPyPyPy-y-HpImImHpHpPy
1901) 5'-W G A A CG G W-3' ImPyPyPyImIm-y-PyPyImHpHpPy
1902) 5'-W G A A CG C W-3' ImPyPyPyImPy-y-ImPyImHpHpPy
1903) 5'-W G A A CC G W-3' ImPyPyPyPyIm-y-PyImImHpHpPy
1904) 5'-W G A A CC C W-3' ImPyPyPyPyPy-y-ImImImHpHpPy
CA 02281930 1999-08-18
WO g8I37067 PCT/US98/01714
-1S5-
TABLE
lOG:
12-ring
Hairpin
Polyamides
for recognition
of 8-by
5'-WGACWNNW-3'
DNA aromatic amino acid sequence
sequence
1905} 5'-W GA C T T T W-3' ImPyPyHpHpHp-y-PypypyImHpPy
1906) 5'-W GA C T T A W-3' ImPyPyHpHpPy-y-HppyPyImHpPy
1907) 5'-W GA C T T G W-3' ImPyPyHpHpIm-y-PypypyImHpPy
1908) 5'-W GA C T T C W-3' ImPyPyHpHpPy-y-ImPyPyImHpPy
1909) 5'-W GA C T A T W-3' ImpyPyHpPyHp-y-PyHppyImHpPy
1910) 5'-W GA C T A A W-3' ImPyPyHpPyPy-y-HpHpPyImHpPy
1911) 5'-W GA C T A G W-3' ImPyPyHpPyIm-y-PyHpPyImHpPy
1912) 5'-W GA C T A C W-3 ImPyPyHpPyPy-y-ImHpPyImHpPy
T
1913) 5'-W GA C T G T W-3' ImPyPyHpImHp-y-PyPyPyImHpPy
1914) 5'-W GA C T G A W-3' ImPyPyHpImPy-y-HpPyPyImHpPy
1915) 5'-W GA C T G G W-3' TmPyPyHpImIm-y-PyPyPyImHpPy
1916) 5'-W GA C T G C W-3' ImPyPyHpImPy-y-ImPyPyImHpPy
1917) 5'-W GA C T C T W-3' ImPyPyHpPyHp-y-PyImPyImHpPy
1918) 5'-W GA C T C A W-3' ImpyPyHpPyPy-y-HpImPyImHpPy
1919) 5'-W GA C T C G W-3' ImPyPyHpPyIm-y-PyImPyImHppy
1920) 5'-W GA C T C C W-3' ImPyPyHpPyPy-y-ImImPyImHpPy
1921) 5'-W GA C A T T W-3' ImPyPyPyHpHp-y-PypyHpImHpPy
1922) 5'-W GA C A T A W-3' ImPyPyPyHpPy-y-HppyHpImHpPy
1923) 5'-W GA C A T G W-3' ImPyPyPyHpIm-y-PyPyHpImHpPy
1924) 5'-W GA C A T C W-3' ImPyPyPyHpPy-y-ImPyHpImHpPy
1925} 5'-W GA C A A T W-3' ImPyPyPyPyHp-y-PyHpHpImHpPy
1926) 5'-W GA C A A A W-3' ImPyPyPyPyPy-y-HpHpHpImHpPy
1927) 5'-W GA C A A G W-3' ImPyPyPyPyIm-y-PyHpHpImHpPy
1928) 5'-W GA C A A C W-3' ImPyPypyPyPy-y-ImHpHpImHpPy
1929) 5'-W GA C A G T W-3' ImPyPyPyImHp-y-PypyHpImHpPy
1930) 5'-W GA C A G A W-3' ImPyPyPyImPy-y-HpPyHpImHpPy
1931) 5'-W GA C A G G W-3' ImPyPyPyImIm-y-PypyHpImHpPy
1932) 5'-W GA C A G C W-3' ImPyPyPyImPy-y-ImPyHpImHpPy
. 1933) 5'-W GA C A C T W-3' ImPyPyPyPyHp-y-PyImHpImHppy
1934) 5'-W GA C A C A W-3' ImPyPyPyPyPy-y-HpImHpImHpPy
1935) 5'-W GA C A C G W-3' ImPyPyPyPyIm-y-PyImHpImHpPy
1936) 5'-W GA C A C C W-3' ImPyPyPyPyPy-y-ImImHpImHpPy
CA 02281930 1999-08-18
WO 98/37067 PCT/~7598/01714
-156-
TABLE
107:
12-ring
Hairpin
Polyamides
for
recognition
of 8-by
5'-WGACSNNW-3'
DNA aromatic amino acid sequence
sequence
1937) 5' -WG A C G T T W-3' ImPyPyImHpHp-y-PyPyPyImHpPy
1938) 5' -WG A C G T A W-3' ImPyPyImHpPy-y-HpPyPyImHpPy
1939) 5' -WG A C G T G W-3' ImPyPyImHpIm-y-PyPyPyImHpPy
1940) 5' -WG A C G T C W-3' ImPyPyImHpPy-y-ImPyPyImHpPy
1941) 5' -WG A C G A T W-3' ImPyPyImPyHp-y-PyHpPyImHpPy
1942) 5' -WG A C G A A W-3' ImPyPyImPyPy-y-HpHpPyImHpPy
1943) 5' -WG A C G A G W-3' ImPyPyImPyIm-y-PyHpPyImHpPy
1944 5' -WG A C G A C W-3' ImPyPyImPyPy-y-ImHpPyImHpPy
)
1945) 5' -WG A C G G T W-3' ImPyPyImImHp-y-PyPyPyImHpPy
1946) 5' -WG A C G G A W-3' ImPyPyImImPy-y-HpPyPyImHpPy
1947) 5' -WG A C G C T W-3' ImPyPyImPyHp-y-PyImPyImHpPy
1948) 5' -WG A C G C A W-3' ImPyPyImPyPy-y-HpImPyImHpPy
1949) 5' -WG A C C T T W-3' ImPyPyPyHpHp-y-PyPyImImHpPy
1950) 5' -WG A C C T A W-3' ImPyPyPyHpPy-y-HpPyImImHpPy
1951) 5' -WG A C C T G W-3' ImPyPyPyHpIm-y-PyPyImImHpPy
1952) 5' -WG A C C T C W-3' ImPyPyPyHpPy-y-ImPyImImHpPy
1953) 5' -WG A C C A T W-3' ImPyPyPyPyHp-y-PyHpImImHpPy
1954) 5' -WG A C C A A W-3' ImPyPyPyPyPy-y-HpHpImImHpPy
1955) 5' -WG A C C A G W-3' ImPyPyPyPyIm-y-PyHpImImHpPy
1956) 5' -WG A C C A C W-3' ImPyPyPyPyPy-y-ImHpImImHpPy
1957) 5' -WG A C C G T W-3' ImPyPyPyImHp-y-PyPyImImHpPy
1958) 5' -WG A C C G A W-3' ImPyPyPyImPy-y-HpPyImImHpPy
1959) 5' -WG A C C C T W-3' ImPyPyPyPyHp-y-PyImImImHpPy
1960) 5' -WG A C C C A W-3' ImPyPyPyPyPy-y-HpImImImHpPy
1961) 5' -WG A C G G G W-3' ImPyPyImImIm-y-PyPyPyImHpPy
1962) 5' -WG A C G G C W-3' ImPyPyImImPy-y-ImPyPyImHpPy
1963) 5' -WG A C G C G W-3' ImPyPyImPyIm-y-PyImPyImHpPy
1964) 5' -WG A C G C C W-3' ImPyPyImPyPy-y-ImImPyImHpPy
1965) 5' -WG A C C G G W-3' ImPyPyPyImIm-y-PyPyImImHpPy
19 6 5' -WG A C C G C W- ImPyPyPyImPy-y- ImPyimImHpPy
6 ) 3
'
1967) 5' -WG A C C C G W-3' ImPyPyPyPyIm-y-PyImImImHpPy
1968) 5' -WG A C C C C W-3' ImPyPyPyPyPy-y-ImImImImHpPy
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-I57-
TABLE
108:
12-ring
Hairpin
Polyamides
for recognition
of 8-by
5'-WGTGWNNW-3'
DNA aromatic amino acid sequence
sequence
1969) 5'-W GT G T T T W-3' ImHpImHpHpHp-y-PYPyPYPyPyPy
1970) 5'-W GT G T T A W-3' ImHpImHpHppy-y-HpPYPyPyPyPy
1971) 5'-W GT G T T G W-3' ImHpImHpHpIm-y-PyPypypypypy
1972) 5'-W GT G T T C W-3' ImHpImHpHpPy-y-ImPyPyPypypy
1973) 5'-W GT G T A T W-3' ImHpImHpPyHp-y-PyHpPyPyPYPy
1974) 5'-W GT G T A A W-3' ImHpImHpPYPy-y-HpHpPyPyPYpy
1975) 5'-W GT G T A G W-3' ImHpImHpPyIm-y-PyHpPyPyPyPy
1976) 5'-W GT G T A C W-3' ImHpImHpPyPy-y-ImHpPyPyPYPY
1977) 5'-W GT G T G T W-3' ImHpImHpImHp-y-PyPYPyPyPyPy
1978) 5'-W GT G T G A W-3' ImHpImHpImPy-y-HpPYPyPyPyPy
1979) 5'-W GT G T G G W-3' ImHpImHpImIm-y-PyPYPyPyPyPy
1980) 5'-W GT G T G C W-3' ImHpImHpImPy-y-ImPyPyPYPyPy
1981) 5'-W GT G T C T W-3' ImHpImHpPYHp-y-PyImPYPYPyPy
1982} 5'-W GT G T C A W-3' ImHpImHpPYPy-y-HpImPyPyPyPy
1983) 5'-W GT G T C G W-3' ImHpImHpPyIm-y-PyImPyPyPyPy
1984) 5'-W GT G T C C W-3' ImHpImHpPYPy-y-ImImPYPyPypy
1985) 5'-W GT G A T T W-3' ImHpImPYHpHp-y-PyPyHpPyPyPy
1986) 5'-W GT G A T A W-3' ImHpImPyHpPy-y-HpPYHpPyPyPy
1987) 5'-W GT G A T G W-3' ImHpImPyHpIm-y-PYPyHpPyPyPy
1988) 5'-W GT G A T C W-3' ImHpImPyHpPy-y-ImPYHpPyPyPy
1989) 5'-W GT G A A T W-3' ImHpImPyPyHp-y-PYHpHpPyPyPy
19 9 0 5'-W GT G A A A W- 3 ImHpImPyPyPy-y-HpHpHpPyPyPy
) '
1991) 5'-W GT G A A G W-3' ImHpImPyPyIm-y-PyHpHpPYPyPy
1992) 5'-W GT G A A C W-3' ImHpImPyPyPy-y-ImHpHpPyPyPy
1993) 5'-W GT G A G T W-3' ImHpImPyImHp-y-PYPyHpPYPYPy
1994) 5'-W GT G A G A W-3' ImHpImPyImPy-y-HpPyHpPyPyPy
1995) 5'-W GT G A G G W-3' ImHpImPYImIm-y-PypyHpPyPyPy
. 1996) 5'-W GT G A G C W-3' ImHpImPyImPy-y-ImPyHpPyPyPy
1997) 5'-W GT G A C T W-3' ImHpImPyPyHp-y-PYImHpPyPYPy
1998) 5'-W GT G A C A W-3' ImHpImPyPyPy-y-HpImHpPypyPy
1999) 5'-W GT G A C G W-3' ImHpImPYPYIm-y-pyImHpPYPYPy
2000) 5'-W GT G A C C W-3' ImHpImPyPyPy-y-ImImHpPyPYPy
CA 02281930 1999-08-18
WO 98137067 PCTILJS98/01714
-158-
TABLE
109:
12-ring
Hairpin
Polyamides
for recognition
of 8-by
5'-WGTGSNNW-3'
DNA aromatic amino acid sequence
sequence
2001) 5' -WG T G G T T W-3' ImHpImImHpHp-y-pypypypypypy
2002) 5' =WG T G G T A W-3' ImHpImImHpPy-y-HpPyPyPyPyPy
2003) 5' -WG T G G T G W-3' ImHpImImHpIm-y-PyPyPyPyPyPy
2004) 5' -WG T G G T C W-3' ImHpImImHpPy-y-ImPyPyPyPyPy
2005) 5' -WG T G G A T W-3' ImHpImImPyHp-y-PyHpPyPyPyPy
2006) 5' -WG T G G A A W-3' ImHpImImPyPy-y-HpHpPyPyPyPy
2007) 5' -WG T G G A G W-3' ImHpImImPyIm-y-PyHpPyPyPyPy
2008) 5' -WG T G G A C W-3' ImHpImImPyPy-y-ImHpPypyPyPy
2009) 5' -WG T G G G T W-3' ImHpImImImHp-y-PyPyPyPyPyPy
2 010 5' -WG T G G G A W- 3 ImHpImImImPy-y-HpPyPyPyPyPy
) '
2011) 5' -WG T G G C T W-3' ImHpImImPyHp-y-pyImPyPyPyPy
2 012 5' -WG T G G C A W-3 ImHpImImPyPy-y-HpImPyPyPyPy
) '
2013) 5' -WG T G C T T W-3' ImHpImPyHpHp-y-PyPyImPyPyPy
2014) 5' -WG T G C T A W-3' ImHpImPyHpPy-y-HpPyImPyPyPy
2015) 5' -WG T G C T G W-3' ImHpImPyHpIm-y-PyPyImPyPyPy
2016) 5' -WG T G C T C W-3' ImHpImPyHpPy-y-ImPyImPyPyPy
2017) 5' -WG T G C A T W-3' ImHpImPyPyHp-y-PyHpImPyPyPy
2018) 5' -WG T G C A A W-3' ImHpImPyPyPy-y-HpHpImPyPyPy
2019) 5' -WG T G C A G W-3' ImHpImPyPyIm-y-PyHpImPyPyPy
2020) 5' -WG T G C A C W-3' ImHpImPyPyPy-y-ImHpImPyPyPy
2021) 5' -WG T G C G T W-3' ImHpImPyImHp-y-PyPyImPyPyPy
2022) 5' -WG T G C G A W-3' ImHpImPyImPy-y-HpPyImPyPyPy
2023) 5' -WG T G C C T W-3' ImHpImPyPyHp-y-PyImImPyPyPy
2024) 5' -WG T G C C A W-3' ImHpImPyPyPy-y-HpImImPyPyPy
2025) 5' -WG T G G G G W-3' ImHpImImImIm-y-PyPyPyPyPyPy
2026) 5' -WG T G G G C W-3' ImHpImImImPy-y-ImPyPyPyPyPy
2027) 5' -WG T G G C G W-3' ImHpImImPyIm-y-PyImPyPyPyPy
2028) 5' -WG T G G C C W-3' ImHpImImPyPy-y-ImImPyPyPyPy
2029) 5' -WG T G C G G W-3' ImHpImPyImIm-y-PyPyImPyPyPy
2030) 5' -WG T G C G C W-3' ImHpImPyImPy-y-ImPyImPyPyPy
2031) 5' -WG T G C C G W-3' ImHpImPyPyIm-y-PyImImPyPyPy
2032) 5' -WG T G C C C W-3' ImHpImPyPyPy-y-ImImImPyPyPy
CA 02281930 1999-08-18
WO 98137067 PCT/US98/01714
-159-
t-At3Ll;
110:
12-ring
Hairpin
Polyamides
for
recogmt~on
of
8-by
5'-WGTTWNNW-3'
DNA aromatic amino acid sequence
sequence
2033) 5'-W G T T W-3' ImHpHpHpHpHp-y-pypypypypypy
T
T
T
2034) 5''-W G T T T A W-3' ImHpHpHpHpPy-y-HpPyPyPypypy
T
2035) 5'-W GT T T T G W-3' ImHpHpHpHpIm-y-Pypypypypypy
2036) 5'-W GT T T T C W-3' ImHpHpHpHpPy-y-ImPYPYPYPYP
y
2037) 5' GT T T A T W-3' ImHpHplipPyHp-y-PYHpPYPYPyPy
-W
2038) 5'-W GT T T A A W-3' ImHpHpHpPypy-Y-HpHpPyPyPypy
2039) 5' GT T T A G W-3' ImHpHpHpPyIm-Y-PyHpPyPyPypy
-W
2040) 5'-W GT T T A C W-3' ImHpHpHpPYPy-y-ImHppyPYpypy
2041) 5' GT T T G T W-3' ImHpHpHpImHp-Y-PypypypyPYPy
-W
2042) 5'-W GT T T G A W-3' ImHpHpHpImPy-y-HpPyPypypypy
2043) 5' GT T T G G W-3' ImHpHpHpImIm-y-pypypypypypy
-W
2044) 5'-W GT T T G C W-3' ImHpHpHpImPy-y-ImPYPYPYPyPy
2045) 5' GT T T C T W-3' ImHplipHpPyHp-y-pyImPYPyPyPy
-W
2046) 5'-W GT T T C A W-3' ImHpHpHpPyPy-Y-HpImPyPyPyPy
2047) 5'-W GT T T C G W-3' ImHpHpHpPyIm-y-PyImPYPYPYPy
2048) 5' GT T T C C W-3' ImHpHpHpPyPy-y-ImImPyPyPyPy
-W
2049) 5'-W GT T A T T W-3' ImHpHpPyHpHp-Y-pypyHpPyPyPy
2050) 5' GT T A T A W-3' ImHpHpPyHpPy-Y-HpPyHppyPYPy
-W
2051) 5' GT T A T G W-3' ImHpHpPyHpIm-y-PypyHppypypY
-W
2052) 5' GT T A T C W-3' ImHpHpPyHpPy-y-ImPyHpPYPyPy
-W
2053) 5' GT T A A T W-3' ImApHppyPyHp-y-pyHpHpPyPyPy
-W
2054) 5'-W GT T A A A W-3' ImHpHpPyPypy-y-HpHpHpPyPyPy
2055) 5'-W GT T A A G W-3' ImHpHpPyPyIm-y-PyHpHppyPyPy
2056) 5'-W GT T A A C W-3' ImHpHpPYPYPy-Y-ImHpHpPYPypy
2057) 5'-W GT T A G T W-3' ImHpHpPyImHp-y-pypygpPyPyPy
2058) 5'-W GT T A G A W-3' ImHpHpPyImPy-y-HpPyHpPyPypy
2059) 5'-W GT T A G G W-3' ImHpHpPyImIm-y-pypyHppypypy
2060) 5'-W GT T A G C W-3' ImHpHpPyImPy-y-ImPyHppypyPy
2061) 5' GT T A C T W-3' ImHpHpPyPyHp-y-Pyl~ppypyp~,
-W
2062) 5'-W GT T A C A W-3' ImHpHpPyPyPy-y-HpImHpPYPypy
2063) 5'-W GT T A C G W-3' ImHpHpPyPYIm-y-Pyl~ppypypY
2064) 5' GT T A C C W-3' ImHpHpPyPyPy-Y-ImImHpPYPYpy
-W
CA 02281930 1999-08-18
WO 98137067 PCT/US98/OI714
-160-
TABLE
111:
12-ring-I-lairpin
Polyamides
for
recognition
of
8-by
5'-WGTTSNNW-3'
DNA aromatic amino acid sequence
sequence
2065) 5' -WG T T G T TW-3' ImHpHpImHpHp-y-PyPyPyPyPyPy
2066) 5' -WG T T G T AW-3' ImHpHpImHpPy-y-HpPyPyPyPyPy
2067) 5' -WG T T G T GW-3' ImHpHpImHpIm-y-PyPyPyPyPyPy
2068) 5' -WG T T G T CW-3' ImHpHpImHpPy-y-ImPyPyPyPyPy
2069) 5' -WG T T G A TW-3' ImHpHpImPyHp-y-PyHpPyPyPyPy
2070) 5' -WG T T G A AW-3' ImHpHpImPyPy-y-HpHpPyPyPyPy
2071) 5' -WG T T G A GW-3' ImHpHpImPyIm-y-PyHpPyPyPyPy
2072) 5' -WG T T G A CW-3' ImHpHpImPyPy-y-ImHpPyPyPyPy
2073) 5' -WG T T G G TW-3' ImHpHpImImHp-y-PyPyPyPypypy
2074) 5' -WG T T G G AW-3' ImHpHpImImPy-y-HpPyPyPyPyPy
2075) 5' -WG T T G C TW-3' ImHpHpImPyHp-y-PyImPyPyPyPy
2076) 5' -WG T T G C AW-3' ImHpHpImPyPy-y-HpImPyPyPyPy
2077) 5' -WG T T G G GW-3' ImHpHpImImIm-y-PyPyPyPyPypy
2078) 5' -WG T T G G CW-3' ImHpHpImImPy-y-ImPyPyPyPyPy
2079) 5' -WG T T G C GW-3' ImHpHpImPyIm-y-PyImPyPyPyPy
2080) 5' -WG T T G C CW-3' ImHpHpImPyPy-y-ImImPyPyPyPy
2081) 5' -WG T T C T TW-3' ImlipHpPyHpHp-y-PyPyImPyPyPy
2082) 5' -WG T T C T AW-3' ImHpHpPyHpPy-y-HpPyImPyPyPy
2083) 5' -WG T T C T GW-3' ImHpHpPyHpIm-y-PyPyImPyPyPy
2084) 5' -WG T T C T CW-3' ImHpHpPyHpPy-y-ImPyImPyPyPy
2085) 5' -WG T T C A TW-3' ImHpHpPyPyHp-y-PyHpImPyPyPy
2086) 5' -WG T T C A AW-3' ImHpHpPyPyPy-y-HpHpImPyPyPy
2087) 5' -WG T T C A GW-3' ImHpHpPyPyIm-y-PyHpImPyPyPy
2088) 5' -WG T T C A CW-3' ImHpHpPyPyPy-y-ImHpImPyPyPy
2089) 5' -WG T T C G TW-3' ImHpHpPyImHp-y-PyPyImPyPyPy
2090) 5' -WG T T C G AW-3' ImHpHpPyImPy-y-HpPyImPyPyPy
2091) 5' -WG T T C C TW-3' ImHpHpPyPyFip-y-PyImImPyPyPy
2092) 5' -WG T T C C AW-3' ImHpHpPyPyPy-y-HpImImPyPyPy
2093) 5' -WG T T C G GW-3' ImHpHpPyImIm-y-PyPyImPyPyPy
2094) 5' -WG T T C G CW-3' ImHpHpPyImPy-y-ImPyImPyPyPy
2095) 5' -WG T T C C GW-3' ImHpHpPyPyIm-y-PyImImPyPyPy
2096) 5' -WG T T C C CW-3' ImHpHpPyPyPy-y-ImImImPyPyPy
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-161-
TABLE
I 12:
12-ring
Hairpin
Polyamides
for
recognition
of 8-by
5'-WGTAWNNW-3'
DNA aromatic amino acid sequence
sequence
2097) 5' -WG T AT T T W-3' ImHpPyHpHpHp-y-pypypyHppypy
2098) 5' -WG T AT T A W-3' ImHpPyHpHpPy-y-HpPyPyHpPyPy
2099) 5' -WG T AT T G W-3' ImHpPyApHpIm-y-PyPypyHpPyPy
2100) 5' -WG T AT T C W-3' ImHpPyHpHpPy-y-ImPyPyHpPyPy
2101) 5' -WG T AT A T W-3' ImHpPyHpPyHp-y-PyHpPyHppyPy
2102) 5' -WG T AT A A W-3' ImHpPyHpPyPy-y-HpHpPyHpPyPy
2103) 5' -WG T AT A G W-3' ImHpPyHpPyIm-y-PyHpPyHpPyPy
2104) 5' -WG T AT A C W-3' ImHpPyHpPyPy-y-ImHpPyHpPyPy
2105) 5' -WG T AT G T W-3' ImHpPyHpImHp-y-pypypyHppypy
2106) 5' -WG T AT G A W-3' ImHpPyHpImPy-y-HpPyPyHpPyPy
2107 5' -WG T AT G G W-3 ImHpPyHpImIm-y-PyPypyI-Ippypy
) '
2108) 5' -WG T AT G C W-3' ImHpPyHpImPy-y-ImPyPyHpPypy
2109) 5' -WG T AT C T W-3' ImHpPyHpPyHp-y-PyImPyHpPyPy
2110) 5' -WG T AT C A W-3' ImHpPyHpPyPy-y-HpImPyHpPyPy
2111) 5' -WG T AT C G W-3' ImHpPyHpPyIm-y-PyImPyHpPyPy
2112) 5' -WG T AT C C W-3' ImHpPyHpPyPy-y-ImImPyHpPyPy
2113) 5' -WG T AA T T W-3' ImHpPyPyHpHp-y-PyPyHpHpPyPy
2114) 5' -WG T AA T A W-3' ImHpPyPyHpPy-y-HpPyHpHpPyPy
2115) 5' -WG T AA T G W-3' ImHpPyPyHpIm-y-PyPyHpHpPyPy
2116) 5' -WG T AA T C W-3' ImHpPyPyHpPy-y-ImPyHpHpPyPy
2117) 5' -WG T AA A T W-3' ImHpPyPyPyHp-y-PyHpApHpPyPy
2118 5' -WG T AA A A W-3 ImHpPyPyPyPy-y-HpHpHpHpPyPy
) '
2119 5' -WG T AA A G W-3 ImHpPyPyPyIm-y-PyHpHpHpPyPy
) '
2120) 5' -WG T AA A C W-3' ImHpPyPyPyPy-y-ImHpHpHpPyPy
2121) 5' -WG T AA G T W-3' ImHpPyPyImHp-y-PypyHpgpPypy
2122) 5' -WG T AA G A W-3' ImHpPyPyImPy-y-HppyHpHpPyPy
2123 5' -WG T AA G G W-3' ImHppyPyImIm-y-PyPyHpHpPyPy
)
2124) 5' -WG T AA G C W-3' ImHpPyPyImPy-y-ImPyHpHpPyPy
2125) 5' -WG T AA C T W-3' ImApPyPyPyHp-y-pyImHpHpPyPy
2126) 5' -WG T AA C A W-3' ImHpPyPyPyPy-y-HpImHpHpPyPy
2127) 5' -WG T AA C G W-3' ImHppyPyPyIm-y-PyImHpHpPyPy
2128) 5' -WG T AA C C W-3' ImHpPyPypyPy-y-ImImHpHpPyPy
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-162-
TABLE
1 I3:
I2-ring-Hairpin
Polyamides
for recognition
of 8-by
S'-WGTASNNW-3'
DNA aromatic amino acid scquence
sequence
2129) 5' -W GT AG T T W-3' ImHpPyImHpHp-y-PyPyPyHpPyPy
2130) 5''-W GT AG T A W-3' ImHpPyImHpPy-y-HpPyPyHpPyPy
2131) 5' -W GT AG T G W-3' ImHpPyImHpIm-y-PyPyPyHpPyPy
2132) 5' -W GT AG T C W-3' ImHpPyImHpPy-y-ImPyPyHpPyPy
2133) 5' -W GT AG A T W-3' ImHpPyImPyHp-y-PyHpPyHpPyPy
2134) 5' -W GT AG A A W-3' ImHpPyImPyPy-y-HpHpPyHpPyPy
2135} 5' -W GT AG A G W-3' ImHpPyImPyIm-y-PyHpPyHpPyPy
213 6 5' -W GT AG A C W-3 ImHpPyImPypy-y- ImHpPyHpPyPy
) '
2137) 5' -W GT AG G T W-3' ImHpPyImImHp-y-PyPyPyHpPyPy
213 8 5' -W GT AG G A W-3 ImHpPyImImPy-y-HpPyPyHpPyPy
) '
213 9 5' -W GT AG C T W-3 ImHpPyImPyHp-y-PyImPyHpPyPy
) '
2140) 5' -W GT AG C A W-3' ImHpPyImPyPy-y-HpImPyHpPyPy
2141) 5' -W GT AG G G W-3' ImHpPyImImIm-y-PyPyPyHppyPy
2142) 5' -W GT AG G C W-3' ImHpPyImImPy-y-ImPyPyHpPyPy
2143 ) 5' -W GT AG C G W-3 ImHpPyImPyIm-y-PyImPyHpPyPy
'
2144) 5' -W GT AG C C W-3' ImHpPyImPyPy-y-ImImPyHpPyPy
2145) 5' -W GT AC T T W-3' ImHpPyPyHpHp-y-PyPyImHpPyPy
2146) 5' -W GT AC T A W-3' ImHpPyPyHpPy-y-HppyImHpPyPy
2147} 5' -W GT AC T G W-3' ImHpPyPyHpIm-y-PyPyImHpPyPy
2148) 5' -W GT AC T C W-3' ImHpPyPyHpPy-y-ImPyImHpPyPy
2149) 5' -W GT AC A T W-3' ImHpPyPyPyHp-y-PyHpImHpPyPy
2150) 5' -W GT AC A A W-3' ImHpPyPyPyPy-y-HpHpImHpPyPy
2151) 5' -W GT AC A G W-3' ImHpPyPyPyIm-y-PyHpImHpPyPy
2152) 5' -W GT AC A C W-3' ImHpPyPypyPy-y-ImHpImHpPyPy
2153) 5' -W GT AC G T W-3' ImHpPyPyImHp-y-PyPyImHpPyPy
2154) 5' -W GT AC G A W-3' ImHpPyPyImPy-y-HpPyImHpPyPy
2155) 5' -W GT AC C T W-3' ImHpPyPyPyHp-y-PyImImHpPyPy
2156) 5' -W GT AC C A W-3' ImHpPypyPyPy-y-HpImImHpPyPy
2157) 5' -W GT AC G G W-3' ImHpPyPyImIm-y-PyPyImHpPyPy
2158) 5' -W GT AC G C W-3' ImHpPyPyImPy-y-ImPyImHpPyPy
2159) 5' -W GT AC C G W-3' ImHpPyPyPyIm-y-PyImImHpPyPy
2160) 5' -W GT AC C C W-3' ImHpPyPyPyPy-y-ImImImHpPyPy
_~.,.,,... _ , , , , .,.
CA 02281930 1999-08-18
WO 98/37067 , PCT/US98/01714
-163-
I
Al3Lt~
I
14:
12-ring
Hairpin
Polyamides
for
recognition
of
8-by
5'-WGTCWNNW-3'
DNA aromatic amino acid sequence
sequence
2161) 5'-W GT C T T T W-3' ImHpPyHpHpHp-y-Pypypylmpypy
2162) 5' GT C T T A W-3' ImHpPyHpHpPy-y-HpPyPyImPyPy
-~n1
2163 ) 5' GT C T T G W-3 ImHpPyHpHpIm-y-PyPypyImPyPy
-W '
2164) 5'-W GT C T T C W-3' ImHpPYHpHpPy-y-ImPypyImPyPy
2165) 5'-W GT C T A T W-3' ImHpPyHpPyHp-y-PyHpPyImPyPy
2166) 5'-W GT C T A A W-3' ImHpPyHpPyPy-y-HpHpPyImpyPy
2167) 5'-W GT C T A G W-3' ImHppyHppYIm_Y_pYHppyImPyPy
2168) 5'-W GT C T A C W-3' ImHpPyHpPypy-y-ImHpPyImPyPy
2169) 5'-W GT C T G T W-3' ImHpPYHpImHp-y-PypypyImPyPy
2170) 5'-W GT C T G A W-3' ImHpPyHpImPy-y-HpPyPyImPyPy
2171) 5' GT C T G G W-3' ImHpPyHpImIm-y-PypypyzmPyPy
-W
2172) 5' GT C T G C W-3' ImHpPyHpImPy-y-ImPyPyImPyPy
-W
2173 ) 5' GT C T C T W-3' ImHpPyHpPyHp-y-PyImPyImPyPy
-W
2174) 5' GT C T C A W-3' ImHpPyHpPYPy-y-HpImPyImPyPy
-W
2175) 5' GT C T C G W-3' ImHppyHpPyIm-y-pyImPYImPyPy
-W
2176) 5' GT C T C C W-3' ImHpPyHpPyPy-y-ImImPyImPyPy
-W
2177 ) 5' GT C A T T W-3' ImHpPyPyHpHp-y-pypyHpImPYPy
-W
2178) 5' GT C A T A W-3' ImHpPYPyHpPy-y-HpPYHpImPyPy
-W
2179) 5' GT C A T G W-3' ImHpPyPyHpIm-y-PyPyHpImPyPy
-W
2180) 5'-W GT C A T C W-3' ImHppypYHPPY_Y-ImPyHpImPyPy
2181) 5' GT C A A T W-3' ImHpPyPyPYHp-y-PyHpHpImPypy
-W
2182) 5' GT C A A A W-3' ImHpPYPyPypy-Y-HpHpHpImPyPy
-W
2183 ) 5' GT C A A G W-3' ImHpPyPyPyIm-Y-PyHpHpImPyPy
-W
2184) 5' GT C A A C W-3' ImHpPyPypypy-Y-I~pHpImPyPy
-W
2185) 5' GT C A G T W-3' ImHpPyPyImHp-y-PypyHpImPyPy
-W
2186) 5'-W GT C A G A W-3' ImHppypylmpY_Y_HpPyHpImPyPy
2187) 5'-W GT C A G G W-3' ImHpPyPyImIm-y-PypygpImPyPy
2188) 5' GT C A G C W-3' ImHpPyPyImPy-
-W y -ImPyHpImPyPy
2189) 5'-W GT C A C T W-3' ImHpPyPyPyHp-Y-PyImHpImPyPy
2190) 5' GT C A C A W-3' ImHppypypypY_Y-HpImHpImpyPy
-W
2191) 5' GT C A C G W-3' ImHpPypypylm-y-PyImHpImPyPy
-W
2192) 5'-W GT C A C C W-3' ImHpPyPyPypy_y-ImImHpImPyPy
CA 02281930 1999-08-18
WO 98/37067 , PCT/US98/01714
-164-
TABLE
115:
12-ring
Hairpin
Polyamides
for
recognition
of
8-by
5'-WGTCSNNW-3'
DNA aromatic amino acid sequence
sequence
2193) 5' -WG T C G TT W-3' ImHpPyImHpHp-y-PyPyPyImPyPy
2194) 5' -WG T C G TA W-3' ImHpPyImHpPy-y-HpPyPyImPyPy
2195) 5' -WG T C G TG W-3' ImHpPyImHpIm-y-PyPyPyImPyPy
2196) 5' -WG T C G TC W-3' ImHpPyImHpPy-y-ImPyPyImPyPy
2197) 5' -WG T C G AT W-3' ImHpPyImPyHp-y-PyHpPyImPyPy
2198) 5' -WG T C G AA W-3' ImHpPyImPyPy-y-HpHpPyImPyPy
2199) 5' -WG T C G AG W-3' ImHpPyImPyIm-y-PyHpPyImPyPy
2200) 5' -WG T C G AC W-3' ImHpPyImPyPy-y-ImHpPyImPyPy
2201) 5' -WG T C G GT W-3' ImHpPyImImHp-y-PyPyPyImPyPy
2202) 5' -WG T C G GA W-3' ImHpPyImImPy-y-HpPyPyImPyPy
2203) 5' -WG T C G CT W-3' ImHpPyImPyHp-y-PyImPyImPyPy
2204) 5' -WG T C G CA W-3' ImHpPyImPyPy-y-HpImPyImPyPy
2205) 5' -WG T C C TT W-3' ImHpPyPyHpHp-y-PyPyImImPyPy
2206) 5' -WG T C C.TA W-3' ImHpPyPyHpPy-y-HpPyImImPyPy
2207) 5' -WG T C C TG W-3' ImHpPyPyHpIm-y-PyPyImImPyPy
2208) 5' -WG T C C TC W-3' ImHpPyPyHpPy-y-ImPyImImPyPy
2209) 5' -WG T C C AT W-3' ImHpPyPyPyHp-y-PyHpImImPyPy
2210) 5' -WG T C C AA W-3' ImHpPyPyPyPy-y-HpHpImImPyPy
2211) 5' -WG T C C AG W-3' ImHpPyPyPyIm-y-PyHpImImPyPy
2212) 5' -WG T C C AC W-3' ImHpPyPyPyPy-y-ImHpImImPyPy
2213) 5' -WG T C C GT W-3' ImHpPyPyImHp-y-PyPyImImPyPy
2214) 5' -WG T C C GA W-3' ImHpPyPyImPy-y-HpPyImImPyPy
2215) 5' -WG T C C CT W-3' ImHpPyPyPyHp-y-PyImImImPyPy
2216) 5' -WG T C C CA W-3' ImHpPyPyPyPy-y-HpImImImPyPy
2217) 5' -WG T C G GG W-3' ImHpPyImImIm-y-PyPyPyImPyPy
2218) 5' -WG T C G GC W-3' ImHpPyImImPy-y-ImPyPyImPyPy
2219) 5' -WG T C G CG W-3' ImHpPyImPyIm-y-PyImPyImPyPy
2220) 5' -WG T C G CC W-3' ImHpPyImPyPy-y-ImImPyImPyPy
2221) 5' -WG T C C GG W-3' ImHpPyPyImIm-y-PyPyImImPyPy
2222) 5' -WG T C C GC W-3' ImHpPyPyImPy-y-ImPyImImPyPy
2223) 5' -WG T C C CG W-3' ImHpPyPyPyIm-y-PyImImImPyPy
2224) 5' -WG T C C CC W-3' ImHpPyPyPyPy-y-ImImImImPyPy
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-165-
TABLE 116:
12-ring
Hairpin
Polyamides
for
recognition
of
8-by
5'WCGGWNNW-3'
'
DNA aromatic amino acid sequence
sequence
2225) 5'W C G G TT T W-3' PyImImHpHpHp-y-PyPypypypylm
2226) 5'W C G G TT A W-3' PyImImHpHpPy-y-HpPyPyPyPyim
2227 5' C G G TT G W-3' PyImImHpHpIm-y-PyPyPyPyPyIm
) W
2228) 5'W C G G TT C W-3' PyImImHpHpPy-y-ImPyPyPyPyIm
2229) 5'W C G G TA T W-3' PyImImHpPyHp-y-PyHpPyPyPyIm
223 0 5' C G G TA A W-3 ' PyImImHpPyPy-y-HpHpPyPyPyIm
) W
2231) 5'W C G G TA G W-3' PyImImHpPyIm-y-PyHpPyPyPyIm
2232) 5'W C G G TA C W-3' PyImImHpPyPy-y-ImHpPyPyPyIm
2233) 5'W C G G TG T W-3' PyImImHpImHp-y-PyPyPyPyPyIm
2234 5' C G G TG A W-3 ' PyImImHpImPy-y-HpPyPyPyPyIm
) W
2235) 5'W C G G TG G W-3' PyImImHpImIm-y-PyPyPypypyIm
2236) 5'W C G G TG C W-3' PyImImHpImPy-y-ImPyPyPyPyIm
2237) 5'W C G G TC T W-3' PyImImHpPyHp-y-PyImPyPyPyIm
223 8 5' C G G TC A W-3 ' PyImImHpPyPy-y-HpImPyPyPyIm
) W
223 9 5' C G G TC G W-3 ' PyImImHpPyIm-y-PyImPyPyPyIm
) W
2240) 5'W C G G TC C W-3' PyImImHpPyPy-y-ImImPyPyPyIm
2241) 5'W C G G AT T W-3' PyImImPyHpHp-y-PyPyHpPyPyIm
2242) 5'W C G G AT A W-3' PyImImPyHpPy-y-HpPyHpPyPyIm
2243 5' C G G AT G W-3 ' PyImImPyHpIm-y-PyPyHpPyPyIm
) W
2244) 5'W C G G AT C W-3' PyImImpyHpPy-y-ImPyHpPyPyIm
2245) 5'W C G G AA T W-3' PyImImPyPyHp-y-PyHpHpPyPyIm
2246) 5'W C G G AA A W-3' PyImImPyPyPy-y-HpHpHpPyPyIm
2247 5' C G G AA G W-3 ' PyImImPyPyIm-y-PyHpHpPyPyIm
) W
2248) 5'W C G G AA C W-3' PyImImPyPyPy-y-ImHpHpPyPyIm
2249) 5'W C G G AG T W-3' PyImImPyImHp-y-PyPyHpPyPyIm
2250) 5'W C G G AG A W-3' PyImImPyImPy-y-HpPyHpPyPyIm
2251) 5' C G G AG G W-3' PyImImPyImIm-y-PypyHpPyPyIm
W
2252) 5'W C G G AG C W-3' PyImImPyImPy-y-ImPyHpPyPyIm
2253 5' C G G AC T W-3 ' PyImImPyPyHp-y-PyImHpPyPyIm
) W
2254) 5'W C G G AC A W-3'
PyImImPyPyPy-y-HpImHpPyPyIm
2255) 5'W C G G AC G W-3' PyImImPyPyIm-y-PyImHpPyPyIm
2256) 5'W C G G AC C W-3' PyImImPyPyPy-y-ImImHpPyPyIm
CA 02281930 1999-08-18
WU 98137067 PCT/US98/01714
-166-
TABLE
117:
12-ring
Hairpin
Polyamides
for
recognition
of
8-by
5'WCGGSNNW-3'
DNA aromatic amino acid sequence
sequence
2257) 5' W C G G GT T W-3' PyImImImHpHp-y-PyPyPyPyPyIm
2258) 5' W C G G GT A W-3' PyImImImHpPy-y-HpPyPyPyPyIm
2259) 5' W C G G GT G W-3' PyImImImHpIm-y-PyPyPyPyPyIm
2260) 5' W C G G GT C W-3' PyImImImHpPy-y-ImPyPyPyPyIm
2261) 5' W C G G GA T W-3' PyImImImPyHp-y-PyHpPyPyPyIm
2262) 5' W C G G GA A W-3' PyImImImPyPy-y-HpHpPyPyPyIm
2263) 5' W C G G GA G W-3' PyImImImPyIm-y-PyHpPyPyPyIm
2264) 5' W C G G GA C W-3' PyImImImPyPy-y-ImHpPyPyPyIm
2265) 5' W C G G GG T W-3' PyImImImImHp-y-PyPyPyPyPyIm
2266) 5' W C G G GG A W-3' PyImImImImPy-y-HpPyPyPyPyIm
2267) 5' W C G G GC T W-3' PyImImImPyHp-y-PyIircPyPyPyIm
226$) 5' W C G G GC A W-3' PyImImImPyPy-y-HpImPyPyPyIm
2269) 5' W C G G CT T W-3' PyImImPyHpHp-y-PyPyImPyPyIm
2270) 5' W C G G CT A W-3' PyImImPyHpPy-y-HpPyImPyPyIm
2271) 5' W C G G CT G W-3' PyImImPyHpIm-y-PyPyImPyPyIm
2272) 5' W C G G CT C W-3' PyImImPyHpPy-y-ImPyImPyPyIm
2273) 5' W C G G CA T W-3' PyImImPyPyHp-y-PyHpImPyPyIm
2274) 5' W C G G CA A W-3' PyImImPyPyPy-y-HpHpImPyPyIm
2275) 5' W C G G CA G W-3' PyImImPyPyIm-y-PyHpImPyPyIm
2276) 5' W C G G CA C W-3' PyImImPyPyPy-y-ImHpImPyPyIm
2277 5' W C G G CG T W-3 ' PyImImPyImHp-y-PyPyImPyPyIm
)
2278) 5' W C G G CG A W-3' PyImImPyImPy-y-HpPyImPyPyIm
227 9 5' W C G G CC T W-3 ' PyImImPyPyHp-y-PyImImPyPyIm
)
2280) 5' W C G G CC A W-3' PyImImPyPyPy-y-HpImImPyPyim
G83) 5' W C G G GG G W-3' PyImImImImIm-y-PyPyPyPyPyIm
G84) 5' W C G G GG C W-3' PyImImImImPy-y-ImPyPyPyPyIm
G85) 5' W C G G GC G W-3' PyImImImPyIm-y-PyImPyPyPyIm
G86 ) 5' W C G G GC C W-3 ' PyImImImPyPy-y-ImImPyPyPyIm
G87 ) 5' W C G G CG G W-3 ' PyImImPyImIm-y-PyPyImPyPyIm
G88) 5' W C G G CG C W-3' PyImImPyImPy-y-ImPyImPyPyIm
G89) 5' W C G G CC G W-3' PyImImPyPyIm-y-PyImImPyPyIm
G90) 5' W C G G CC C W-3' PyImImPyPyPy-y-ImImImPyPyIm
CA 02281930 1999-08-18
WO 98/37067 . PCT/US98/01714
-167-
TABLE 12-ring
118: Hairpin
Polyamides
for
recognition
of
8-by
5'-WCGTWNNW-3'
DNA aromatic amino acid sequence
sequence
2281) 5'W C G T T T TW-3' PyImHpHpHpHp-y-PyPyPyPyPyIm
2282) 5'W C G T T T AW-3' PyImHpHpHpPy-y-HpPyPyPyPyIm
2283 ) 5' C G T T T GW-3 ' PyImHpHpHpIm-y-PyPyPyPyPyIm
W
2284) 5'W C G T T T CW-3' PyImHpHpHpPy-y-ImPyPyPyPyIm
2285) 5'W C G T T A TW-3' PyImHpHpPyHp-y-PyHpPyPyPyIm
2286) 5'W C G T T A AW-3' PyImHpHpPyPy-y-HpHpPyPyPyIm
2287) 5'W C G T T A GW-3' PyImHpHpPyIm-y-PyHpPyPypyIm
2288) 5'W C G T T A CW-3' PyImHpHpPyPy-y-ImHpPyPyPyIm
2289) 5'W C G T T G TW-3' PyImHpHpImHp-y-PyPyPyPyPyIm
2290) 5'W C G T T G AW-3' PyImHpHpImPy-y-HpPypyPypylm
2291) 5'W C G T T G GW-3' PyImHpHpImIm-y-PyPyPyPyPyIm
2292) 5'W C G T T G CW-3' PyImHpHpImPy-y-ImPyPyPyPyIm
2293) 5'W C G T T C TW-3' PyImHpHpPyHp-y-PyTmPyPyPyIm
2294} 5'W C G T T C AW-3' PyImHpHpPyPy-y-HpImPyPyPyIm
2295) 5'W C G T T C GW-3' PyImHpHpPyIm-y-PyImPyPyPyIm
2296) 5'W C G T T C CW-3' PyImHpHpPyPy-y-ImImPyPyPyIm
2297) 5'W C G T A T TW-3' PyImHpPyHpHp-y-PyPyHpPyPyIm
2298) 5'W C G T A T AW-3' PyImHpPyHpPy-y-HpPyHpPyPyIm
2299) 5'W C G T A T GW-3' PyImHpPyHpIm-y-PyPyHpPyPyIm
2300} 5'W C G T A T CW-3' PyImHpPyHpPy-y-ImPyHpPyPyIm
2301) 5'W C G T A A TW-3' PyImHpPyPyHp-y-PyHpHpPyPyIm
2302) 5'W C G T A A AW-3' PyImHpPyPyPy-y-HpHpHpPyPyIm
2303) 5'W C G T A A GW-3' PyImHpPyPyim-y-PyHpHpPyPyim
2304) 5'W C G T A A CW-3' PyImHpPyPyPy-y-ImHpHpPyPyIm
2305) 5'W C G T A G TW-3' PyImHpPyImHp-y-PyPyHpPyPyIm
2306) 5'W C G T A G AW-3' PyImHpPyImPy-y-HpPyHpPyPyIm
2307) 5'W C G T A G GW-3' PyImHpPyImIm-y-PyPyHpPyPyIm
2308) 5'W C G T A G CW-3' PyImHpPyImPy-y-ImPyHpPyPyIm
2309) 5'W C G T A C TW-3' PyImHpPyPyHp-y-PyImHpPyPyIm
2310) 5'W C G T A C AW-3' PyImHpPyPyPy-y-HpImHpPyPyIm
2311) 5'W C G T A C GW-3' PyImHpPyPyIm-y-PyImHpPyPyIm
2312 ) 5' C G T A C CW-3 ' PyImHpPyPypy-y- ImImHpPyPyIm
W
CA 02281930 1999-08-18
WO 98137067 PCT/US98/01714
-168-
TABLE I 19: 12-ring-Hairpin Polyamides far recognition of 8-by 5'-WCGTSNNW-3'
DNA sequence aromatic amino acid sequence
2313 ) 5' W C G T G T T W-3 ' PyImHpImHpHp-Y-PypypypypyIm
2314 ) 5' W C G T G T A W-3 ' PyImHpImHpPy-y-Hppypypypylm
2315) 5'W C G T G T G W-3' PyImHpImHpIm-y-PyPyPyPypyIm
2316 ) 5' W C G T G T C W-3 ' PyImHpImHpPy-y- ImPyPyPyPyIm
2317 ) 5' W C G T G A T W-3 ' PyImHpImPyHp-y-PyHpPyPyPyIm
2318) 5'W C G T G A A W-3' PyImHpImPyPy-y-HpHpPyPyPyIm
2319) 5'W C G T G A G W-3' PyImHpImPyIm-Y-PyHpPyPypyIm
2320) 5'W C G T G A C W-3' PyImHpImPyPy-y-ImHpPyPyPyIm
2321) 5'W C G T G G T W-3' PyImHpImImHp-y-pypypypypyim
2322) 5'W C G T G G A W-3' PyImHpImImPy-y-HPPyPyPyPyIm
2323) 5'W C G T G C T W-3' PyImHpImPyHp-y-pyImPyPyPyIm
2324) 5'W C G T G C A W-3' PyImHpImPyPy-y-HpImPyPyPyIm
2325) 5'W C G T G G G W-3' PyImHpImImIm-y-PyPyPyPyPyIm
2326) 5'W C G T G G C W-3' PyImApImImPy-y-ImPyPyPyPyIm
2327) 5'W C G T G C G W-3' PyImHpImPyIm-y-PyImPyPyPyIm
2328) 5'W C G T G C C W-3' PyImHpImPyPy-y-ImImPyPyPyIm
2329) 5'W C G T CT T W-3' PyImHpPyHpHp-y-PypyImPyPyIm
2330) 5' C G T CT A W-3' PyImHpPyHpPy-y-HpPyImPyPyIm
W
2331) 5'W C G T CT G W-3' PyImHpPyI3pIm-y-PyPyImPyPyIm
2332) 5'W C G T CT C W-3' PyImHpPyHpPy-y-ImpyImPyPyIm
2333 ) 5' C G T CA T W-3' PyImHpPyPyHp-y-PyHpImPyPyIm
W
2334 ) 5' C G T CA A W-3 ' PyImHpPyPyPy-y-HpHpImPyPyIm
W
2335) 5'W C G T CA G W-3' PyImHppypylm-y-PyHpImPyPyIm
2336) 5'W C G T CA C W-3' PyImHpPyPyPy-y-ImHpImPyPyIm
2337 ) 5' C G T CG T W-3 ' PyImHpPyImHp-y-pypyImPyPyim
W
2338) 5'W C G T CG A W-3' PyImHpPyImPy-y-HpPyImPyPyIm
2339) 5'W C G T CC T W-3' PyImHpPyPyHp-y-PyImImPyPyIm
2340) 5'W C G T CC A W-3' PyImHpPyPyPy-y-HpImImPyPyIm
2341) 5'W C G T CG G W-3' PyImHpPyImIm-y-pypyImPyPyIm
2342) 5'W C G T CG C W-3' PyImHpPyImPy-y-ImpyImPyPyIm
2343 ) 5' C G T CC G W-3 ' PyImHpPyPyIm-y-PyImImPyPyIm
W
2 3 44 ) 5' C G T CC C W- 3 PyImHpPyPyPy-y- ImImImPyPyIm
W '
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-169-
1A13LIr
120:
12-ring
Hairpin
Polyamides
for
recognition
of
8-by
5'-WCGAWNNW-3'
DNA aromatic amino acid sequence
sequence
2345) 5'W C GA T T T W-3' PyImPyHpHpHp-y-pypypyHppylm
2346) 5'W C GA T T A W-3' PyImPyHpHpPy-y-HpPyPyHpPyIm
2347) 5'W C GA T T G W-3' PyImpyHpHpIm-y-pyPypyHpPyIm
2348) 5'W C GA T T C W-3' PyImPyHpHpPy-y-ImPyPyHpPyIm
2349) 5'W C GA T A T W-3' PyImPyHpPyHp-y-PyHpPyHpPyIm
2350) 5'W C GA T A A W-3' pyImPyHpPyPy-y-HpHpPyHpPyIm
2351) 5'W C GA T A G W-3' PyImPyApPyIm-y-PyHpPyHpPyIm
2352) 5'W C GA T A C W-3' PyImPyHpPyPy-y-ImHpPyHpPyIm
2353) 5'W C GA T G T W-3' PyImPyHpImHp-y-Pypypygppylm
2354 ) 5' C GA T G A W-3 ' PyImPyHpImPy-y-HpPyPyHpPyIm
W
2355) 5'W C GA T G G W-3' PyImPyHpImIm-y-PyPyPyHpPyIm
2356) 5'W C GA T G C W-3' PyImPyHpImPy-y-ImPyPyHpPyIm
2357) 5'W C GA T C T W-3' PyImPyHpPyHp-y-PyImPyHpPyIm
2358) 5'W C GA T C A W-3' PyImPyHpPyPy-y-HpImPyHpPyIm
2359) 5'W C GA T C G W-3' PyImPyHpPyIm-y-PyImPyHpPyIm
2360) 5'W C GA T C C W-3' PyImPyHpPyPy-y-ImImPyHpPyIm
2361) 5'W C GA A T T W-3' PyImPyPyHpHp-y-PypyHpHpPyIm
2362) 5'W C GA A T A W-3' PyImPyPyHpPy-y-HpPyHpHpPyIm
2363) 5'W C GA A T G W-3' PyImPyPyHpIm-y-PypyHpHpPyIm
2364) 5'W C GA A T C W-3' PyImPyPyHpPy-y-ImPyHpHpPyIm
2365) 5'W C GA A A T W-3' PyImPyPyPyHp-y-PyHpHpHpPyIm
2366) 5'W C GA A A A W-3'
PyImPyPyPyPy-y-HpHpHpHpPyIm
2367) 5'W C GA A A G W-3' PyImPyPypylm-y-PyHpHpHpPyIm
2368) 5'W C GA A A C W-3' PyImPyPyPyPy-y-ImHpHpHpPyIm
2369) 5'W C GA A G T W-3' PyImPyPyImHp-y-PyPyHpHpPyIm
2370) 5'W C GA A G A W-3' PyImPyPyImPy-y-HpPyHpHpPyIm
2371) 5'W C GA A G G W-3' PyImPyPyImIm-y-PyPyHpHpPyIm
2372) 5'W C GA A G C W-3' yImPypyImPy-y-ImPyHpHpPyIm
P
. 2373 ) 5' C GA A C T W-3 ' PyImPyPypyHp-y-PyImHpHpPyIm
W
2374 ) 5' C GA A C A W-3' PyImPyPyPyPy-y-HpImHpHpPyIm
W
2375) 5'W C GA A C G W-3' PyImPyPyPyIm-y-PyImHpHpPyIm
2376) 5'W C GA A C C W-3' PyImPyPyPyPy-y-ImImHpIipPyIm
CA 02281930 1999-08-18
WO 98137067 PCT/US98/01714
-170-
TABLE
121:
12-ring
Hairpin
Polyamides
for
recognition
of
8-by
5'-WCGASNNW-3'
DNA aromatic amino acid sequence
sequence
2377) 5'W C G A GT T W-3' PyImPyImHpHp-y-PyPyPyHpPyIm
2378) 5'W C G A GT A W-3' PyImPyImHpPy-y-HpPyPyHppyIm
2379) 5'W C G A GT G W-3' PyImPyImHpIm-y-PyPyPyHpPyIm
2380) 5'W C G A GT C W-3' PyImPyImHpPy-y-ImPyPyHpPyIm
2381) 5'W C G A GA T W-3' PyImPyImPyHp-y-PyHpPyHpPyIm
2382) 5'W C G A GA A W-3' PyImPyImPyPy-y-HpHpPyHpPyIm
2383) 5'W C G A GA G W-3' PyImPyImPyIm-y-PyHpPyHpPyIm
2384) 5'W C G A GA C W-3' PyImPyImPyPy-y-ImHpPyHpPyIm
2385) 5'W C G A GG T W-3' PyImPyImImHp-y-PyPyPyHpPyIm
2386) 5'W C G A GG A W-3' PyImPyImImPy-y-HpPyPyHpPyIm
2387) 5'W C G A GC T W-3' PyImPyImPyHp-y-PyImPyHpPyIm
2388) 5'W C G A GC A W-3' PyImPyImPyPy-y-HpImPyHpPyIm
2389) 5'W C G A GG G W-3' PyImPyImImIm-y-PyPyPyHpPyIm
2390) 5'W C G A GG C W-3' PyImPyImImPy-y-ImPyPyHpPyIm
2391) 5'W C G A GC G W-3' PyImPyImPyIm-y-PyImPyHpPyIm
2392) 5'W C G A GC C W-3' PyImPyImPyPy-y-ImImPyHpPyim
2393) 5'W C G A CT T W-3' PyImPyPyHpHp-y-PyPyImHpPyIm
2394) 5'W C G A CT A W-3' PyImPyPyHpPy-y-HpPyImHpPyIm
2395) 5'W C G A CT G W-3' PyImPyPyHpIm-y-PyPyImHpPyIm
2396) 5'W C G A CT C W-3' PyImPyPyHpPy-y-ImPyImHpPyIm
2397) 5'W C G A CA T W-3' PyImPyPyPyHp-y-PyHpImHpPyIm
2398) 5'W C G A CA A W-3' PyImPyPyPyPy-y-HpHpImHpPyIm
2399) 5'W C G A CA G W-3' PyImPyPyPyIm-y-PyHpImHpPyIm
2400) 5'W C G A CA C W-3' PyImPyPyPyPy-y-ImHpImHpPyIm
2401) 5'W C G A CG T W-3' PyImPyPyImHp-y-PyPyImHpPyIm
2402) 5'W C G A CG A W-3' PyImPyPyImPy-y-HpPyImHpPyIm
2403) 5'W C G A CC T W-3' PyImPyPyPyHp-y-PyImImHpPyIm
2404 5' C G A CC A W-3 PyImPyPyPyPy-y-HpImImHpPyIm
) W '
2405) 5'W C G A CG G W-3' PyImPyPyImIm-y-PyPyImHpPyIm
2406) 5'W C G A CG C W-3' PyImPyPyImPy-y-ImPyImFFpPyIm
2407) 5'W C G A CC G W-3' PyImPyPyPyIm-y-PyImImHpPyIm
2408) 5'W C G A CC C W-3' PyImPyPyPyPy-y-ImImImHpPyIm
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/OI714
-171-
TABLE 12-ring
I22: Hairpin
Polyamides
for
recognition
of
8-by
5'-WCGCWNNW-3'
DNA aromatic amino acid sequence
sequence
2409) 5'W CG C T T T W-3' PyImPyHpHpHp-y-pypypyImPyIm
2410 ) 5' CG C T T A W-3 ' PyImPyHpHpPy-y-HpPyPyImPyIm
TnT
2411) 5'W CG C T T G W-3' PyImPyHpHpIm-y-PypypyImPyIm
2412) 5'W CG C T T C W-3' PyImPyHpHpPy-y-ImPyPyImPyIm
2413 ) 5' CG C T A T W-3 ' PyImPyHpPyHp-y-PyHpPyImPyIm
W
2414 ) 5' CG C T A A W-3 ' PyImPyHpPyPy-y-HpHpPyImPyIm
W
2415 ) 5' CG C T A G W-3 T PyImPyHpPyIm-y-PyHpPyImPyIm
W
2416) 5'W CG C T A C W-3' PyImPyHpPyPy-y-ImHpPyImPyIm
2417) 5'W CG C T G T W-3' PyImPyHpImHp-y-PyPypyImPyIm
2418 ) 5' CG C T G A W-3 ' PyImPyHpItttPy-y-HpPyPyImPyIm
W
2419 ) 5' CG C T G G W-3' PyImPyHpImIm-y-PyPyPyImPyIm
W
2420) 5'W CG C T G C W-3' PyImPyHpImPy-y-ImPyPyImPyIm
2421) 5'W CG C T C T W-3' PyImPyHpPyHp-y-PyImPyImPyIm
2422) 5'W CG C T C A W-3' PyImPyHpPyPy-y-HpImPyImPyIm
2423 ) 5' CG C T C G W-3' PyImPyHpPyIm-y-PyImPyImPyIm
W
2424) 5'W CG C T C C W-3' PyImPyHpPyPy-y-ImImPyImPyIm
2425) 5'W CG C A T T W-3' PyImPyPyHpHp-y-pyPyHpimPyIm
2426 ) 5' CG C A T A W-3 ' PyImPyPyHppy-y-HpPyHpImPyIm
W
2427 ) 5' CG C A T G W-3 ' PyImPypyHpIm-y-PyPyHpImPyIm
W
2428) 5'W CG C A T C W-3' PyImPyPyHpPy-y-ImPyHpImPyIm
2429) 5'W CG C A A T W-3' PyImPyPyPyHp-y-PyHpHpImPyIm
2430) 5'W CG C A A A W-3' PyImPyPyPyPy-y-HpHpHpImPyIm
2431) 5'W CG C A A G W-3' PyImPyPyPyIm-y-PyHpHpImPyIm
2432) 5'W CG C A A C W-3' PyImPyPyPyPy-y-ImHpHpImPyIm
2433) 5'4JCG C A G T W-3' PyImPyPyImHp-y-PyPyHpImPyIm
- 2434) 5'W CG C A G A W-3' PyImPyPyImPy-y-HpPyHpImPyIm
2435) 5'W CG C A G G W-3' PyImPyPyImIm-y-PyPyHpImPyIm
24 3 6 5' CG C A G C W-3 ' PyImPyPyImPy-y- ImPyHpImPyIm
) W
2437 ) 5' CG C A C T W-3' pyImPyPyPyHp-y-PyImHpImPyIm
W
2438) 5'W CG C A C A W-3' PyImPyPyPyPy-y-HpImHpImPyIm
_ 2439) 5'W CG C A C G W-3' PyImPyPyPyIm-y-PyImHpImPyIm
2440) 5'W CG C A C C W-3' PyImPyPyPyPy-y-ImImHpImPyim
CA 02281930 1999-08-18
WO 9$/37067 PCT/US98/01714
-172-
TABLE 123:
12-ring
Hairpin
Polyamides
for
recognition
of
8-by
5'-WCGCSNNW-3'
DNA aromatic amino acid sequence
sequence
2441) 5' W C GC GT T W-3' PyImPyImApHp-y-PyPyPyImPyIm
2442) 5' W C GC GT A W-3' PyImPyImHpPy-y-HpPyPyImPyIm
2443) 5' W C GC GT G W-3' PyImPyImHpIm-y-PyPyPyImPyIm
2444) 5' W C GC GT C W-3' PyImPyImHpPy-y-ImPyPyImPyIm
2445) 5' W C GC GA T W-3' PyImPyImPyHp-y-PyHpPyImPyIm
2446) 5' W C GC GA A W-3' PyImPyImPyPy-y-HpHpPyImPyim
2447) 5' W C GC GA G W-3' PyImPyImPyIm-y-PyHpPyImPyIm
2448) 5' W C GC GA C W-3' PyImPyImPyPy-y-ImHpPyImPyIm
2449) 5' W C GC GG T W-3' PyImPyImImHp-y-PyPyPyImPyim
2450) 5' W C GC GG A W-3' PyImPyImImPy-y-HpPyPyImPyIm
2451) 5' W C GC GC T W-3' PyImPyImPyHp-y-PyImPyImPyIm
IS 2452) 5' W C GC GC A W-3' PyImPyImPyPy-y-HpImPyImPyIm
2453) 5' W C GC CT T W-3' PyImPyPyHpHp-y-PyPyImImPyIm
2454 5' W C GC CT A W-3 ' PyImPyPyHpPy-y-HpPyImImPyIm
)
2455) 5' W C GC CT G W-3' PyImPyPyHpIm-y-PyPyImImPyIm
2456 5' W C GC CT C W-3' PyImPyPyHpPy-y-ImPyImImPyIm
)
2457 5' W C GC CA T W-3' PyImPyPyPyHp-y-PyHpImImPyIm
)
2458) 5' W C GC CA A W-3' PyImPyPyPyPy-y-HpHpImImPyIm
2459) 5' W C GC CA G W-3' PyImPyPyPyIm-y-PyHpImImPyIm
2460) 5' W C GC CA C W-3' PyImPyPyPyPy-y-ImHpImImPyIm
2461) 5' W C GC CG T W-3' PyImPyPyImHp-y-PyPyImImPyIm
2462 5' W C GC CG A W-3' PyImPyPyImPy-y-HpPyImImPyIm
)
2463) 5' W C GC CC T W-3' PyImPyPyPyHp-y-PyImImImPyIm
2464) 5' W C GC CC A W-3' Py3mPyPyPyPy-y-HpImImImPyIm
G91) 5' W C GC GG G W-3' PyImPyImImIm-y-PyPyPyImPyIm
G92 ) 5' W C GC GG C W-3' PyImPyImImPy-y-ImPyPyImPyIm
G93 ) 5' W C GC GC G W-3' PyImPyImPyIm-y-PyImPyImPyIm
G94) 5' W C GC GC C W-3' PyImPyImPyPy-y-ImImPyImPyIm
G95) 5' W C GC CG G W-3' PyImPyPyImIm-y-PyPyImImPyIm
G96) 5' W C GC CG C W-3 ' PyImPyPyImPy-y-ImPyImImPyIm
G97 ) 5' W C GC CC G W- 3 PyImPyPyPyIm-y-PyImImImPyIm
'
G98) 5' W C GC CC C W-3' PyImPyPyPyPy-y-ImImImImPyIm
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-173-
TABLE
124:
12-ring
Hairpin
Polyamides
for
recognition
of 8-by
S'-WCCGWNNW-3'
DNA aromatic amino acid sequence
sequence
2465) 5'W C C G T T TW-3' PyPyImHpHpHp-y-PypypypyImIm
S 2466) 5'W C C G T T AW-3' PyPyImHpHpPy-y-HpPyPypyImlm
2467) 5'W C C G T T GW-3' PyPyImHpHpIm-y-pyPypypylmlm
2468) 5'W C C G T T CW-3' PyPyImHpHpPy-y-ImPyPyPyImIm
2469) 5'W C C G T A TW-3' PyPyImHpPyHp-y-PyHpPyPyImIm
247 0 5' C C G T A AW-3 ' PyPyImHppyPy-y-HpHpPyPyImIm
) W
2471) 5'W C C G T A GW-3' PyPyImHpPyIm-y-PyHpPyPyImIm
2472) 5' C C G T A CW-3' PyPyImHpPyPy-y-ImHpPyPyImIm
W
2473) 5'W C C G T G TW-3' PyPyImHpImHp_y-PyPypypylmlm
2474) 5'W C C G T G AW-3' PyPyImHpImPy-y-HpPyPyPyImIm
2475) 5'W C C G T G GW-3' PyPyImHpImIm-y-pyPypypylmlm
1S 2476) 5'W C C G T G CW-3' PyPyImHpImPy-y-ImpyPyPyImIm
2477 5' C C G T C TW-3 ' PyPyImHpPyHp-y-PyImPyPyImIm
) W
2478) 5'W C C G T C AW-3' PyPyImHpPyPy-y-HpImPyPyImIm
247 9 5' C C G T C GW-3 ' PyPyImHpPyIm-y-PyImPypyImlm
) W
2480) 5'W C C G T C CW-3'
PyPyImHpPypy-y-ImImPyPyImIm
2481) 5'W C C G A T TW-3' PyPyImPyHpHp-y-PyPyHpPyImIm
2482) 5'W C C G A T AW-3' PyPyImPyHpPy-y-HpPyHppyImIm
2483) 5'W C C G A T GW-3' PyPyImPyHpIm-y-PyPyHpPyImIm
2484) 5'W C C G A T CW-3' PyPyImPyHpPy-y-ImPyHpPyImIm
2485) 5'W C C G A A TW-3' PyPyImPyPyHp-y-PyHpHppyImlm
2S 2486) 5'W C C G A A AW-3' PyPyImPyPyPy-y-HpHpHpPyImIm
2487) 5'W C C G A A GW-3' PyPyImPyPyIm-y-PyHpHpPyImIm
2488) 5'W C C G A A CW-3' PyPyImPyPyPy-y-ImHpHpPyImIm
2489) 5'W C C G A G TW-3' PyPyImPyImHp-y-PyPyHpPyImIm
2490) 5'W C C G A G AW-3' PyPyImPyImPy-y-HppyHpPyImIm
2491) 5'W C C G A G GW-3' PyPyImPyImIm-y-PypyHpPyImIm
2492) 5'W C C G A G CW-3' PyPyImPyImPy-y-ImPyHpPyImIm
2493 5' C C G A C TW-3 ' PyPyImPypyHp-y-PyImHppyImIm
) W
24 94 5' C C G A C AW-3 ' PyPyImPyPyPy-y-HpImHpPyImIm
) W
_ 2495) 5'W C C G A C GW-3' PyPyImPyPyIm-y-PyImHpPyImIm
3S 2496) 5'W C C G A C CW-3'
PyPyImPyPyPy-y-ImImHpPyImIm
CA 02281930 1999-08-18
WO 98137067 , PCT/US98/01714
-174-
TABLE
125:
12-ring-Hairpin
Polyamides
for
recognition
of
8-by
5'-WCCGSNNW-3'
DNA aromatic amino acid sequence
sequence
2497) 5'W C C G G T TW-3' PyPyImImHpHp-y-PyPyPyPyImIm
2498} 5''W C C G G T AW-3' PyPyImImHpPy-y-HpPyPyPyImIm
2499) 5'W C C G G T GW-3' PyPyImImHpIm-y-PyPyPyPyImIm
2500) 5'W C C G G T CW-3' PyPyImImHpPy-y-ImPyPyPyImIm
2501) 5'W C C G G A TW-3' PyPyImImPyHp-y-PyHpPyPyImIm
2502) 5'W C C G G A AW-3' PyPyImImPyPy-y-HpHpPyPyImIm
2503 5' C C G G A GW-3 ' PyPyImImPyIm-y-PyHpPyPyImIm
) W
2504 5' C C G G A CW-3 ' PyPyImImPyPy-y-ImHpPyPyImIm
) W
2505) 5'W C C G G G TW-3' PyPyImImImHp-y-PyPyPyPyImIm
2506) 5'W C C G G G AW-3' PyPyImImImPy-y-HpPyPyPyImIm
2507) 5'W C C G G C TW-3' PyPyImImPyHp-y-PyImPyPyImIm
2508) 5'W C C G G C AW-3' PyPyImImPyPy-y-HpImPyPyImIm
2509) 5'W C C G C T TW-3' PyPyImPyHpHp-y-PyPyImPyImIm
2510 5' C C G C T AW-3' PyPyImPyHpPy-y-HpPyImPyImIm
) W
2511) 5'W C C G C T GW-3' PyPyImPyHpIm-y-PyPyImPyImIm
2512 5' C C G C T CW-3 ' PyPyImPyHpPy-y-ImPyImPyImIm
) W
2513 5' C C G C A TW-3' PyPyImPyPyHp-y-PyHpImPyImIm
) W
2514 5' C C G C A AW-3 ' PyPyImPyPyPy-y-HpHpImPyImIm
) W
2515 5' C C G C A GW-3 ' PyPyImPyPyIm-y-PyHpImPyImIm
} W
2516) 5'W C C G C A CW-3' PyPyImPyPyPy-y-ImHpImPyImIm
2517 5' C C G C G TW-3 ' PyPyImPyImHp-y-PyPyImPyImIm
) W
2 518 5' C C G C G AW-3 ' PyPyImPyImPy-y-HpPyImPyImIm
) W
2519 5' C C G C C TW-3 ' PyPyImPyPyHp-y-PyImImPyImIm
) W
2520) 5'W C C G C C AW-3' PyPyImPyPyPy-y-HpImImPyImIm
G99) 5'W C C G G G GW-3' PyPyImImImIm-y-PyPyPyPyImIm
6100) 5'W C C G G G CW-3' PyPyImImImPy-y-ImPyPyPyImIm
6101) 5'W C C G G C GW-3' PyPyImImPyIm-y-PyImPyPyImIm
6102) 5'W C C G G C CW-3' PyPyImImPyPy-y-ImImPyPyImIm
6103 5' C C G C G GW-3 ' PyPyImPyImIm-y-PyPyImPyImIm
) W
6104) 5'W C C G C G CW-3' PyPyImPyImPy-y-ImPyImPyImIm
6105) 5'W C C G C C GW-3' PyPyImPyPyIm-y-PyImImPyImIm
6106) 5'W C C G C C CW-3' PyPyImPyPyPy-y-ImImImPyImIm
~w_ ...~,.. . . ,
CA 02281930 1999-08-18
WO 98137067 PCT/US98/01714
-175-
1'A13LE
I26:
12-ring
Hairpin
Polyamides
for
recognition
of
8-by
5'-WCCTWNNW-3'
DNA aromatic amino acid sequence
sequence
2521) 5'W C C TT T T W-3' PyPyHpHpHpHp-y-PyPyPypyImIm
2522) 5'W C C TT T A W-3' PyPyHpHpHpPy-y-HpPyPyPyImIm
2523) 5'W C C TT T G W-3' PyPyHpHpHpIm-y-PyPyPyPyImIm
2524) 5'W C C TT T C W-3' PyPyHpHpHpPy-y-ImPyPypyImlm
2525) 5'W C C TT A T W-3' PyPyHpHpPyHp-y-PyHpPyPyImIm
2526) 5'W C C TT A A W-3' PyPyHpHpPyPy-y-HpHpPypyImIm
2527 ) 5' C C TT A G W-3' PyPyHpHpPyIm-y-PyHpPyPyImIm
W
2528) 5'W C C TT A C W-3' PyPyHpHpPyPy-y-ImHppyPyImIm
2529) 5'W C C TT G T W-3' PyPyHpHpImHp-y-PyPyPyPyImIm
2530) 5'W C C TT G A W-3'
PyPyHpHpImPy-y-HpPyPyPyImIm
2531) 5'W C C TT G G W-3' PyPyHpHpImIm-y-pypypypyImlm
2532) 5'W C C TT G C W-3' PyPyHpHpImPy-y-ImPyPyPyImIm
2533) 5'W C C TT C T W-3' PyPyHpHpPyHp-y-PyImPyPyImIm
2534 ) 5' C C TT C A W-3' PyPyHpHpPyPy-y-HpImPyPyImIm
W
2535) 5'W C C TT C G W-3' PyPyHpI-ipPyIm-y-PyImPyPyImIm
2536) 5'W C C TT C C W-3' PypyHpHpPyPy-y-ImImPyPyImIm
2537) 5'W C C TA T T W-3' PyPyIipPyHpHp-y-PyPyHpPyImIm
2538) 5'W C C TA T A W-3' PyPyHpPyHpPy-y-HpPyHpPyImIm
2539) 5'W C C TA T G W-3' PyPyHpPyHpIm-y-PyPyHppyImlm
2540 ) 5' C C TA T C W-3 PyPyHpPyHpPy-y-ImPyHpPyImIm
W '
2541) 5'W C C TA A T W-3' PyPyHpPyPyHp-y-PyHpHpPyImIm
2542) 5'W C C TA A A W-3' PyPyHpPyPyPy-y-HpHplipPyImIm
2543) 5'W C C TA A G W-3' PyPyHpPyPyIm-y-PyHpHpPyImIm
2544) 5'W C C TA A C W-3' PyPyHpPyPyPy-y-ImHpHpPyImIm
2545) 5'W C C TA G T W-3' PyPyHpPyImHp-y-PyPyHpPyImIm
2546) 5'W C C TA G A W-3' PyPyHpPyImPy-y-HpPyHpPyImIm
2547 ) 5' C C TA G G W-3 PyPyHpPyImIm-y-PyPyHpPyImIm
W '
2548) 5'W C C TA G C W-3' PyPyHpPyImPy-y-ImPyFipPyImIm
2549) 5'W C C TA C T W-3' PypyHpPyPyHp-y-PyImHpPyImIm
2550) 5'W C C TA C A W-3' PyPyHpPyPyPy-y-HpImHpPyImIm
2551) 5'W C C TA C G W-3' PyPyHpPypyIm-y-PyImHpPyImIm
2552) 5'W C C TA C C W-3' PyPyHpPyPyPy-y-ImImHpPyImIm
CA 02281930 1999-08-18
WO 98137067 , PCTIUS98/01714
-176-
TABLE
127:
12-ring
Hairpin
Polyamides
for
recognition
of 8-by
5'-WCCTSNNW-3'
DNA aromatic amino acid sequence
sequence
2553 5' C C T GT T W-3 ' PyPyHpImHpHp-y-PyPyPyPyImIm
) W
2554) 5'W C C T GT A W-3' PyPyHpImHpPy-y-HpPyPyPyImIm
2555) 5'W C C T GT G W-3' PyPyHpImFipIm-y-PyPyPyPyImIm
2556) 5'W C C T GT C W-3' PyPyHpImHpPy-y-ImPyPyPyImIm
2557 5' C C T GA T W-3 ' PyPyHpImPyHp-y-PyHpPyPyImIm
) W
2558) 5'W C C T GA A W-3' PyPyHpImPyPy-y-HpHpPyPyImIm
2559) 5'W C C T GA G W-3' PyPyHpImPyIm-y-PyHpPyPyImIm
2560) 5'W C C T GA C W-3' PyPyHpImPyPy-y-ImHpPyPyImIm
2561} 5'W C C T GG T W-3' PyPyHpImImHp-y-PyPyPypyImlm
2562) 5'W C C T GG A W-3' PyPyHpImImPy-y-HpPyPyPyImIm
2563) 5'W C C T GC T W-3' PyPyHpImPyHp-y-PyImPyPyImIm
2564) 5'W C C T GC A W-3' PyPyHpImPyPy-y-HpImPyPyImIm
2565) 5'W C C T GG G W-3' PypyHpImImIm-y-PyPyPyPyImIm
2566) 5'W C C T GG C W-3' PyPyHpImImPy-y-ImPyPyPyImIm
2567 5' C C T GC G W-3 ' PyPyHpImPyIm-y-PyImPyPyImIm
) W
2568) 5'W C C T GC C W-3' PyPyHpImPyPy-y-ImImPyPyImIm
2569) 5'W C C T CT T W-3' PyPyHpPyHpHp-y-PyPyImpyImlm
2570) 5'W C C T CT A W-3' PyPyHpPyHpPy-y-HpPyImPyImIm
2571) 5'W C C T CT G W-3' PyPyHpPyHpIm-y-PyPyImPyImIm
2572) 5'W C C T CT C W-3' PyPyHpPyHpPy-y-ImPyImPyImIm
2573) 5'W C C T CA T W-3' PyPyHpPyPyHp-y-PyHpImPyImIm
2574) 5'W C C T CA A W-3' PyPyHpPyPyPy-y-HpHpImPyImIm
2575) 5'W C C T CA G W-3' PyPyHpPyPyIm-y-PyHpImPyImIm
2 57 5' C C T CA C W-3 ' PyPyHpPyPyPy-y- ImHp ImPyImIm
6 } W
2577) 5'W C C T CG T W-3' PyPyHpPyImHp-y-PyPyImpyImIm
2578) 5'W C C T CG A W-3' PyPyHpPyImPy-y-HpPyImPyImIm
2579) 5'W C C T CC T W-3' PyPyHpPyPyF-Ip-y-PyImImPyImIm
2580) 5'W C C T CC A W-3' PypyHpPyPyPy-y-HpImImPyImIm
2581) 5'W C C T CG G W-3' PyPyHpPyImIm-y-PyPyImPyImIm
2582) 5'W C C T CG C W-3' PyPyHpPyImPy-y-ImPyImPyImIm
2583) 5'W C C T CC G W-3' PyPyHpPyPyIm-y-PyImImPyImIm
2584) 5'W C C T CC C W-3' PyPyHpPyPyPy-y-ImImImPyImIm
CA 02281930 1999-08-18
WO 98137067 PCTIUS98/01714
-177-
1A13LE
128:
12-ring
Hairpin
Polyamides
for
recognition
of
8-by
5'-WCCAWNNW-3'
DNA aromatic amino acid sequence
sequence
2585) 5'W CC A T T T W-3' PyPyPyHpHpHp-y-PyPypygpImIm
2586) 5'W CC A T T A W-3' PyPyPyHpHpPy-y-HpPyPyHpImIm
2587) 5'W CC A T T G W-3' PyPypyHpHpIm-y-PyPypyHpImIm
2588) 5'W CC A T T C W-3' PyPyPyHpHpPy-y-ImPyPyHpImIm
2589 ) 5' CC A T A T W-3' PyPyPyHpPyHp-y-PyHpPyHpImIm
W
2590) 5'W CC A T A A W-3' PyPyPyHpPyPy-y-HpHpPyHpImIm
2591) 5'W CC A T A G W-3' PyPyPyHpPyIm-y-PyHpPyHpImIm
2592) 5'W CC A T A C W-3' PyPyPyHpPyPy-y-ImHpPyHpImIm
2593) 5'W C C A T G T W-3' PyPyPyHpImHp-y-PyPyPyHpImIm
2594) 5'W C C A T G A W-3' PyPyPyHpImPy-y-HpPyPyHpImIm
2595) 5'W C C A T G G W-3' PyPyPyHpImIm-y-PypypyHpImIm
2596) 5'W C C A T G C W-3' PyPyPyHpImPy-y-ImPyPyHpImIm
2597) 5'W C C A T C T W-3' PyPyPyHpPyHp-y-pyImPyHpImIm
2598) 5'W C C A T C A W-3' PyPyPyHpPypy-y-HpImPyHpImIm
2599) 5'W C C A T C G W-3' PyPyPyHpPyIm-y-PyImPyHpImIm
2600) 5'W C CA T C C W-3' PyPyPyHpPyPy-y-ImImPyHpImIm
2601) 5'W C CA A T T W-3' PyPyPyPyHpHp-y-PyPyHpHpImIm
2602) 5'W C CA A T A W-3' PyPyPyPyHpPy-y-HpPyHpHpImIm
2603) 5'W C CA A T G W-3' PyPyPyPyHpIm-y-PypyHpHpImIm
2604) 5'W C CA A T C W-3' PyPyPyPyHpPy-y-ImPyHpHpImIm
2605) 5'W C CA A A T W-3' PyPyPyPypyHp-y-pyHpHpHpImIm
2606) 5'W C CA A A A W-3' PyPyPyPyPyPy-y-HpHpHpHpImIm
2607) 5'W C CA A A G W-3' PyPyPypypyIm-y-PyHpHpHpImIm
2608) 5'W C CA A A C W-3' PyPyPyPyPyPy-y-ImHpHpHpImIm
2609) 5'W C CA A G T W-3' PyPyPyPyImHp-y-PyPyHpHpImIm
2610 ) 5' C CA A G A W-3 PyPyPyPyImPy-y-HpPyHpHpImIm
W '
2611) 5'W C CA A G G W-3' PyPyPyPyImIm-y-PyPyHpHpImIm
2 612 ) 5' C CA A G C W-3 yPyPyPyImPy-y- ImPyHpHpImIm
W P '
2613) 5'W C CA A C T W-3' PyPyPyPypyHp-y-PyImHpHpImIm
2 614 ) 5' C CA A C A W-3 PyPyPyPypypy-y-HpI~pHpImIm
W '
_ 2615) 5'W C CA A C G W-3' pyPypypypylm-y-pyi~pHpimim
2616) 5'W C CA A C C W-3' PypyPypypypy-y-ImImHpHpImIm
CA 02281930 1999-08-18
WO 98/37067 PCTIUS98/01714
-178-
TABLE
129:
12-ring
Hairpin
Polyamides
for recognition
of 8-by
S'-WCCASNNW-3'
DNA aromatic amino acid sequence
sequence
2617 ) 5' C CA GT T W-3 PyPyPyImHpHp-y-PyPyPyHpImIm
W '
2618) 5'~W C CA GT A W-3' PyPyPyImHpPy-y-HpPyPyHpImIm
2619) 5'W C CA GT G W-3' PyPyPyImHpIm-y-PyPyPyHpImIm
2620) 5'W C CA GT C W-3' PyPyPyImHpPy-y-ImPyPyHpImIm
2621) 5'W C CA GA T W-3' PyPypyImPyHp-y-PyHpPyHpImIm
2622) 5'W C CA GA A W-3' PyPypyImPyPy-y-HpHpPyHpImIm
2623) 5'W C CA GA G W-3' PyPyPyImPyIm-y-PyHpPyHpImIm
2624) 5'W C CA GA C W-3' PyPyPyImPyPy-y-ImHpPyHpImIm
2625) 5'W C CA GG T W-3' PyPyPyImImHp-y-PyPyPyHpImIm
2626) 5'W C CA GG A W-3' PyPyPyImImPy-y-HpPyPyHpImIm
2627) 5'W C CA GC T W-3' PyPyPyImPyHp-y-PyImPyHpImIm
2628) 5'W C CA GC A W-3' PyPyPyImPyPy-y-HpImPyHpImIm
2629) 5'W C CA GG G W-3' PyPyPyImImIm-y-PyPyPyHpImIm
2630) 5'W C CA GG C W-3' PyPyPyImImPy-y-ImPyPyHpImIm
2631) 5'W C CA GC G W-3' PyPyPyImPyIm-y-PyImPyHpImIm
2632) 5'W C CA GC C W-3' PyPyPyImPyPy-y-ImImPyHpImIm
2633) 5'W C CA CT T W-3' PyPyPyPyHpHp-y-PyPyImHpImIm
2634) 5'W C CA CT A W-3' PyPyPyPyHpPy-y-HpPyImHpImIm
2635) 5' C CA CT G W-3' PyPyPyPyHpIm-y-PyPyImHpImIm
W
2636) 5'W C CA CT C W-3' PyPyPyPyHpPy-y-ImPyImHpImIm
2637) 5'W C CA CA T W-3' PyPyPyPyPyHp-y-PyHpImHpImIm
2638) 5'W C CA CA A W-3' PyPyPyPyPyPy-y-HpHpImHpImIm
2639) 5'W C CA CA G W-3' PyPyPyPyPyIm-y-PyHpImHpImIm
2640) 5'W C CA CA C W-3' PyPyPyPyPyPy-y-ImHpImHpImIm
2641) 5'W C CA CG T W-3' PyPyPyPyImHp-y-PyPyImHpImIm
2642) 5'W C CA CG A W-3' PyPyPyPyImPy-y-HpPyImHpImIm
2643) 5'W C CA CC T W-3' PyPyPyPyPyHp-y-PyImImHpImIm
2644) 5'W C CA CC A W-3' PyPyPyPyPyPy-y-HpImImHpImIm
2645) 5'W C CA CG G W-3' PyPyPyPyImIm-y-PyPyImHpImIm
2646) 5'W C CA CG C W-3' PyPyPyPyImPy-y-ImPyImHpImIm
2647) 5'W C CA CC G W-3' PyPyPyPyPyIm-y-PyImImHpImIm
2648) 5'W C CA CC C W-3' pypypyPyPyPy-y-ImImImHpImIm
CA 02281930 1999-08-18
WO 98/37067 . PCT/US98/01714
-179-
'TABLE 130: 12-ring Hairpin Polyamides for recognition of 8-by 5'-WCCCWNNW-3'
DNA sequence aromatic amino acid sequence
2649) 5'W C C C T T T W-3' PyPyPyHpHpHp-y-PyPypyImImIm
2650) 5'W C C C T T A W-3' PyPyPyHpHpPy-y-HpPyPyImImIm
2651) 5'W C C C T T G W-3' PyPyPyHpHpIm-y-PyPyPyImImIm
2652) 5'W C C C T T C W-3' PyPyPyHpHpPy-y-ImPyPyImImIm
2653) 5'W C C C T A T W-3' PyPyPyHpPyHp-y-PyHpPyImImIm
2654} 5'W C C C T A A W-3' PyPyPyHpPyPy-y-HgHpPyImImIm
2655) 5'W C C C T A G W-3' PyPyPyHpPyIm-y-PyHpPyImImIm
2656) 5'W C C C T A C W-3' PyPyPyHpPyPy-y-ImHpPyImImIm
2657) 5'W C C C T G T W-3' PyPyPyHpImHp-y-PyPypyImImIm
2658) 5'W C C C T G A W-3' PyPyPyHpImPy-y-HpPyPyImImIm
2659) 5'W C C C TG G W-3' PyPypyHpImIm-y-PyPyPyImImIm
2660) 5'W C C C TG C W-3' PyPyPyHpImPy-y-ImPyPyImImIm
2661} 5'W C C C TC T W-3' PyPyPyHpPyHp-y-PyImPyImImIm
2662) 5'W C C C TC A W-3' PyPyPyHpPyPy-y-HpImPyImImIm
2663) 5'W C C C TC G W-3' PyPyPyHpPyIm-y-PyImPyImImIm
2664) 5'W C C C TC C W-3 T PyPyPyHpPyPy-y-ImImPyImImIm
2665) 5'W C C C AT T W-3' PyPyPyPyHpHp-y-PyPyHpImImIm
2666) 5'W C C C AT A W-3' PyPyPyPyHpPy-y-HpPyHpImImIm
2667} 5'W C C C AT G W-3' PyPyPyPyHpIm-y-PyPyHpImImIm
2668) 5'W C C C AT C W-3' PyPyPyPyHpPy-y-ImPyHpImImIm
2669) 5'W C C C AA T W-3' PyPyPyPyPyHp-y-PyHpHpImImIm
2670) 5'W C C C AA A W-3' PyPyPyPyPyPy-y-HpHpHpImImIm
2671) 5'W C C C AA G W-3' PyPyPyPyPyIm-y-PyHpHpImImIm
2 672 ) 5' W C C C A A C W-3 ' PyPyPyPyPyPy-y- ImHpHpImImIm
2673) 5'W C C C A G T W-3' PyPyPyPyImHp-y-PyPyHpImImim
2674) 5'W C C C A G A W-3' PyPyPyPyImPy-y-HpPyHpImImIm
2675) 5'W C C C A G G W-3' PyPyPyPyImIm-y-pyPyHpImImIm
2676) 5'W C C C A G C W-3' PyPypypylmpy-y-ImPyHpImImIm
2677) 5'W C C C A C T W-3' PyPyPyPyPyHp-y-PyImHpImImIm
2678) 5'W C C C A C A W-3' Pypypypypypy-y-HpImFipImImIm
2679) 5'W C C C A C G W-3' Pypypypypylm-y-pyImHpImImIm
2680) 5'W C C C A C C W-3' PyPyPyPyPyPy-y-ImImHpImImIm
CA 02281930 1999-08-18
WO 98/37067 PCT/LJS98/OI714
-180-
TABLE 131: 12-ring Hairpin Polyamides far recognition of 8-by 5'-WCCCSNNW-3'
DNA sequence aromatic amino acid sequence
2681) 5'W C C C G T T W-3' PyPyPyImApHp-y-PyPyPyImImIm
2 6 82 ) 5' C C C G TA W-3 ' PyPypyImHppy-y-HpPyPyImImIm
W'
2683) 5'W C C C G TG W-3' PyPyPyImHpIm-y-PyPyPyImImIm
2684) 5'W C C C G TC W-3' PyPyPyImHpPy-y-ImPyPyImImIm
2685) 5'W C C C G AT W-3' pyPyPyImPyHp-y-PyHpPyImImIm
2686) 5'W C C C G AA W-3' PyPyPyImPyPy-y-HpHpPyImImIm
2687) 5'W C C C G AG W-3' PyPyPyImPyIm-y-PyHpPyImImIm
2688) 5'W C C C G AC W-3' PyPyPyImPyPy-y-ImHpPyImImIm
2689) 5'W C C C G GT W-3' PyPyPyImImHp-y-PypypyzmImIm
2690) 5'W C C C G GA W-3' PyPypyImImPy-y-HpPyPyImImIm
2691) 5'W C C C G CT W-3' PyPyPyImPyHp-y-PyImPyImImIm
2692) 5'W C C C G CA W-3' PyPyPyImpypy_y-HpImPyImImIm
2693) 5'W C C C C TT W-3' PyPyPyPyHpHp-y-PyPyImIm3mIm
2694) 5'W C C C C TA W-3' PyPyPyPyFipPy-y-HpPyImImImIm
2695) 5'W C C C C TG W-3' PyPyPyPyHpIm-y-PyPyImImImIm
2696) 5'W C C C C TC W-3' pyPyPyPyIipPy-y-ImPyImImImIm
2697) 5'W C C C C AT W-3' PyPyPyPyPyHp-y-PyHpImImImIm
2698) 5' C C C C AA W-3' PyPyPyPyPyPy-y-HpHpImImImIm
W
2699) 5'W C C C C AG W-3' PyPyPyPyPyIm-y-PyHpImImImIm
2690) 5'W C C C C AC W-3' PypypyPyPyPy-y-ImHpImImImIm
2701) 5'W C C C C GT W-3' PyPyPyPyImHp-y-PyPyImImImIm
2702) 5'W C C C C GA W-3' PyPyPyPyImPy-y-HpPyImImImIm
2703) 5'W C C C C C T W-3' PyPyPyPyPyHp-y-PyImImImImIm
2704) 5'W C C C C C A W-3' PyPyPyPyPypy-y-HpImImImImIm
6107 ) 5' W C C C G G G W-3' PyPyPyImImIm-y-PyPyPyImImIm
6108) 5'W C C C G G C W-3' PyPyPyImImPy-y-ImPyPyImImIm
6109) 5'W C C C G C G W-3' PyPyPyImPyIm-y-PyImPyImImIm
6110) 5'W C C C G C C W-3' PyPyPyImPyPy-y-ImImPyImImIm
6111) 5' W C C C C G G W-3' PypyPyPyImIm-y-PyPyImImImIm
6112 ) 5' W C C C C G C W-3 ' PyPyPyPyImPy-y- ImPyImImImIm
6113 ) 5' W C C C C C G W-3 ' PyPypypypylm-y-pyImImImImIm
6114) 5'W C C C C C C W-3' pypypypypypy-y-ImImImImImIm
,. ,
CA 02281930 1999-08-18
WO 98137067 PCT/US98/01714
-181-
1-Al3Lt; 132:
12-ring
Hairpin
Polyamides
for
recognition
of
8-by
5'-WCAGWNNW-3'
DNA aromatic amino acid sequencc
sequence
' 2705) 5'W C A G T T TW-3' PyPyImHpHpHp-y-pypypypyHplm
' 5 2706) 5'W C A G T T AW-3'
PypyImHpHpPy-y-HpPyPyPyHpIm
270?) 5'W C A G T T GW-3' PyPyImHpHpIm-y-pypypypyHpIm
2708) 5'W C A G T T CW-3' PyPyImHpHpPy-y-ImPyPyPyHpIm
2709} 5'W C A G T A TW-3' PyPyImHpPyHp-y-PyHpPyPyHpIm
2700) 5'W C A G T A AW-3' PyPyImHpPyPy-y-HpHpPyPyFipIm
2711) 5' C A G T A GW-3 ' PyPyImHpPyIm-y-PyHpPyPyHpIm
W
2712) 5'W C A G T A CW-3'
PyPyImHpPyPy-y-ImHppyPyHpIm
2713) 5'W C A G T G TW-3'
PyPyImHpImHp-y-PyPyPyPyHpIm
2714 5' C A G T G AW-3 ' PyPyImHpImPy-y-HpPyPyPyHpIm
) W
2715) 5'W C A G T G GW-3' PyPyImHpImIm-y-PypypypyHplm
2716) 5'W C A G T G CW-3'
PyPyImHpImPy-y-ImPyPyPyHpIm
2717) 5'W C A G T C TW-3'
PyPyImHpPyHp-y-PyImPyPyHpIm
2718) 5'W C A G T C AW-3' PyPyImHpPyPy-y-HpImPyPyHpIm
2719) 5'W C A G T C GW-3' PyPyImHpPyIm-y-PyImPyPyHpIm
2720) 5'W C A G T C CW-3' PyPyImHpPyPy-y-ImImPyPyHpIm
2721) 5'W C A G A T TW-3' PyPyImPyHpHp-y-PyPyHppyHplm
2722) 5'W C A G A T AW-3' PypyImPyHpPy-y-HpPyHpPyHpIm
2723) 5'W C A G A T GW-3' PyPyImPyHpIm-y-PyPyHpPyHpIm
2724) 5'W C A G A T CW-3'
PyPyImPyHpPy-y- ImPyFipPyHpIm
2725) 5'W C A G A A TW-3' PyPyImPyPyHp-y-PyHpHpPyHpIm
2726) 5'W C A G A A AW-3' PyPyImPyPyPy-y-HpHpHpPyHpIm
2727) 5'W C A G A A GW-3' 'PyPyImPyPyIm-y-PyHpHpPyHpIm
2728) 5'W C A G A A CW-3' PyPyImPyPyPy-y-ImHpHpPyHpIm
2729) 5'W C A G A G TW-3' PyPyImPyImHp-y-pypyHpPyHpIm
2730) 5'W C A G A G AW-3'
' PyPyImPyImPy-y-HpPyHpPyHpIm
2731) 5'W C A G A G GW-3' PyPyImPyImIm-y-PyPyHpPyHpIm
2732) 5'W C A G A G CW-3' PyPyImPyImPy-y-ImPyHpPyHpIm
2733) 5'W C A G A C TW-3'
PyPyImPyPyHp-y-PyImHpPyHpIm
2734) 5'W C A G A C AW-3' PyPyImPyPyPy-y-HpImHpPyHpIm
2735) 5'W C A G A C GW-3' PyPyImPyPyIm-y-pyImHpPyHpIm
2736) 5'W C A G A C CW-3'
PyPyImPyPyPy-y-ImImHpPyHpIm
CA 02281930 1999-08-18
WO 98137067 PCT/US98/01714
-182-
TABLE 133: 12-ring Hairpin Polyamides for recognition of 8-by S'-WCAGSNNW-3'
DNA sequence aromatic amino acid sequence
2737) 5'W C A G G T T W-3' PyPyImImHpHp-y-PyPyPyPyHpIm
2738) 5~'W C A G G T A W-3' PyPyImImHpPy-y-HpPyPyPyHpIm
2739) 5'W C A G G T G W-3' PyPyImImHpIm-y-PyPyPyPyHpIm
2740) 5'W C A G G T C W-3' PyPyImImHpPy-y-ImPyPyPyHpIm
2741) 5'W C A G G A T W-3' PyPyImImPyHp-y-PyHpPyPyHpIm
2742) 5'W C A G G A A W-3' PyPyImImPyPy-y-HpHpPyPyHpIm
2743) 5'W C A G G A G W-3' PyPyImImPyIm-y-PyHpPyPyHpIm
2744) 5'W C A G G A C W-3' PyPyImImPyPy-y-ImHpPyPyHpIm
2745) 5'W C A G G G T W-3' PyPyImImImHp-y-PyPyPyPyHpim
2746) 5'W C A G G G A W-3' PyPyImImImPy-y-HpPyPyPyHpIm
2747) 5'W C A G G C T W-3' PyPyImImPyHp-y-PyImPyPyHpIm
2748) 5'W CA G G C A W-3' PyPyImImPyPy-y-HpImPyPyHpIm
2749) 5'W CA G C T T W-3' PyPyImPyHpHp-y-PyPyImPyHpIm
2750} 5'W CA G C T A W-3' PyPyImPyHpPy-y-HpPyImPyHpIm
2751) 5'W CA G C T G W-3' PyPyImPyHpIm-y-PyPyImPyHpIm
2752) 5'W CA G C T C W-3' PyPyImPyHpPy-y-ImPyImPyHpIm
2753) 5'W CA G C A T W-3' PyPyImPyPyHp-y-PyHpImPyHpIm
2754) 5'W C A G C A A W-3' PyPyImPyPyPy-y-HpHpImPyHpIm
2755) 5'W C A G C A G W-3' PyPyImPyPyIm-y-PylipImPyHpIm
2756) 5'W C A G C A C W-3' PyPyImPyPyPy-y-ImHpImPyHpIm
2757} 5'W C A G C G T W-3' PyPyImPyImHp-y-PyPyImPyHpIm
2758} 5'W CA G C G A W-3' PyPyImPyImPy-y-HpPyImPyHpIm
2759) 5'W CA G C C T W-3' PyPyImPyPyHp-y-PyImImPyHpIm
2760) 5'W CA G C C A W-3' PyPyImPyPyPy-y-HpImImPyHpIm
2761) 5'W CA G G G G W-3' PyPyImImImIm-y-PyPyPyPyHpIm
2762) 5'W CA G G G C W-3' PyPyImImImPy-y-ImPyPyPyHpIm
2763) 5'W CA G G C G W-3' PyPyImImPyIm-y-PyImPyPyHpIm
2764) 5'W CA G G C C W-3' PyPyImImPyPy-y-ImImPyPyHpIm
2765) 5'W CA G C G G W-3' PyPyImPyImIm-y-PyPyImPyHpIm
2766) 5'W CA G C G C W-3' PyPyImPyImPy-y-ImPyImPyHpIm
2767) 5'W CA G C C G W-3' PyPyImPyPyim-y-PyImImPyHpIm
2768} 5'W CA G C C C W-3' PyPyImPyPyPy-y-ImImImPyHpIm
CA 02281930 1999-08-18
WO 98/37067
-183-
PCT/US98101714
TABLE 134:
12-ring
Hairpin
Polyamides
for recognition
of 8-by
5'-WCATWNNW-3
DNA sequence aromatic amino acid sequence
2769) 5'W C A T PyPyHpHpHpHp-y-pypypypyHpIm
T T T W-3'
2770) .5'W C A T A W-3' PyPyHpHpHpPy-y-HpPyPypyHplm
T T
2771) 5'W C A T T G W-3' PyPyHpHpHpIm-y-PypypypyHpim
T
2772) 5'W C A T T C W-3' PyPyHpHpHpPy-y-ImPyPyPyHpIm
T
2773) 5'W C A T A T W-3' PyPyHpHpPyHp-y-pyHppypyHpIm
T
2774) 5'W C A T A A W-3' PyPyHpHpPyPy-y-HpHpPyPyHpIm
T
2775} 5'W C A T A G W-3' PyPyHpHpPyIm-y-pygppypyHplm
T
2776) 5'W C A T A C W-3' PyPyHpHpPyPy-y-ImHpPypygpIm
T
2777) 5'W C A T G T W-3' PyPyHpHpImHp-y-PypypypyHplm
T
2778) 5'W C A T G A W-3' PyPyHpHpImPy-y-HpPyPyPyHpIm
T
2779) 5'W C A T G G W-3' PyPyHpHpImIm-y-pypypypyHpIm
T
2780) 5'W C A T G C W-3' PyPyHpHpImPy-y-ImPyPyPyHpIm
T
2781) 5'W C A T C T W-3' PyPyHpHpPyHp-y-PyImPyPyHpIm
T
2782) 5'W C A T C A W-3' PyPyHpHpPyPy-y-HpImPyPyHpIm
T
2783) 5'W C A T C G W-3' PyPyHpHpPyIm-y-pyImPyPyHpIm
T
2784) 5'W C A T C C W-3' PyPyHpHpPyPy-y-ImImPyPyHpIm
T
2785) 5'W C A T T T W-3' PyPyHpPyHpHp-y-PyPyHppyHpIm
A
2786) 5'W C A T T A W-3' PyPyI-ippygpp~,_y-HpPyHpPyHpIm
A
2787) 5'W C A T T G W-3' PyPyHpPyHpIm-y-pypyHppyHpIm
A
2788) 5'W C A T T C W-3' PyPyHpPyHpPy-y-ImPyHpPyHpIm
A
2789) 5'W C A T A T W-3' yPyHpPyPyHp-y-PyHpHpPyHpIm
A P
2790) 5'W C A T A A W-3' PypyHpPyPypy-y-HpHpHpPyHpIm
A
2791) 5'W C A T A G W-3' PypyHppypylm-y-PyHpHpPyHpIm
A
2792) 5'W C A T A C W-3' PyPyHpPyPyPy-y-ImHpHpPyHpim
A
2793) 5'W C A T G T W-3' pyPyHpPyImHp-y-pypygppyHpIm
A
2794) 5'W C A T G A W-3' PyPyHpPyImPy-y-HpPyHpPyHpIm
A
2795) 5'W C A T G G W-3' PyPyHpPyImIm-y-pypygppyHPIm
A
2796) 5'W C A T G C W-3' PyPyHpPyImPy-y-ImPyHpPyHpIm
A
2797) 5'W C A T C T W-3' PyPyHpPyPyHp-y-PyImHpPyHpIm
A
2798) 5'W C A T C A W-3' PyPyHpPyPyPy-y-HpImHpPyHpIm
A
2799) 5'W C A T C G W-3' PyPyHpPyPyIm-y-PyImHpPyHpIm
A
2800) 5'W C A T C C W-3' PyPyHpPyPyPy-y-ImImHpPyHpIm
A
CA 02281930 1999-08-18
WO 98/37067
-184-
PCT/US98/01714
TABLE 135: 12-ring Hanpm
Polyamides for recogmt~on
of 8-by 5'-WCATSNNW-3'
DNA sequence aromatic
amino acid sequence
2801) 5'W C PyPyHpImHpHp-y-pypypypyHprm
A T G T T PyPyHpImHpPy-y-HpPyPyPyHpIm
W-3' PyPyHpImHpIm-y-pypypypyHplm
2802) 5'W C PyPyHpImHppy-y-ImPyPypyHplm
A T G T A PyPyHpImPyHp-y-pygppypyHplm
W-3' PyPyHpImPyPy-y-HpHppypyHpIm
2803) 5'W C PyPyHpImPyIm-y-pyHppypyHpIm
A T G T G PyPyHpImPyPy-y-ImHppypyHplm
W-3' PypyHpImImHp_y-pypypypyHplm
2804) 5'W C PyPyHpImImPy-y-HppypypyHpIm
A T G T C PypyHpImPyHp-y-pyImPyPyHpIm
W-3' PyPyHpImpypy_y-HpImPyPyHpIm
2805) 5'W C PyPyHpImImIm-y-pypypypyHpim
A T G A T PyPyHpImImPy-y-ImpypypyHpIm
W-3' PyPyHpImPyIm-y-pylmpypyHpIm
2806) 5'W C PypyHpImPyPy-y-ImImPyPyHpIm
A T G A A PyPyHppyHpHp-y-pypyimPyHpIm
W-3' PyPyHpPyHpPy-y-HppyImPyHpIm
2807) 5'W PypyHpPyHpIm-y-PypyImPyHpIm
C A T G A pyPyHpPyHpPy-y-ImPyImPyHpIm
G W-3' PypyHpPypygp-y_pyHpImPyHpIm
2808) 5'W C PyPyHpPyPypy-y-HpHpImPyHpIm
A T G A C PyPygppypylm-y_pyHpImPyHpIm
W-3' PyPyHpPypypy-y-ImHpImPyHpIm
2809) 5'W C PypyHppyl~p-y-pypyImPyHpIm
A T G G T PyPyHpPyImPy-y-HpPyImPyHpIm
W-3' PyPyHpPypyHp-y-pyImImPyHpIm
2810) 5'W C PyPyHpPyPypy-y-HpImImPyHpIm
A T G G A pypyHppyImIm-y-pypyImPyHpIm
W-3' PyPyHppylmpy_y_ImpyImPyHpIm
2811) 5'W C PyPyHpPyPyIm-y-pyImImPyHpIm
A T G C T PyPyHpPyPyPy-y-ImImImPyHpIm
W-3'
2812) 5'W
C A T G C
A W-3'
2813) 5'W C
A T G G G
W-3'
2814) 5'W C
A T G G C
W-3'
2815) 5'W C
A T G C G
W-3'
2816) 5'W C
A T G C C
W-3'
2817) 5'W
C A T C T
T W-3'
2818) 5'W C
A T C T A
W-3'
2819) 5'W C
A T C T G
W-3'
2820) 5'W C
A T C T C
W-3'
2821) 5'W C
A T C A T
W-3'
2822) 5'W
C A T C A
A W-3'
2823) 5'W C
A T C A G
W-3'
2824) 5'W C
A T C A C
W-3'
2825) 5'W C
A T C G T
W-3'
2826) 5'W C
A T C G A
W-3'
2827) 5'W
C A T C C
T W-3'
2828) 5'W C
A T C C A
W-3'
2829) 5'W C
A T C G G
W-3'
2830) 5'W C
A T C G C
W-3'
2831) 5'W C
A T C C G
W-3'
2832) 5'W
C A T C C
C W-3'
CA 02281930 1999-08-18
WO 98/37067
-18S-
PCT1US98/Ol ? 14
TABLE
136:
12-ring
Hairpin
Polyamides
for recognition
of 8-by
5'-WCAAWNNW-3'
DNA aromatic amino acid sequence
sequence
' 2833) 5'W C PyPYpyHpHpHp-y-pypypyHpHpim
A
A
T
T
T
W-3'
' S 2834) 5'W C T A W-3' pypypyHpHppy_y_HppypyHpHpIm
A
A
T
2835) 5'W C A T T G W-3' PyPyPyHpHpIm-y-PypypygpHplm
A
2836) 5'W C A AT T C W-3' PYPypyHpHpPy-y-ImPyPyHpHpIm
2837) 5'W C A AT A T W-3' PyPyPyHppyHp-Y_pyHppyHpHpIm
2838) 5'W C A AT A A W-3' PYPyPyHpPYPy-y-HpHpPyHpHpIm
2839) 5'W C A AT A G W-3' PyPyPyHpPyIm-y-PyHpPYHpHpIm
2840) 5'W C A AT A C W-3' PyPyPYHpPYPy-Y-ImHppyHpHpIm
2841) 5'W C A AT G T W-3' PyPypyHpImHp-y-pypypygpHpIm
2842) 5'W C A AT G A W-3' PyPypyHpImPy-Y-HpPyPyHpHpIm
2843) 5'W C A AT G G W-3' PYPyPyHpImIm-Y-PypypYHpHpIm
1S 2844) 5'W C A AT G C W-3'
PYPyPyHpImPy-y-ImPyPyHpHpIm
2845) 5'W C A AT C T W-3' PyPypyHpPYHp-y-PyImPyHpHpIm
2846) 5'W C A AT C A W-3' PyPyPyHpPyPy-y-HpImPyHpHpIm
2847) 5'W C A AT C G W-3' PyPypyHppYIm-y-PYImPyHpHpIm
2848) 5'W C A AT C C W-3' Pypypygppypy_Y_ImImPyHpHpIm
2849) 5'W C A AA T T W-3' PyPypypygpHp-y-PYPYHpHpHpIm
2850) 5'W C A AA T A W-3' PyPyPyPYHpPy-Y-HpPyHpHpHpim
2851) 5'W C A AA T G W-3' PyPyPypyHpIm-y-PYpyHpHpHpIm
2852) 5'W C A AA T C W-3' PyPyPyPyHpPy-y-ImPyHpHpHpIm
2853) 5'W C A AA A T W-3' PypypypypYHp_Y_pYHpHpHpHpIm
2854) 5'W C A AA A A W-3' PyPyPYPyPyPy-Y-HpHpHpHpHpIm
2855) 5'W C A AA A G W-3' PYPyPyPyPyIm-y-PyHpHpHpHpIm
2856) 5'W C A AA A C W-3' PYPypypypypy-y_ImHpHpHpHpIm
2857) 5'W C A AA G T W-3' PyPyPYPyImHp-Y-PypyHpHpHpIm
2858) 5'W C A AA G A W-3' Pypypypylmpy_y-HpPYHpHpHpIm
2859) 5'W C A AA G G W-3' PyPyPypyImlm-y-PYPYHpHpHpIm
2860 ) 5' C A AA G C W-3 ' PyPyPypyImpY_y_ ImPYHpHpHpIm
W
2861) 5'W C A AA C T W-3' PYPyPyPyPyHp-Y-PyImHpHpHpIm
2862) 5'W C A AA C A W-3' PyPyPYpypypy-y-HpImHpHpHpIm
2863) 5'W C A AA C G W-3' PyPypypypYlm_y_pyImHpHpHpIm
3S 2864 ) 5' C A AA C C W-3 ' pypypypypypy-y_ ImImHpHpHpIm
W
CA 02281930 1999-08-18
WO 98137067
PCT/US98101714
-186-
TABLE
137:
12-ring
Hairpin
Polyamides
for
recognition
of
8-by
5'-WCAASNNW-3'
DNA aromatic amino acid sequence
sequence
2865) 5'W C A A GT T w-3' PyPyPyImHpHp-y-pypypyHpHpIm
2866) - C A A GT A W-3' PyPyPyImHpPy-y-HpPyPyHpHpIm
5'
W
2867) 5'W C A A GT G W-3' PyPyPyImHpIm-y-PyPyPyHpHpIm
2868) 5'W C A A GT C W-3' PyPyPyImHpPy-y-ImPyPyHpHpIm
2869) 5'W C A A GA T W-3' PyPyPyImPyHp-y-PyHpPyHpHpIm
2870) 5'W C A A GA A W-3' PyPyPyImPyPy-y-HpHpPyHpHpIm
2871) 5'W C A A GA G W-3' PyPyPyImPyIm-y-PyHpPyHpHpIm
2872) 5'W C A A GA C W-3' PyPyPyImPyPy-y-ImHpPyHpHpIm
2873) 5'W C A A GG T W-3' PyPyPyImImHp-y-PyPyPyHpHpIm
2874) 5'W C A A GG A W-3' PyPyPyImImPy-y-HpPyPyHpHpIm
2875) 5'W C A A GC T W-3' PyPyPyImPyHp-y-PyImPyHpF3pIm
2876) 5'W C A A GC A W-3' PyPyPyImPyPy-y-HpImPyHpHpIm
2877) 5'W C A A GG G W-3' PyPyPyImImIm-y-PyPyPyHpHpIm
2878) 5'W C A A GG C W-3' PyPyPyImImPy-y-ImPyPyHpHpIm
2879) 5'W C A A GC G W-3' PyPyPyImPyIm-y-PyImPyHpHpIm
2880) 5'W C A A GC C W-3' PyPyPyImPyPy-y-ImImPyHpHpIm
2881) 5' C A A CT T W-3' PyPyPyPyHpllp-y-PyPyImHpHpIm
W
2882) 5'W C A A CT A W-3' PyPyPyPyHpPy-y-HpPyImHpHpIm
2883) 5'W C A A CT G W-3' PyPyPyPyHpIm-y-PypyImHpHpIm
2884) 5'W C A A CT C W-3' PyPyPyPyHpPy-y-ImPyImHpHpIm
2885) 5'W C A A CA T W-3' PyPyPyPyPyHp-y-PyHpImHpHpIm
2886) 5'W C A A CA A W-3' PyPyPyPyPyPy-y-HpHpImHpHpIm
2887) 5'W C A A CA G W-3' PyPyPyPyPyIm-y-PyHpImHpHpIm
2888) 5'W C A A CA C W-3' pyPypypypypy-y-I~pImHpHpIm
2889) 5'W C A A CG T W-3' PyPyPyPyImHp-y-PyPyImHpfIpIm
2890) 5'W C A A CG A W-3' PyPyPyPyImPy-y-HpPyImHpHpIm
2891) 5'W C A A CC T W-3' PyPyPyPyPyHp-y-PyImImHpHpIm
2892) 5'W C A A CC A W-3' PyPyPyPyPyPy-y-HpImImHpHpIm
2893) 5'W C A A CG G W-3' PyPyPyPyImIm-y-PyPyImHpHpIm
2894) 5'W C A A CG C W-3' PypypypyImPy-y-ImPyImHpHpIm
2895) 5'W C A A CC G W-3' PyPyPyPyPyIm-y-PyImImHpHpIm
3$ 2896) 5'W C A A CC C W-3' PyPyPyPyPyPy-y-ImImImHpHpIm
CA 02281930 1999-08-18
WO 98/37067
PCT/US98/01714
-187-
TABLE 138: 12-ring
Hairpin Polyamides
for recognition
of 8-by 5'-WCACWNNW-3'
DNA aromatic amino acid sequence
sequence
2897) 5'W C A C TT T W-3' PyPyPyHpHpHp-y-PyPyPyImHpIm
2898) 5'W C A C TT A W-3'
PYPYPYHPHPPY-y-HPPYPYI~PIm
2899) 5'W C A C TT G W-3' PyPyPyHpHpIm-y-PyPypyl~plm
2900) 5'W C A C TT C W-3' PYPYPyHpHppy_y-ImPYPyImHpIm
2901) 5'W C A C TA T W-3' PyPyPyHpPyHp-y-PyHpPyImHpIm
2902) 5'W C A C TA A W-3' PyPyPyHpPyPy-y-HpHpPyImHpIm
2903) 5'W C A C TA G W-3' PyPyPyHpPyIm-y-PyHpPyImHpIm
2904) 5'W C A C T A C W-3' PyPyPyHpPyPy-y-ImHpPyImHpIm
2905) 5'W C A C T G T W-3' PYpypygpl~p-y_pypypyl~plm
2906) 5'W C A C T G A W-3' PyPyPyHpImPy-y-HpPyPyImHpIm
2907) 5'W C A C T G G W-3' PyPyPyHpImIm-y-PypypyImHpIm
2908) 5'W C A C T G C W-3' PyPyPyHpImPy-y-ImPyPyImHpIm
2909) 5'W C A C T C T W-3' PyPyPyHpPyHp-y-PyImPyImHpIm
2910) 5'W C A C T C A W-3' PyPyPyHpPyPy-y-HpImPyImHpIm
2911) 5'W C A C TC G W-3' PyPyPyHpPyIm-y-PyImPyImHpIm
2912) 5'W C A C TC C W-3' PyPyPyHpPypy-y-ImImPyImHpIm
2913} 5'W C A C AT T W-3' PyPyPyPyHpHp-y-PypyHpImHpIm
2914) 5'W C A C AT A W-3' PyPyPyPyHpPy-y-HpPyHPImHpIm
2915) 5'W C A C AT G W-3' PyPyPyPyHpIm-y-PyPyHpImHpIm
2916) 5'W C A C AT C W-3' PyPyPypyHPPy-y-ImPyHpImHpIm
2917) 5'W C A C AA T W-3' PyPyPyPyPyHp-y-PyHpHpImHpIm
2918) 5'W C A C AA A W-3' PyPyPyPyPypy-y-HpHpHPImHpIm
2919) 5'W C A C AA G W-3' ~PyPyPyPyPyIm-y-PyHpHpImHpIm
2920) 5'W C A C AA C W-3' PyPyPyPyPypy-y-ImHpHpImHpIm
2921) 5'W C A C AG T W-3' PyPyPyPyImHp-y-PyPyHpImHpIm
2922) 5'W C A C AG A W-3' PyPyPyPyImPy-y-HpPyHpImHpIm
2923) 5'W C A C AG G W-3' PyPyPyPyImIm-y-PyPyHpImHpIm
2924) 5'W C A C AG C W-3' PyPyPyPyImPy-y-ImPyHPImHpIm
- 2925) 5'W C A C AC T W-3' PypypypypyHp-y_pyl~pImHpIm
2926) 5'W C A C AC A W-3' PyPyPyPyPyPy-y-HpImHpImHpIm
- 2927) 5'W C A C AC G W-3' PyPyPyPyPyIm-y-PyImHpImHpIm
2928) 5'W C A C AC C W-3' PyPyPyPyPyPy-y-ImImHpImHpIm
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-188-
TABLE
139:
12-ring
Hairpin
Polyamides
for recognition
of 8-by
5'-WCACSNNW-3'
DNA aromatic amino acid sequence
sequence
2929) 5'W C A CG T T W-3' PyPyPyImHpHp-y-PyPyPyImHpIm
2930) 5~'WC A CG T A W-3' PyPyPyImHpPy-y-HpPyPyImHpIm
2931) 5'W C A CG T G W-3' PyPyPyImHpIm-y-PyPyPyImHpIm
2932) 5'W C A CG T C W-3' PyPyPyImHpPy-y-ImPyPyImHpIm
2933) 5'W C A CG A T W-3' PyPyPyImPyHp-y-PyHpPyImHpIm
2934) 5'W C A CG A A W-3' PyPyPyImPyPy-y-HpHpPyImHpIm
2935) 5'W C A CG A G W-3' PyPyPyImPyIm-y-PyHpPyImHpIm
2936) 5'W C A CG A C W-3' PyPyPyImPyPy-y-ImHpPyImHpIm
2937) 5'W C A CG G T W-3' PyPyPyImImHp-y-PyPyPyImHpIm
2938) 5'W C A CG G A W-3' PyPyPyImImPy-y-HpPyPyImHpIm
2939) 5'W C A CG C T W-3' PyPyPyImPyHp-y-PyImPyImHpIm
2940) 5'W C A CG C A W-3' PyPyPyImPyPy-y-HpImPyImHpIm
2941) 5'W C A CC T T W-3' PyPyPyPyHpHp-y-PyPyImImI~ipIm
2942) 5'W C A CC T A W-3' PyPyPyPyHpPy-y-HpPyImImHpIm
2943) 5'W C A CC T G W-3' PyPyPyPyHpIm-y-PyPyImImHpIm
2944) 5'W C A CC T C W-3' PyPyPyPyHpPy-y-ImPyImImHpIm
2945) 5'W C A CC A T W-3' PyPyPyPyPyHp-y-PyHpImImHpIm
2946) 5'W C A CC A A W-3' PyPyPyPyPyPy-y-HpHpImImHpIm
2947) 5'W C A CC A G W-3' PyPyPyPyPyIm-y-PyHpImImHpIm
2948) 5'W C A CC A C W-3' PyPyPyPyPyPy-y-ImApImImHpIm
2949) 5'W C A CC G T W-3' PyPyPyPyImHp-y-PyPyImImHpIm
2950) 5'W C A CC G A W-3' PyPyPyPyImPy-y-HpPyImImHpIm
2951) 5'W C A CC C T W-3' ~PyPyPyPyPyHp-y-PyImImImHpim
2952) 5'W C A CC C A W-3' PyPyPyPyPyPy-y-HpImImImHpIm
2953) 5'W C A CG G G W-3' PyPyPyImImIm-y-PyPyPyImHpIm
2954) 5'W C A CG G C W-3' PyPyPyImImPy-y-ImPyPyImHPIm
2955) 5'W C A CG C G W-3' PyPyPyImPyIm-y-PyImPyImHpIm
2956) 5'W C A CG C C W-3' PyPyPyImPyPy-y-ImImPyImHpIm
2957) 5'W C A CC G G W-3' PyPyPyPyImIm-y-PyPyImImHpIm
2958) 5'W C A CC G C W-3' PyPyPyPyImPy-y-ImPyImImHpIm
2959) 5'W C A CC C G W-3' PyPyPyPyPyIm-y-PyImImImHpIm
2960) 5'W C A CC C C W-3' PyPyPyPyPyPy-y-ImImImImHpIm
CA 02281930 1999-08-18
WO 98/37067 PCT/US98101714
-189-
1A13Lt; I2-ring
140: Hairpin
Polyamides
for
recognition
of
8-by
5'-WCTGWNNW-3'
DNA aromatic amino acid sequence
sequence
' 2961) 5'W C TG T T T W-3'
PyHpImHpHpHp-y-PyPyPyPyPyIm
2962) ~5'W C TG T T A W-3'
PyHpImHpHpPy-y-HpPyPyPyPyIm
2963) 5'W C TG T T G W-3' PyHpImHpHpIm-y-Pypypypypylm
2964) 5'W C TG T T C W-3'
PyHpImHpHpPy-y-ImPyPyPyPyIm
2965) 5'W C TG T A T W-3' PyHpImHpPyHp-y-pyHpPyPyPyIm
2966) 5'W C TG T A A W-3' PyHpImHpPyPy-y-HpHpPyPypyIm
2967) 5'W C TG T A G W-3' PyHpImHpPyIm-y-PyHpPyPyPyIm
296$) 5'W C TG T A C W-3' PyHpImHpPyPy-y-ImHpPyPYPyIm
2969) 5'W C TG T G T W-3' PyHpImHpImHp-Y-PypypypyPyIm
2970) 5'W C TG T G A W-3' PyHpImHpImPy-y-HpPyPyPyPyIm
2971) 5'W C TG T G G W-3' PyHpImHpImIm-y-PypypypypyIm
I5 2972) 5'W C TG T G C W-3' PyHpImHpImPy-y-ImPyPyPyPyIm
2973) 5'W C TG T C T W-3' PyHpImHpPyHp-y-PyImPyPyPyIm
2974) 5'W C TG T C A W-3' PyHpImHpPyPy-y-HpImPyPyPyIm
2975) 5'W C TG T C G W-3' PyHpImHpPyIm-y-PyImPyPyPyIm
2976) 5'W C TG T C C W-3' PyHpImHpPyPy-y-ImImPyPyPyIm
2977) 5'W C TG A T T W-3' PyHpImPyHpHp-y-pypyHpPyPyIm
2978) 5'W C TG A T A W-3' PyHpImPyHpPy-y-HpPyHpPyPyIm
2979) 5'W C TG A T G W-3' PyHpImPyHpIm-y-PyPyHpPyPyIm
2980) 5' C TG A T C W-3' PyHpImPyHpPy-y-ImPyHpPyPyIm
W
2981) 5'W C TG A A T W-3' PyHpImPyPyHp-y-PyHpHpPyPyIm
2982) 5'W C TG A A A W-3' PyHpImPyPyPy-y-HpHpHpPyPyIm
2983) 5'W C TG A A G W-3' PyHpImPyPyIm-y-PyHpHpPyPyim
2984) 5'W T GA A C W-3' PyHpImPyPyPy-y-ImHpHpPyPyIm
C
2985) 5'W T GA G T W-3' PyHpImPyImHp-y-PyPyHpPyPyIm
C
2986) 5'W T GA G A W-3' PyHpImPyImPy-y-HpPyHpPyPyIm
C
2 9 87 5' T GA G G W-3 ' PyHpImPyImIm-y-Pypygppypylm
) W
C
2988) 5'W T GA G C W-3' PyHpImPyImPy-y-ImPyHpPyPyIm
C
2989) 5'W T GA C T W-3' PyHpImPyPyHp-y-PyImHpPyPyIm
C
2990) 5'W T GA C A W-3' PyHpImPyPyPy-y-HpImHpPyPyIm
C
2991) 5'W T GA C G W-3' PyHpImPyPyIm-y-PyImHpPyPyIm
C
2992) 5'W T GA C C W-3' PyHpImPyPyPy-y-ImImHpPyPyIm
C
CA 02281930 1999-08-18
WO 98/37067 PCTIUS98/01714
-190-
TABLE 141:
12-ring
Hairpin
Polyamides
for
recognition
of
8-by
5'-WCTGSNNW-3'
DNA aromatic amino acid sequence
sequence
2993) 5'W C TG G T T W-3' PyHpIrnImHpHp-~-PyPyPyPyPyIm
2994) 5.'WC TG G T A W-3' PyHpImImHpPy-y-HpPyPyPyPyIm
2995) 5'W C TG G T G W-3' PyHpImImHpIm-y-PyPyPyPyPyIm
2996) 5'W C TG G T C W-3' PyHpImImHpPy-y-ImPyPyPyPyIm
2997) 5'W C TG G A T W-3' PyHpImImPyHp-'y-PyHpPyPyPyIm
2998) 5'W C TG G A A W-3' PyHpImImPyPy-~y-HpHpPyPyPyIm
2999) 5'W C TG G A G W-3' PyHpImImPyIm-'y-PyHpPyPyPyIm
3000) 5'W C TG G A C W-3' PyHpImImPyPy-y-ImHpPyPyPyIm
3001) 5'W C TG G G T W-3' PyHpImImImHp-y-PyPyPyPyPyIm
3002) 5'W C TG G G A W-3' PyHpIrnImImPy-y-HpPyPyPyPyim
3003) 5'W C TG G C T W-3' PyHpImImPyHp-y-PyImPyPyPyIm
3004) 5'W C TG G C A W-3' PyHpImImPyPy-y-HpImPyPyPyIm
3005) 5'W C TG C T T W-3' PyHpImPyHpHp-y-PyPyImPyPyIm
3006) 5'W C TG C T A W-3' PyHpImPyHpPy-~y-HpPyImPyPyIm
3007 ) 5' C TG C T G W-3' PyHpImPyHpIm-y-PyPyImPyPyIm
W
3008) 5'W C TG C T C W-3' PyHpImPyFipPy-y-ImPyImPyPyIm
3009) 5'W C TG C A T W-3' PyHpImPyPyHp-y-PyHpImPyPyim
3 O 10 5' C TG C A A W-3 PyHpImPyPyPy-y-HpHpImPyPyIm
) W '
3011) 5'W C TG C A G W-3' PyHpImPyPyIm-~y-PyHpImPyPyim
3012) 5'W C TG C A C W-3' PyHpImPyPyPy-~y-ImHpImPyPyIm
3013) 5'W C TG C G T W-3' PyHpImPyImHp-y-PyPyImPyPyIm
3 014 5' C TG C G A W-3 PyHpImPyImPy-'y-HpPyImPyPyIm
) W '
3015) 5'W C TG C C T W-3' 'PyHpImPyPyHp-y-PyImImPyPyIm
3016) 5'W C TG C C A W-3' PyHpImPyPyPy-y-HpImImPyPyIm
3017) 5'W C TG G G G W-3' PyHpImImImIm-y-PyPyPyPyPyIm
3018) 5'W C TG G G C W-3' PyHpImImImPy-y-ImPyPyPyPyIm
3019) 5'W C TG G C G W-3' PyHpImImPyIm-y-PyImPyPyPyIm
3020) 5'W C TG G C C W-3' PyHpImImPyPy-y-ImImPyPyPyIm
3021) 5'W C TG C G G W-3' PyHpImPyImIm-y-PyPyImPyPyIm
3022) 5'W C TG C G C W-3' PyHpImPyImPy-y-ImPyImPyPyIm
3023) 5'W C TG C C G W-3' PyHpImPyPyIm-y-PyImImPyPyIm
3024) 5'W C TG C C C W-3' PyHpImPyPyPy-y-ImImImPyPyIm
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-191-
TABLE 142: r recognition of 8-by 5'-WCTTWNNW-3'
12-ring
Hairpin
Polyamides
fo
DNA sequence
aromatic amino acid sequence
3025) 5'W C T T PyHpHpHpHpHp-y-pypypypypylm
T T T W-3'
' 5 3026) ~ 5'W C T PyHpHpHpHpPy-y-HpPyPyPypylm
T T T A
W-3'
3027) 5'W C T T PyHpHpHpHpIm-y-PyPypypypylm
T T G W-3'
3 028 5' W C T PyHpHpHpHpPy-y-ImPyPypypylm
) T T T C
W-3 '
3029) 5'W C T T A PyHpHpHpPyHp-y-pyHpPypypylm
T T
W-3'
3030) 5'W C T T A A W-3' PyHpHpHpPyPy-y-Hpgppypypylm
T
3031) 5'W C T T A G W-3' PyHpHpHpPyIm-y-PyI-lppypypylm
T
3032) 5'W C T T A C W-3' PyHpHpHpPyPy-y-ImHPPYPYPyIm
T
3033) 5'W C T T G T W-3' PyHpHpHpImHp-y-Pypypypypylm
T
3034) 5'W C T T G A W-3' PyHpHpHpImPy-y-HpPYPYPYPyIm
T
3035) 5'W C T T G G W-3' PyHpHpHpImIm-y-pypypypypylm
T
3036) 5'W C T T G C W-3' PyHpHpHpImPy-y-ImPyPyPyPyIm
T
3037) 5'W C T T C T W-3' PyHpHpHpPyHp-y-Pylmpypypylm
T
3038) 5'W C T T C A W-3' PyHpHpHpPyPy-y-HpImPyPypylm
T
3 03 5' W C T C G W- 3 ' PyHPHpHpPyIm-y-PyImPyPyPyIm
9 ) T T
3 04 5' W C T C C W-3 ' PyHpHpHpPyPy-y- ImImPyPyPyIm
0 ) T T
3041) 5'W C T T T T W-3' PyHpHpPyHpHp-y-PypyHpPyPyim
A
3 042 5' W C T T A W-3 ' PyHpHpPyHpPy-y-HpPyHpPYPyIm
) T A
3043) 5'W C T T T G W-3' PyHpHpPyHpIm-y-pypygppypylm
A
3044) 5'W C T T T C W-3' PyFipI-IpPyHpPy-y-ImPyHpPyPyIm
A
3045) 5'W C T T A T W-3'
A pYHPHPPYPYHP-Y-pYHPHPPYPYIm
3046) 5'W C T T A A W-3' PyHpHpPyPyPy-y-HpgpHPPyPyIm
A
3047) 5'W C T T A G W-3' ' PyHpHpPyPyIm-y-pyHpHpPyPyIm
A
3 04 5' W C T A C W-3 ' PyHpHpPyPyPy-y- ImHpHpPyPyIm
8 ) T A
3049) 5'W C T T G T W-3' PyHpHpPyImHp-y-PypyHpPypyIm
A
3 050 5' W C T G A W-3 ' PyHpHpPyImPy-y-HpPyHpPypyIm
) T A
3051) 5'W C T T G G W-3' PyHpHpPyImIm-y-PypyHppypylm
A
3052) 5'W C T T G C W-3' PyHpHpPyImPy-y-ImPyHPPYPyIm
A
' 3053) 5'W C T T C T W-3' PyHpHpPyPyHp-y-pylmgppypy=m
A
3054) 5'W C T T C A W-3' PyHpHppypypy-Y-HpImHpPyPyIm
A
3055) 5'W C T T C G W-3' PyHpHpPyPyIm-y-pylmI-ippypylm
A
3056) 5'W C T T C C W-3' PyHpHpPyPyPy-y-ImImHpPyPyIm
A
CA 02281930 1999-08-18
WO 98/37067 PCTIUS98101714
-192-
TABLE
143:
12-ring
Hairpin
Polyamides
for
recognition
of
8-by
5'-WCTTSNNW-3'
DNA aromatic amino acid sequence
sequence
3057) 5'W C T TG T T W-3' PyHpHpImHpHp-y-PyPyPyPyPyIm
3058) 5'W C T TG T A W-3' PyHpHpImHpPy-y-HpPyPyPyPyIm
3059) 5'W C T TG T G W-3' PyHpHpImHpIm-y-PyPyPyPyPyIm
3060) 5'W C T TG T C W-3' PyHpHpImHpPy-y-ImPyPyPyPyIm
3061) 5' C T TG A T W-3' PyHpHpImPyHp-y-PyHpPyPyPyIm
W
3062) 5'W C T TG A A W-3' PyHpHpImPyPy-y-HpHpPyPyPyIm
3063) 5'W C T TG A G W-3' PyHpHpImPyIm-y-PyHpPyPyPyIm
3064) 5'W C T TG A C W-3' PyHpHpImPyPy-y-ImHpPyPyPyIm
3065) 5'W C T TG G T W-3' PyHpHpImImHp-y-PyPyPyPyPyIm
3066) 5'W C T TG G A W-3' PyHpHpImImPy-y-HpPyPyPyPyIm
3067) 5'W C T TG C T W-3' PyHpHpImPyHp-y-PyImPyPyPyIm
3068) 5'W C T TG C A W-3' PyHpHpImPyPy-y-HpImPyPyPyIm
3069) 5'W C T TG G G W-3' PyHpHpImImIm-y-PyPyPyPyPyIm
3 07 0 5' C T TG G C W-3 ' PyHpHpImImPy-y- ImPyPyPyPyIm
) W
3071) 5'W C T TG C G W-3' PyHpHpImPyIm-y-PyImPyPyPyIm
3072) 5'W C T TG C C W-3' PyHpHpImPyPy-y-ImImPyPyPyIm
3073) 5'W C T TC T T W-3' PyHpHpPyHpHp-y-PyPyImPyPyIm
3 074 5' C T TC T A W-3 ' PyHpHpPyHpPy-y-HpPyImPyPyIm
) W
3 07 5 5' C T TC T G W-3 ' PyHpHpPyHpIm-y-PyPyImPyPyIm
) W
3076) 5'W C T TC T C W-3' PyHpHpPyHpPy-y-ImPyImPyPyIm
3077) 5'W C T TC A T W-3' PyHpHpPyPyHp-y-PyHpImPyPyIm
3 07 8 5' C T TC A A W-3 ' PyHpHpPyPyPy-y-HpHpImPyPyIm
) W
3079) 5'W C T TC A G W-3' 'PyHpFIpPyPyIm-y-PyHpImPyPyIm
3080) 5'W C T TC A C W-3' PyHpHpPyPyPy-y-ImHpImPyPyIm
3081) 5'W C T TC G T W-3' PyHpHpPyImHp-y-PyPyImPyPyIm
3 082 5' C T TC G A W-3 ' PyHpHpPyImPy-y-HpPyImPyPyIm
) W
3083) 5'W C T TC C T W-3' PyHpHpPyPyHp-y-PyImImPyPyIm
3084) 5'W C T TC C A W-3' PyHpHpPyPyPy-y-HpImImPyPyIm
3085) 5'W C T TC G G W-3' PyHpHpPyImIm-y-PyPyImPyPyIm
3086) 5'W C T TC G C W-3' PyHpHpPyImPy-y-ImPyImPyPyIm
3087) 5'W C T TC C G W-3' PyHpHpPyPyIm-y-PyImImPyPyIm
3088) 5'W C T TC C C W-3' PyHpHpPyPyPy-y-ImImImPyPyIm
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-193-
TABLE
144:
12-ring
Hairpin
Polyamides
for
recognition
of
8-by
5'-WCTAWNNW-3'
DNA aromatic amino acid sequence
sequence
3089) 5'W C T A TT T W-3' PyHpPyHpHpHp-y-PyPypyHpPyIm
S 3090) 5'W C T A TT A W-3' PyHpPyHpHpPy-y-HpPyPyHpPyIm
3091) 5'W C T A TT G W-3' PyHpPyHpHpIm-y-Pypypygppylm
3092) 5'W C T A TT C W-3' PyHpPyHpHpPy-y-ImPyPyHpPyIm
3093) 5'W C T A TA T W-3' PyHpPyHpPyHp-y-pyHpPyHpPyIm
3 0 94 5' C T A TA A W-3 ' PyHpPyHpPyPy-y-HpHpPyHpPyIm
) W
3 095 5' C T A TA G W-3 ' PyHpPyHpPyIm-y-PyHpPyHpPyIm
) W
3096) 5'W C T A TA C W-3'
pYHPPYHPPYPY-Y-ImHppyHppyIm
3097) 5'W C T A TG T W-3'
PYHPPYHPImHp-y-PyPyPyHpPyim
3 098 5' C T A TG A W-3 ' PyHppyHpImPy-y-HpPyPyHpPyIm
) W
3099) 5'W C T A TG G W-3' PyHpPyHpImIm-y-Pypypygppylm
3100) 5'W C T A TG C W-3'
PyHpPyHpImPy-y-ImPyPyHpPyIm
3101) 5'W C T A TC T W-3' PyHpPyHpPyHp-y-PyImPyHpPyIm
3102 5' C T A TC A W-3 ' PyHpPyHpPyPy-y-HpImPyHpPyIm
) W
3103 5' C T A TC G W-3 ' PyHppyHppylm-y_pyImPYHpPyIm
) W
3104 5' C T A TC C W-3' PyHpPyHpPyPy-y-ImImPyHpPyIm
) W
3105) 5'W C T A AT T W-3' PyHpPyPyHpHp-y-PypyHpHpPyIm
3106) 5'W C T A AT A W-3' PyHpPyPyHpPy-y-HpPyHpHpPyIm
3107) 5'W C T A AT G W-3' PyHpPyPyHpIm-y-PyPyHpHpPyIm
3108) 5'W C T A AT C W-3' PyHpPyPyHpPy-y-ImPyHpHpPyIm
3109) 5'W C T A AA T W-3' PyHpPyPyPyHp-y-PyHpHpHpPyIm
3110 5' C T A AA A W-3 ' PyHpPyPyPyPy-y-HpHpHpHpPyIm
) W
3111) 5'W C T A AA G W-3' PyHpPyPyPyIm-y-PyHpHpHpPyIm
3112) 5'W C T A AA C W-3' PyHpPyPyPyPy-y-ImHPHpHppyIm
3113 5' C T A AG T W-3 ' PyHpPyPyImHp-y-PyPyHpHpPyIm
) W
3114 5' C T A AG A W-3' PyHpPyPyImPy-y-HpPyHpHpPyIm
) W
3115) 5'W C T A AG G W-3' PyHpPyPyImIm-y-pyPyHpHpPyIm
3116) 5'W C T A AG C W-3'
PYHPPYPYImPy-y-ImPyHpHpPyIm
3117 5' C T A AC T W-3 ' PyHpPyPyPyHp-y-PyImHpHpPyIm
) W
3118 5' C T A AC A W-3 ' PyHpPyPyPyPy-y-HpImHpHpPyIm
) W
3119 5' C T A AC G W-3 ' PyHpPyPyPyIm-y-PyImHpHpPyIm
) W
3120) 5'W C T A AC C W-3' PyHpPyPyPyPy-y-ImImHpHpPyIm
CA 02281930 1999-08-18
WO 98137067 PCT/US98/01714
-194-
TABLE
145:
I2-ring
Hairpin
Yolyamides
for recognition
of 8-by
5'-WCTASNNW-3'
DNA aromatic amino acid sequence
sequence
3121) 5'W C T A GT T W-3' PyHpPyImHpHp-y-PyPyPyHpPyIm
3122 ) ~5' C T A GT A W-3 PyHpPyImHpPy-y-HpPyPyHpPyIm
W '
3123 ) 5' C T A GT G W-3 PyHpPyImHpIm-y-PyPyPyHpPyIm
W '
3124) 5'W C T A GT C W-3' PyHpPyImHpPy-y-ImPyPyHpPyIm
3125 ) 5' C T A GA T W-3 PyHpPyImPyHp-y-PyHpPyHpPyIm
W '
3126) 5'W C T A GA A W-3' PyHpPyImPyPy-y-HpHpPyHpPyIm
3127 ) 5' C T A GA G W-3 PyHpPyImPyIm-y-PyHpPyHpPyIm
W '
3128 ) 5' C T A GA C W-3 PyHpPyImPyPy-y-ImHpPyHpPyIm
W '
3129) 5'W C T A GG T W-3' PyHpPyImImHp-y-PyPyPyHpPyIm
313 0 5' C T A GG A W- 3 PyHpPyImImPy-y-HpPyPyHpPyIm
) W '
3131) 5'W C T A GC T W-3' PyHpPyImPyHp-y-PyImPyHpPyIm
3132 ) 5' C T A GC A W-3 PyHpPyImPyPy-y-HpImPyHpPyIm
W '
3133) 5'W C T A GG G W-3' PyHpPyImImIm-y-PyPyPyHpPyIm
3134) 5'W C T A GG C W-3' PyHpPyImImPy-y-ImPyPyHpPyIm
33.35) 5'W C T A GC G W-3' PyHpPyImPyIm-y-PyImPyHpPyIm
3136) 5'W C T A GC C W-3' PyHpPyImPyPy-y-ImImPyHpPyIm
3137 ) 5' C T A CT T W-3 PyHpPyPyHpHp-y-PyPyImHpPyIm
W '
313 8 5' C T A CT A W-3 PyHpPyPyHpPy-y-HpPyImHpPyIm
) W '
3139) 5'W C T A CT G W-3' PyHpPyPyHpIm-y-PyPyImHpPyIm
3140 ) 5' C T A CT C W-3 PyHpPyPyHpPy-y- ImPyImHpPyIm
W '
3141) 5'W C T A CA T W-3' PyHpPyPyPyHp-y-PyHpImHpPyIm
3142) 5'W C T A CA A W-3' PyHpPyPyPyPy-y-HpHpImHpPyIm
3143 ) 5' C T A CA G W-3' ~ PyHpPyPyPyIm-y-PyHpImHpPyIm
W
3144) 5'W C T A CA C W-3' PyHpPyPyPyPy-y-ImHpImHpPyIm
3145) 5'W C T A CG T W-3' PyHpPyPyImHp-y-PyPyImHpPyIm
3146) 5'W C T A CG A W-3' PyHpPyPyImPy-y-HpPyImHpPyIm
3147 ) 5' C T A CC T W-3' PyHpPyPyPyHp-y-PyImImHpPyIm
W
3148) 5'W C T A CC A W-3' PyHpPyPyPyPy-y-HpImImHpPyIm
3149) 5'W C T A CG G W-3' PyHpPyPyImIm-y-PyPyImHpPyIm
3150) 5'W C T A CG C W-3' PyHpPyPyImPy-y-ImPyImHpPyIm
3151) 5'W C T A CC G W-3' PyHpPyPyPyIm-y-PyImImHpPyIm
3152) 5'W C T A CC C W-3' PyHpPyPyPyPy-y-ImImImHpPyIm
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-195-
TABLE 14b: 12-ring Hairpin Polyamides for recognition of 8-by 5'-WCTCWNNW-3'
DNA sequence aromatic amino acid sequence
3153) 5'W C T C T T T W-3' PyHpPyHpHpHp-y-PyPyPyImPyIm
3154 ) 5~' W C T C T T A W- 3 ' PyHpPyHpHpPy-y-HpPyPyImPyIm
3155 ) 5' C T CT T G W-3 ' PyHpPyHpHpIm-y-PyPyPyImPyTm
W
3156) 5'W C T CT T C W-3' PyHpPyHpHpPy-y-ImPyPyImPyIm
3157 ) 5' C T CT A T W-3' PyHpPyHpPyHp-y-PyHpPyImPyIm
W
3158) 5'W C T CT A A W-3' PyHpPyHpPyPy-y-HpHpPyImPyIm
3159) 5'W C T CT A G W-3' PyHpPyHpPyIm-y-PyHpPyImPyIm
3160) 5'W C T CT A C W-3' PyHpPyHpPyPy-y-ImHpPyImPyIm
3161) 5'W C T CT G T W-3' PyHpPyHpImHp-y-PyPyPyImPyIm
3162) 5'W C T CT G A W-3' PyHpPyHpImPy-y-HpPyPyImPyIm
3163) 5'W C T CT G G W-3' PyHpPyHpImIm-y-PyPyPyImPyIm
3164) 5'W C T CT G C W-3' PyHpPyHpImPy-y-ImPyPyImPyIm
3165 ) 5' C T CT C T W-3 ' PyHpPyHpPyHp-y-PyImPyImPyIm
W
3166 ) 5' W C T C T C A W-3 ' PyHpPyHpPyPy-y-HpImPyImPyIm
3167 ) 5' W C T C T C G W-3' PyHpPyHpPyIm-y-PyImPyImPyIm
3168) 5'W C T C T C C W-3' PyHpPyHpPyPy-y-ImImPyImPyIm
3169) 5'W C T C A T T W-3' PyHpPyPyHpHp-y-PyPyHpImPyIm
3170) 5'W C T C A T A W-3' PyHpPyPyHpPy-y-HpPyHpImPyIm
3171) 5' W C T C A T G W-3' PyHpPyPyHpIm-y-PyPyHpImPyIm
3172) 5'W C T C A T C W-3' PyHpPyPyHpPy-y-ImPyHpImPyIm
3173) 5'W C T C A A T W-3' PyHpPyPyPyHp-y-PyHpHpImPyIm
3174 ) 5'W C T C AA A W-3' PyHpPyPyPyPy-y-HpHpHpImPyIm
3175) 5'W C T C AA G W-3' 'PyHpPyPyPyIm-y-PyHpHpImPyIm
317 6 ) 5'W C T C AA C W-3 ' PyHpPyPyPypy-y- ImHpHpImPyIm
3177) 5'W C T C AG T W-3' PyHpPyPyImHp-y-PyPyHpImPyIm
317 8 ) 5'W C T C AG A W-3 ' PyHpPyPyImPy-y-HpPyHpImPyIm
317 9 ) 5'W C T C AG G W-3 ' PyHpPyPyImIm-y-PyPyHpImPyIm
3180) 5'W C T C AG C W-3' PyHpPyPyImPy-y-ImPyHpImPyIm
3181) 5'W C T C AC T W-3' PyHpPyPyPyHp-y-PyImHpImPyIm
3182 ) 5'W C T C AC A W-3 ' PyHpPyPyPyPy-y-HpImHpImPyIm
3183 ) 5'W C T C AC G W-3 ' PyHpPyPyPyIm-y-PyImHpImPyIm
3184) 5'W C T C AC C W-3' PyHpPyPyPyPy-y-ImImHpImPyIm
CA 02281930 1999-08-18
WO 98/37067
PCT/US98101714
-196-
TABLE
147:
12-ring
Hairpin
Polyamides
for recognition
of 8-by
5'-WCTCSNNW-3'
DNA aromatic amino acid sequence
sequence
3185) 5'W C T C GT T W-3' PyHpPyImHpHp-y-PyPyPyImPyIm
3186) 5~'WC T C GT A W-3' PyHpPyImHpPy-y-HpPyPyImPyIm
3187 ) 5' C T C GT G W-3 ' PyHpPyImHpIm-y-PyPyPyImPyIm
W
3188) 5'W C T C GT C W-3' PyHpPyImHpPy-y-ImPyPyImPyIm
3189 ) 5' C T C GA T W-3 ' PyHpPyImPyHp-y-PyHpPyImPyIm
W
3190) 5'W C T C GA A W-3' PyHpPyImPyPy-y-HpHpPyImPyIm
3191) 5'W C T C GA G W-3' PyHpPyImPyIm-y-PyHpPyImPyIm
3192 ) 5' C T C GA C W-3 ' PyHpPyImPyPy-y- ImHpPyImPyIm
W
3193 ) 5' C T C GG T W-3' PyHpPyImImHp-y-PyPyPyImPyIm
W
3194 ) 5' C T C GG A W-3 ' PyHpPyImImPy-y-HpPyPyImPyIm
W
3195) 5'W C T C GC T W-3' PyHpPyImPyHp-y-PyImPyImPyIm
3196) 5'W C T C GC A W-3' PyHpPyImPyPy-y-HpImPyImPyIm
3197 ) 5' C T C CT T W-3' PyHpPyPyHpHp-y-PyPyImImPyIm
W
3198 ) 5' C T C CT A W-3' PyHpPyPyHpPy-y-HpPyImImPyIm
W
3199 ) 5' C T C CT G W-3 ' PyHpPyPyHpIm-y-PyPyImImPyIm
W
3200) 5'W C T C CT C W-3' PyHpPyPyHpPy-y-ImPyImImPyIm
3201) 5'W C T C CA T W-3' PyHpPyPyPyHp-y-PyHpImImPyIm
3202) 5'W C T C CA A W-3' PyHpPyPyPyPy-y-HpHpImImPyIm
3203 ) 5' C T C CA G W-3' PyHpPyPyPyIm-y-PyHpImImPyIm
W
3204) 5'W C T C CA C W-3' PyHpPyPyPyPy-y-ImHpImImPyIm
3205) 5'W C T C CG T W-3' PyHpPyPyImHp-y-PyPyImImPyIm
3206 ) 5' C T C CG A W-3 ' PyHpPyPyImPy-y-HpPyImImPyIm
W
3207) 5'W C T C CC T W-3' PyHpPyPyPyHp-y-PyImImImPy3m
3208) 5'W C T C CC A W-3' PyHpPyPyPyPy-y-HpImImImPyIm
3209) 5'W C T C GG G W-3' PyHpPyImImIm-y-PyPyPyImPyIm
3210) 5'W C T C GG C W-3' PyHpPyImImPy-y-ImPyPyImPyIm
3211) 5'W C T C GC G W-3' PyHpPyImPyIm-y-PyImPyImPyIm
3212) 5'W C T C GC C W-3' PyHpPyImPyPy-y-ImImPyImPyIm
3213 ) 5' C T C CG G W-3' PyHpPyPyImIm-y-PyPyImImPyIm
W
3214) 5'W C T C CG C W-3' PyHpPyPyImPy-y-ImPyImImPyIm
3215) 5'W C T C CC G W-3' PyHpPyPyPyIm-y-PyImImImPyIm
3216) 5'W C T C CC C W-3' PyHpPyPyPyPy-y-ImImImImPyIm
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/OI714
-197-
TABLE 148: 12-ring (3-Hairpin
Polyamides for recognition
of 8-by 5'-WGGGWNNW-3'
-
DNA aromatic amino acid sequence
sequence
' 1233(3) 5' -W G G G T T T W-3' ImImIm-(3-HpHp-y-pypy-(3-pypypy
S 1234(3) 5' -W G G G T T A W-3' ImImIm-(3-HpPy-Y-HpPy-(3-Pypypy
1235(3) 5' -W G G G T T G W-3' ImImIm-(3-HpIm-y-Pypy-~-pypypy
' 1236(3) 5' -W G G G T T C W-3' ImImIm-(3-HpPy-Y-ImPy-(3-Pypypy
1237(3) 5'-WG G G T AT W-3' ImImIm-J3-PyHp-Y-pyHp-(3-Pypypy
1238(3) 5'-WG G G T AA W-3' ImImIm-(3-PyPy-y-HpHp-(3-PyPypy
1239(3) 5'-WG G G T AG W-3' ImImIm-(3-Pylm-y-PyHp-(3-pypypy
12403) 5'-WG G G T AC W-3' ImImIm-(3-PyPy-y-ImHp-~3-pypypy
12413) 5'-WG G G T GT W-3' ImImIm-~-ImHp-y-pypy-~-pypypy
1242(3) 5'-WG G G T GA W-3' ImImIm-(3-ImPy-y-HpPy-~3-PyPypy
1243(3) 5'-WG G G T GG W-3' ImImIm-/3-Imlm-y-pypy-p-pypypy
12443) 5'-WG G G T GC W-3' ImImIm-~3-ImPy-Y-ImPy-[3-PyPyPy
1245(3) 5' -W G G G T C T W-3' ImImIm-~3-PyHp-Y-Pylm-~-Pypypy
12463) 5' -W G G G T C A W-3' ImImIm-(3-PyPy-y-Helm-~3-pypypy
12473) 5' -W G G G T C G W-3' ImImIm-~3-Pyim-Y-PyIm-(3-PyPyPy
12483) 5' -W G G G T C C W-3' ImImIm-(3-PyPy-y-ImIm-(3-PyPyPy
1249~i) 5' -WG G GA T T W-3' ImImIm-(3-HpHp-y-pypy-j3-pypypy
1250(3) 5' -WG G GA T A W-3' ImImIm-/3-HpPy-y-HpPy-p-pypypy
1251(3) 5' -WG G GA T G W-3' ImImIm-(3-HpIm-y-PyPy-~3-pypypy
1252(3) 5' -WG G GA T C W-3' ImImIm-(3-HpPy-y-ImPy-(3-Pypypy
12533) 5' -WG G GA A T W-3' ImImIm-(3-PyHp-y-PyHp-~3-Pypypy
1254(3) 5' -WG G GA A A W-3' ImImIm-~i-Pypy-y-HpHp-a_pypypy
1255(3) 5' -WG G GA A G W-3' ImImIm-(3-PyIm-y-pyHp-(3-PyPyPy
1256(3) 5' -WG G GA A C W-3' ImImIm-~3-PyPy-y-I~p_~_pypypy
1257(3) 5' -WG G GA G T W-3' ImImIm-(3-ImHp-Y-PyPY-~-pYPYPY
1258(3) 5' -WG G GA G A W-3' ImImIm-~3-ImPy-y-HpPy-(3-PyPyPy
1259(3) 5' -WG G GA G G W-3' ImImIm-(3-Im=m-y-pypy-~3-pypypy
1260~i) 5' -WG G GA G C W-3' ImImIm-(3-ImPy-y-ImPy-~3-PyPyPy
1261(3) 5' -WG G GA C T W-3' ImImIm-(3-PyHp-Y-pylm_~3_pypypy
12623) 5' -WG G GA C A W-3' ImImIm-(3-PyPy-y-Hplm-(3-PyPyPy
1263(3) 5' -WG G GA C G W-3' ImImIm-(3-
P ylm-y-Pylm-p-Pypypy
1264(3) 5' -WG G GA C C W-3' ImImIm-(3-PyPy-y-Imlm-~3-Pypypy
CA 02281930 1999-08-18
WO 98/37067
PCT/US98/01714
-198-
TABLE
149:
12-ring
(3-Hairpin
Polyamides
for
recognition
of
8-by
S'-WGGGSNNW-3'
DNA aromatic amino acid sequence
sequence
1265 (3)5' -WG G G G TT W-3' ImImImIm-(3-Hp-y-Py-~-PyPyPyPy
1266 (3)~ -WG G G G TA W-3' ImImImIm-~-Py-y-Hp-~i-PyPyPyPy
5'
1267 (3)5' -WG G G G TG W-3' ImImImIm-(3-Im-y-Py-(3-PyPyPyPy
1268 (3)5' -WG G G G TC W-3' ImImImIm-(3-Py-y-Im-~i-PyPyPyPy
1269 ~3)5' -WG G G G AT W-3' ImImImIm-(3-Hp-y-Py-(3-PyPyPyPy
1270 (3)5' -WG G G G AA W-3' ImImImIm-(3-Py-y-Hp-~3-PyPyPyPy
1271 (3)5' -WG G G G AG W-3' ImImImIm-(3-Im-y-Py-(3-PyPyPyPy
1272 ~)5' -WG G G G AC W-3' ImImImIm-(3-Py-y-Im-(3-PyPyPyPy
1275 (3)5' -WG G G G CT W-3' ImImImIm-(3-Hp-y-PyImPy-(3-PyPy
1276 (3)5' -WG G G G CA W-3' ImImImIm-(3-Py-y-HpImPy-~i-PyPy
1277 (3)5' -WG G G C TT W-3' ImImIm-(3-HpHp-y-PyPyIm-(3-PyPy
1278 ~3)5' -WG G G C TA W-3' ImImIm-~3-HpPy-y-HpPyIm-(3-PyPy
1279 (3)5' -WG G G C TG W-3' ImImIm-~3-HpIm-y-PyPyIm-~3-PyPy
1280 (3)5' -WG G G C TC W-3' ImImIm-(3-HpPy-y-ImPyIm-p-PyPy
1281 (3)5' -WG G G C AT W-3' ImImIm-(3-PyHp-y-PyHpIm-(3-PyPy
1282 (3)5' -WG G G C AA W-3' ImImIm-(3-PyPy-y-HpHpIm-p-PyPy
1283 (3)5' -WG G G C AG W-3' ImImIm-(3-PyIm-y-PyHpIm-(3-PyPy
1284 (3)5' -WG G G C AC W-3' ImImIm-(3-PyPy-y-ImHpIm-(3-PyPy
1285 (3)5' -WG G G C GT W-3' ImImIm-(3-ImHp-y-PyPyIm-(3-PyPy
1286 ~3)5' -WG G G C GA W-3' ImImIm-(3-ImPy-y-HpPyIm-(3-PyPy
1287 (3)5' -WG G G C CT W-3' ImImIm-(3-PyHp-y-PyImIm-~3-PyPy
2S 1288 (3)5' -WG G G C CA W-3' ImImIm-~i-PyPy-y-HpImIm-J3-PyPy
G52 5' -WG G G G CC W-3' ImImImIm-~3-Py-y-ImImPy-~3-PyPy
(3)
G53 5' -WG G G C GG W-3' ImImIm-(3-ImIm-y-PyPyIm-(3-PyPy
(3)
G54 5' -WG G G C GC W-3' ImImIm-~3-ImPy-y-ImPyIm-(3-PyPy
(3)
G55 5' -WG G G C CG W-3' ImImIm--Pylm-y-Pylmim-~3-PyPy
~3)
G56 5' -WG G G C CC W-3' ImImIm--PyPy-y-ImImIm-(3-PyPy
(3)
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-199-
TABLE -Hairpin
150: Polyamides
12-ring for
(3 recognition
of
8-by
S'-WGGTWNNW-3'
.
DNA aromatic amino acid sequence
sequence
1289(3) 5' -W G GT T T T W-3' ImIm-(3-HpHpHp-y-pypypy-~3-pypy
12903} 5' -W G GT T T A W-3' ImIm-(3-HpHpPy-y-HpPyPy-(3-PyPy
S 1291} ~ -W G GT T T G W-3' ImIm-~3-HpHpIm-y-Pypypy-(3-pypy
5'
1292(3) 5' -W G GT T T C W-3' ImIm-(3-HpHpPy-y-ImPypy-~i-Pypy
1293(3) 5' -W G GT T A T W-3' ImIm-G3-HpPyHp-y-pyHpPy-~3-pyPy
12943} 5' -W G GT T A A W-3' ImIm-(3-HpPyPy-y-HpHpPy-~3-PyPy
1295(3) 5' -W G GT T A G W-3' Imlm-(3-HpPyIm-y-PyHpPy-(3-PyPy
12963) 5' -W G GT T A C W-3' ImIm-~I-HpPypy-y-ImHppy_~_pyp~,
12973) 5' -W G GT T G T W-3' Imam-~3-HpImHp-y-pypypy-(3-pypy
12983) 5' -W G GT T G A W-3' ImIm-(3-HpImPy-y-HpPyPy-(3-PyPy
12993) 5' -W G GT T G G W-3' ImIm-~-HpImIm-y-PyPyPy-~3-Pypy
1300) 5' -W G GT T G C W-3' ImIm-(3-HpImPy-y-ImPyPy-(3-PYPy
1301(3) 5' -W G GT T C T W-3' Imam-p-HpPyHp-y-PyImPy-p-pypy
1302(3) 5' -W G GT T C A W-3' ImIm-~-HpPyPy-y-HpImPy-(3-PYPy
1303(3) 5' -W G GT T C G W-3' ImIm-p-HpPyIm-y-PyImPy-~3-PyPy
1304(3) 5' -W G GT T C C W-3' ImIm-(3-HpPyPy-y-ImImPy-(3-PyPy
1305(3) 5' -W G GT A T T W-3' Imlm-(3-PYHpHp-y-PyPYHp-~3-PyPy
1306~i) 5' -W G GT A T A W-3' ImIm-~3-PyHpPy-y-HpPyHp-(3-PyPy
13073) 5' -W G GT A T G W-3' ImIm-~3-PyHpIm-y-PyPyHp-(3-PyPy
13083) 5' -W G GT A T C W-3' Imam-(3-PyHpPy-y-ImPyHp-p-pyPy
1309(3) 5' -W G GT A A T W-3' ImIm-p-PyPyHp-y-PyHpHp-(3-PyPy
1310(3) 5' -W G GT A A A W-3' ImIm-p-PyPyPy-y-HpHpHp-/3-PyPy
2S 1311(3) 5' -W G GT A A G W-3' ImIm-~i-PyPyIm-y-PyHpHp--Pypy
1312(3) 5' -W G GT A A C W-3' ImIm-(3-PyPYPy-y-ImHpHp-~3-PyPy
1313(3) 5' -W G GT A G T W-3' Imlm-[3-PyImHp-y-PypyHp-(3-PYPy
13143) 5' -W G GT A G A W-3' Imlm-~i-pyImPy-y-HpPyHp-(3-pypy
1315(3) 5' -W G GT A G G W-3' Imlm-(3-PyImIm-y-PyPYHp-(3-PyPy
1316(3} 5' -W G GT A G C W-3' Imlm-~i-PyImPy-y-ImPyHp-(3-PyPy
1317~i) 5' -W G GT A C T W-3' ImIm-(3-PyPyHp-y-PyImHp-p-pypy
1318(3) 5' -W G GT A C A W-3' ImIm-(3-PyPyPy-y-HpImHp-p-PyPy
1319~i) 5' -W G GT A C G W-3' ImIm-(3-PyPyIm-y-PyImHp-~3-Pypy
1320(3) 5' -W G GT A C C W-3' ImIm-(3-PyPYPy-y-ImImHp-p-PyPy
CA 02281930 1999-08-18
WO 98137067 PCT/US98/01714
-200-
TABLE 151: 12-ring (3-Hairpin Polyamides for recognition of 8-by 5'-WGGTSNNW-
3'
DNA sequence aromatic amino acid sequence
1321(3) 5' -W G G T G T T W-3' ImIm-(i-ImHpHp-y-PyPyPy-(3-PyPy
1322(3) 5' -W G G T G T A W-3' Imlm-J3-ImHpPy-y-HpPyPy-~3-PyPy
1323(3) 5' -W G G T G T G W-3' ImIm-(3-ImHpIm-y-PyPyPy-p-PyPy
1324(3) 5' -W G G T G T C W-3' ImIm-(3-ImHpPy-y-ImPyPy-(3-PyPy
1325(3) 5' -W G G T G A T W-3' Imlm-(3-ImPyHp-y-PyHpPy-~3-PyPy
1326(3) 5' -WG G T G AA W-3' ImIm-(3-ImPyPy-y-HpHpPy-(3-PyPy
1327(3) 5' -WG G T G AG W-3' ImIm-~i-ImPyIm-y-PyHpPy-(3-PyPy
1328(3) 5' -WG G T G AC W-3' ImIm-(3-ImPyPy-y-ImHpPy-J3-Pypy
1329(3) 5' -WG G T G GT W-3' ImIm-(3-ImImHp-y-PyPyPy-(3-PyPy
1330(3) 5' -WG G T G GA W-3' ImIm-(3-ImImPy-y-HpPyPy-(3-PyPy
1331(3) 5' -WG G T G CT W-3' ImIm-(3-ImPyHp-y-PyImPy-(3-PyPy
1332(3) 5' -WG G T G CA W-3' ImIm-(3-ImPyPy-y-HpImPy-~3-PyPy
1333(3) 5' -WG G T G GG W-3' Imlm-(3-ImImIm-y-PypyPy-(3-PyPy
1334(3) 5' -W G G T G G C W-3' Imam-(3-ImImPy-y-ImPyPy-~i-PyPy
13353) 5' -W G G T G C G W-3' ImIm-p-ImPyIm-y-PyImPy-(3-PyPy
1336(3) 5' -W G G T G C C W-3' ImIm-(3-ImPyPy-y-ImImPy-~-PyPy
1337) 5' -W G G T C T T W-3' ImIm-~3-PyHpHp-y-PyPyIm-(3-PyPy
13383) 5' -W G G T C T A W-3' ImIm-(3-PyHpPy-y-HpPyIm-(3-PyPy
1339(3) 5' -W G G T C T G W-3' ImIm-~i-PyHpIm-y-PyPyIm-(3-PyPy
13403) 5' -W G G T C T C W-3' ImIm-(3-PyHpPy-y-ImPyIm-~3-PyPy
13413) 5' -W G G T C A T W-3' ImIm-~i-PyPyHp-y-PyHpIm-(3-PyPy
13423) 5' -W G G T C A A W-3' Imlm-(3-PyPyPy-y-HpHpIm-(3-PyPy
1343(3) 5' -W G G T C A G W-3' ImIm-(3-PyPyIm-y-PyFipIm-(3-PyPy
13440 5' -W G G T C A C W-3' ImIm-~i-PyPyPy-y-imHpIm-(3-PyPy
1345(3) 5' -W G G T C G T W-3' ImIm-(3-PyImHp-y-PyPyIm-(3-PyPy
1346(3) 5' -W G G T C G A W-3' Imlm-(3-PyImPy-y-HpPyIm-(3-PyPy
13470 5' -W G G T C C T W-3' Imlm-(3-PyPyHp-y-PyImIm-~3-PyPy
1348(3) 5' -W G G T C C A W-3' ImIm-(3-PyPyPy-y-HpImIm-(3-PyPy
1349~i) 5' -W G G T C G G W-3' Imlm-(3-PyImIm-y-PyPyIm-~3-PyPy
1350(3) 5' -W G G T C G C W-3' Imlm-(3-PyImPy-y-ImPyIm-(3-PyPy
1351(3) 5' -W G G T C C G W-3' ImIm-(3-PyPyIm-y-PyImIm-(3-PyPy
1352ø) 5' -W G G T C C C W-3' Imlm-~3-PyPyPy-y-ImImIm-~i-PyPy
CA 02281930 1999-08-18
WO 98137067 PCT/US98/OI714
-201-
TABLE 152: 12-ring
(3-Hairpin Polyamides
for recognition
of 8-by 5'-WGGAVVNNW-3'
-
DNA sequence aromatic amino acid sequence
1353(3) 5' -W G T T T W-3' ImIm-~3-HpHpHp-y-pypypy-(3-pypy
G A
1354(3) '5'-W G T T A W-3' ImIm-~3-HpHpPy-y-HpPyPy-(3-PyPy
G A
1355(3) 5' -W G T T G W-3' ImIm-(3-HpHp3m-y-PypyPy-~3-PyPy
G A
1356(3) 5' -W G T T C W-3' ImIm-~-HpHpPy-y-ImPyPy-[3-PyPy
G A
1357(3) 5' -W G T A T W-3' ImIm-(3-HpPyHp-y-PyHpPy-~-pypy
G A
13583) 5'-W G T A A W-3' ImIm-(3-HpPyPy-y-HpHpPy-(3-PyPy
G A
13593) 5'-W G GA T A G W-3' ImIm-(3-HpPyIm-y-PyHpPy-(3-PyPy
1360(3) 5'-W G GA T A C W-3' ImIm-~3-HppyPy-y-ImHppy_~3_pypy
1361(3) 5'-W G GA T G T W-3' ImIm-~3-HpImHp-y-pypypy_~_pypy
1362(3) 5'-W G GA T G A W-3' ImIm-(3-HpImPy-y-HpPyPy-(3-pypy
1363(3) 5'-W G GA T G G W-3' Imlm-~3-HpImIm-y-PyPyPy-(3-PyPy
1364(3) 5'-W G GA T G C W-3' Imlm-~3-HpImPy-y-ImPyPy-(3-PyPy
1365(3) 5'-W G GA T C T W-3' ImIm-R-HpPyHp-y-PyImPy-(3-PyPy
13663) 5'-W G GA T C A W-3' ImIm-(3-HpPyPy-y-HpImPy-(3-PyPy
13673) 5'-W G GA T C G W-3' ImIm-(3-HpPyIm-y-PyIrr~Py-(3-PyPy
1368(3) 5'-W G GA T C C W-3' ImIm-(3-HpPyPy-y-ImImpy-(3-Pypy
1369(3) 5'-W G GA A T T W-3' Imlm-p-PyHpHp-y-PypyHp-(3-PyPy
1370(3) 5'-W G GA A T A W-3' ImIm-(3-PyHpPy-y-HpPyHp-/3-PyPy
1371(3) 5'-W G GA A T G W-3' ImIm-J3-PyHpIm-y-PyPyHp-(3-PyPy
1372(3) 5'-W G GA A T C W-3' Imlm-~3-pyHpPy-y-ImPyHp-j3-PyPy
13733) 5'-W G GA A A T W-3' ImIm-(3-PyPyHp-y-pyHpHp-~i-Pypy
1374(3) 5'-W G GA A A A w-3' ImIm-(3-PyPyPy-y-HpHpHp-(3-PyPy
13753) 5'-W G GA A A G W-3' Imlm-(3-PyPyIm-y-PyHpHp-~3-PyPy
1376(3) 5'-W G GA A A C W-3' ImIm-~i-Pypypy-y-I~pHp_(3_pyp~,
13773) 5'-W G GA A G T W-3' Imam-a-pyImHp-y-PypyHp-~3-PyPy
13783) 5'-W G GA A G A W-3' ImIm-~3-pyImPy-y-HpPyHp-~3-PyPy
1379(3) 5'-W G GA A G G W-3' Imlm-(3-PyImIm-y-PypyHp-~3-Pypy
1380(3) 5'-W G GA A G C W-3' Imlm-(3-PyImPy-y-ImPyHp-~3-PyPy
1381~i) 5'-W G GA A C T W-3' ImIm-~3-PyPyHp-y-PyImHp-(3-PyPy
1382~i) 5'-W G GA A C A W-3' Imlm_(3_pypypy_y_Hp=~p-(3-pypy
1383(3) 5'-W G GA A C G W-3' ImIm-(3-PyPyim-y-pyImHp-(3-PyPy
13843) 5'-W G GA A C C W-3' ImIm-(3-PypyPy-y-ImImHp-~3-Pypy
CA 02281930 1999-08-18
WO 98/370b7 PCT/US98/01714
-202-
TABLE
153:
12-ring
(3-Hairpin
Polyamides
for recognition
of 8-by
5'-WGGASNNW-3'
DNA aromatic amino acid sequence
sequence
1385(3) 5' -WG G A GT T W-3' ImIm-~i-ImHpHp-y-PyPyPy-~3-PYPy
13863) ' -WG G A GT A W-3' ImIm-~i-ImHpPy-y-HpPyPy-~3-PyPy
5'
1387(3) 5' -WG G A GT G W-3' Imlm-~3-ImHpIm-y-PyPyPy-~3-PyPy
1388(3) 5' -WG G A GT C W-3' ImIm-~i-ImHpPy-y-ImPyPy-~3-PyPy
1389(3) 5' -WG G A GA T W-3' ImIm-~3-TmPyHp-y-PyHpPy-(3-PyPy
1390(3) 5' -WG G A GA A W-3' ImIm-~i-ImPyPy-y-HpHpPy-(3-PyPy
13913) 5' -WG G A GA G W-3' ImIm-~3-ImPyIm-y-PyHpPy-(3-PyPy
1392(3) 5' -WG G A GA C W-3' ImIm-(3-ImPyPy-y-ImHpPy-(3-PyPy
13933) 5' -WG G A GG T W-3' ImIm-(3-ImImHp-y-PyPyPy-[3-PyPy
13943) 5' -WG G A GG A W-3' ImIm-(3-ImImPy-y-HpPyPy-(3-PyPy
1395(3) 5' -WG G A GC T W-3' ImIm-(3-ImPyHp-y-PyImPy-(3-PyPy
13963) 5' -WG G A GC A W-3' Imlm-(3-ImPyPy-y-HpImPy-(3-PyPy
1397(3) 5' -WG G A GG G W-3' Imlm-(3-ImImIm-y-PyPyPy-(3-PyPy
1398(3) 5' -WG G A GG C W-3' ImIm-/3-ImImPy-y-ImPYPy-(3-PyPy
1399(3) 5' -WG G A GC G W-3' ImIm-(3-ImPyIm-y-PyImPy-(3-PyPy
1400(3) 5' -WG G A GC C W-3' ImIm-~-ImPyPy-y-ImImPy-(3-PyPy
1401~i) 5' -WG G A CT T W-3' Imlm-(3-PyHpHp-y-PYPyIm-/3-PyPy
1402(3) 5' -WG G A CT A W-3' ImIm-(3-PyHpPy-y-HpPyIm-R-PyPy
1403(3) 5' -WG G A CT G W-3' ImIm-(3-PyHpIm-y-PyPy3m-~3-PyPy
14043) 5' -WG G A CT C W-3' ImIm-~-PyHpPy-y-ImPyIm-(3-PyPy
14053) 5' -WG G A CA T W-3' ImIm-~3-PyPyHp-y-PyHpIm-(3-PyPy
1406~i) 5' -WG G A CA A W-3' ImIm-(3-PyPyPy-y-HpHpIm-p-PyPy
1407(3) 5' -WG G A CA G W-3' ~ImIm-(3-PyPyIm-y-PyHpIm--PyPy
1408(3) 5' -WG G A CA C W-3' ImIm-(i-PyPyPy-y-ImHpIm-(i-PyPy
1409~i) 5' -WG G A CG T W-3' ImIm-(i-PyImHp-y-PyPyIm-(3-PyPy
1410(3) 5' -WG G A CG A W-3' Imlm-(3-PyImPy-y-HpPyIm-~-PyPy
1411) 5' -WG G A CC T W-3' ImIm-~3-PyPyHp-y-PyImIm-(3-PyPy
1412(3) 5' -WG G A CC A W-3' ImIm-(3-PyPyPy-y-HpImIm-(3-PyPy
1413(3) 5' -WG G A CG G W-3' ImIm-~3-PyImIm-y-PyPYIm-~i-PyPy
1414(3) 5' -WG G A CG C W-3' Imam-~3-PyImPy-y-ImPyIm-p-PyPy
1415p) 5' -WG G A CC G W-3' ImIm-~i-PyPyIm-y-PyImIm-(3-PyPy
1416(3) 5' -WG G A CC C W-3' Imlm-(3-PyPyPy-y-ImImIm-~i-PyPy
_~__... _.._ ? , . ,
CA 02281930 1999-08-18
WO 98/37067
-203-
PCT/US98/01714
TABLE 154:
12-ring
(3-Hairpin
Polyamides
for recognition
of 8-by
5'-WGGCWNNW-3'
-
DNA sequence aromatic amino acid sequence
1417(3) ImImPy-~3-HpHp-y-PyPy-(3-ImPyPy
5' -W
G G C
T T T
W-3'
1418(3) 5' -W G G T A W-3' ImImPy-(3-HpPy-y-HpPy-/3-ImPyPy
C T
1419(3) 5' -W G G T G W-3' ImImPy-~3-HpIm-y-Pypy-(3-Impypy
C T
14200 5' -W G G T C W-3' ImImPy-~-HpPy-y-ImPy-(3-ImPypy
C T
14213) 5' -W G G A T W-3' ImImPy-(3-PyHp-y-pygp-~-ImPyPy
C T
1422(3) 5' -W G G A A W-3' ImImPy-(3-Pypy-y-HpHp_~3-ImPyPy
C T
1423(3) 5' -W G G A G W-3' ImImPy-(3-Pylm-y-pygp-~3-ImPyPy
C T
1424(3) 5' -W G G A C W-3'
C T ImImPy-(3-PyPy-y-ImHp-~i-ImPyPy
1425(3) 5' -W G G G T W-3'
C T ImImPy-(3-ImHp-y-PyPy-(3-ImPyPy
1426) 5' -W G G G A W-3' ImImPy-~3-ImPy-y-HpPy-~-ImPyPy
C T
1427(3) 5' -W G G G G W-3' ImImPy-(3-ImIm-y-Pypy-~-ImPyPy
C T
1428(3) 5' -W G G G C W-3' ImImPy-(3-ImPy-y-ImPy-/3-ImPyPy
C T
1429(3) 5' -W G G C T W-3' ImImPy-(3-PyHp-y-pyIm-(3-ImPyPy
C T
1430(3) 5' -W G G C A W-3' ImImPy-~3-pypy-y-HpIm-J3-ImPyPy
C T
1431(3) 5' -W G G C G W-3' ImImPy-~3-pylm-y-pylm_(~_ImPyPy
C T
14323) 5' -W G G C C W-3' ImImPy-(3-pypy-y-Imlm-(3-ImPyPy
C T
14330 5' -W G G T T W-3' ImImPy-(3-HpHp-y-Pypy-~3-ImPyPy
C A
1434~i) 5' -W G G T A W-3' ImImPy-(3-HpPy-y-HpPy-(3-ImPyPy
C A
14353) 5' -W G G T G W-3' ImImPy-(3-Hplm-y-Pypy-~3-ImPyPy
C A
14363) 5' -W G G T C W-3'
C A ImImPy-~i-HpPy-y-ImPy-(3-ImPyPy
1437(3) 5' -W G G A T W-3' ImImPy-(3-PyHp-y-pyHp-(3-ImPyPy
C A
1438~i) 5' -W G G A A W-3' ImImPy-(3-PyPy-y-HpHp-(3-ImPyPy
C A
1439(3) 5' -W G G A G W-3' Imlmpy-a-pyim-y-pyHp-(3-ImPyPy
C A
1440(3) 5' -W G G A C W-3'
C A ImImPy-(3-PyPy-y-ImHp-~3-ImPyPy
14413) 5' -W G G G T W-3'
C A ImImPy-~3-ImHp-y-PyPy-(3-ImPyPy
14423) 5' -W G G G A W-3' ImImPy-~3-ImPy-y-HpPy-(3-ImPyPy
C A
1443(3) 5' -W G G G G W-3' ImImPy-p-Imlm-y-PyPy-R-ImPyPy
C A
1444(3) 5'-W G G G C W-3' ImImPy-~3-ImPy-y-Impy-(3-ImPyPy
C A
1445(3) 5' -W G G C T W-3' ImImPy-(3-pyHp-y-pylm-~i-ImPyPy
C A
1446(3) 5' -W G G C A W-3' ImImPy-(3-PyPy-y-Hplm-(3-ImPyPy
C A
1447(3) 5' -W G G C G W-3' ImImPy-(3-Pylm-y-Pylm-/3-ImPyPy
C A
14483) 5' -W G G C C W-3' ImImPy-(3-pypy-y-ImIm-/3-ImPypy
C A
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-204-
TABLE
155:
12-ring
(3-Hairpin
Polyamides
for recognition
of 8-by
S'-WGGCSNNW-3'
-
DNA aromatic amino acid sequence
sequence
1449R) 5'-W G GC G T T W-3' ImIm-(3-ImHpHp-y-PyPy-~3-ImPyPy
14503) ~5'-W G GC G T A W-3' Imlm-~3-ImHpPy-y-HpPy-(3-ImPyPy
1451(3) 5'-W G GC G T G W-3' ImIm-(3-ImHpIm-y-PyPy-(3-ImPyPy
1452(3) 5'-W G GC G T C W-3' Imlm-(3-ImHpPy-y-ImPy-(3-ImPyPy
14530 5'-W G GC G A T W-3' ImIm-(3-ImPyHp-y-PyHp-(3-ImPyPy
1454(3) 5'-W G GC G A A W-3' ImIm-(3-ImPyPy-y-HpHp-~3-ImPyPy
14553) 5'-W G GC G A G W-3' Imlm-~-ImPyIm-y-PyHp-(3-ImPyPy
1456(3) 5'-W G GC G A C W-3' ImIm-(3-ImPyPy-y-ImHp-(3-ImPyPy
1457~i) 5'-W G GC G G T W-3 Imlm-(3-ImImHp-y-PyPy-(3-ImPyPy
14583) 5'-W G GC G G A W-3' ImIm-~-ImImPy-y-HpPy-~-ImPyPy
1459(3) 5'-W G GC G C T W-3' ImIm-(3-ImPyHp-y-PyIm-(3-ImPyPy
1460(3) 5'-W G GC G C A W-3' Imlm-(3-ImPyPy-y-HpIm-(3-ImPyPy
14613) 5'-W G GC C T T W-3' Imlm-p-PyHpHp-y-Py-(3-ImImPyPy
1462(3) 5'-W G GC C T A W-3' ImIm-~3-PyHpPy-y-Hp-~-ImImPyPy
14633) 5'-W G GC C T G W-3' ImIm-/3-PyHpIm-y-Py-~i-ImImPyPy
1464(3) 5'-W G GC C T C W-3' Imlm-(3-PyHpPy-y-Im-(3-ImImPyPy
1465~i) 5'-W G GC C A T W-3' ImIm-(3-PyPyHp-y-Py-p-ImImPyPy
.
1466(3) 5'-W G GC C A A W-3' ImIm-[3-PyPyPy-y-Hp-/3-ImImPyPy
1467(3) 5'-W G GC C A G W-3' ImIm-(3-PyPyIm-y-Py-(3-ImImPyPy
14683) 5'-W G GC C A C W-3' ImIm-p-PyPyPy-y-Im-(3-ImImPyPy
1469p) 5'-W G GC C G T W-3' Imlm-(3-PyImHp-y-Py-(3-ImImPyPy
1470(3) 5'-W G GC C G A W-3' Imlm-(3-PyImPy-y-Hp-~3-ImImPyPy
14713) 5'-W G GC C C T W-3' ' ImIm-J3-PyPyHp-y-PyImImIm-(3-Py
1472(3) 5'-W G GC C C A W-3' Imlm-~3-PyPyPy-y-HpImImIm-(3-Py
G57(3) 5'-W G GC G G G W-3' Imlm-(3-ImImIm-y-PyPy-(3-ImPyPy
G58(3) 5'-W G GC G G C W-3' Imlm-J3-ImImPy-y-ImPy-(3-ImPyPy
G59~) 5'-W G GC G C G W-3' ImIm-~3-ImPyIm-y-PyIm-~3-ImPyPy
G60(3) 5'-W G GC G C C W-3' ImIm-(3-ImPyPy-y-ImIm-(3-ImPyPy
G6l~i) 5'-W G GC C G G W-3' ImIm-(3-PyImIm-y-Py-(3-ImImPyPy
G62~3) 5'-W G GC C G C W-3' ImIm-(3-PyImPy-y-Im-(3-ImImPyPy
G63(3) 5'-W G GC C C G W-3' ImIm-(3-PyPyIm-y-PyImImIm-(3-Py
G64(3) 5'-W G GC C C C W-3' ImIm-(3-PyPyPy-y-ImImImIm-(3-Py
CA 02281930 1999-08-18
WO X8/37067 PCT/US98/01714
-2U5-
TABLE 156:
12-ring
(3-Hairpin
Polyamides
for recognition
of 8-by
5'-WGCGWNNW-3'
.
DNA aromatic amino acid sequence
sequence
1473(3) 5'-WG C G T TT W-3'
ImPyIm-(3-HpHp-y-PyPyPy-(3-ImPy
1474(3) ~5'-WG C G T TA W-3' ImPyIm-(3-HpPy-y-Hppypy-~3_Impy
1475(3) 5'-WG C G T TG W-3' ImPyIm-(3-Hplm-y-PyPyPy-~3-ImPy
1476(3) 5'-WG C G T TC W-3' ImPyIm-(3-HpPy-y-ImPyPy-(3-ImPy
1477(3) 5'-WG C G T AT W-3' ImPyIm-~-PyHp-y-pyHpPy-(3-ImPy
1478) 5'-WG C G T AA W-3' ImPyIm-~3-PyPy-y-HpHpPy-(3-ImPy
1479(3) 5'-WG C G T AG W-3' ImPyIm-(3-PyIm-y-pyHppy-(3-ImPy
14803) 5'-WG C G T AC W-3' ImPyIm-(3-PyPy-y-ImHpPy-(3-ImPy
1481(3) 5'-WG C G T GT W-3' ImPyIm-(3-ImHp-y-pypypy-~3-ImPy
14823) 5'-WG C G T GA W-3' ImPyIm-(3-ImPy-y-HpPyPy-p-ImPy
1483(3) 5'-WG C G T GG W-3' ImPyIm-(3-ImIm-y-Pypypy-(3-ImPy
14843) 5'-WG C G T GC W-3' ImPyIm-~3-ImPy-y-ImPyPy-j~-ImPy
1485(3) 5'-WG C G T CT W-3' ImPyIm-(3-PyHp-Y-PyImPy-(3-ImPy
1486(3) 5'-WG C G T CA W-3' ImPyIm-~3-PyPy-y-HpImPy-(3-ImPy
1487(3) 5'-WG C G T CG W-3' ImPyIm-(3-Pylm-y-PyImPy-~3-Irr~Py
1488(3) 5'-WG C G T CC W-3' ImPyIm-(3-PyPy-y-ImImPy-~i-ImPy
14893) 5'-WG C G A TT W-3' ImPyIm-~-HpHp-Y-PypyHp-/3-ImPy
1490(3) 5'-WG C G A TA W-3' ImPyIm-~-HpPy-y-HpPyHp-(3-ImPy
1491(3) 5'-WG C G A TG W-3' ImPyIm-(3-HpIm-y-PyPyHp-(3-ImPy
1492(3) 5'-WG C G A TC W-3' ImPyIm-(3-HpPy-y-ImPyHp-~-ImPy
1493(3) 5'-WG C G A AT W-3' ImPyIm-~3-PyHp-y-pyHpHp-(3-ImPy
14940 5'-WG C G A AA W-3' ImPyIm-(3-pyPy-y-HpHpHp-(3-ImPy
1495(3) 5'-WG C G A AG W-3' ImPyIm-(3-PyIm-y-PyHpHp-~3-ImPy
1496(3) 5'-WG C G A AC W-3' ImPyIm-(3-Pypy-y-ImHpHp-~3-ImPy
1497(3) 5'-WG C G A GT W-3' ImPyIm-~-ImHp-y-PyPyHp-(3-ImPy
1498(3) 5'-WG C G A GA W-3' ImPyIm-(3-ImPy-y-HpPyHp-(3-ImPy
1499(3) 5'-WG C G A GG W-3' ImPyIm-(3-Imlm-y-PyPyHp-p-ImPy
1490(3) 5'-WG C G A GC W-3' ImPyIm-/3-ImPy-y-ImPyHp-(3-ImPy
1501(3) 5'-WG C G A CT W-3' ImPyIm-(3-PyHp-y-PyImHp-(3-ImPy
1502(3) 5'-WG C G A CA W-3' ImPyIm-~3-PyPy-Y-HpImHp-p-ImPy
1503(3) 5'-WG C G A CG W-3' ImPyIm-(3-PyIm-y-pyImHp-a-ImPy
1504(3) 5'-WG C G A CC W-3' ImPyIm-p-PyPy-y-ImImHp-p-ImPy
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-206-
TABLE
157:
12-ring
(3-Hairpin
Polyamides
for recognition
of 8-by
5'-WGCGSNNW-3'
-
DNA aromatic amino acid sequence
sequence
15053) 5'-W G C G GT T W-3' Im-(3-ImImHpHp-y-PyPyPy-(3-ImPy
1506(3) 5'-W G C G GT A W-3' Im-(3-ImImHpPy-y-HpPyPy-(3-ImPy
1507(3) 5'-W G C G GT G W-3' Im-(3-ImImHpIm-y-PyPyPy-(3-ImPy
1508(3) 5'-W G C G GT C W-3' Im-(3-ImImHpPy-y-ImPyPy-(3-ImPy
1509(3) 5'-W G C G GA T W-3' Im-(3-ImImPyHp-y-PyHpPy-(3-ImPy
1510(3) 5'-W G C G GA A W-3' Im-(3-ImImPyPy-y-HpHpPy-(3-Impy
1511~i) 5'-W G C G GA G W-3' Im-(3-ImImPyIm-y-PyHpPy-(3-ImPy
1512(3) 5'-W G C G GA C W-3' Im-(3-ImImPyPy-y-ImHpPy-(3-ImPy
1513(3) 5'-W G C G GG T W-3' Im-~3-ImImImHp-y-PyPyPy-p-ImPy
153-4(3) 5'-W G C G GG A W-3' Im-~3-ImImImPy-y-HpPyPy-(3-ImPy
1515(3) 5'-W G C G GC T W-3' Im-p-ImImPyHp-y-PyImPy-(3-ImPy
1516(3) 5'-W G C G GC A W-3' Im-~-ImImPyPy-y-HpImPy-~3-ImPy
1517(3) 5'-W G C G CT T W-3' ImPyIm-(3-HpHp-y-PyPyIm-~i-ImPy
1518(3) 5'-W G C G CT A W-3' ImPyIm-(3-HpPy-y-HpPyIm-~3-ImPy
1519(3) 5'-W G C G CT G W-3' ImPyIm-a-HpIm-y-PyPyIm-(3-ImPy
1520(3) 5'-W G C G CT C W-3' ImPyIm-(3-HpPy-y-ImPyIm-(3-ImPy
15213) 5'-W G C G CA T W-3' ImPyIm-(3-PyAp-y-PyHpIm-(3-ImPy
1522(3) 5'-W G C G CA A W-3' ImPyIm-(3-PyPy-y-HpHpIm-(3-ImPy
1523(3) 5'-W G C G CA G W-3' ImPyIm-(3-PyIm-y-PyHpIm-(3-ImPy
1524(3) 5'-W G C G CA C W-3' ImPyIm-~3-PyPy-y-ImHpIm-(3-ImPy
1525(3) 5'-W G C G CG T W-3' ImPyIm-(3-ImHp-y-PyPyIm-~3-ImPy
15263) 5'-W G C G CG A W-3' ImPyim-(3-ImPy-y-HpPyIm-(3-ImPy
1527) 5'-W G C G CC T W-3' ImPyIm-~i-PyHp-y-PyImIm-(3-ImPy
1528(3) 5'-W G C G CC A W-3' ImPyIm-~-PyPy-y-HpImIm-(3-ImPy
G65~) 5'-W G C G GG G W-3' Im-~i-ImImImIm-y-PyPyPy-~i-ImPy
G66~3) 5'-W G C G GG C W-3' Im-p-ImImImPy-y-ImPyPy-(3-ImPy
G67(3) 5'-W G C G GC G W-3' Im-(3-ImImPyIm-y-PyImPy-/3-ImPy
G68(3) 5'-W G C G GC C W-3' Im-(3-ImImPyPy-y-ImImPy-p-ImPy
G69(3) 5'-W G C G CG G W-3' ImPyIm-(3-ImIm-y-PyPyIm-(3-ImPy
G70~3) 5'-W G C G CG C W-3' ImPyIm-(3-ImPy-y-ImPyIm-~3-ImPy
G71(3) 5'-W G C G CC G W-3' ImPyIm-~i-PyIm-y-PyImIm-p-ImPy
G72(3) 5'-W G C G CC C W-3' ImPyIm-(3-PyPy-y-ImImIm-(3-ImPy
,,
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/OI714
-207-
TABLE 158:
12-ring
~3-Hairpin
Polyamides
for recognition
of 8-by
5'-WGCTWNNW-3'
-
DNA aromatic amino acid sequence
sequence
' 1529(3) 5' G C T T T TW-3' ImPy-~3-HpHpHp-y-Pypypy_~3-ImPy
-W
15303) - G C T T T AW-3' ImPy-~i-HpHpPy-y-HpPyPy-~3-ImPy
5'
-W
1531(3) 5' G C T T T GW-3' ImPy-(3-HpHpIm-y-Pypypy-a-ImPy
-W
15323) 5' G C T T T CW-3' ImPy-(3-HpHpPy-y-ImPyPy-(3-ImPy
-W
15333) 5' G C T T A TW-3' ImPy-~3-HpPyHp-y-pyHpPy-~i-ImPy
-W
1534(3) 5' G C T T A AW-3' ImPy-~3-HpPyPy-y-HpHpPy-(3-ImPy
-W
15353) 5' G C T T A GW-3' ImPy-(3-HpPyIm-y-PyHpPy-(3-ImPy
-W
1536~i) 5'-W G C T T A CW-3' ImPy-~;-Hppypy_y_I~ppy-~_Impy
15373) 5' G C T T G TW-3' ImPy-(1-HpImHp-y-PyPypy-(3-ImPy
-W
1538(3) 5' G C T T G AW-3' ImPy-/3-HpImPy-y-HpPyPy-~i-ImPy
-W
1539(3) 5' G C T T G GW-3' ImPy-~-HpImIm-y-Pypypy-(3-Impy
-W
1540p) 5' G C T T G CW-3' ImPy-a-HpImPy-y-ImPyPy-~3-ImPy
-W
1541(3) 5' G C T T C TW-3' ImPy-(3-HppyHp-y-pyImPy-~3-ImPy
-W
1542~i) 5' G C T T C AW-3' ImPy-(3-HpPyPy-y-HpImPy-~-ImPy
-W
15433) 5' G C T T C GW-3' ImPy-~3-HpPyIm-y-pyImPy-p-ImPy
-W
15443) 5' G C T T C CW-3' ImPy-~3-HpPyPy-y-ImImPy-(3-ImPy
-W
1545(3) 5' G C T A T TW-3' ImPy-(1-pyHpHp-y-pypyHp-(3-ImPy
-W
15463) 5' G C T A T AW-3' Impy-(3-PyHppy-y-HppyHp-~i-ImPy
-W
1547(3) 5' G C T A T GW-3' ImPy-(3-PyHpIm-y-pypyHp-~3-ImPy
-W
1548(3) 5' G C T A T CW-3' ImPy-(3-PyHpPy-y-ImPyHp-p-ImPy
-W
1549~i) 5' G C T A A TW-3' ImPy-(3-PyPyHp-y-pyHpHp-~i-ImPy
-W
1550p) 5' G C T A A AW-3' ImPy-(3-PyPyPy-y-HpHpHp_~3-ImPy
-W
1551(3) 5' G C T A A GW-3' ImPy-~-Pypylm-y_pyHpHp-(3-ImPy
-W
1552(3) 5' G C T A A CW-3' ImPy-p-Pypypy-y-I~pHp-(3-ImPy
-W
1553(3) 5' G C T A G TW-3' ImPy-~-PyImHp-y-PypyHp-(3-ImPy
-W
1554(3) 5' G C T A G AW-3' ImPy-p-PyImPy-y-HpPyHp-/3-ImPy
-W
1555(3) 5' G C T A G GW-3' Impy-(3-PyImIm-y-pypyHp-(3-ImPy
-W
1556(3) 5' G C T A G CW-3' ImPy-~3-PyImPy-y-ImPyHp-(3-ImPy
-W
I557(3) 5' G C T A C TW-3' ImPy-(3-PyPyHp-y-PyImHp-p-ImPy
-W
15583) 5' G C T A C AW-3' ImPy-(3-Pypypy-Y_Hpl~p_~3_ImPy
-W
1559(3) 5' G C T A C GW-3' ImPy-R-Pypylm-Y-PyImHp-/3-ImPy
-W
1560~i) 5' G C T A C CW-3' Impy-~i-pypypy-y-ImImHp-(3-ImPy
-W
CA 02281930 1999-08-18
WO 98/37067
PCT/US98/01714
-208-
TABLE
159:
12-ring
(3-Hairpin
Polyamides
for recognition
of 8-by
5'-WGCTSNNW-3'
DNA aromatic amino acid sequence
sequence
15613) 5'-W G C TG T T W-3' ImPy-j3-ImHpHp-y-PyPyPy-(3-ImPy
1562(3) 5'-W G C TG T A W-3' ImPy-~3-ImHpPy-y-HpPyPy-(3-ImPy
1563(3) 5'-W G C TG T G W-3' ImPy-(3-ImHpIm-y-PyPyPy-(3-ImPy
1564(3) 5'-W G C TG T C W-3' ImPy-(3-ImHpPy-y-ImPyPy-(3-ImPy
1565(3) 5'-W G C TG A T W-3' ImPy-(3-ImPyHp-y-PyHppy-(3-ImPy
1566(3) 5'-W G C TG A A W-3' Impy-(3-ImPyPy-y-HpHpPy-(3-ImPy
1567(3) 5'-W G C TG A G W-3' ImPy-p-ImPyIm-y-PyHpPy-p-ImPy
1568(3) 5'-W G C TG A C W-3' ImPy-(3-ImPyPy-y-ImHpPy-(3-ImPy
1569(3) 5'-W G C TG G T W-3' ImPy-~3-ImImHp-y-PyPyPy-(3-ImPy
1570(3) 5'-W G C TG G A W-3' ImPy-(3-ImImPy-y-HpPyPy-(3-ImPy
15713) 5'-W G C TG C T W-3' ImPy-(3-ImPyHp-y-PyImPy-(3-ImPy
1572(3) 5'-W G C TG C A W-3' ImPy-~-ImPyPy-y-HpImPy-(3-ImPy
1573~i) 5'-W G C TG G G W-3' ImPy~-(3-ImImIm-y-PyPyPy-(3-ImPy
1574(3) 5'-W G C TG G C W-3' ImPy-[3-ImImPy-y-ImPyPy-p-ImPy
1575(3) 5'-W G C TG C G W-3' ImPy-(3-ImPyIm-y-PyImPy-(3-ImPy
15760 5'-W G C TG C C W-3' ImPy-(3-ImPyPy-y-ImImPy-(3-ImPy
1577(3) 5'-W G C TC T T W-3' ImPy-(3-PyHpHp-y-PyPyIm-(3-ImPy
1578(3) 5'-W G C TC T A W-3' ImPy-(3-PyHpPy-y-HpPyIm-(3-ImPy
1579(3) 5'-W G C TC T G W-3' ImPy-(3-PyHpIm-y-PyPyIm-/3-ImPy
1580(3) 5'-W G C TC T C W-3' ImPy-(3-PyHpPy-y-ImPyIm-(3-ImPy
1581(3) 5'-W G C TC A T W-3' ImPy-(3-PyPyHp-y-PyHpIm-/3-ImPy
1582(3) 5'-W G C TC A A W-3 ImPy-(3-PyPyPy-y-HpHpIm-(3-ImPy
T
1583(3) 5'-W G C TC A G W-3' 'Impy-J3-Pypylm-y-PyHpIm-(3-ImPy
1584(3) 5'-W G C TC A C W-3' ImPy-~3-PyPyPy-y-ImHpIm-(3-ImPy
15853) 5'-W G C TC G T W-3' ImPy-(3-PyImHp-y-PypyIm-~-ImPy
1586(3) 5'-W G C TC G A W-3' ImPy-(3-PyImPy-y-HpPyIm-~i-ImPy
1587(3) 5'-W G C TC C T W-3' ImPy-(3-PyPyHp-y-PyImIm-(3-ImPy
1588(3) 5'-W G C TC C A W-3' ImPy-~3-PyPyPy-y-HpImIm-(3-ImPy
1589~i) 5'-W G C TC G G W-3' ImPy-(3-PyImIm-y-PyPyIm-(3-ImPy
1590~i) 5'-W G C TC G C W-3' ImPy-~3-PyImPy-y-ImPyIm-(3-ImPy
15913) 5'-W G C TC C G W-3' ImPy-p-PyPyIm-y-PyImIm-(3-ImPy
1592(3) 5'-W G C TC C C W-3' ImPy-p-PyPyPy-y-ImImIm-p-ImPy
,..
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-209-
TABLE 160: 12-ring ~i-Hairpin Polyamides for recognition of 8-by 5'-WGCAWNNW-
3'
DNA sequence aromatic amino acid sequence
1593(3) 5' -W G C A T T T W-3' ImPy-~-HpHpHp-y-Pypypy-(3-ImPy
1594(3) 5' -W G C A T T A W-3' ImPy-~3-HpHpPy-y-HpPyPy-p-ImPy
1595(3) 5' -W G C A T T G W-3' ImPy-~i-HpHpIm-y-pypypy-(3-ImPy
1596(3) 5' -W G C A T T C W-3' ImPy-~3-HpHpPy-y-ImPyPy-(3-ImPy
1597) 5'-WG C A T A TW-3' ImPy-(3-HpPyHp-y-PyHpPy-~3-ImPy
1598(3) 5'-WG C A T A AW-3' ImPy-(~-HpPyPy-y-HpHpPy-(3-ImPy
1599(3) 5'-WG C A T A GW-3' ImPy-~3-HpPyIm-y-PyHpPy-~3-ImPy
1600(3) 5'-WG C A T A CW-3' ImPy-~3-HpPyPy-y-ImHpPy-p-ImPy
1601(3) 5'-WG C A T G TW-3' ImPy-p-HpImHp-y-PyPyPy-(3-ImPy
1602~i) 5'-WG C A T G AW-3' ImPy-(3-HpImPy-y-HpPyPy-(3-ImPy
1603(3) 5'-WG C A T G GW-3' ImPy-~3-HpImIm-y-Pypypy-(3-ImPy
IS 16043) 5'-WG C A T G CW-3' ImPy-~-HpImPy-y-ImPyPy-(3-ImPy
1605(3) 5'-WG C A T C TW-3' ImPy-~i-HpPyHp-y-pylmPy-(3-ImPy
1606(3) 5'-WG C A T C AW-3' ImPy-(3-HpPyPy-y-HpImPy-(3-ImPy
16073) 5'-WG C A T C GW-3' ImPy-(3-HpPyIm-y-PyImPy-~-ImPy
1608(3) 5'-WG C A T C CW-3' ImPy-~3-HpPyPy-y-ImImPy-~3-ImPy
1609~i) 5'-WG C A A T TW-3' ImPy-~-PyHpHp-y-PypyHp-(3-ImPy
16103) 5'-WG C A A T AW-3' ImPy-~3-pyHpPy-y-HpPyHp-~-ImPy
16113) 5'-WG C A A T GW-3' ImPy-(3-PyHpIm-y-PypyHp-p-ImPy
1612(3) 5'-WG C A A T CW-3' ImPy-~3-PyHpPy-y-ImPyHp-p-ImPy
1613(3) 5'-WG C A A A TW-3' ImPy-(3-PypyHp-y-pyHpHp-(3-ImPy
1614(3) 5'-WG C A A A AW-3' Impy-(3-PyPyPy-y-HpHpHp-(3-Impy
1615(3) 5'-WG C A A A GW-3' ~ImPy-~3-pypylm-y-PyHpHp-~3-ImPy
16163) 5'-WG C A A A CW-3' ImPy-R-PyPypy-y-I~pHp-~3-ImPy
1617(3) 5'-WG C A A G TW-3' ImPy-(3-pyl~p_y-pypyHp-~-ImPy
16183) 5'-WG C A A G AW-3' ImPy-(3-PyImPy-y-HpPyHp-(3-ImPy
1619(3) 5'-WG C A A G GW-3' ImPy-(3-PyImIm-y-PypyHp-~i-ImPy
1620(3) 5'-WG C A A G CW-3' ImPy-J3-PyImPy-y-ImPyHp-(3-ImPy
16213) 5'-WG C A A C TW-3' ImPy-(3-pypyHp-Y-pYI~Pv-ImPy
1622(3) 5'-WG C A A C AW-3' ImPy-~3-Pypypy-y-Hpl~p_~3_ImPy
1623(3) 5'-WG C A A C GW-3' ImPy-(3-PyPyIm-y-py=mt-tp_~3_ImPy
1624(3) 5'-WG C A A C CW-3' ImPy-~3-pypypy-y_ImImHp-~3-ImPy
CA 02281930 1999-08-18
WO 98/37067 PCTIi1S98/01714
-210-
TABLE 161:
12-ring
~3-Hairpin
Polyamides
for recognition
of 8-by
5'-WGCASNNW-3'
-
DNA aromatic amino acid sequence
sequence
1625(3) 5' -WG C A G TT W-3' ImPy-(3-ImHpHp-y-PyPyPy-~3-ImPy
1626~i) ~ -WG C A G TA W-3' ImPy-[3-ImHpPy-y-HpPyPy-p-ImPy
5'
1627(3) 5' -WG C A G TG W-3' ImPy-(3-ImHpIm-y-PyPyPy-/3-ImPy
1628(3) 5' -WG C A G TC W-3' ImPy-(3-ImHpPy-y-ImPyPy-(3-ImPy
1629(3) 5' -WG C A G AT W-3' ImPy-p-ImPyHp-y-PyHpPy-~-ImPy
1630(3) 5' -WG C A G AA W-3' ImPy-(3-ImPyPy-y-HpHpPy-~i-ImPy
1631(3) 5' -WG C A G AG W-3' ImPy-~i-ImPyIm-y-PyHpPy-(i-ImPy
1632(3) 5' -WG C A G AC W-3' ImPy-[3-ImPyPy-y-ImHpPy-(3-ImPy
16333) 5' -WG C A G GT W-3' ImPy-(3-ImImHp-y-PyPyPy-(3-ImPy
16343) 5' -WG C A G GA W-3' ImPy-p-ImImPy-y-HpPyPy-(3-ImPy
1635(3) 5' -WG C A G CT W-3' ImPy-~3-ImPyHp-y-PyImPy-~3-ImPy
1636(3) 5' -WG C A G CA W-3' ImPy-(3-ImPyPy-y-HpImPy-(3-ImPy
1637) 5' -WG C A G GG W-3' ImPy-(3-ImImIm-y-PyPyPy-~i-ImPy
1638(3) 5' -WG C A G GC W-3' ImPy-~3-ImImPy-y-ImPyPy-~3-ImPy
1639(3) 5' -WG C A G CG W-3' ImPy-J3-ImPyIm-y-PyImPy-~i-ImPy
1640(3) 5' -WG C A G CC W-3' ImPy-~i-ImPyPy-y-ImImPy-(3-ImPy
1641(3) 5' -WG C A C TT W-3' ImPy-(3-PyHpHp-y-PyPyIm-[3-ImPy
1642(3) 5' -WG C A C TA W-3' ImPy-(3-PyHpPy-y-HpPyIm-~3-ImPy
16433) 5' -WG C A C TG W-3' ImPy-(3-PyHpIm-y-PyPyIm-(3-ImPy
1644(3) 5' -WG C A C TC W-3' ImPy-~3-PyHpPy-y-ImPyIm-(3-ImPy
1645(3) 5' -WG C A C AT W-3' ImPy-~-PyPyHp-y-PyHpIm-(3-ImPy
16463) 5' -WG C A C AA W-3' ImPy-(3-PyPyPy-y-HpHpIm-(3-ImPy
1647(3) 5' -WG C A C AG W-3' ImPy-(3-PyPyIm-y-PyHpIm-(3-ImPy
1648(3) 5' -WG C A C AC W-3' ImPy-(3-PyPyPy-y-ImHpIm-(3-ImPy
1649(3) 5' -WG C A C GT W-3' ImPy-(3-PyImHp-y-PyPyIm-~3-ImPy
1650~i) 5' -WG C A C GA W-3' ImPy-(3-PyImPy-y-HpPyIm-(3-ImPy
1651~i) 5' -WG C A C CT W-3' ImPy-~3-PyPyHp-y-PyImIm-(3-ImPy
1652(3) 5' -WG C A C CA W-3' ImPy-(3-PyPyPy-y-HpImIm-(3-ImPy
1653(3) 5' -WG C A C GG W-3' ImPy-(3-PyImIm-y-PyPyIm-p-ImPy
1654(3) 5' -WG C A C GC W-3' ImPy-f3-PyImPy-y-ImPyIm-(3-ImPy
1655(3) 5' -WG C A C CG W-3' ImPy-(3-PyPyIm-y-PyImIm-(3-ImPy
1656~i) 5' -WG C A C CC W-3' ImPy-p-PyPyPy-y-ImImIm-(3-ImPy
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-211-
TABLE 162: 12-ring
~3-Hairpin Polyamides
for recognition
of 8-by S'-WGCCWNNW-3'
-
DI'TA sequence aromatic amino acid sequence
' 1657R) 5' -W G T T T W-3' ImPyPy-~-HpHp-y-pypy-(3-ImImPy
C C
1658(3) 5' -W G T T A W-3' ImPyPy-(3-HpPy-y-HpPy-~3-ImImPy
C C
16593) 5' -W G T T G W-3' ImPyPy-(3-HpIm-y-PyPy-(3-ImImPy
C C
1660~i) 5' -W G T T C W-3' ImPyPy-/~-HpPy-y-ImPy-(3-ImImPy
C C
1661(3) 5' -W G T A T W-3'
C C ImPyPy-(3-PyHp-y-PyHp-(3-ImImPy
1662(3) 5'-WG C C T A A W-3' ImPyPy-~3-pypy-y-HpHp-(3-ImImPy
IO 1663(3) 5'-WG C C T A G W-3' ImPyPy-(3-pylm-y-pyHp-(3-ImImPy
1664(3) 5'-WG C C T A C W-3' ImPyPy-~-pypy-y-I~p-~3-ImImPy
16653) 5'-WG C C T G T W-3' ImpyPy-~-ImHp-y-pypy_~3_ImImPy
16663) 5'-WG C C T G A W-3' ImPyPy-(3-ImPy-y-HpPy-(3-ImImPy
1667(3) 5'-WG C C T G G W-3' ImPyPy-(3-Imlm-y-pypy-~3-ImImPy
1668(3) 5'-WG C C T G C W-3' ImPyPy-J3-Impy-y-Impy-(3-Imlmpy
1669(3) 5'-WG C C T C T W-3' ImPyPy-(3-PyHp-y-pyIm-(3-ImImPy
1670(3) 5'-WG C C T C A W-3' ImPyPy-(3-PyPy-y-Hplm-~3-ImImPy
1671(3) 5'-WG C C T C G W-3' ImPyPy-~3-pylm-y-PyIm-(3-ImImPy
1672(3) 5'-WG C C T C C W-3' ImPypy-~-PyPy-y-Imlm-(3-ImImpy
16733) 5'-WG C C A T T W-3' ImPyPy-~3-HpHp-y-pypy_~-ImImPy
1674(3) 5'-WG C C A T A W-3' ImPyPy-(3-HpPy-y-HpPy-(i-ImImPy
1675(3) 5'-WG C C A T G W-3' ImPyPy-p-HpIm-y-pypy-~-ImImPy
1676(3) 5'-WG C C A T C W-3' ImPyPy-(3-HpPy-y-ImPy-~3-ImImPy
1677(3) 5'-WG C C A A T W-3' ImPyPy-~3-PyHp-y-PyHp-(3-ImImPy
1678(3) 5'-WG C C A A A W-3' ImPyPy-R-Pypy-y-HpHp-(3-ImImPy
16793) 5'-WG C C A A G W-3' ImPyPy-~3-PyIm-y-pyHp-~i-ImImPy
1680(3) 5'-WG C C A A C W-3' ImPyPy-(3-pypy-y-I~p-a-ImImPy
1681(3) 5'-WG C C A G T W-3' ImPyPy-~i-ImHp-y-PyPy-p-ImImPy
1682(3) 5'-WG C C A G A W-3' ImPyPy-(3-ImPy-y-HpPy-~3-ImImPy
1683~i) 5'-WG C C A G G W-3' ImPyPy-~3-Imim-y-Pypy-(3-ImImPy
1684(3) 5'-WG C C A G C W-3' ImPyPy-j3-ImPy-y-ImPy-~3-ImImPy
16853) 5'-WG C C A C T W-3' ImPyPy-(3-PyHp-y-Pylm-(3-ImImPy
1686(3) 5'-WG C C A C A W-3' ImPyPy-(3-PyPy-y-Hplm-~3-ImImPy
1687(3) 5'-WG C C A C G W-3' ImPyPy-(3-Pylm-y-PyIm-~3-ImImPy
1688~i) 5'-WG C C A C C W-3' ImPyPy-(3-PyPy-y-ImIm-(3-ImImPy
CA 02281930 1999-08-18
WO 98/37067 PCT/US98101714
-212-
TABLE 163:
12-ring
(3-Hairpin
Polyamides
for recognition
of 8-by
5'-WGCCSNNW-3'
DNA aromatic amino acid sequence
sequence
1689(3) 5'-WG C C G T TW-3' ImPy-(3-ImHpHp-y-PyPy-~3-ImImPy
16903) ~5'-WG C C G T AW-3' ImPy-(3-ImHpPy-y-HpPy-(3-ImImPy
1691(3) 5'-WG C C G T GW-3' ImPy-(3-ImHpim-y-PyPy-(3-ImImPy
1692(3) 5'-WG C C G T CW-3' ImPy-(3-ImHpPy-y-ImPy-(3-ImImPy
1693(3) 5'-WG C C G A TW-3' ImPy-~3-ImPyHp-y-PyHp-(3-ImImPy
1694(3) 5'-WG C C G A AW-3' ImPy-(3-ImPyPy-y-HpHp-(3-ImImPy
16953) 5'-WG C C G A GW-3' ImPy-(3-ImPyIm-y-PyHp-~3-ImImPy
16963) 5'-WG C C G A CW-3' ImPy-~-ImPyPy-y-ImHp-(3-ImImPy
16973) 5'-WG C C G G TW-3' ImPy-(3-ImImHp-y-PyPy-(3-ImImPy
16983) 5'-WG C C G G AW-3' ImPy-(3-ImImPy-y-HpPy-(3-ImImPy
1699(3) 5'-WG C C G C TW-3' ImPy-(3-ImPyHp-y-PyIm-~3-ImImPy
17003) 5'-WG C C G C AW-3' ImPy-~i-ImPyPy-y-Hplm-~3-ImImPy
170/(3) 5'-WG C C C T TW-3' ImPy-~3-PyHpHp-y-Py-/3-ImImImPy
1702(3) 5'-WG C C C T AW-3' ImPy-p-PyHpPy-y-Hp-J3-ImImImPy
1703(3) 5'-WG C C C T GW-3' ImPy-(~-PyHpIm-y-Py-(3-ImImImPy
1704(3) 5'-WG C C C T CW-3' ImPy-(3-PyHpPy-y-Im-(3-ImImImPy
1705(3) 5'-WG C C C A TW-3' ImPy-(3-PyPyAp-y-Py-(3-ImImImPy
1706(3) 5'-WG C C C A AW-3' ImPy-(3-PyPyPy-y-Hp-(3-ImImImPy
1707(3) 5'-WG C C C A GW-3' ImPy-(3-PyPyIm-y-Py-~3-ImImImPy
1708(3) 5'-WG C C C A CW-3' ImPy-(3-PyPyPy-y-Im-(3-ImImImPy
1709(3) 5'-WG C C C G TW-3' ImPy-(3-PyImHp-y-Py-(3-ImImImPy
17100 5'-WG C C C G AW-3' ImPy-(3-PyImPy-y-Hp-(3-ImImImPy
G73~3) 5'-WG C C G G GW-3' 'ImPy-p-ImImIm-y-PyPy-~i-ImImPy
G74(3) 5'-WG C C G G CW-3' ImPy-~3-ImImPy-y-ImPy-~i-ImImPy
G75(3) 5'-WG C C G C GW-3' ImPy-(3-ImPyIm-y-PyIm-p-ImImPy
G76(3) 5'-WG C C G C CW-3' ImPy-(3-ImPyPy-y-Imlm-~i-ImImPy
G77~3) 5'-WG C C C G GW-3' ImPy-(3-PyImIm-y-Py-(3-ImImImPy
G78(3) 5'-WG C C C G CW-3' ImPy-(3-PyImPy-y-Im-~3-ImImImPy
...~. , . ,
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-213-
TABLE 164: 12-ring Hairpin
(3- Polyamides
for recognition
of 8-by
5'-WGAGWNNW-3'
.
DNA aromatic amino acid sequence
sequence
1713(3) 5' G AG T T T W-3' Im-(3-ImHpHpHp-y-pypypypY-(3-PY
-W
1714(3) 5' G AG T T A W-3' Im-(3-ImHpHppy-y-HppypypY_~_pY
-W
1715(3) .5' G AG T T G W-3' Im-(3-ImHpHpIm-y-pypypypy_~_py
-W
1716(3) 5'-W G AG T T C W-3' Im-(3-ImHpIipPy-y-ImPYPYPy-~-py
1717(3) 5' G AG T A T W-3' Im-(3-ImHpPyHp-y-PYHpPYPy-(3-pY
-W
1718(3) 5' G AG T A A W-3' Im-~3-ImHpPyPY-y-HpHpPyPy-(3-Py
-W
1719(3) 5' G AG T A G W-3' Im-(3-ImHpPyIm-y-PyHpPyPy-(3-Py
-W
1720(3) 5' G AG T A C W-3' Im-~3-ImHppypY_y_Iml.lppypY-(3-pY
-W
1721(3) 5' G AG T G T W-3' Im-~3-ImHpImHp-y-pypypypY-p-pY
-W
1722(3) 5' G AG T G A W-3' Im-(3-ImHpImPY-y-HpPypyPY-(3-py
-W
1723(3) 5' G AG T G G W-3' Im-p-ImHpImIm-y-Pypypypy-~3-pY
-W
1724(3) 5' G AG T G C W-3' Im-~3-ImHpImPy-y-ImPyPYPy-(3-Py
-W
1725~i) 5' G AG T C T W-3' Im-/3-ImHpPyHp-y-PyImPYPy-~3-Py
-W
17263) 5' G AG T C A W-3' Im-~3-ImHpPyPy-y-HpImPYPy-(3-Py
-W
1727(3) 5' G AG T C G W-3' Im-(3-ImHpPyIm-y-PYImPYPy-(3-Py
-W
1728(3) 5' G AG T C C W-3' Im-(3-ImHpPypY-y-ImImPyPy-J3-py
-W
1729) 5' G AG A T T W-3' Im-/3-ImPyHpHp-y-pypYHppy-(3-pY
-W
17300 5' G AG A T A W-3' Im-p-ImPyHpPy-y-HpPyHpPy-(3-py
-W
1731(3) 5' G AG A T G W-3' Im-(3-ImPYHpIm-y-pypygppy-(3-Py
-W
1732~i) 5' G AG A T C W-3' Im-(3-ImpyHppy-y-ImpyHpPy-(3-Py
-W
1733(3) 5' G AG A A T W-3' Im-p-ImPyPyHp-y-PyHpHpPy-(3-Py
-W
1734(3) 5' G AG A A A W-3' Im-~-ImPyPYPy-y-HpHpHpPy-(3-Py
-W
1735~i) 5' G AG A A G W-3' Im-~i-ImPyPYIm-y-pyHpHpPy-~3-Py
-W
1736(3) 5' G AG A A C W-3' 'Im-~3-ImPyPyPy-y-ImHpHpPy-~3-Py
-W
1737(3) 5' G AG A G T W-3' Im-(3-ImPYImHp-y-pypygpPy-(3-Py
-W
1738(3) 5' G AG A G A W-3' Im-~i-ImPYImPy-y-HpPyHpPy-(3-Py
-W
17393) 5' G AG A G G W-3' Im-(3-ImPYImIm-y-PYPyHpPy-(3-py
-W
17403) 5' G AG A G C W-3' Im-(3-ImPyImPy-y-ImPyHpPy-(3-Py
-W
1741~i) 5' G AG A C T W-3' Im-~3-ImPyPyHp-y-PyImHpPy-(3-Py
-W
1742(3) 5' G AG A C A W-3' Im-(3-ImPyPyPy-y-HpImHpPy-(3_pY
-W
1743(3) 5' G AG A C G W-3' Im-(3-ImPyPyIm-y-PyImHpPy-(3-Py
-W
1744(3) 5' G AG A C C W-3' Im-(3-ImPyPyPy-y-ImImHpPy-(3-Py
-W
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-214-
TABLE 165: 12-ring (3-Hairpin Polyamides for recognition of 8-by 5'-WGAGSNNW-
3'
DNA sequence aromatic amino acid sequence
1745(3) 5' -W G A G G T T W-3' Im-(3-ImImHpHp-y-PyPyPyPy-~3-Py
1746(3) 5' -W G A G G T A W-3' Im-(3-ImImHpPy-y-HpPyPyPy-(3-Py
1747(3) 5' -W G A G G T G W-3' Im-(3-ImImHpIm-y-PyPyPyPy-(3-Py
1748(3) 5' -W G A G G T C W-3' Im-(3-ImImHpPy-y-ImPyPyPy-(3-Py
1749(3) 5' -W G A G G A T W-3' Im-(3-ImImPyHp-y-PyHpPyPy-~3-Py
17503) 5' -W G A G G A A W-3' Im-(3-ImImPyPy-y-HpHpPyPy-/3-Py
17513) 5' -W G A G G A G W-3' Im-~3-ImImPyIm-y-PyHpPyPy-(3-Py
1752(3) 5' -W G A G G A C W-3' Im-(3-ImImPyPy-y-ImHpPyPy-~3-Py
1753(3) 5' -W G A G G G T W-3' Im-(3-ImImImHp-y-PyPyPyPy-(3-Py
1754(3) 5' -W G A G G G A W-3' Im-(3-ImImImPy-y-HpPyPyPy-~3-Py
1755(3) 5'-W G A G G C T W-3' Im-(3-ImImPyHp-y-PyImPyPy-(3-Py
1756(3) 5' -W G A G G C A W-3' Im-(3-ImImPyPy-y-HpImPyPy-~3-Py
17573) 5' -W G A G C T T W-3' Im-(3-ImPyHpHp-y-PyPyImPy-(3-Py
1758j3) 5' -W G A G C T A W-3' Im-~3-ImPyHpPy-y-HpPyImPy-~3-Py
1759(3) 5' -W G A G C T G W-3' Im-~-ImPyHpIm-y-PyPyImPy-J3-Py
17603) 5' -W G A G C T C W-3' Im-~3-ImPyHpPy-y-ImPyImPy-(3-Py
1761~i) 5' -W G A G C A T W-3' Im-/3-ImPyPyHp-y-PyHpImPy-(3-Py
1762(3) 5' -W G A G C A A W-3' Im-(3-ImPyPyPy-y-HpHpImPy-~3-Py
1763(3) 5' -W G A G C A G W-3' Im-(3-ImPyPyIm-y-PyHpImPy-(3-Py
1764(3) 5' -W G A G C A C W-3' Im-(3-ImPyPyPy-y-ImHpImPy-(3-Py
17653) 5' -W G A G C G T W-3' Im-~3-ImPyImHp-y-PyPyImPy-~3-Py
1766~i) 5'-WG A G C GA W-3' Im-(3-IrnPyImPy-y-HpPyImPy-(3-Py
1767(3) 5'-WG A G C CT W-3' 'Im-~3-ImPyPyHp-y-PyImImPy-/3-Py
1768(3) 5'-WG A G C CA W-3' Im-j3-ImPyPyPy-y-HpImImPy-(3-Py
1769(3) 5'-WG A G G GG W-3' Im-(3-ImImImIm-y-PyPyPyPy-[3-Py
1770(3) 5'-WG A G G GC W-3' Im-(3-ImImImPy-y-ImPyPyPy-~-Py
1771(3) 5'-WG A G G CG W-3' Im-(3-ImImPyIm-y-PyImPyPy-(3-Py
1772(3) 5'-WG A G G CC W-3' Im-p-ImImPyPy-y-ImImPyPy-~3-Py
17733) 5'-WG A G C GG W-3' Im-~i-ImPyImIm-y-PyPyImPy-(3-Py
1774(3) 5'-WG A G C GC W-3' Im-(3-ImPyImPy-y-ImPyImPy-~i-Py
1775(3) 5'-WG A G C CG W-3' Im-(3-ImPyPyIm-y-PyImimPy-p-Py
1776(3) 5'-WG A G C CC W-3' Im-~i-ImPyPyPy-y-ImImImPy-(i-Py
W.. . ~.. ,
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-215-
1 ABLE
166: 12-ring
~3-Hairpin
Polyamides
for recognition
of 8-by
5'-WGATWNNW-3'
DNA aromatic amino acid sequence
sequence
1777(3) 5' GA T T T T W-3' ImPy-(3-HpHpHp-y-PYPyPy-(3-HpPy
-W
1778(3) 5' GA T T T A W-3' ImPy-~3-HpHpPy-y-HpPYPy-~3-HpPy
. -W
17793) 5' GA T T T G W-3' ImPy-(3-HpHpIm-y-PyPyPy-(3-HpPy
-W
1780(3) 5' GA T T T C W-3' ImPy-(3-HpHpPy-y-ImPYPy-~3-HpPy
-W
17810 5' GA T T A T W-3' ImPy-(3-HppyHp-y-PYHpPy-(3-HpPy
-W
17823) 5' GA T T A A W-3' ImPy-/3-HpPyPy-y-HpHpPy-(3-HpPy
-W
1783(3) 5' GA T T A G W-3' ImPy-(3-HpPYIm-y-PyHpPy-~3-HpPy
-W
1784(3) 5' GA T T A C W-3' ImPy-(3-HpPYPy-y-ImHpPy-~-HpPy
-W
17853) 5' GA T T G T W-3'
-W ImPy-/3-HpImHp-y-PyPypY-(3 _HppY
1786(3) 5' GA T T G A W-3'
-W ImPy-~3-HpImPy-y-HpPYpy-~3-Hppy
1787~i) 5' GA T T G G W-3' ImPy-(3-HpImIm-y-Pypypy-(3-Hppy
-W
1788(3) 5' GA T T G C W-3' ImPy-(3-HpImPy-y-ImPyPy-(3-Hppy
-W
17893) 5' GA T T C T W-3' ImPy-(3-HpPyHp-y-PyImPy-(3-HpPy
-W
17903) 5' GA T T C A W-3' ImPy-~3-HppyPy-y-HpImPy-~i-HpPy
-W
1791(3) 5' GA T T C G W-3' ImPy-(3-HpPyIm-y-pylmPy-~i-HpPy
-W
17923) 5' GA T T C C W-3' ImPy-(3-HpPYPy-y-ImImPy-R-HpPy
-W
17933) 5' GA T A T T W-3' ImPy-~-PyHpHp-y-PYPyHp-(3-HpPy
-W
1794(3) 5' GA T A T A W-3' ImPy-(3-PyHpPy-y-HpPyHp-(3-HpPy
-W
17953) 5' GA T A T G W-3' ImPy-(3-PYHpIm-y-pypyHp-(3-HpPy
-W
1796~i) 5' GA T A T C W-3' ImPy-(3-PYHpPy-y-ImPYHp-~3-HpPy
-W
1797(3) 5' GA T A A T W-3' ImPy-(3-PyPyHp-y-pyHpHp-(3-HpPy
-W
1798(3) 5' GA T A A A W-3' Impy-(3-PyPyPY-y-HpHpHp-(3-HpPy
-W
1799(3) 5' GA T A A G W-3' ImPy-(3-PyPyIm-y-pyHpHp-/3-HpPy
-W
1800(3) 5' GA T A A C W-3' ImPy-~3-PyPyPy-y-ImHpHp-(3-HpPy
-W
1801(3) 5' GA T A G T W-3'
-W ImPy-(3-PyImHp-y-pypyHp-p-Hppy
18023) 5' GA T A G A W-3' ImPy-~i-pyImPy-y-HpPYHp-(3-HpPy
-W
18033) 5' GA T A G G W-3' Impy-~3-pylmIm-y-pypygp-~3-HppY
-W
1804(3) 5' GA T A G C W-3' ImPy-(3-PyImPy-y-ImPyHp-(3-HpPy
-W
1805(3) 5' GA T A C T W-3' ImPy-(3-pypyHp-y-PyImHp-~i-Hppy
-W
1806(3) 5' GA T A C A W-3' ImPy-(3-PYPyPy-y-HpImHp-~3-HpPy
-W
1807(3) 5' GA T A C G W-3' ImPy-~i-PyPyIm-y-PyImHp-(3-HpPy
-W
1808(3) 5' GA T A C C W-3' ImPy-(3-PyPyPy-y-ImImHp-(3-HpPY
-W
CA 02281930 1999-08-18
WO 98/37067 PCTIUS98/01714
-216-
TABLE 167: 12-ring (3-Hairpin Polyamides for recognition of 8-by 5'-WGATSNNW-
3' -
DNA sequence aromatic amino acid sequence
1809(3) 5' -W G A T G T T W-3' ImPy-~-ImHpHp-y-PyPyPy-p-HpPy
1810(3) 5' -W G A T G T A W-3' ImPy-(3-ImHpPy-y-HpPyPy-~3-HpPy
1811(3) 5' -W G A T G T G W-3' ImPy-~i-ImHpIm-y-PyPyPy-~3-HpPy
1812(3) 5' -W G A T G T C W-3' ImPy-(3-ImHpPy-y-ImPyPy-J3-HpPy
1813(3) 5' -W G A T G A T W-3' ImPy-~3-ImPyHp-y-PyHpPy-(3-HpPy
1814(3) 5' -W G A T G A A W-3' ImPy-(3-ImPyPy-y-HpHpPy-(3-HpPy
1815(3) 5' -W G A T G A G W-3' ImPy-~-ImPyIm-y-PyHpPy-(3-HpPy
1816(3) 5' -W G A T G A C W-3' ImPy-(3-ImPyPy-y-ImHpPy-~i-HpPy
18173) 5' -W G A T G G T W-3' ImPy-p-ImImHp-y-PyPyPy-(3-HpPy
1818(3) 5' -W G A T G G A W-3' ImPy-~3-ImImPy-y-HpPyPy-p-HpPy
1819(3) 5' -W G A T G C T W-3' ImPy-~i-ImPyHp-y-PyImPy-(3-HpPy
1820(3) 5' -W G A T G C A W-3' ImPy-(3-ImPyPy-y-HpImPy-~3-HpPy
1821(3) 5' -W G A T G G G W-3' ImPy-~3-ImImIm-y-PyPyPy-(3-HpPy
1822(3) 5' -W G A T G G C W-3' ImPy-(3-ImImPy-y-ImPyPy-(3-HpPy
1823~i) 5' -W G A T G C G W-3' ImPy-(3-ImPyIm-y-PyImPy-p-HpPy
18243) 5' -W G A T G C C W-3' ImPy-[3-ImPyPy-y-ImImPy-(3-HpPy
1825(3) 5' -W G A T C T T W-3' ImPy-(3-PyHpHp-y-PyPyIm-(3-HpPy
1826(3) 5' -W G A T C T A W-3' ImPy-~3-PyHpPy-y-HpPyIm-(3-HpPy
1827) 5' -W G A T C T G W-3' ImPy-(3-PyHpIm-y-PyPyIm-~-HpPy
1828(3) 5'-WG A T C T CW-3' ImPy-(3-PyHpPy-y-ImPyIm-/3-HpPy
1829(3) 5'-WG A T C A TW-3' ImPy-~3-PyPyHp-y-PyHpIm-p-HpPy
18303) 5'-WG A T C A AW-3' ImPy-(3-PyPyPy-y-HpHpIm-(3-HpPy
18313) 5'-WG A T C A GW-3' 'ImPy-(3-PyPyIm-y-PyHpIm-~i-HpPy
1832(3) 5'-WG A T C A CW-3' ImPy-(3-PyPyPy-y-ImHpIm-~3-HpPy
1833(3) 5'-WG A T C G TW-3' ImPy-(3-PyImHp-y-PyPyIm-(3-HpPy
18343) 5'-WG A T C G AW-3' ImPy-(3-PyImPy-y-HpPyIm-(3-HpPy
18353) 5'-WG A T C C TW-3' ImPy-p-PyPyHp-y-PyImIm-(3-HpPy
1836~i) 5'-WG A T C C AW-3' ImPy-(3-PyPyPy-y-HpImIm-~-HpPy
1837(3) 5'-WG A T C G GW-3' ImPy-~3-PyImIm-y-PyPyIm-~3-HpPy
1838(3) 5'-WG A T C G CW-3' ImPy-~3-PyImPy-y-ImPyIm-(3-HpPy
18393) 5'-WG A T C C GW-3' ImPy-(3-PyPyIm-y-PyImIm-(3-HpPy
18403) 5'-WG A T C C CW-3' ImPy-(3-PyPyPy-y-ImImIm-(3-HpPy
f , ,
CA 02281930 1999-08-18
WO 98'37067 PCT/US98/01714
-217-
~1'ABLE 168;
12-ring ~3-Hairpin
Polyamides
for recognition
of 8-by 5'-WGAAWNNW-3'
-
DNA aromatic amino acid sequence
sequence
1841(3) 5' G A A TT T W-3' ImPy-(3-HpHpHp-y-pyPypy-(3-HpPy
-W
1842(3) 5' G A A TT A W-3' ImPy-[3-HpHpPy-y-HpPyPy-~3-HpPy
-W
18433) 5' G A A TT G W-3' ImPy-(3-HpHpIm-y-Pypypy-~3-HppY
-W
1844(3) 5' G A A TT C W-3' ImPy-~i-HpHpPy-y-ImPYPy-~3-HpPy
-W
1845(3) 5' G A A TA T W-3' ImPy-(3-HpPyHp-y-PyHpPy-(3-HpPy
-W
18463) 5' G A A TA A W-3' ImPy-(3-HppyPy-y-HpHppy-[3-HpPy
-W
1847(3) 5' G A A TA G W-3' ImPy-~3-HpPYIm-y-PYHpPy-(3-HpPy
-W
1848(3) 5' -W G A A T A C W-3' ImPy-(3-HpPYPy-y-ImHpPy-(3-HpPy
1849(3) 5' -W G A A T G T W-3' ImPy-~3-HpImHp-y-Pypypy-(3-HpPy
1850(3) 5' -W G A A T G A W-3' ImPy-~-HpImPy-y-HpPyPy-(3-HpPy
1851(3) 5' -W G A A T G G W-3' ImPy-(3-HpImIm-y-PyPyPy-(3-HpPy
1852(3) 5' -WG A A TG C W-3' ImPy-~3-HpImPy-y-ImPyPy-(3-HpPy
1853(3) 5' -WG A A TC T W-3' ImPy-(3-HpPyHp-y-PYImPy-(3-HpPy
1854(3) 5' -WG A A TC A W-3' ImPy-(3-HpPyPy-y-HpImPy-(3-HpPy
1855(3) 5' -WG A A TC G W-3' ImPy-(3-HpPyim-y-PyImPy-~-HpPy
1856(3) 5' -WG A A TC C W-3' ImPy-(3-HpPyPy-y-ImImPy-(3-HpPy
18573) 5' -WG A A AT T W-3' ImPy-~3-PyHpHp-y-PyPyHp-~3-HpPy
18583) 5' -WG A A AT A W-3' ImPy-~3-PYHpPy-y-HpPyHp-~3-HpPy
1869(3) 5' -W G A A A T G W-3' ImPy-(3-PyHpIm-y-PypyHp-~3-HpPy
1860(3) 5' -W G A A A T C W-3' ImPy-(3-PYHpPy-y-ImPyHp-(3-HpPy
18613) 5' -W G A A A A T W-3' ImPy-~-PYPyHp-y-PyHpHp-(3-HpPy
1862(3) 5'-WG A A A A A W-3' ImPy-(3-Pypypy-y-HpHpHp-(3-HpPy
1863(3) 5'-WG A A A A G W-3' ImPy-~i-PyPYIm-y-PyHpHp-(3-HpPy
1864~i} 5'-WG A A A A C W-3' ImPy-(3-PYPyPy-y-ImHpHp-~3-HpPy
1865(3) 5'-WG A A A G T W-3' ImPy-(3-PyImHp-y-PYPYHp-~3-HpPy
1866(3) 5'-WG A A A G A W-3' ImPy-(3-PyImPy-y-HppyHp-p-HpPy
1867(3) 5'-WG A A A G G W-3' ImPy-~3-PyImIm-y-PYPyHp-p-HpPy
1868(3) 5'-WG A A A G C W-3' ImPy-J3-PyImPy-y-ImPyHp-(3-Hppy
1869(3) 5'-WG A A A C T W-3' ImPy-/3-PyPyHp-y-PYImHp-~3-HpPy
1870(3) 5'-WG A A A C A W-3' ImPy-(3-PyPyPy-y-HpImHp-(3-HpPy
1871(3) 5'-WG A A A C G W-3' ImPy-~3-PyPYIm-y-PyImHp-p-HpPy
1872(3) 5'-WG A A A C C W-3' ImPy-(3-PyPyPy-y-ImImHp-(3-HpPy
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-218-
TABLE 169:
12-ring
-Hairpin
Polyamides
for recognition
of 8-by
5'-WGAASN1VW-3'
DNA aromatic amino acid sequence
sequence
1873(3) 5' -WG A A G TT W-3' ImPy--ImHpHp-y-PyPyPy--HpPy
1874(3) . -WG A A G TA W-3' ImPy--ImHpPy-y-HpPyPy--HpPy
5'
1875(3) 5' -WG A A G TG W-3' ImPy--ImHpIm-y-PyPyPy--HpPy
1876(3) 5' -WG A A G TC W-3' ImPy--ImHpPy-y-ImPyPy--HpPy
1877 ) 5' -WG A A G AT W-3' ImPy--ImPyHp-y-PyHpPy--HpPy
18783) 5' -WG A A G AA W-3' ImPy--ImPyPy-y-HpHpPy--HpPy
1879) 5' -WG A A G AG W-3' ImPy--ImPyIm-y-PyHpPy--HpPy
1880) 5' -WG A A G AC W-3' ImPy--ImPyPy-y-ImHpPy--HpPy
18813) 5' -WG A A G GT W-3' ImPy--ImImHp-y-PyPyPy--HpPy
18823) 5' -WG A A G GA W-3' ImPy--ImImPy-y-HpPyPy--HpPy
1883(3) 5' -WG A A G CT W-3' ImPy--ImPyHp-y-PyImPy--HpPy
1884(3) 5' -WG A A G CA W-3' ImPy--ImPyPy-y-HpImPy--HpPy
1885) 5' -WG A A G GG W-3' ImPy--ImImIm-y-PyPyPy--HpPy
1886) 5' -WG A A G GC W-3' ImPy--ImImPy-y-ImPyPy--HpPy
1887) 5' -WG A A G CG W-3' ImPy--ImPyIm-y-PyImPy--HpPy
1888) 5' -WG A A G CC W-3' ImPy--ImPyPy-y-ImImPy--HpPy
1889~i) 5' -WG A A C TT W-3' ImPy--PyHpHp-y-PyPyIm-(3-HpPy
18903) 5' -WG A A C TA W-3' ImPy--PyHpPy-y-HpPyIm--HpPy
1891(3) 5' -WG A A C TG W-3' ImPy--PyHpIm-y-PyPyIm--HpPy
1892) 5' -WG A A C TC W-3' ImPy--PyHpPy-'y-ImPyIm--HpPy
1893(3) 5' -WG A A C AT W-3' ImPy--PyPyHp-y-PyHpIm--HpPy
1894(3) 5' -WG A A C AA W-3' ImPy--PyPyPy-y-HpHpIm--HpPy
18953) 5' -WG A A C AG W-3' ImPy--PyPyIm-y-PyHpIm--HpPy
1896(3) 5' -WG A A C AC W-3' ImPy--PyPyPy-y-ImHpIm--HpPy
1897p) 5' -WG A A C GT W-3' ImPy--PyImHp-y-PyPyIm--HpPy
1898(3) 5' -WG A A C GA W-3' ImPy--PyImPy-y-HpPyIm--HpPy
1899(3) 5' -WG A A C CT W-3' ImPy--PyPyHp-y-PyImIm--HpPy
1900) 5' -WG A A C CA W-3' ImPy--PyPyPy-y-HpImIm--HpPy
1901(3) 5' -WG A A C GG W-3' ImPy--PyImIm-y-PyPyIm--HpPy
1902) 5' -WG A A C GC W-3' ImPy--PyImPy-y-ImPyIm--HpPy
1903) 5' -WG A A C CG W-3' ImPy--PyPyIm-y-PyImIm--HpPy
1904~i) 5' -WG A A C CC W-3' ImPy--PyPyPy-y-ImImIm--HpPy
r , ,
CA 02281930 1999-08-18
WO 9t1~370b7 PCT/US98/01714
-219-
'TABLE 170: 12-ring (3-Hairpin Polyamides for recognition of 8-by S'-WGACWNNW-
3' -
DNA sequence aromatic amino acid sequence
- 1905~i) 5' -W G A C T T T W-3' ImPyPy-~3-HpHp-y-PyPy-(3-ImHpPy _
1906(3) ~5' -W G A C T T A W-3' ImPyPy-(3-Hppy-y-Hppy_R-ImHpPy
1907~i) 5' -W G A C T T G W-3' ImPyPy-(3-Hplm-y-PyPy-(3-ImHpPy
1908(3) 5'-W G A CT T C W-3' ImPyPy-~-HpPy-y-ImPy-(3-ImHpPy
1909(3) 5'-W G A CT A T W-3' ImPyPy-~3-pyHp-y-PyHp-(3-ImHpPy
19103) 5'-W G A CT A A W-3' ImPyPy-~3-Pypy-y-HpFip-(3-ImHpPy
1911(3) 5'-W G A CT A G W-3' ImPyPy-(3-Pylm-y-PyHp-~i-ImHpPy
1912 5'-W G A CT A C W-3'
) ImPyPy-~i-PyPy-y-ImHp-p-ImHpPy
19133) 5'-W G A CT G T W-3' ImPyPy-p-ImHp-y-pypy-(3-I~ppy
19143) 5'-W G A CT G A W-3' ImPyPy-(3-ImPy-y-HpPy-(3-ImHpPy
1915(3) 5'-W G A CT G G W-3' ImPyPy-j3-ImIm-y-Pypy-p-ImHpPy
1916(3) 5'-W G A CT G C W-3' ImPyPy-(3-ImPy-y-ImPy-(3-ImHpPy
19173) 5'-W G A CT C T W-3' ImPyPy-(3-pygp-y-pyIm-~i-ImHpPy
19183) 5'-W G A CT C A W-3' ImPyPy-~-PyPy-y-HpIm-p-ImHpPy
1919(3) 5'-W G A CT C G W-3' ImPyPy-~3-PyIm-y-PyIm-(3-ImHpPy
1920~i) 5'-W G A CT C C W-3' ImPyPy-(3-PyPy-y-ImIm-(3-ImHpPy
1921(3) 5'-W G A CA T T W-3' ImPyPy-~i-HpHp-y-Pypy-(3-ImHpPy
1922(3) 5'-W G A CA T A W-3' ImPyPy-(3-HpPy-y-HpPy-(3-ImHpPy
1923(3) 5'-W G A CA T G W-3' ImPyPy-(3-HpIm-y-PyPy-p-ImHpPy
19243) 5'-W G A CA T C W-3' ImPyPy-(3-HpPy-y-ImPy-~-ImHpPy
1925(3) 5'-W G A CA A T W-3' ImPyPy-(3-PyHp-y-PyHp-(3-ImHpPy
1926(3) 5'-W G A CA A A W-3' ImPyPy-(3-pypy-y-HpHp-(3-ImHpPy
1927(3) 5'-W G A CA A G W-3' ImPypy-(3-pylm-y-pyHp-~i-ImHpPy
1928) 5'-W G A CA A C W-3' ImPyPy-p-PyPy-y-ImHp-p-ImHpPy
1929(3) 5'-W G A CA G T W-3' ImPyPy-(3-ImHp-y-PyPy-~3-ImHpPy
19303) 5'-W G A CA G A W-3' ImPyPy-(3-ImPy-y-HpPy-(3-ImHpPy
1931(3) 5'-W G A CA G G W-3' ImPyPy-(3-Imlm-y-PyPy-(3-ImHpPy
19323) 5' -W G A C A G C W-3' ImPyPy-(3-Impy-y-ImPy-(3-ImHpPy
19333) 5' -W G A C A C T W-3' ImPyPy-~3-PyHp-y-PyIm-(3-ImHpPy
19343) 5' -W G A C A C A W-3' ImPyPy-(3-PyPy-y-Hplm-(3-ImHpPy
19350 5' -W G A C A C G W-3' ImPyPy-R-pylm-y_pylm_(3-ImHpPy
1936(3) 5' -W G A C A C C W-3' ImPyPy-p-Pypy-y-ImIm-(3-ImHpPy
CA 02281930 1999-08-18
WO 98137067 PCT/US98101714
-220-
TABLE
171:
12-ring
(3-Hairpin
Polyamides
for recognition
of 8-by
5'-WGACSNNW-3'
-
DNA aromatic amino acid sequence
sequence
1937(3) 5'-W GA C G T TW-3 T ImPy-(3-ImHpHp-y-PyPy-(3-ImHpPy
1938(3) 5'-W GA C G T AW-3' ImPy-(3-ImHpPy-y-HpPy-(3-ImHpPy
1939(3) 5'-W GA C G T GW-3' ImPy-[3-ImHpIm-y-PyPy-(3-ImHpPy
1940(3) 5'-W GA C G T CW-3' ImPy-(3-ImHpPy-y-ImPy-(3-ImHpPy
1941(3) 5'-W GA C G A TW-3' ImPy-(3-ImPyHp-y-PyHp-(3-ImHpPy
1942~i) 5'-W GA C G A AW-3' ImPy-(3-ImPyPy-y-HpHp-~3-ImHpPy
1943(3) 5'-W GA C G A GW-3' ImPy-~3-ImPyIm-y-PyHp-(3-ImHpPy
19443) 5'-W GA C G A CW-3' ImPy-(3-ImPyPy-y-ImHp-(3-ImHpPy
19453) 5'-W GA C G G TW-3' ImPy-(3-ImImHp-y-PyPy-p-ImHpPy
19463) 5'-W GA C G G AW-3' ImPy-(3-ImImPy-y-HpPy-(3-ImHpPy
1947(3) 5'-W GA C G C TW-3' ImPy-(3-ImPyHp-y-PyIm-(3-ImHpPy
1948(3) 5'-W GA C G C AW-3' ImPy-(3-ImPyPy-y-HpIm-J3-ImHpPy
19493) 5'-W GA C C T TW-3' ImPy-~3-PyHpHp-y-Py-~3-ImImHpPy
1950(3) 5'-W GA C C T AW-3' ImPy-(3-PyHpPy-y-Hp-(3-ImImHpPy
1951(3) 5'-W GA C C T GW-3' ImPy-(3-PyHpim-y-Py-(3-ImImHpPy
19523) 5'-W GA C C T CW-3' ImPy-(3-PyHpPy-y-Im-(3-ImImHpPy
1953(3) 5'-W GA C C A TW-3' ImPy-(3-PyPyHp-y-Py-p-ImImHpPy
1954(3) 5'-W GA C C A AW-3' ImPy-(3-PyPyPy-y-Hp-p-ImImHpPy
1955(3) 5'-W GA C C A GW-3' ImPy-(3-PyPyIm-y-Py-(3-ImImHpPy
1956(3) 5'-W GA C C A CW-3' ImPy-(3-PyPyPy-y-Im-(3-ImImHpPy
1957(3) 5'-W GA C C G TW-3' ImPy-/3-PyImHp-y-Py-p-ImImHpPy
1958(3) 5'-W GA C C G AW-3' ImPy-(3-PyImPy-y-Hp-~3-ImImHpPy
1959(3) 5'-W GA C C C TW-3' ImPy-p-PyPyHp-y-PyImImIm-(3-Py
1960(3) 5'-W GA C C C AW-3 T ImPy-(3-PyPyPy-y-HpImImIm-(3-Py
1961(3) 5'-W GA C G G GW-3' ImPy-(3-ImImIm-y-PyPy-~-ImHpPy
19623) 5'-W GA C G G CW-3' ImPy-(3-ImImPy-y-ImPy-p-ImHpPy
1963(3) 5'-W GA C G C GW-3' ImPy-~i-ImPyIm-y-Pylm-(3-ImHpPy
1964(3) 5'-W GA C G C CW-3' ImPy-(3-ImPyPy-y-ImIm-(3-ImHpPy
1965~i) 5'-W GA C C G GW-3' ImPy-(3-PyImIm-y-Py-(3-ImImHpPy
1966~i) 5'-W GA C C G CW-3' ImPy-~3-PyImPy-y-Im-~3-ImImHpPy
1967(3) 5'-W GA C C C GW-3' ImPy-(3-PyPyIm-y-PyImImIm-(3-Py
1968(3) 5'-W GA C C C CW-3' ImPy-(3-PyPyPy-y-ImImImIm--Py
.~. , , ,
CA 02281930 1999-08-18
WO 98/?7067 PCT/US98101714
-221-
~hABLE 2:
17 12-ring
[3-Hairpin
Polyamides
for
recognition
of
8-by
5'-WGTGVVNIVW-3'
-
DNA aromatic amino acid sequence
sequence
1969(3) 5' G TG T T T W-3' Im-(3-ImHpHpHp-y-pypypypy-(3-py
-W
1970(3) 5' G TG T T A W-3' Im-(3-ImHpHpPy-y-HpPyPYPy-(3-py
-W
19713) 5' G TG T T G W-3' Im-(3-ImHpHpIm-y-PypypypY-~j-py
-W
1972(3) 5' G TG T T C W-3' Im-~3-ImHpHpPy-y-ImPyPYPy-(3-Py
-W
19733) 5' G TG T A T W-3' Im-(3-ImHpPYHp-y-PYHpPyPy-(3-Py
-W
1974(3) 5' G TG T A A W-3' Im-~-ImHpPyPy-y-HpHpPyPy-(3-Py
-W
1975(3) 5' G TG T A G W-3' Im-(3-ImHpPyIm-y-pYHpPYPy-p-py
-W
1976(3) 5' G TG T A C W-3' Im-(3-ImHpPyPy-y-ImHpPyPy-(3-Py
-W
19773) 5' G TG T G T W-3' Im-p-ImHpImHp-y-PypypypY-~-py
-W
1978(3) 5' G TG T G A W-3' Im-(3-ImHpImPy-y-HpPyPyPy-~3-Py
-W
1979(3) 5' G TG T G G W-3' Im-~-ImHpImIm-y-PYPyPyPy-(3-Py
-W
19803) 5' G TG T G C W-3' Im-(3-ImHpImPy-y-ImPyPYPy-~3-py
-W
1981(3) 5' G TG T C T W-3' Im-(3-ImHppyHp-y-pyImPyPy-(3-Py
-W
1982(3) 5' G TG T C A W-3' Im-~i-ImHpPYPy-y-HpImPyPy-(3-Py
-W
19833) 5' G TG T C G W-3' Im-(3-ImHpPyIm-y-PyImPyPy-(3-Py
-W
1984(3) 5' G TG T C C W-3' Im-p-ImHpPYPy-y-ImImPyPy-~3-Py
-W
19853) 5' G TG A T T W-3' Im-(3-ImPyHpHp-y-PypyHpPy-(3-Py
-W
1986(3) 5' G TG A T A W-3' Im-~3-ImPYHpPy-y-HpPYHpPy-~i-py
-W
1987(3) 5' G TG A T G W-3' Im-(3-ImPYHpIm-y-PYPYHpPy-(3-Py
-W
1988(3) 5' G TG A T C W-3' Im-p-ImPyHpPy-y-ImPYHpPy-p-Py
-W
1989(3) 5' G TG A A T W-3' Im-~-ImPYPYHp-y-pyI-IpHppy-~i-py
-W
1990(3) 5' G TG A A A W-3' Im-(3-ImPYPyPy-y-HpHpHpPy-(3-Py
-W
1991(3) 5' G TG A A G W-3' Im-(3-ImPyPyIm-y-PYHpHpPy-(3-Py
-W
1992(3) 5' G TG A A C W-3' Im-p-ImPyPYPy-y-ImHpI-IpPy-p-Py
-W
19933) 5' G TG A G T W-3' Im-(3-ImPyImHp-y-PyPyHpPy-(3-Py
-W
19943) 5' G TG A G A W-3' Im-~3-ImPyImPy-y-HpPyHpPy-~3-py
-W
19950 5' G TG A G G W-3' Im-(3-ImPyImIm-y-PyPyHpPy-(3-Py
-W
19963) 5' G TG A G C W-3' Im-p-ImPyImPy-y-ImPYHpPy-~3-py
-W
1997(3) 5' G TG A C T W-3' Im-(3-ImPyPyHp-y-PyImHpPy-p-Py
-W
1998(3) 5' G TG A C A W-3' Im-p-ImPyPyPy-y-HpImHpPy-p-Py
-W
1999~i) 5' G TG A C G W-3' Im-(3-ImPyPyIm-y-PYImHpPy-(3-Py
-W
20003) 5' G TG A C C W-3' Im-/3-ImpyPypy-y-ImImHpPy-(3-Py
-W
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-222-
TABLE
173:
I2-ring
(3-Hairpin
Poiyamides
for recognition
of 8-by
5'-WGTGSNNW-3'
DNA aromatic amino acid sequence
sequence
2001(3) 5'-W G TG G T T W-3' Im-~3-ImImHpHp-y-PyPyPyPy-(3-Py
2002(3) '5'-W G TG G T A W-3' Im-~3-ImImHpPy-y-HpPyPyPy-~-Py
20033) 5'-W G TG G T G W-3' Im-/3-ImImHpIm-y-PyPyPyPy-(3-Py
20043) 5'-W G TG G T C W-3' Im-p-ImImHpPy-y-ImPyPyPy-(3-Py
2005~i) 5'-W G TG G A T W-3' Im-p-ImImPyHp-y-PyHpPyPy-~3-Py
2006~i) 5'-W G TG G A A W-3' Im-p-ImImPyPy-y-HpHpPyPy-p-Py
20070 5'-W G TG G A G W-3' Im-p-ImImPyIm-y-PyHpPyPy-p-Py
20083) 5'-W G TG G A C W-3' Im-~3-ImImPyPy-y-ImHpPyPy-p-Py
2009(3) 5'-W G TG G G T W-3' Im-(3-ImImImHp-y-PyPyPyPy-p-Py
20103) 5'-W G TG G G A W-3' Im-~3-ImImImPy-y-HpPyPyPy-(3-Py
2011(3) 5'-W G TG G C T W-3' Im-~3-ImIrnPyHp-y-PyImPyPy-(3-Py
2012(3) 5'-W G TG G C A W-3' Im-~i-ImImPyPy-y-HpImPyPy-(3-Py
2013(3) 5'-W G TG C T T W-3' Im-p-ImPyHpHp-y-PyPyImPy-p-Py
20143) 5'-W G TG C T A W-3' Im-(3-ImPyHpPy-y-HpPyImPy-(3-Py
20153) 5'-W G TG C T G W-3' Im-(3-ImPyHpIm-y-PyPyImPy-~3-Py
20160 5'-W G TG C T C W-3' Im-(3-ImPyHpPy-y-ImPyImPy-(3-Py
2017(3) 5'-W G TG C A T W-3' Im-(3-ImPyPyHp-y-PyHpImPy-(3-Py
2018(3) 5'-W G TG C A A W-3' Im-(3-ImPyPyPy-y-HpHpImPy-~i-Py
2019) 5'-W G TG C A G W-3' Im-~-ImPyPyIm-y-PyHpImPy-(3-Py
2020(3) 5'-W G TG C A C W-3' Im-~i-ImPyPyPy-y-ImHpImPy-~3-Py
2021(3) 5'-W G TG C G T W-3' Im-(3-ImPyImHp-y-PyPyImPy-(3-Py
2022~i) 5'-W G TG C G A W-3' Im-(1-ImPyImPy-y-HpPyImPy-(3-Py
2023(3) 5'-W G TG C C T W-3' ~Im-(3-ImPyPyHp-y-PyImImPy-p-Py
2024) 5'-W G TG C C A W-3' Im-~i-ImPyPyPy-y-HpImImPy-(3-Py
2025R) 5'-W G TG G G G W-3' Im-(3-ImImImIm-y-PyPyPyPy-(3-Py
2026(3) 5'-W G TG G G C W-3' Im-R-ImImImPy-y-ImPyPyPy-(3-Py
2027(3) 5'-W G TG G C G W-3' Im-~3-ImImPyIm-y-PyImPyPy-(3-Py
20283) 5'-W G TG G C C W-3' Im-~i-ImImPyPy-y-ImImPyPy-p-Py
20293) 5'-W G TG C G G W-3' Im-(3-mPyImIm-y-PyPyImPy-~3-Py
2030(3) 5'-W G TG C G C W-3' Im-(3-ImPyImPy-y-ImPyImPy-(3-Py
2031(3) 5'-W G TG C C G W-3' Im-~3-ImPyPyIm-y-PyImImPy-~i-Py
2032(3) 5'-W G TG C C C W-3' Im-(3-ImPyPyPy-y-ImImImPy-(3-Py
i_
CA 02281930 1999-08-18
WO 98/37067
-223-
PCT/US98l01714
TABLE 174:
12-ring
(3-Hairpin
Polyamides
for recogmUon
of 8-by
S'-WGTTWNNW-3'
DNA sequence aromatic amino acid sequence
2033(3) 5' -W G T ImHp-/3-HpApHp-y-pypypy_a_pypY
T T T T
W-3'
2034(3) ~ 5' -W G ImHp-(3-HpHpPy-y-HpPyPy-~3-pypy
T T T T
A W-3'
20353) 5' -W G T ImHp-(3-HpHpIm-y-pypypy-R_pypy
T T T G
W-3'
20363) 5' -W G T ImHp-(3-HpHpPy-y-ImPyPy-(3-PyPy
T T T C
W-3'
2037(3) 5' -W G T ImHp-(3-HpPYHp-y-pyHpPy-(3-PYPy
T T A T
W-3'
2038(3) 5' -W G T A A W-3' ImHp-J3-HpPYPy-y-HpHpPy-(3-Pypy
T T
2039(3) 5' -W G T A G W-3' ImHp-~3-HpPYIm-y-PyHpPy-(3-PYPy
T T
2040(3} 5' -W G T A C W-3' ImHp_~3_Hppypy_y_ImHppy-(3_pypy
T T
20413) 5' -W G T G T W-3' ImHp-(3-HpImHp-y_PyPypy-(3-pypY
T T
2042(3) 5' -W G T G A W-3' ImHp-(3-Hplmpy_y_HpPyPy-(3-PyPy
T T
20433) 5' -W G T G G W-3' ImHp-~i-HpImIm-y-PypypY-~3_pypy
T T
2044(3} 5' -W G T G C W-3' _ _
T T Imp R HpImPy y ImPyPy-(3-PyPy
2045(3) 5' -W G T C T W-3 ImHp-(3-HpPyHp-y-PYImPy-~-PyPy
T T T
20463) 5' -W G T C A W-3' ImHp-(3-Hppypy_y_HpImPy-~3-pypy
T T
20473) 5' -W G T C G W-3' ImHp-(3-HpPyIm-y-PYImPy-J3-pypY
T T
2048(3) 5'-W G T C C W-3' ImHp-~3-Hppypy_y_ImImpy-(3-PYPy
T T
20493) 5' -W G T T T W-3'
T A ImHp-~-PyHpHp-y-PyPyHp-p-PyPy
20503) 5'-W G T T A W-3' ImHp-~3-PyHpPy-y-HpPYHp-(3-PyPy
T A
2051(3) 5' -W G T T G W-3' ImHp-(3-PYHpIm-y-PypyHp-(3_pypy
T A
20523) 5' -W G T T C W-3' ImHp-~i-PyHppy-y-ImPYHp-(3-Pypy
T A
2053J3) 5' -W G T A T W-3' ImHp-~3-pypyHp_y_pyHpHp-~3-pypy
T A
2054(3) 5' -W G T A A W-3' ImHp-(3-PYPYpy-y_HpHpHp-~i-pypY
T A
2055(3) 5' -W G T A G W-3' ImHp-~3-PyPYIm-y-PyHpHp-(3-PYPy
T A
2056(3) 5' -W G T A C W-3' ImHp-(3-PyPYPy-y-ImHpHp-~3-pypY
T A
2057~i) 5' -W G T G T W-3' ImHp-(3-pylmHp_y_pypYHp_~3_PyPy
T A
2058(3) 5' -W G T G A W-3' ImHp-(3-PyImPY-y-Hppygp-(3-PyPy
T A
2059~i) 5' -W G T G G W-3' ImHp-~-PyImIm-y-pyPyHp-(3-pypy
T A
20603) 5' -W G T G C W-3' ImHp-~3-PyImPy-y_ImPYHp-~3-Pypy
T A
2061~i) 5' -W G T C T W-3' Imp-(3_pypyHp_y_pyl~p_a-pYpy
T A
2062(3) 5' -W G T C A W-3' ImHp-(3-pypypy-y_HpImHp-/3-PyPy
T A
20633) 5' -W G T C G W-3' ImHp-(3-PYPyIm-y-pylmHp-p_pypy
T A
2064(3) 5' -W G T C C W-3' ImHp-/3-PyPYPY-y-ImImHp-(3-Pypy
T A
CA 02281930 1999-08-18
WO 98137067 PCT/US98/01714
-224-
TABLE
175:
12-ring
(3-Hairpin
Polyamides
for recognition
of 8-by
5'-WGTTSNNW-3'
-
DNA aromatic amino acid sequence
sequence
2065(3) 5'-W G TT G T T W-3' ImHp-(3-ImHpHp-y-PyPyPy-~-PyPy
20663) ~5'-W G TT G T A W-3' ImHp-(3-ImHpPy-y-HpPYPy-(3-PYPy
20673) 5'-W G TT G T G W-3' ImHp-(3-ImHpIm-y-PYPYPy-~3-PYPy
2068(3) 5'-W G TT G T C W-3' ImHp-(3-ImHpPy-y-ImPYPy-(3-PyPy
2069(3) 5'-W G TT G A T W-3' ImHp-p-ImPYHp-y-PyHpPy-p-PyPy
2070(3) 5'-W G TT G A A W-3' ImHp-(3-ImPyPy-y-HpHpPy-(3-PyPy
2071(3) 5'-W G TT G A G W-3' ImHp-p-ImPyIm-y-PyHpPy-(3-PYPy
20723) 5'-W G TT G A C W-3' ImHp-(3-ImPYPy-y-ImHpPy-(3-PYPy
2073(3) 5'-W G TT G G T W-3' ImHp-a-ImImHp-y-PyPYPy-(3-PYPy
20743) 5'-W G TT G G A W-3' ImHp-p-ImImPy-y-HpPyPy-(3-PYPy
2075(3) 5'-W G TT G C T W-3' ImHp-p-ImPyHp-y-PyImPy-(3-PYPy
2076(3) 5'-W G TT G C A W-3' ImHp-p-ImPyPy-y-HpImPy-(3-PYPy
2077(3) 5'-W G TT G G G W-3' ImHp-~3-ImImIm-y-PyPYPy-(3-PyPy
2078(3) 5'-W G TT G G C W-3' ImHp-(3-ImImPy-y-ImPyPy-(3-PYPy
2079R) 5'-W G TT G C G W-3' ImHp-(3-ImPYIm-y-PyImPy-~-PYPy
2080(3) 5'-W G TT G C C W-3' ImHp-(3-ImPyPy-y-ImImPy-(3-PYPy
2081(3) 5'-W G TT C T T W-3' ImHp-(3-PYHpHp-y-PYPYIm-(3-PYPy
2082(3) 5'-W G TT C T A W-3' ImHp-(3-PYHpPy-y-HpPyIm-(3-PYPy
2083(3) 5'-W G TT C T G W-3' ImHp-(3-PYHpIm-y-PyPYIm-~3-PyPy
2084(3) 5'-W G TT C T C W-3' ImHp-(3-PYHpPy-y-ImPyIm-p-PyPy
20853) 5'-W G TT C.A T W-3' ImHp-(3-PYPyHp-y-PYHpIm-(3-PyPy
2086(3) 5'-W G TT C A A W-3' ImHp-p-PYPYPy-y-HpHpIm-(3-PyPy
2087(3) 5'-W G TT C A G W-3' ' ImHp-p-PyPYIm-y-PyHpIm-(3-PyPy
20883) 5'-W G TT C A C W-3' ImHp-J3-PYPyPy-y-ImHpIm-(3-PYPy
2089(3) 5'-W G TT C G T W-3' ImHp-(3-PyImHp-y-PyPYIm-~3-PyPy
2090(3) 5'-W G TT C G A W-3' ImHp-~i-PYImPy-y-HpPYIm-~3-PYPy
2091(3) 5'-W G TT C C T W-3' ImHp-(3-PYPyHp-y-PyImIm-(3-PyPy
2092(3) 5'-W G TT C C A W-3' ImHp-p-PYPyPy-y-HpImIm-p-PyPy
2093~i) 5'-W G TT C G G W-3' ImHp-p-PYImIm-y-PYPyIm-(3-PyPy
2094(3) 5'-W G TT C G C W-3' ImHp-[3-PYImPy-y-ImPYIm-(3-PYPy
2095(3) 5'-W G TT C C G W-3' ImHp-(3-PYPyIm-y-PyImIm-p-PYPy
2096(3) 5'-W G TT C C C W-3' ImHp-(3-PYPyPy-y-ImImIm-~3-PyPy
......~_.......-.. n
CA 02281930 1999-08-18
WO 98/37067 PCT/US98IOI714
-225-
TABLE 176: r recognition of 8-by 5'-WGTAWNNW-3'
12-ring -
~3-Hairpin
Polyamides
fo
DNA aromatic amino acid sequence
sequence
2097(3) 5' G A T T W-3' ImHp-/3-HpHpHp-y-pypypy_p_pypy
-W T T
20983) 5' G A TT A W-3' ImHp-(3-HpHpPy-y-HpPYPy-(3-PYPy
-W T
2099(3) 5' G A TT G W-3' ImHp-(3-HpHpIm-y-Pypypy-(3-pypY
-W T
' 2100(3) 5' G A TT C W-3'
-W T ImHp-p-HpHpPy-y-ImPyPy-~3-PYPy
2101) 5' G A TA T W-3' ImHp-(3-HpPYHp-y-PYHpPy-~i-Pypy
-W T
2102(3) 5' G A TA A W-3' ImHp-~3-HpPYPy-y-HpHpPy-~3-PYpY
-W T
2103(3) 5' G A TA G W-3' ImHp-(3-HpPyIm-Y-PYHpPy-~3-PYPy
-W T
2104(3) 5' G A TA C W-3' I~p_~_HppypY-Y_I~ppy-~_PypY
-W T
2105(3) 5' G A TG T W-3' I~p_~_Hpl~p_Y_pypypy-a-pYpY
-W T
21063) 5' G A TG A W-3' Imi-Ip-~_Hplmpy_y_HpPYpy-(3-pypy
-W T
21073) 5' G A TG G W-3' ImHp-(3-HpImIm-y-PypypY-(3-pypY
-W T
2108~i) 5' G A TG C W-3' ImHp-~-HpImPy-y-ImPyPy-(3-pypy
-W T
2109(3) 5' G A TC T W-3' ImHp-(3-HpPyHp-y-PyImPy-(3-PYPy
-W T
21103) 5' G A TC A W-3' ImHp-(3-HpPyPy-y-HpImPy-~3-Pypy
-W T
2111(3) 5' G A TC G W-3' ImHp-(3-HpPyIm-y-PyImPy-(3-Pypy
-W T
21123) 5' G A TC C W-3' ImHp-~3-HpPyPy-y-ImImPy-(3-PyPy
-W T
2113(3) 5' G A AT T W-3' ImHp-(3-PyHpHp-y-pypygp-(~-pypy
-W T
2114) 5' G A AT A W-3' ImHp-(3-PYHpPy-y-HpPyHp-(3-PyPy
-W T
2115(3) 5' G A AT G W-3' ImHp-~3-pyHplm-y-PypyHp-(3-Pypy
-W T
2116(3) 5' G A AT C W-3' ImHp-p-pygppY_y_ImPYHp-(3-PYPy
-W T
2117(3) 5' G A AA T W-3' ImHp-(3-PyPyHp-y-pYHpHp-(3-PYPy
-W T
2118(3} 5' G A AA A W-3' ImHp-(3-PyPyPy-Y-HpHpHp-/3-Pypy
-W T
2119(3) 5' G A AA G W-3' 'ImHp-p-pypylm-y-PYHpHp-(3-PyPy
-W T
21203) 5' G A AA C W-3' I~p_R_p~,p~,py_y_I~pHp-p-PyPY
-W T
21213) 5' G A AG T W-3' I~p_~_p~,I~p_y-pYpYHp-~-pYpY
-W T
2122(3) 5' G A AG A W-3' ImHp-~i-pylmpy_y_HppYHp-~-pypY
-W T
2123(3) 5' G A AG G W-3' ImHp-p-PYImIm-y-Pypygp-(3-pYPy
-W T
2124(3) 5' G A AG C W-3' ImHp-R-PYImPY-y-ImPYHp-~3-Pypy
-W T
2125(3) 5' G A AC T W-3' ImHpPyPYPyHp-Y-PyImHp-(3-PyPy
-W T
2126(3) 5' G A AC A W-3' ImHpPyPYPYPy-y-Hpl~p_~3-pypy
-W T
2127(3) 5' G A AC G W-3' ImHpPyPYPYIm-y-PYImHp-(3-PYpY
-W T
2128(3) 5' G A AC C W-3' ImHpPYPYPYPY-Y-ImImHp-(3-PyPY
-W T
CA 02281930 1999-08-18
WO 98/37067 PCT/US98101714
-22G-
TABLE 177: 1-Iairpin
12-ring Polyamides
p- for
recognition
of
8-by
5'-WGTASNNW-3'
-
DNA aromatic amino acid sequence
sequence
2129(3) 5' -WG T A G T T W-3' ImHp-(3-ImHpHp-y-PyPyPy-~3-PyPy
21303) ~ -WG T A G T A W-3' ImHp-(3-ImHpPy-y-HpPyPy-~3-PyPy
5'
21313) 5' -WG T A G T G W-3' ImHp-(3-ImHpIm-y-PyPypy-p-PyPy
2132(3) 5' -WG T A G T C W-3' ImHp-(3-ImHpPy-y-ImPyPy-[3-PyPy
21333) 5' -WG T A G A T W-3' ImHp-(3-ImPyHp-y-PyHpPy-(3-Pypy
2134(3) 5' -WG T A G A A W-3' ImHp-(3-ImPyPy-y-HpHpPy-~3-PyPy
2135(3) 5' -WG T A G A G W-3' ImHp-(3-ImPyIm-y-PyHpPy-~3-PyPy
2136(3) 5' -WG T A G A C W-3' ImHp-(3-ImPyPy-y-ImHpPy-~3-PyPy
21373) 5' -WG T A G G T W-3' ImHp-(3-ImImHp-y-PypyPy-~3-PyPy
21383) 5' -WG T A G G A W-3' ImHp-(3-ImImPy-y-HpPyPy-~-PyPy
2139(3) 5' -WG T A G C T W-3' ImHp-/3-ImPyHp-y-PyImPy-(3-PyPy
2140(3) 5' -WG T A G C A W-3' ImHp-(3-ImpyPy-y-HpImPy-(3-PyPy
2141(3) 5' -WG T A G G G W-3' ImHp-(3-ImImIm-y-PyPyPy-p-PyPy
2142(3) 5' -WG T A G G C W-3' ImHp-(3-ImImPy-y-ImPyPy-~i-PyPy
2143(3) 5' -WG T A G C G W-3' ImHp-(3-ImPyIm-y-PyImPy-(3-PyPy
2144(3) 5' -WG T A G C C W-3' ImHp-~3-ImPyPy-y-ImImPy-~i-PyPy
2145(3) 5' -WG T A C T T W-3' ImHp-(3-PyHpHp-y-PyPyIm-R-PyPy
2146(3) 5' -WG T A C T A W-3' ImHp-(3-PyHpPy-y-HpPyIm-(3-PyPy
2147(3) 5' -WG T A C T G W-3' ImHp-j3-PyHpIm-y-PyPyIm-(3-PyPy
2148(3) 5' -WG T A C T C W-3' ImHp-(3-PyHpPy-y-ImPyIm-p-PyPy
2149(3) 5' -WG T A C A T W-3' ImHp-R-PyPyHp-y-PyHpIm-(3-PyPy
2150(3) 5' -WG T A C A A W-3' ImHp-(3-PyPyPy-y-HpHpIm-(3-PyPy
2151(3) 5' -WG T A C A G W-3' ImHp-~3-PyPyIm-y-PyHpIm-(3-PyPy
2152(3) 5' -WG T A C A C W-3' ImHp-(3-PyPyPy-y-ImHpim-~3-PyPy
2153(3) 5' -WG T A C G T W-3' ImHp-(3-PyImHp-y-PyPyIm-(3-PyPy
2154) 5' -WG T A C G A W-3' ImHp-(3-PyImPy-y-HpPyIm-(3-PyPy
2155(3) 5' -WG T A C C T W-3' ImHp-~i-PyPyHp-y-PyImIm-p-PyPy
2156(3) 5' -WG T A C C A W-3' ImHp-(3-PyPyPy-y-HpImIm--PyPy
2157(3) 5' -WG T A C G G W-3' ImHp-(3-PyImIm-y-PyPyIm-(3-PyPy
2158(3) 5' -WG T A C G C W-3' ImHp--PyImPy-y-ImPyIm-(3-PyPy
21593) 5' -WG T A C C G W-3' ImHp-~3-PyPyIm-y-PyImIm-(3-PyPy
21603) 5' -WG T A C C C W-3' ImHp-(3-PyPyPy-y-ImImIm-p-PyPy
,. , .
CA 02281930 1999-08-18
WO 98/37067 PCT/US98/01714
-227-
1A13LE 178: 12-ring
~3-Hairpin Polyamides
for recognition
of 8-by 5'-WGTCWNNW-3'
DNA aromatic amino acid sequence
sequence
2161(3) 5'-W G TC T T T W-3' ImHppy_~3_HpHp_y_pypy_~3-ImPyPy
21623) ~5'-W G TC T T A W-3' ImHpPy-J3-Hppy_y_Hppy-(3-ImPyPy
2163~i) 5'-W G TC T T G W-3' ImHpPy-~3-HpIm-y-PyPy-~3-ImPyPy
' 2164(3) 5'-W G TC T T C W-3'
ImHpPy-(3-HpPy-y-ImPy-~3-ImPyPy
2165~i) 5'-W G TC T A T W-3' ImHpPy-~3-PyHp-y_pyHp-(3-ImPyPy
21663) 5'-W G TC T A A W-3' ImHpPy-(3-Pypy-y-HpHp-(3-ImPyPy
2167(3) 5'-W G TC T A G W-3' ImHpPy-(3-Pylm-y-PyHp-a-ImPyPy
2168(3) 5'-W G TC T A C W-3'
ImHpPy-~i-PyPy-y-ImHp-p-ImPyPy
2169(3) 5'-W G TC T G T W-3' ImHpPy-(3-ImHp-y-pypy_R-ImPyPy
2170(3) 5'-W G TC T G A W-3' ImHpPy-(3-ImPy-y-HpPy-~3-ImPyPy
2171(3) 5'-W G TC T G G W-3' ImHpPy-(3-Imlm_y_pypy_~3-ImpyPy
2172(3) 5'-W G TC T G C W-3' ImHppy_~_Impy_y_Imp~,_(3-ImPyPy
2173(3) 5'-W G TC T C T W-3' ImHpPy-~3-PyHp-y-Pylm-(3-ImPyPy
21743) 5'-W G TC T C A W-3' ImHpPy-~3-Pypy-y-HpIm-(3-ImPyPy
2175(3) 5'-W G TC T C G W-3' ImHpPy-p-pyIm-y-PyIm-(3-ImPyPy
2176~i) 5'-W G TC T C C W-3' ImHpPy-(3-PyPy-y-Imlm-~3-ImPyPy
2177(3) 5'-W G TC A T T W-3' ImHpPy-~3-HpHp-y-Pypy-(3-ImPyPy
2178(3) 5'-W G TC A T A W-3' ImHpPy-(3-HpPy-y-HpPy-(3-ImPyPy
2179(3) 5'-W G TC A T G W-3' ImHpPy-(3-HpIm-y-PyPy-~i-ImPyPy
2180J3) 5'-W G TC A T C W-3' ImHpPy-~3-HpPy-y-ImPy-p-ImPyPy
21813) 5'-W G TC A A T W-3' ImHppy_(~_pyHp_y_pyHp_R-ImPyPy
2182~i) 5'-W G TC A A A W-3' ImApPy-(1-Pypy-y-HpHp-(3-ImPyPy
2183(3) 5' -W G T C A A G W-3' ImHpPy-(3-PyIm-y-PyHp-(3-ImPyPy
2184(3) 5' -W G T C A A C W-3' ImHpPy-(3-PyPy-y-ImHp-(3-ImPyPy
2185(3) 5' -W G T C A G T W-3' ImFipPy-~3-ImHp-y_pyp~,_~_ImPyPy
2186(3) 5' -W G T C A G A W-3' ImHpPy-(3-ImPy-y-HpPy-p-ImPyPy
2187(3) 5'-W G TC A G G W-3' ImHpPy-(3-ImIm-y-PyPy-(3-ImPyPy
2188(3) 5'-W G TC A G C W-3'
ImHpPy-(3-ImPy-y-ImPy-~3-ImPyPy
2189(3) 5'-W G TC A C T W-3' ImHpPy-~i-PyHp-y-PyIm-(3-ImPyPy
2190~i) 5'-W G TC A C A W-3' ImHpPy-(3-PyPy-y-HpIm-/3-ImPyPy
2191(3) 5'-W G TC A C G W-3' ImHpPy-(3-PyIm-y-PyIm-(3-ImPyPy
2192(3) 5'-W G TC A C C W-3' ImHpPy-(3-PyPy-y-Imlm-(3-ImPyPy
CA 02281930 1999-08-18
WO 981370b7 PCT/US98/01714
-228-
TABLE 179:
12-ring
~3-Hairpin
Polyamides
for recognition
of 8-by
5'-WGTCSNNW-3'
DNA aromatic amino acid sequence
sequence
2193(3) 5'-WG T C G T TW-3' ImHp-(3-ImHpHp-y-PyPy-J3-ImPyPy
2194~i) 5'-WG T C G T AW-3' ImHp-(3-ImHpPy-y-HpPy-(3-ImPyPy
21953) 5'-WG T C G T GW-3' ImHp-j3-ImHpIm-y-PyPy-(3-ImPyPy
2196(3) 5'-WG T C G T CW-3' ImHp-~-ImHpPy-y-ImPy-(3-ImpyPy
21973) 5'-WG T C G A TW-3' ImHp-~3-ImPyHp-y-PyFip-(3-ImPyPy
2198(3) 5'-WG T C G A AW-3' ImHp-(3-ImPyPy-y-HpHp-(3-ImPyPy
2199(3) 5'-WG T C G A GW-3' ImHp-J3-ImPyIm-y-PyHp-(3-ImPyPy
22003) 5'-WG T C G A CW-3' ImHp-~i-ImPyPy-y-ImHp-(3-ImpyPy
2201(3) 5'-WG T C G G TW-3' ImHp-(3-ImImHp-y-PyPy-~3-ImPyPy
2202(3) 5'-WG T C G G AW-3' ImHp-(3-ImImPy-y-HpPy-p-ImPyPy
2203) 5'-WG T C G C TW-3' ImHp-(3-ImPyHp-y-PyIm-p-ImPyPy
2204~i) 5'-WG T C G C AW-3' ImHp-p-ImPyPy-y-HpIm-[3-ImpyPy
22053) 5'-WG T C C T TW-3' ImHp-(3-PyHpHp-y-Py-p-ImImPyPy
2206(3) 5'-WG T C C T AW-3' ImHp-(3-PyHpPy-y-Hp-(3-ImImPyPy
2207(3) 5'-WG T C C T GW-3' ImHp-(3-PyHpim-y-Py-(3-ImImPyPy
2208(3) 5'-WG T C C T CW-3' ImHp-~i-PyHpPy-y-Im-(3-ImImPyPy
2209(3) 5'-WG T C C A TW-3' ImHp-(3-PyPyHp-y-Py-(3-ImImPyPy
2210(3) 5'-WG T C C A AW-3' ImHp-(3-PyPypy-y-Hp-~3-ImImPyPy
22113) 5'-WG T C C A GW-3' ImHp-~3-PyPyIm-y-Py-~i-ImImpyPy
2212(3) 5'-WG T C C A CW-3' ImHp-(3-PypyPy-y-Im-~3-ImImPyPy
2213(3) 5'-WG T C C G TW-3' ImHp-(3-PyImHp-y-py-(3-ImImpyPy
2214(3) 5'-WG T C C G AW-3' ImHp-(3-PyImPy-y-Hp-~i-ImImPyPy
2215(3) 5'-WG T C C C TW-3' 'ImHp-~i-PyPyHp-y-PyImImIm-(3-Py
2216(3) 5'-WG T C C C AW-3' ImHp-(i-PyPyPy-y-HpImImIm-(3-Py
2217(3) 5'-WG T C G G GW-3' ImHp-~i-ImImIm-y-PyPy-(3-ImPyPy
2218(3) 5'-WG T C G G CW-3' ImHp-p-ImImPy-y-ImPy-~3-ImPyPy
22193) 5'-WG T C G C GW-3' ImHp-~3-ImPyIm-y-PyIm-p-ImPyPy
2220(3) 5'-WG T C G C CW-3' ImHp-(3-ImPyPy-y-ImIm-~-ImPyPy
22210 5'-WG T C C G GW-3' ImHp-(3-PyImIm-y-Py-(3-ImImPyPy
2222(3) 5'-WG T C C G CW-3' ImHp-(3-PyImPy-y-Im-~i-ImImPyPy
2223(3) 5'-WG T C C C GW-3' ImHp-(3-PyPyIm-y-PyImImIm-p-Py
2224~i) 5'-WG T C C C CW-3' ImHp-(3-PyPyPy-y-ImImImIm-~i-Py
