COLORANTS DE TRANSFERT D'ENERGIE A FLUORESCENCE ACCRUE

ENERGY TRANSFER DYES WITH ENHANCED FLUORESCENCE

Abrégé français

On propose de nouveaux coupleurs permettant de lier un colorant donneur à un accepteur dans un colorant fluorescent à transfert d'énergie. Ces coupleurs facilitent le transfert efficace d'énergie entre un colorant donneur et un colorant accepteur dans un colorant à transfert d'énergie. L'un de ces coupleurs permettant de lier un colorant donneur à un colorant accepteur dans un colorant fluorescent à transfert d'énergie possède la structure générale R21Z,C(O)R22R28, où R2 est un alkyle en C1 à C5 lié au colorant donneur, C(O) est un groupement carbonyle, Z est un NH, un soufre ou un oxygène, R22 est un substituant comprenant un alcène, un diène, un alcyne et un cycle à 5 ou 6 atomes possédant au moins un lien insaturé ou une structure cyclique condensée lié au groupement carbonyle, et R28 comprend un groupement fonctionnel reliant le coupleur au colorant accepteur.

Abrégé anglais

Novel linkers for linking a donor dye to an acceptor dye in an energy
transfer fluorescent dye are provided. These linkers facilitate the efficient
transfer
of energy between a donor and acceptor dye in an energy transfer dye. One of
these linkers for linking a donor dye to an acceptor dye in an energy transfer
fluorescent dye has the general structure R21Z,C(O)R22R28 where R2, is a C1-5
alkyl
attached to the donor dye, C(O) is a carbonyl group, Z, is either NH, sulfur
or
oxygen, R22 is a substituent which includes an alkene, diene, alkyne, a five
and six
membered ring having at least one unsaturated bond or a fused ring structure
which is attached to the carbonyl carbon, and R28 includes a functional group
which attaches the linker to the acceptor dye.

Revendications

CLAIMS
1. An energy transfer dye comprising:
a xanthene donor dye capable of absorbing light at a first wavelength and
emitting excitation energy in response thereto;
a 4,7-dichlororhodamine acceptor dye capable of absorbing excitation energy
emitted by the donor dye and fluorescing at a second wavelength in response
thereto; and
a linker linking the 4'-, 5- or 6-ring position of the donor dye to the 4'-, 5-
or 6-
ring position of the acceptor dye.
2. The energy transfer dye of Claim 1 in which the donor dye is a fluorescein
dye.
3. The energy transfer dye of Claim 2 in which the linker links the 5- or 6-
ring
position of the donor dye to the 5- or 6-ring position of the acceptor dye.
4. The energy transfer dye of Claim 2 in which the linker links the 4'-ring
position of
the donor dye to the 5- or 6-ring position of the acceptor dye.
5. The energy transfer dye of Claim 2 which further comprises a linking group
suitable for attaching the energy transfer dye to another substance.
6. The energy transfer dye of Claim 5 in which the linking group is attached
to the 5-
or 6-ring position of the donor dye.
7. The energy transfer dye of Claim 5 in which the linking group is attached
to the 4'-
position of the acceptor dye.
8. The energy transfer dye of Claim 1 which comprises structural formula (la)
or (lb):
-99-

<IMG>
wherein:
R1, R2, R3 and R4 are each, independently of one another, selected from
hydrogen and alkyl, or alternatively R1 and R5, R2 and R6, R3 and R8 and/or R4
and R9 may be
taken together with the atoms to which they are bonded to form a 5, 6 or 7-
membered ring;
R5, R6, R7, R9 and R10 are each, independently of one another, selected from
hydrogen, fluorine, chlorine, bromine, iodine, carboxyl, alkyl, alkene,
alkyne, sulfonate,
sulfone, amino, ammonium, amido, nitrile, alkoxy, phenyl and substituted
phenyl, or
alternatively, R6 and R7 and/or R9 and R10 may be taken together with the
atoms to which they
are bonded to form a benzo group;
R8 is selected from hydrogen, fluorine, chlorine, bromine, iodine, carboxyl,
alkyl, alkene, alkyne, sulfonate, sulfone, amino, ammonium, amido, nitrile,
alkoxy, phenyl,
substituted phenyl and linking group;
X1 and X3 are each, independently of one another, selected from hydrogen,
fluorine, chlorine, bromine, iodine, carboxyl, alkyl, alkene, alkyne,
sulfonate, sulfone, amino,
ammonium, amido, nitrile and alkoxy;
L is the linker linking the donor and acceptor dyes;
-100-

R11, R12, R13, R15 and R16 are each, independently of one another, selected
from
hydrogen, fluorine, chlorine, bromine, iodine, carboxyl, alkyl, alkene,
alkyne, sulfonate,
sulfone, amino, ammonium, amido, nitrile, alkoxy, phenyl and substituted
phenyl, or
alternatively, R12 and R13 and/or R15 and R16 may be taken together with the
atoms to which
they are bonded to form a benzo group;
R14 is selected from hydrogen, fluorine, chlorine, bromine, iodine, carboxyl,
alkyl, alkene, alkyne, sulfonate, sulfone, amino, ammonium, amido, nitrile,
alkoxy, phenyl,
substituted phenyl and linking group;
X11, X12, X13 and X15 are each, independently of one another, selected from
hydrogen, fluorine, chlorine, bromine, iodine, carboxyl, alkyl, alkene,
alkyne, sulfonate,
sulfone, amino, ammonium, amido, nitrile and alkoxy; and
X14 is selected from hydrogen, fluorine, chlorine, bromine, iodine, carboxyl,
alkyl, alkene, alkyne, sulfonate, sulfone, amino, ammonium, amido, nitrile,
alkoxy and linking
group.
9. The energy transfer dye of Claim 1 in which the linker comprises a
functional
group selected from an alkene, a diene, an alkyne, a five membered ring having
at least one
unsaturated bond, a six membered ring having at least one unsaturated bond and
a fused ring
structure.
10. The energy transfer dye of Claim 1 in which the acceptor dye is selected
from
DR110-2, DR6G-2, DTMR and DROX.
11. A fluorescently-labeled reagent comprising an energy transfer dye
covalently
attached to a reagent, wherein:
the reagent is selected from a protein, a polypeptide, a polysaccharide, a
nucleoside or
nucleotide (nucleosides/tide), an oligonucleotide, an oligonucleotide analog,
a lipid, a solid
support, an organic polymer and an inorganic polymer; and
the energy transfer dye comprises:
a xanthene donor dye capable of absorbing light at a first wavelength and
emitting
excitation energy in response thereto;
-101-

a 4,7-dichlororhodamine acceptor dye capable of absorbing the excitation
energy
emitted by the donor dye and fluorescing at a second wavelength in response
thereto; and
a linker linking the 4'-, 5- or 6-ring position of the xanthene donor dye to
the 4'-, 5-
or 6-ring position of the acceptor dye.
12. The fluorescently-labeled reagent of Claim 11 in which the reagent is a
nucleoside/tide.
13. The fluorescently-labeled reagent of Claim 12 in which the donor dye is a
fluorescein dye.
14. The fluorescently-labeled reagent of Claim 13 in which the linker links
the 5- or 6-
ring position of the donor dye to the 5- or 6-ring position of the acceptor
dye.
15. The fluorescently-labeled reagent of Claim 13 in which the linker links
the 4'-ring
position of the donor dye to the 5- or 6-ring position of the acceptor dye.
16. The fluorescently labeled nucleoside/tide of Claim 13 in which the energy
transfer
dye is covalently linked to the nucleobase of the nucleoside/tide at the 5- or
6-ring position of
the donor dye or the 4'-ring position of the acceptor dye.
17. The fluorescently labeled nucleoside/tide of Claim 16 in which the energy
transfer
dye is covalently linked to the nucleobase of the nucleoside/tide by way of
acetylenic amido or
alkenic amido linkage.
18. The fluorescently labeled nucleoside/tide of Claim 17 in which the
acetylenic
amido or alkenic amido linkage is selected from -C .ident.C-CH2-NH-C(O)-, 3-
amino-1-propyn-1-
yl, -C .ident.C-CH2-NH-C(O)-(CH2)5-C(O)-, -C=CH-C(O)-NH-(CH2)5-NH-C(O)- and
-C .ident.C-CH2-O-CH2-CH2-NR-, where R is hydrogen, a protecting group or
alkyl.
19. The fluorescently-labeled nucleoside/tide of Claim 12 in which the linker
linking
the donor and acceptor dyes comprises a functional group selected from an
alkene, a diene, an
-102-

alkyne, a five membered ring having at least one unsaturated bond, a six
membered ring
having at least one unsaturated bond and a fused ring structure.
20. The fluorescently-labeled nucleoside/tide of any one of Claims 12-19 in
which the
energy transfer dye comprises structural formula (Ia) or (lb)
<IMG>
wherein:
R1, R2, R3 and R4 are each, independently of one another, selected from
hydrogen and alkyl, or alternatively R1 and R5, R2 and R6, R3 and R8 and/or R4
and R9 may be
taken together with the atoms to which they are bonded to form a 5, 6 or 7-
membered ring;
R5, R6, R7, R9 and Rio are each, independently of one another, selected from
hydrogen, fluorine, chlorine, bromine, iodine, carboxyl, alkyl, alkene,
alkyne, sulfonate,
sulfone, amino, ammonium, amido, nitrile, alkoxy, phenyl and substituted
phenyl, or
alternatively, R6 and R7 and/or R9 and R10 may be taken together with the
atoms to which they
are bonded to form a benzo group;
R8 is selected from hydrogen, fluorine, chlorine, bromine, iodine, carboxyl,
alkyl, alkene, alkyne, sulfonate, sulfone, amino, ammonium, amido, nitrile,
alkoxy, phenyl and
-103-

substituted phenyl, or, altematively R8 comprises the covalent attachment to
the
nucleoside/tide;
X1 and X3 are each, independently of one another, selected from hydrogen,
fluorine, chlorine, bromine, iodine, carboxyl, alkyl, alkene, alkyne,
sulfonate, sulfone, amino,
ammonium, amido, nitrile and alkoxy;
L is the linker linking the donor and acceptor dyes;
R11, R12, R13, R15 and R16 are each, independently of one another, selected
from
hydrogen, fluorine, chlorine, bromine, iodine, carboxyl, alkyl, alkene,
alkyne, sulfonate,
sulfone, amino, ammonium, amido, nitrile, alkoxy, phenyl and substituted
phenyl, or
alternatively, R12 and R13 and/or R15 and R16 may be taken together with the
atoms to which
they are bonded to form a benzo group;
R14 is selected from hydrogen, fluorine, chlorine, bromine, iodine, carboxyl,
alkyl, alkene, alkyne, sulfonate, sulfone, amino, ammonium, amido, nitrile,
alkoxy, phenyl and
substituted phenyl, or, alternatively R14 comprises the covalent attachment to
the
nucleoside/tide;
X11, X12, X13 and X15 are each, independently of one another, selected from
hydrogen, fluorine, chlorine, bromine, iodine, carboxyl, alkyl, alkene,
alkyne, sulfonate,
sulfone, amino, ammonium, amido, nitrile and alkoxy; and
X14 is selected from hydrogen, fluorine, chlorine, bromine, iodine, carboxyl,
alkyl, alkene, alkyne, sulfonate, sulfone, amino, ammonium, amido, nitrile and
alkoxy, or,
alternatively X14 comprises the covalent attachment to the nucleoside/tide,
with the proviso that only one of R8, R14 or X14 comprises the covalent
attachment to the nucleoside/tide.
21. The fluorescently labeled nucleoside/tide of Claim 20 in which the
nucleoside/tide
is a 2'-deoxyribonucleoside.
22. The fluorescently labeled nucleoside/tide of Claim 20 in which the
nucleoside/tide
is a 2'-deoxyribonucleotide.
23. The fluorescently labeled nucleoside/tide of Claim 22 in which the 2'-
deoxyribonucleotide is a 2'-deoxyribonucleoside-5'-triphosphate.
-104-

24. The fluorescently labeled nucleoside/tide of Claim 20 in which the
nucleoside/tide
is a terminating nucleotide.
25. The fluorescently labeled nucleoside/tide of Claim 24 in which the
terminating
nucleotide is a 2',3'-dideoxynucleoside-5'-triphosphate.
26. The fluorescently-labeled reagent of Claim 11 in which the reagent is an
oligonucleotide or oligonucleotide analog.
27. The fluorescently-labeled oligonucleotide or analog of Claim 26 in which
the
energy transfer dye is attached to the 5'-terminus of the oligonucleotide or
oligonucleotide
analog.
28. The fluorescently-labeled oligonucleotide or analog of Claim 26 in which
the
energy transfer dye is attached to the 3'-terminus of the oligonucleotide or
oligonucleotide
analog.
29. The fluorescently-labeled oligonucleotide of Claim 26 in which the energy
transfer
dye is attached to a nucleobase of the oligonucleotide or oligonucleotide
analog.
30. A kit for analyzing a nucleic acid, comprising a set of four different
terminating
nucleotides, each of which terminates a template-dependent primer extension
reaction at a
different template nucleotide and comprises a fluorescent label capable of
producing a
detectable, spectrally resolvable fluorescent signal, wherein at least one of
the fluorescent
labels is an energy transfer dye comprising:
a xanthene donor dye capable of absorbing light at a first wavelength and
emitting excitation energy in response thereto;
a 4,7-dichlororhodamine acceptor dye capable of absorbing the excitation
energy emitted by the donor dye and fluorescing at a second wavelength in
response thereto;
and
a linker linking the 4'-, 5- or 6-ring position of the donor dye to the 4'-, 5-
or 6-
ring position of the acceptor dye,
-105-

and wherein the energy transfer dye is attached to the terminating nucleotide
at the 4'-,
5- or 6-ring position of the donor or acceptor dye.
31. The kit of Claim 30 in which the linker linking the donor and acceptor
dyes
comprises a functional group selected from an alkene, a diene, an alkyne, a
five membered
ring having at least one unsaturated bond, a six membered ring having at least
one unsaturated
bond and a fused ring structure.
32. The kit of Claim 30 in which the donor dye is a fluorescein dye.
33. The kit of Claim 32 in which the terminating nucleotide is attached to the
4'-ring
position of the acceptor dye.
34. The kit of Claim 32 in which the terminating nucleotide is attached to the
5- or 6-
ring position of the donor dye.
35. The kit of Claim 30 in which the energy transfer dye comprises structural
formula
(Ia) or (Ib):
<IMG>
wherein:
-106-

R1, R2, R3 and R4 are each, independently of one another, selected from
hydrogen and alkyl, or alternatively R1 and R5, R2 and R6, R3 and R8 and/or R4
and R9 may be
taken together with the atoms to which they are bonded to form a 5, 6 or 7-
membered ring;
R5, R6, R7, R9 and R10 are each, independently of one another, selected from
hydrogen, fluorine, chlorine, bromine, iodine, carboxyl, alkyl, alkene,
alkyne, sulfonate,
sulfone, amino, ammonium, amido, nitrile, alkoxy, phenyl and substituted
phenyl, or
alternatively, R6 and R7 and/or R9 and R10 may be taken together with the
atoms to which they
are bonded to form a benzo group;
R8 is selected from hydrogen, fluorine, chlorine, bromine, iodine, carboxyl,
alkyl, alkene, alkyne, sulfonate, sulfone, amino, ammonium, amido, nitrile,
alkoxy, phenyl and
substituted phenyl, or, alternatively R8 comprises the covalent attachment to
the terminating
nucleotide;
X1 and X3 are each, independently of one another, selected from hydrogen,
fluorine, chlorine, bromine, iodine, carboxyl, alkyl, alkene, alkyne,
sulfonate, sulfone, amino,
ammonium, amido, nitrile and alkoxy;
L is the linker linking the donor and acceptor dyes;
R11, R12, R13, R15 and R16 are each, independently of one another, selected
from
hydrogen, fluorine, chlorine, bromine, iodine, carboxyl, alkyl, alkene,
alkyne, sulfonate,
sulfone, amino, ammonium, amido, nitrile, alkoxy, phenyl and substituted
phenyl, or
alternatively, R12 and R13 and/or R15 and R16 may be taken together with the
atoms to which
they are bonded to form a benzo group;
R14 is selected from hydrogen, fluorine, chlorine, bromine, iodine, carboxyl,
alkyl, alkene, alkyne, sulfonate, sulfone, amino, ammonium, amido, nitrile,
alkoxy, phenyl and
substituted phenyl, or, alternatively R14 comprises the covalent attachment to
the terminating
nucleotide;
X11, X12, X13 and X15 are each, independently of one another, selected from
hydrogen, fluorine, chlorine, bromine, iodine, carboxyl, alkyl, alkene,
alkyne, sulfonate,
sulfone, amino, ammonium, amido, nitrile and alkoxy; and
-107-

X14 is selected from hydrogen, fluorine, chlorine, bromine, iodine, carboxyl,
alkyl, alkene, alkyne, sulfonate, sulfone, amino, ammonium, amido, nitrile and
alkoxy, or,
alternatively X14 comprises the covalent attachment to the terminating
nucleotide,
with the proviso that only one of R8, -R14 or X14 comprises the covalent
attachment to the terminating nucleotide.
36. The kit of Claim 30 in which the labels of the terminating nucleotides are
excitable
by a single light source.
37. The kit of Claim 30, wherein in each of the four different terminating
nucleotides,
the fluorescent label is an energy transfer dye comprising:
a xanthene donor dye capable of absorbing light at a first wavelength and
emitting excitation energy in response thereto;
a 4,7-dichlororhodamine acceptor dye capable of absorbing the excitation
energy emitted by the donor dye and fluorescing at a second wavelength in
response thereto;
and
a linker linking the 4'-, 5- or 6-ring position of the donor dye to the 4'-, 5-
or 6-
ring position of the acceptor dye,
and wherein each energy transfer dye is attached to its respective terminating
nucleotide at the 4'-, 5- or 6-ring position of the donor or acceptor dye.
38. The kit of Claim 37 in which each linker linking each donor and acceptor
dye
comprises a functional group selected from an alkene, a diene, an alkyne, a
five membered
ring having at least one unsaturated bond, a six membered ring having at least
one unsaturated
bond and a fused ring structure.
39. The kit of Claim 37 in which each donor dye is a fluorescein dye.
40. The kit of Claim 37 in which each energy transfer dye is attached to its
respective
terminating nucleotide at the 4'-ring position of the acceptor dye.
41. The kit of Claim 37 in which each energy transfer dye is attached to its
respective
terminating nucleotide at the 5- or 6-ring position of the donor dye.
-108-

42. The kit of Claim 37 in which each energy transfer dye comprises structural
formula
(Ia) or (Ib):
<IMG>
wherein:
R1, R2, R3 and R4 are each, independently of one another, selected from
hydrogen and alkyl, or alternatively R1 and R5, R2 and R6, R3 and R8 and/or R4
and R9 may be
taken together with the atoms to which they are bonded to form a 5, 6 or 7-
membered ring;
R5, R6, R7, R9 and R10 are each, independently of one another, selected from
hydrogen, fluorine, chlorine, bromine, iodine, carboxyl, alkyl, alkene,
alkyne, sulfonate,
sulfone, amino, ammonium, amido, nitrile, alkoxy, phenyl and substituted
phenyl, or
alternatively, R6 and R7 and/or R9 and R10 may be taken together with the
atoms to which they
are bonded to form a benzo group;
R8 is selected from hydrogen, fluorine, chlorine, bromine, iodine, carboxyl,
alkyl, alkene, alkyne, sulfonate, sulfone, amino, ammonium, amido, nitrile,
alkoxy, phenyl and
substituted phenyl, or, alternatively R8 comprises the covalent attachment to
the respective
terminating nucleotide;
-109-

X1 and X3 are each, independently of one another, selected from hydrogen,
fluorine, chlorine, bromine, iodine, carboxyl, alkyl, alkene, alkyne,
sulfonate, sulfone, amino,
ammonium, amido, nitrile and alkoxy;
L is the linker linking the donor and acceptor dyes;
R11, R12, R13, R15 and R16 are each, independently of one another, selected
from
hydrogen, fluorine, chlorine, bromine, iodine, carboxyl, alkyl, alkene,
alkyne, sulfonate,
sulfone, amino, ammonium, amido, nitrile, alkoxy, phenyl and substituted
phenyl, or
alternatively, R12 and R13 and/or R15 and R16 may be taken together with the
atoms to which
they are bonded to form a benzo group;
R14 is selected from hydrogen, fluorine, chlorine, bromine, iodine, carboxyl,
alkyl, alkene, alkyne, sulfonate, sulfone, amino, ammonium, amido, nitrile,
alkoxy, phenyl and
substituted phenyl, or, alternatively R14 comprises the covalent attachment to
the respective
terminating nucleotide;
X11, X12, X13 and X15 are each, independently of one another, selected from
hydrogen, fluorine, chlorine, bromine, iodine, carboxyl, alkyl, alkene,
alkyne, sulfonate,
sulfone, amino, ammonium, amido, nitrile and alkoxy; and
X14 is selected from hydrogen, fluorine, chlorine, bromine, iodine, carboxyl,
alkyl, alkene, alkyne, sulfonate, sulfone, amino, ammonium, amido, nitrile and
alkoxy, or,
alternatively X14 comprises the covalent attachment to the respective
terminating nucleotide,
with the proviso that only one of R8, R14 or X14 comprises the covalent
attachment to the respective terminating nucleotide.
43. The kit of Claim 37 in which each energy transfer dye comprises the same
donor
dye.
44. The kit of any one of Claims 30-43 that further includes a set of four
nucleoside
triphosphates capable of extending an oligonucleotide primer in a template-
dependent primer
extension reaction.
45. The kit of Claim 44 that further includes a polymerase.
-110-

46. A method of forming a fluorescently labeled oligonucleotide, comprising
the step
of enzymatically extending an oligonucleotide primer in the presence of a
template nucleic
acid and nucleotide triphosphates, wherein the oligonucleotide primer or at
least one of the
nucleotide triphosphates is labeled with an energy transfer dye comprising:
(i) a xanthene donor dye capable of absorbing light at a first wavelength and
emitting excitation energy in response thereto;
(ii) a 4,7-dichlororhodamine acceptor dye capable of absorbing the excitation
energy emitted by the donor dye and fluorescing at a second wavelength in
response thereto;
and
(iii) a linker linking the 4'-, 5- or 6-ring position of the donor dye to the
4'-, 5-
or 6-ring position of the acceptor dye,
and wherein the energy transfer dye is attached to the oligonucleotide primer
or the at
least one nucleotide triphosphate at the 4'-, 5- or 6-ring position of the
donor or acceptor dye.
47. The method of Claim 46 in which the linker comprises a functional group
selected
from an alkene, a diene, an alkyne, a five membered ring having at least one
unsaturated bond,
a six membered ring having at least one unsaturated bond and a fused ring
structure.
48. The method of Claim 46 in which the donor dye is a fluorescein dye.
49. The method of Claim 46 in which the energy transfer dye is attached to the
oligonucleotide primer or the at least one nucleotide triphosphate at the 4'-
ring position of the
acceptor dye.
50. The method of Claim 46 in which the energy transfer dye is attached to the
oligonucleotide primer or the at least one nucleotide triphosphate at the 5-
or 6-ring position of
the donor dye.
51. The method of any one of Claims 46-50 in which the energy transfer dye
comprises
structural formula (la) or (lb):
-111-

<IMG>
wherein:
R1, R2, R3 and R4 are each, independently of one another, selected from
hydrogen and alkyl, or alternatively R1 and R5, R2 and R6, R3 and R8 and/or R4
and R9 may be
taken together with the atoms to which they are bonded to form a 5, 6 or 7-
membered ring;
R5, R6, R7, R9 and R10 are each, independently of one another, selected from
hydrogen, fluorine, chlorine, bromine, iodine, carboxyl, alkyl, alkene,
alkyne, sulfonate,
sulfone, amino, ammonium, amido, nitrile, alkoxy, phenyl and substituted
phenyl, or
alternatively, R6 and R7 and/or R9 and R10 may be taken together with the
atoms to which they
are bonded to form a benzo group;
R8 is selected from hydrogen, fluorine, chlorine, bromine, iodine, carboxyl,
alkyl, alkene, alkyne, sulfonate, sulfone, amino, ammonium, amido, nitrile,
alkoxy, phenyl and
substituted phenyl, or, alternatively R8 comprises the covalent attachment to
the
oligonucleotide primer or the at least one nucleotide triphosphate;
X1 and X3 are each, independently of one another, selected from hydrogen,
fluorine, chlorine, bromine, iodine, carboxyl, alkyl, alkene, alkyne,
sulfonate, sulfone, amino,
ammonium, amido, nitrile and alkoxy;
L is the linker linking the donor and acceptor dyes;
-112-

R11, R12, R13, R15 and R16 are each, independently of one another, selected
from
hydrogen, fluorine, chlorine, bromine, iodine, carboxyl, alkyl, alkene,
alkyne, sulfonate,
sulfone, amino, ammonium, amido, nitrile, alkoxy, phenyl and substituted
phenyl, or
alternatively, R12 and R13 and/or R15 and R16 may be taken together with the
atoms to which
they are bonded to form a benzo group;
R14 is selected from hydrogen, fluorine, chlorine, bromine, iodine, carboxyl,
alkyl, alkene, alkyne, sulfonate, sulfone, amino, ammonium, amido, nitrile,
alkoxy, phenyl and
substituted phenyl, or, alternatively R14 comprises the covalent attachment to
the
oligonucleotide primer or the at least one nucleotide triphosphate;
X11, X12, X13 and X15 are each, independently of one another, selected from
hydrogen, fluorine, chlorine, bromine, iodine, carboxyl, alkyl, alkene,
alkyne, sulfonate,
sulfone, amino, ammonium, amido, nitrile and alkoxy; and
X14 is selected from hydrogen, fluorine, chlorine, bromine, iodine, carboxyl,
alkyl, alkene, alkyne, sulfonate, sulfone, amino, ammonium, amido, nitrile and
alkoxy, or,
alternatively X14 comprises the covalent attachment to the oligonucleotide
primer or the at
least one nucleotide triphosphate,
with the proviso that only one of R8, R14 or X14 comprises the covalent
attachment to the oligonucleotide primer or the at least one nucleotide
triphosphate.
52. The method of Claim 51 in which the oligonucleotide primer is labeled with
the
energy transfer dye.
53. The method of Claim 51 in which the at least one nucleotide triphosphate
is labeled
with the energy transfer dye.
54. The method of Claim 51 in which the enzymatic extension is carried out
with a
polymerase.
55. A method of analyzing a nucleic acid, comprising the steps of
forming a plurality of differently sized fluorescently labeled extended
oligonucleotide primers;
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separating the fluorescently labeled extended oligonucleotide primers based
upon their sizes; and
detecting the fluorescently labeled extended primers based upon their
fluorescence, wherein the fluorescent label of at least one of the
fluorescently labeled extended
oligonucleotide primers is a fluorescent energy transfer dye comprising:
(i) a xanthene donor dye capable of absorbing light at a first wavelength
and emitting excitation energy in response thereto;
(ii) a 4,7-dichlororhodamine acceptor dye capable of absorbing the
excitation energy emitted by the donor dye and fluorescing at a second
wavelength in response
thereto; and
(iii) a linker linking the 4'-, 5- or 6-ring position of the donor dye to the
4'-, 5- or 6-ring position of the acceptor dye,
and wherein the energy transfer dye is linked to the extended oligonucleotide
primer at
the 4'-, 5'- or 6-ring position of the donor or acceptor dye.
56. The method of Claim 55 in which the plurality of differently sized
fluorescently
labeled extended oligonucleotide primers are formed by enzymatically extending
an
oligonucleotide primer including the energy transfer dye in the presence of a
template nucleic
acid, nucleotide triphosphates and at least one terminating nucleotide such
that the primer is
extended until the terminating nucleotide is incorporated into the extended
primer.
57. The method of Claim 55 in which the plurality of differently sized
fluorescently
labeled extended oligonucleotide primers are formed by enzymatically extending
an
oligonucleotide primer in the presence of a template nucleic acid, nucleotide
triphosphates and
at least one terminating nucleotide including the energy transfer dye such
that the primer is
extended until the terminating nucleotide is incorporated into the extended
primer.
58. The method of Claim 55 in which the enzymatic extension is carried out in
the
presence of four different terminating nucleotides, each of which terminates
primer extension
at a different template nucleotide, and wherein each of the different
terminating nucleotides
includes a different, spectrally resolvable fluorescent dye, at least one of
which is the energy
transfer dye.
-114-

59. The method of Claim 58 in which the donor dye is a fluorescein dye.
60. The method of Claim 58 in which the linker of the energy transfer dye
comprises a
functional group selected from an alkene, a diene, an alkyne, a five membered
ring having at
least one unsaturated bond, a six membered ring having at least one
unsaturated bond and a
fused ring structure.
61. The method of Claim 58 in which each energy transfer dye is attached to
its
respective terminating nucleotide at the 4'-position of the 4,7-
dichlororhodamine acceptor dye.
62. The method of Claim 58 in which each energy transfer dye is attached to
its
respective terminating nucleotide at the 5- or 6-ring position of the donor
dye.
63. The method of Claim 58 in which each energy transfer dye comprises
structural
formula (Ia) or (lb):
<IMG>
wherein:
R1, R2, R3 and R4 are each, independently of one another, selected from
hydrogen and alkyl, or alternatively R1 and R5, R2 and R6, R3 and R8 and/or R4
and R9 may be
taken together with the atoms to which they are bonded to form a 5, 6 or 7-
membered ring;
-115-

R5, R6, R7, R9 and Rio are each, independently of one another, selected from
hydrogen, fluorine, chlorine, bromine, iodine, carboxyl, alkyl, alkene,
alkyne, sulfonate,
sulfone, amino, ammonium, amido, nitrile, alkoxy, phenyl and substituted
phenyl, or
alternatively, R6 and R7 and/or R9 and R10 may be taken together with the
atoms to which they
are bonded to form a benzo group;
R8 is selected from hydrogen, fluorine, chlorine, bromine, iodine, carboxyl,
alkyl, alkene, alkyne, sulfonate, sulfone, amino, ammonium, amido, nitrile,
alkoxy, phenyl and
substituted phenyl, or, alternatively R8 comprises the covalent attachment to
the terminating
nucleotide;
X1 and X3 are each, independently of one another, selected from hydrogen,
fluorine, chlorine, bromine, iodine, carboxyl, alkyl, alkene, alkyne,
sulfonate, sulfone, amino,
ammonium, amido, nitrile and alkoxy;
L is the linker linking the donor and acceptor dyes;
R11, R12, R13, R15 and R16 are each, independently of one another, selected
from
hydrogen, fluorine, chlorine, bromine, iodine, carboxyl, alkyl, alkene,
alkyne, sulfonate,
sulfone, amino, ammonium, amido, nitrile, alkoxy, phenyl and substituted
phenyl, or
alternatively, R12 and R13 and/or R15 and R16 may be taken together with the
atoms to which
they are bonded to form a benzo group;
R14 is selected from hydrogen, fluorine, chlorine, bromine, iodine, carboxyl,
alkyl, alkene, alkyne, sulfonate, sulfone, amino, ammonium, amido, nitrile,
alkoxy, phenyl and
substituted phenyl, or, alternatively R14 comprises the covalent attachment to
the terminating
nucleotide;
X11, X12, X13 and X15 are each, independently of one another, selected from
hydrogen, fluorine, chlorine, bromine, iodine, carboxyl, alkyl, alkene,
alkyne, sulfonate,
sulfone, amino, ammonium, amido, nitrile and alkoxy; and
X14 is selected from hydrogen, fluorine, chlorine, bromine, iodine, carboxyl,
alkyl, alkene, alkyne, sulfonate, sulfone, amino, ammonium, amido, nitrile and
alkoxy, or,
alternatively X14 comprises the covalent attachment to the terminating
nucleotide,
with the proviso that only one of R8, R14 or X14 comprises the covalent
attachment to the terminating nucleotide.
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64. The method of Claim 63 in which each energy transfer dye comprises the
same
donor dye.
65. The method of any one of Claims 56-64 in which the enzymatic extension is
carried out with a polymerase.
66. The method of Claim 65 in which the nucleotide triphosphates comprise a
mixture
of dATP, dCTP, dGTP and dTTP.
67. The method of Claim 65 in which the terminating nucleotide is selected
from the
group consisting of ddATP, ddCTP, ddOTP and ddTTP.
68. The method of Claim 65 further comprising the step of determining the
sequence of
the nucleic acid.
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Description

CA 02297589 2000-02-03
ENERGY TRANSFER DYES WITH ENHANCED FLUORESCENCE
BACKGROUND OF THE INVENTION
Field of the Invention
The present invention relates to fluorescent dyes and, more
specifically, energy transfer fluorescent dyes and their use.
Description of Related Art
A variety of fluorescent dyes have been developed for labeling
and detecting components in a sample. In general, fluorescent dyes
preferably have a high quantum yield and a large extinction coefficient
so that the dye may be used to detect small quantities of the component
being detected. Fluorescent dyes also preferably have a large Stokes
shift (i.e., the difference between the wavelength at which the dye has
maximum absorbance and the wavelength at which the dye has
maximum emission) so that the fluorescent emission is readily
distinguished from the light source used to excite the dye. -
One class of fluorescent dyes which has been developed is
energy transfer fluorescent dyes. In general, energy transfer fluorescent
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CA 02297589 2000-02-03
dyes include a donor fluorophore and an acceptor fluorophore. In these
dyes, when the donor and acceptor fluorophores are positioned in
proximity with each other and with the proper orientation relative to each
other, the energy emission from the donor fluorophore is absorbed by
the acceptor fluorophore and causes the acceptor fluorophore to
fluoresce. It is therefore important that the excited donor fluorophore be
able to efficiently absorb the excitation energy of the donor fluorophore
and efficiently transfer the energy to the acceptor fluorophore.
A variety of energy transfer fluorescent dyes have been
1Q described in the literature. For example, U.S. Patent No. 4,996,143 and
WO 95/21266 describe energy transfer fluorescent dyes where the
donor and acceptor fluorophores are linked by an oligonucleotide chain.
Lee, et al., Nucleic Acids Research 20:10 2471-2483 (1992) describes
an energy transfer fluorescent dye which includes 5-carboxy rhodamine
linked to 4'-aminomethyl-5-carboxy fluorescein by the 4'-aminomethyl
substituent on fluorescein.
Several diagnostic and analytical assays have been developed
which involve the detection of multiple components in a sample using
fluorescent dyes, e.g. flow cytometry (Lanier, et al., J. Immunol. 132
151-156 (1984)); chromosome analysis (Gray, et al., Chromosoma 73 9-
27 (1979)); and DNA sequencing. For these assays, it is desirable to
simultaneously employ a set of two or more spectrally resolvable
fluorescent dyes so that more than one target substance can be
detected in the sample at the same time. Simultaneous detection of
multiple components in a sample using multiple dyes reduces the time
required to serially detect individual components in a sample. In the
case of multi-loci DNA probe assays, the use of multiple spectrally
resolvable fluorescent dyes reduces the number of reaction tubes that
are needed, thereby simplifying the experimental protocols and
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CA 02297589 2000-02-03
facilitating the manufacturing of application-specific kits. In the case of
automated DNA sequencing, the use of multiple spectrally resolvable
fluorescent dyes allows for the analysis of all four bases in a single lane
thereby increasing throughput over single-color methods and eliminating
uncertainties associated with inter-lane electrophoretic mobility
variations. Connell, et al., Biotechniques 5 342-348 (1987); Prober, et
al., Science 238 336-341 (1987), Smith, et al., Nature 321 674-679
(1986); and Ansorge, et al., Nucleic Acids Research 15 4593-4602
(1989).
There are several difficulties associated with obtaining a set of
fluorescent dyes for simultaneously detecting multiple target substances
in a sample, particularly for analyses requiring an electrophoretic
separation and treatment with enzymes, e.g., DNA sequencing. For
example, each dye in the set must be spectrally resolvable from the
other dyes. It is difficult to find a collection of dyes whose emission
spectra are spectrally resolved, since the typical emission band half-
width for organic fluorescent dyes is about 40-80 nanometers (nm) and
the width of the available spectrum is limited by the excitation light
source. As used herein the term "spectral resolution" in reference to a
set of dyes means that the fluorescent emission bands of the dyes are
sufficiently distinct, i.e., sufficiently non-overlapping, that reagents to
which the respective dyes are attached, e.g. polynucleotides, can
be distinguished on the basis of the fluorescent signal generated by
the respective dyes using standard photodetection systems, e.g.
employing a system of band pass filters and photomultiplier tubes,
charged-coupled devices and spectrographs, or the like, as exemplified
by the systems described in U.S. Pat. Nos. 4,230,558, 4,811,218, or
in Wheeless et al, pgs. 21-76, in Flow Cytometry: Instrumentation and
Data Analysis (Academic Press, New York, 1985).
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CA 02297589 2000-02-03
The fluorescent signal of each of the dyes must also be
sufficiently strong so that each component can be detected with
sufficient sensitivity. For example, in the case of DNA sequencing,
increased sample loading can not compensate for low fluorescence
efficiencies, Pringle et al., DNA Core Facilities Newsletter, 1 15-21
(1988). The fluorescent signal generated by a dye is generally greatest
when the dye is excited at its absorbance maximum. It is therefore
preferred that each dye be excited at about its absorbance maximum.
A further difficulty associated with the use of a set of dyes is that
the dyes generally do not have the same absorbance maximum. When
a set of dyes are used which do not have the same absorbance
maximum, a trade off is created between the higher cost associated with
providing multiple light sources to excite each dye at its absorbance
maximum, and the lower sensitivity arising from each dye not being
excited at its absorbance maximum.
In addition to the above difficulties, the charge, molecular size,
and conformation of the dyes must not adversely affect the
electrophoretic mobilities of the fragments. The fluorescent dyes must
also be compatible with the chemistry used to create or manipulate the
fragments, e.g., DNA synthesis solvents and reagents, buffers,
polymerase enzymes, ligase enzymes, and the like.
Because of the multiple constraints on developing a set of dyes
for multicolor applications, particularly in the area of four color DNA
sequencing, only a few sets of fluorescent dyes have been developed.
Connell, et al., Biotechniques 5 342-348 (1987); Prober, et al., Science
238 336-341 (1987); and Smith, et al., Nature 321 674-679 (1986).
One class of fluorescent dyes that has been found to be useful in
multicolor applications are rhodamine dyes, e.g., tetramethylrhodamine
(TAMRA), rhodamine X (ROX), rhodamine 6G (R6G), rhodamine 110
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CA 02297589 2000-02-03
(R110), and the like. U.S. Patent 5,366,860. Rhodamine dyes are
particularly attractive relative to fluorescein dyes because (1)
rhodamines are typically more photostable than flucresceins, (2)
rhodamine-labeled dideoxynucleotides are better substrates for
thermostable polymerase enzymes, and (3) the emission spectra of
rhodamine dyes is significantly to the red (higher wavelength) of
fluoresceins.
One drawback associated with currently available rhodamine
dyes, particularly in the context of multiplex detection methods, is the
relatively broad emission spectrum of the rhodamine dyes. This broad
emission spectrum limits spectral resolution between spectrally
neighboring dyes, making the multicomponent analysis of such dye
combinations difficult. A second drawback associated with currently
available rhodamine dyes is that their absorption spectrum does not
match the wavelength of currently available solid state frequency-
doubled green diode lasers, e.g., neodymium solid-state YAG lasers,
which have an emission line at approximately 532 nm. It is highly
advantageous to use such lasers because of their compact size, long
useful life, and efficient use of power.
Energy transfer fluorescent dyes possess several features which
make them attractive for use in the simultaneous detection of multiple
target substances in a sample, such as in DNA sequencing. For
example, a single donor fluorophore can be used in a set of energy
transfer fluorescent dyes so that each dye has strong absorption at a
common wavelength. Then, by varying the acceptor fluorophore in the
energy transfer dye, a series of energy transfer dyes having spectrally
resolvable fluorescence emissions can be generated.
Energy transfer fluorescent dyes also provide a larger effective
Stokes shift than non-energy transfer fluorescent dyes. This is because
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CA 02297589 2000-02-03
the Stokes shift for an energy transfer fluorescent dye is based on the
difference between the wavelength at which the donor fluorophore
maximally absorbs light and the wavelength at which the acceptor
fluorophore maximally emits light. In general, a need exists for
fluorescent dyes having larger Stokes shifts.
The sensitivity of any assay using a fluorescent dye is dependent
on the strength of the fluorescent signal generated by the fluorescent
dye. A need therefore exists for fluorescent dyes which have a strong
fluorescence signal. With regard to energy transfer fluorescent dyes,
the fluorescence signal strength of these dyes is dependent on how
efficiently the acceptor fluorophore absorbs the energy emission of the
donor fluorophore. This, in turn, depends on a variety of variables,
including the proximity of the donor fluorophore to the acceptor
fluorophore and the orientation of the donor fluorophore relative to the
acceptor fluorophore. A need therefore exists for energy transfer
fluorescent dyes in which the orientation between the donor and
acceptor fluorophore is such that energy is efficiently transferred
between the donor and acceptor fluorophore.
SUMMARY OF THE INVENTION
The present invention relates to linkers for linking a donor dye to
an acceptor dye in an energy transfer fluorescent dye. The present
invention also relates to energy transfer fluorescent dyes having
enhanced fluorescence. The present invention also relates to reagents
which include the energy transfer dyes of the present invention,
methods for using the dyes and reagents, and kits within which the dyes
and reagents are included.
One linker according to the present invention for linking a donor
dye to an acceptor dye in an energy transfer fluorescent dye has the
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CA 02297589 2000-02-03
general structure R21Z1C(O)R22R28, as illustrated below, where R21 is a C,_5
alkyl
attached to the donor dye, C(O) is a carbonyl group, Z1 is either NH, sulfur
or
oxygen, R22 is a substituent attached to the carbonyl carbon which includes a
functional group selected from the group consisting of an alkene, diene,
alkyne, a
five or six membered ring having at least one unsaturated bond or a fused ring
structure, and R28 includes a functional group which attaches the linker to
the
acceptor dye. 0
R23
DONOR ~R21,Z1 R2 'ACCEPTOR
The R28 group used in the linker may be any group known in the art
which can be used to attach the R22 group to an acceptor dye. Typically, the
R28
group will be attached to a benzene ring or other aromatic ring structure on
the
acceptor dye. Accordingly, R28 is preferably formed by forming an
electrophilic
functional group on the benzene ring or other aromatic ring structure of the
acceptor dye, such as a carboxylic acids, acid halide, sulfonic acid, ester,
aldehyde, thio, disulfide, isothiocyanate, isocyanate, sulfonyl halide,
maleimide,
hydroxysuccinimide ester, haloacetyl, hydroxysulfosuccinimide ester, imido
ester,
hydrazine, azidonitrophenyl, and azide. The R22 group can then be added to the
acceptor dye, either before or after attachment of the donor dye to the R22
group,
by reacting the electrophilic agent on the acceptor dye with a nucleophile,
such as
an amino, hydroxyl or sulfhydryl nucleophile.
For example, in the embodiment illustrated below, the linker has the
general structure R21Z1C(O)R22R29Z2C(O) where R21 and R22 are as detailed
above, Z, and Z2 are each independently either NH, sulfur or oxygen, and R29
is a
C1_5 alkyl and the terminal carbonyl group is
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CA 02297589 2000-02-03
attached to the ring structure of the acceptor dye. In the variation where
Z2 is nitrogen, the C(O)R22R29Z2 subunit forms an amino acid subunit.
O O
DONOR I-IR21 /R29' RACCEPTO
Z1 R22 Z2 R
In this embodiment, the linker may be formed by the reaction of an
activated carbonyl group (NHS ester) with a amine, hydroxyl or thiol
group. It is noted that a wide variety of other mechanisms for attaching
an R22 group to an acceptor dye are envisaged and are intended to fall
within the scope of the invention.
Particular examples of five or six membered rings which may be
used as R22 in the linker include, but are not limited to cyclopentene,
cyclohexene, cyciopentadiene, cyclohexadiene, furan, thiofuran, pyrrole,
isopyrole, isoazole, pyrazole, isoimidazole, pyran, pyrone, benzene,
pyridine, pyridazine, pyrimidine, pyrazine and oxazine. Examples of
fused ring structures include, but are not limited to indene, benzofuran,
thionaphthene, indole and naphthalene.
A preferred embodiment of this linker is where R21 and R29 are
methylene, Z, and Z2 are NH, and R22 is benzene, as shown below.
0
0
DONOR CHZ'H N"'LACCEPTOR
/ H
One class of energy transfer fluorescent dyes according to the
present invention includes a donor dye which has the following xanthene
ring structure with a 4' ring position
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CA 02297589 2000-02-03
R11 R14
Y1 #R YZ
11 5 R12 15
R13 1
R17
where Y, and Y2 taken separately are either hydroxyl, oxygen, iminium
or amine, the iminium and amine preferably being a tertiary iminium or
amine. R11-R17 may be any substituent which is compatible with the
energy transfer dyes of the present invention, it being noted that the Rõ-
Rõ may be widely varied in order to alter the spectral and mobility
properties of the dyes.
According to this embodiment, the energy transfer dye also
includes an acceptor dye which absorbs the excitation energy emitted
by the donor dye and fluoresces at a second wavelength in response.
The energy transfer dye also includes a linker which attaches the donor
dye to the acceptor dye.
In one variation of this embodiment of energy transfer dyes, the
linker has the general structure R21Z,C(O)R22R28, as illustrated above,
where R21 is a C,_5 alkyl attached to the 4' position of the xanthene donor
dye, C(O) is a carbonyl group, Z, is either NH, sulfur or oxygen, R. is a
substituent attached to the carbonyl carbon which may be either an
alkene, diene, alkyne, a five or six membered ring having at least one
unsaturated bond or a fused ring structure, and Rte includes a functional
group which attaches the linker to the acceptor dye.
In a further variation of this embodiment of energy transfer dyes,
the linker has the general structure R2tZC(O)R22R29Z2C(O), as
illustrated above, where R21 and R22 are as detailed above, Z, and Z2
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CA 02297589 2000-02-03
are each independently either NH, sulfur or oxygen, and R29 is a C,.S
alkyl, and the terminal carbonyl group is attached to the ring structure of
the acceptor dye. In the variation where Z2 is nitrogen, -C(O)R22R29Z2-
forms an amino acid subunit.
In a further preferred variation of this embodiment of energy
transfer dyes, the linker is where R21 and R29 are methylene, Z, and Z2
are NH, and R22 is benzene, as shown below.
0
0
CH2
DONOR ,H H ACCEPTOR
The donor dye may optionally be a member of the class of dyes
where R17 is a phenyl or substituted phenyl. When Y, is hydroxyl and Y2.
is oxygen, and R17 is a phenyl or substituted phenyl, the dye is a
member of the fluorescein class of dyes. When Y, is amine and Y2 is
iminium, and R17 is a phenyl or substituted phenyl, the dye is a member
of the rhodamine class of dyes. Further according to this embodiment,
the acceptor dye may optionally be a member of the xanthene, cyanine,
phthalocyanine and squaraine classes of dyes.
In another embodiment, the energy transfer fluorescent dyes
have donor and acceptor dyes with the general structure
Rõ R,4
Y, Y2
4-
R12 Rn
R13 Rid
Xs X,
Xa
X}
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CA 02297589 2000-02-03
where Y1 and Y, taken separately are either hydroxyl, oxygen, iminium
or amine, the iminium and amine preferably being a tertiary iminium or
amine and R11-R16 are any substituents which are compatible with the
energy transfer dyes of the present invention.
According to this embodiment, as illustrated below, the linker is
attached to one of X, and X4 substituents of each of the donor and
acceptor dyes, preferably the X. substituents of the donor and acceptor
dyes. In this embodiment, the linker is preferably short and/or rigid as
this has been found to enhance the transfer of energy between the
donor and acceptor dyes.
R11 R14
2
R 1
12 5
Y1 VX4
X2 1\ LINKER
I
X1' / X5'
R18' Rt3'
R15 / \ R12
YZ O I Y1
R14' R11'
In another embodiment, the energy transfer fluorescent dyes
include a donor dye which is a member of the xanthene class of dyes,
an acceptor dye which is a member of the xanthene, cyanine,
phthalocyanine and squaraine classes of dyes which is capable of
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CA 02297589 2000-02-03
absorbing the excitation energy emitted by the donor dye and
fluorescing at a second wavelength in response, and a linker attaching
the donor dye to the acceptor dye. According to this embodiment, the
acceptor has an emission maximum that is greater than about 600 nm
or at least about 100 nm greater than the absorbance maximum of the
donor dye.
In addition to the above-described novel energy transfer
fluorescent dyes, the present invention also relates to fluorescent
reagents containing the energy transfer fluorescent dyes. In general,
these reagents include any molecule or material to which the energy
transfer dyes of the invention can be attached and used to detect the
presence of the reagent based on the fluorescence of the energy
transfer dye. In one embodiment, a fluorescent reagent is provided
which includes a nucleoside or a mono-, di- or triphosphate nucletotide
labeled with an energy transfer fluorescent dye. The nucleotide may be
a deoxynucleotide which may be used for example, in the preparation of
dye labeled oligonucleotides. The nucleotide may also be a
dideoxynucleoside which may be used, for example, in dye terminator
sequencing. In another embodiment, the fluorescent reagent includes
an oligonucleotide labeled with an energy transfer fluorescent dye.
These reagents may be used, for example, in dye primer sequencing.
The present invention also relates to methods which use the
energy transfer fluorescent dyes and reagents of the present invention.
In one embodiment, the method includes forming a series of different
sized oligonucleotides labeled with an energy transfer fluorescent dye of
the present invention, separating the series of labeled oligonucleotides
based on size, detecting the separated labeled oligonucleotides based
on the fluorescence of the energy transfer dye.
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CA 02297589 2004-11-19
In one embodiment of this method, a mixture of extended labeled primers is
formed by
hybridizing a nucleic acid sequence with an oligonucleotide primer in the
presence of
deoxynucleotide triphosphates, and at least one dye labeled dideoxynucleotide
triphosphate
and a DNA polymerase. The DNA polymerase serves to extend the primer with the
deoxynucleotide triphosphates until a dideoxynucleotide triphosphate is
incorporated which
terminates extension of the primer. Once terminated, the mixture of extended
primers are
separated and detected based on the fluorescence of the dye on the
deoxynucleoside. In a
variation of this embodiment, four different fluorescently labeled
dideoxynucleotide
triphosphates are used, i.e., a fluorescently labeled dideoxycytosine
triphosphate, a
fluorescently labeled dideoxyadenosine triphosphate, a fluorescently labeled
dideoxyguanosine
triphosphate, and a fluorescently labeled dideoxythymidine triphosphate. In an
alternative
embodiment of this method, the oligonucleotide primer is fluorescently labeled
as opposed to
the deoxynucleotide triphosphate.
The present invention also relates to kits containing the dyes and reagents
for
performing DNA sequencing using the dyes and reagents of present invention.
According to a first aspect of the invention, there is provided an energy
transfer dye
comprising:
a xanthene donor dye capable of absorbing light at a first wavelength and
emitting
excitation energy in response thereto;
a 4,7-dichlororhodamine acceptor dye capable of absorbing excitation energy
emitted
by the donor dye and fluorescing at a second wavelength in response thereto;
and
a linker linking the 4'-, 5- or 6-ring position of the donor dye to the 4'-, 5-
or 6-ring
position of the acceptor dye.
According to a second aspect of the invention, there is provided a
fluorescently-labeled
reagent comprising an energy transfer dye covalently linked to a reagent,
wherein the energy
transfer dye comprises:
a xanthene donor dye capable of absorbing light at a first wavelength and
emitting
excitation energy in response thereto;
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CA 02297589 2004-11-19
a 4,7-dichlororhodamine acceptor dye capable of absorbing the excitation
energy
emitted by the donor dye and fluorescing at a second wavelength in response
thereto; and
a linker linking the 4'-, 5- or 6-ring position of the xanthene donor dye to
the 4'-, 5- or
6-ring position of the acceptor dye.
According to a third aspect of the invention, there is provided a kit for
analyzing a
nucleic acid, comprising a set of four different terminating nucleotides, each
of which
terminates a template-dependent primer extension reaction at a different
template nucleotide
and comprises a fluorescent label capable of producing a detectable,
spectrally resolvable
fluorescent signal, wherein at least one of the fluorescent labels is an
energy transfer dye
comprising:
a xanthene donor dye capable of absorbing light at a first wavelength and
emitting
excitation energy in response thereto;
a 4,7-dichlororhodamine acceptor dye capable of absorbing the excitation
energy
emitted by the donor dye and fluorescing at a second wavelength in response
thereto; and
a linker linking the 4'-, 5- or 6-ring position of the donor dye to the 4'-, 5-
or 6-ring
position of the acceptor dye,
and wherein the energy transfer dye is attached to the terminating nucleotide
at the 4'-,
5- or 6-ring position of the donor or acceptor dye.
According to a fourth aspect of the invention, there is provided a method of
forming a
fluorescently labeled oligonucleotide, comprising the step of enzymatically
extending an
oligonucleotide primer in the presence of a template nucleic acid and
nucleotide triphosphates,
wherein the oligonucleotide primer or at least one of the nucleotide
triphosphates is labeled
with an energy transfer dye comprising:
(i) a xanthene donor dye capable of absorbing light at a first wavelength and
emitting
excitation energy in response thereto;
(ii) a 4,7-dichlororhodamine acceptor dye capable of absorbing the excitation
energy
emitted by the donor dye and fluorescing at a second wavelength in response
thereto; and
(iii) a linker linking the 4'-, 5- or 6-ring position of the donor dye to the
4'-, 5- or 6-
ring position of the acceptor dye,
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CA 02297589 2004-11-19
and wherein the energy transfer dye is attached to the oligonucleotide primer
or the at
least one nucleotide triphosphate at the 4'-, 5- or 6-ring position of the
donor or acceptor dye.
According to a fifth aspect of the invention, there is provided a method of
analyzing a
nucleic acid, comprising the steps of:
forming a plurality of differently sized fluorescently labeled extended
oligonucleotide
primers;
separating the fluorescently labeled extended oligonucleotide primers based
upon their
sizes; and
detecting the fluorescently labeled extended primers based upon their
fluorescence,
wherein the fluorescent label of at least one of the fluorescently labeled
extended
oligonucleotide primers is a fluorescent energy transfer dye comprising:
(i) a xanthene donor dye capable of absorbing light at a first wavelength and
emitting excitation energy in response thereto;
(ii) a 4,7-dichlororhodamine acceptor dye capable of absorbing the excitation
energy emitted by the donor dye and fluorescing at a second wavelength in
response thereto;
and
(iii) a linker linking the 4'-, 5- or 6-ring position of the donor dye to the
4'-, 5-
or 6-ring position of the acceptor dye,
and wherein the energy transfer dye is linked to the extended oligonucleotide
primer at
the 4'-, 5'- or 6-ring position of the donor or acceptor dye.
BRIEF DESCRIPTION OF THE FIGURES
Figure 1 illustrates the modification of a carboxy substituent on a energy
transfer dye to an activated N-hydroxysuccinimidyl (NHS) ester which is then
reacted
with an amino hexyl-oligomer to form a dye labeled oligonucleotide primer.
Figure 2 compares the fluorescence emission strength of a series of energy
transfer dyes of the present invention to other energy transfer dyes and the
acceptor dye
alone.
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i

CA 02297589 2000-02-03
Figures 3A and 3B show several particularly preferred embodiments of
4,7-dichlororhodamine dye compounds which can be used in the energy
transfer dyes of the present invention.
Figures 4A and 4B show preferred generalized synthesis
schemes for the preparation of the 4,7-dichlororhodamine dyes of the
invention.
Figure 4A shows a generalized synthesis wherein the substituent
X, can be other than carboxylate.
Figure 4B shows a generalized synthesis wherein the substituent
X, is carboxylate.
Figure 5 illustrates a set of four dyes (3-carboxy-R110, 5-carboxy-
R6G, 5TMR-B-CF and 5ROX-CF) which are spectrally resolvable from
each other.
Figure 6 illustrates a set of four dyes (3-carboxy-R110, 5-carboxy-
R6G, 5ROX-CF and Cy5-CF) which are spectrally resolvable from each
other.
Figure 7 is a plot of a mixture of labeled oligonucleotides
generated during dye primer sequencing using 5TMR-CF and 5TMR-B-
CF labeled primers.
Figure 8 is a four color plot of dye primer sequencing using a four
dye set including 3-carboxy-R110, 5-carboxy-R6G, 5TMR-CF and
5TMR-B-CF.
Figures 9A-D compare the fluorescence emission strength of a
series of energy transfer dyes of the present invention to the
corresponding acceptor dye alone.
Figure 9A provides the overlaid spectra of 6-CFB-DR1 10-2 and
DR110-2.
Figure 9B provides an overlaid spectra of 5-CFB-DR6G-2 and
DREG-2.
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CA 02297589 2000-02-03
Figure 9C provides an overlaid spectra of 6-CFB-DTMR-2 and
DTMR-2.
Figure 9D provides an overlaid spectra of 6-CFB-DROX-2 and
DROX-2.
Figure 10 illustrates a set of four dyes (5-CFB-DR110-2, 5-CFB-
DR6G-2, 6-CFB-DTMR-2, and 6-CFB-DROX-2) which are spectrally
resolvable from each other.
Figure 11 is a plot of a mixture of labeled oligonucleotides
generated during dye primer sequencing using 6-CFB-DTMR-2 and
DTMR-2 labeled primers.
Figure 12 is a plot of a mixture of labeled oligonucleotides
generated during dye primer sequencing using 5-CF-TMR-2 and 5-CF-
B-TMR-2 labeled primers.
Figure 13 is a four color plot of dye primer sequencing using a
four dye set including 5-CFB-DR1 10-2, 6-CFB-DR6g-2, 5-CFB-DTMR-2,
and 5-CFB-DROX-2.
DETAILED DESCRIPTION
I. Energy Transfer Dye Linkers Of The Present Invention
The present invention relates to novel linkers for linking a donor
dye to an acceptor dye in an energy transfer fluorescent dye. The
present invention also relates to energy transfer fluorescent dyes which
incorporate these linkers. These linkers have been found to faciliate the
efficient transfer of energy between a donor and acceptor dye in an
energy transfer dye.
One linker according to the present invention for linking a donor
dye to an acceptor dye in an energy transfer fluorescent dye has the
general structure R21Z1C(O)R22R2a, as illustrated below, where R2, is a
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CA 02297589 2000-02-03
Cl., alkyl attached to the donor dye, C(O) is a carbonyl group, Z, is
either NH, sulfur or oxygen, R22 is a substituent which includes an
alkene, diene, alkyne, a five and six membered ring having at least one
unsaturated bond or a fused ring structure which is attached to the
carbonyl carbon, and Rte includes a functional group which attaches the
linker to the acceptor dye.
O
~ R2i, Rea
DONOR Zi R22 'ACCEPTOR
In one embodiment of this linker, illustrated below, the linker has
the general structure R21Z1C(O)R22R29Z2C(O) where R21 and R22 are as
detailed above, Z, and Z2 are each independently either NH, sulfur or
oxygen, R29 is a C1_5 alkyl, and the terminal carbonyl group is attached to
the ring structure of the acceptor dye. In the variation where Z2 is
nitrogen, the C(O)R22R29Z2 subunit forms an amino acid subunit.
O O
R21. R29,
DONOR Zj R'22 Z2 ACCEPTOR
Particular examples of five or six membered rings which may be
used as R22 in the linker include, but are not limited to cyclopentene,
cyclohexene, cyclopentadiene, cyclohexadiene, furan, thiofuran, pyrrole,
isopyrole, isoazole, pyrazole, isoimidazole, pyran, pyrone, benzene,
pyridine, pyridazine, pyrimidine, pyrazine and oxazine. Examples of
fused ring structures include, but are not limited to indene, benzofuran,
thionaphthene, indole and naphthalene.
A preferred embodiment of this linker is where R21 and R29 are
methylene, Z, and Z2 are NH, and R22 is benzene, as shown below.
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CA 02297589 2000-02-03
0
O
DONOR CH2H N/~-ACCEPTOR
H
Table 3 illustrates examples of -C(O)R22- subunits of linkers which
may be used in the linkers of the present invention.
II. Energy Transfer Dyes Of The Present Invention
In general, the energy transfer dyes of the present invention
include a donor dye which absorbs light at a first wavelength and emits
excitation energy in response, an acceptor dye which is capable of
absorbing the excitation energy emitted by the donor dye and
fluorescing at a second wavelength in response, and a linker which
attaches the donor dye to the acceptor dye. With regard to all of the
molecular structures provided herein, it is intended that these molecular
structures encompass not only the exact electronic structure presented,
but also include all resonant structures and protonation states thereof.
One class of energy transfer fluorescent dyes according to the
present invention includes a donor dye which is a member of the
xanthene class of dyes, an acceptor dye and a linker which is a member
of the group of linkers described in Section I. As used herein, xanthene
dyes include all molecules having the general structure
Rõ R14
Y, 0 2
Y
R1z Res
R1 R17
-17-

CA 02297589 2000-02-03
where Y, and Y2 taken separately are either hydroxyl, oxygen, iminium
or amine, the iminium and amine preferably being a tertiary iminium or
amine. When Y, is hydroxyl and Y2 is oxygen, and Rõ is a phenyl or
substituted phenyl, the dye is a member of the fluorescein class of dyes.
When Y, is amine and Y2 is iminium, and R17 is a phenyl or substituted
phenyl, the dye is a member of the rhodamine class of dyes.
Rõ-R17 may be any substituent which is compatible with the
energy transfer dyes of the present invention, it being noted that the R11-
R17 may be widely varied in order to alter the spectral and mobility
properties of the dyes. The number indicated in the ring structure
indicates the 4' position on the xanthene ring structure. For the energy
transfer dyes of the present invention in which the linker is attached to
the 4' position of the xanthene ring structure, the R14 substituent
corresponds to the linker.
Examples of R11-R17 substituents include, but not limited to
hydrogen, fluorine, chlorine, bromine, iodine, carboxyl, alkyl, alkene,
alkyne, sulfonate, amino, ammonium, amido, nitrite, alkoxy, phenyl,
substituted phenyl, where adjacent substituents are taken together to
form a ring, and combinations thereof.
In one embodiment, R15 and R15 are taken together to form a
substituted or unsubstituted benzene ring. This class of xanthene dyes
are referred to herein as asymmetric benzoxanthene dyes,
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In another embodiment, Rõ is a phenyl or substituted phenyl
having the general formula
x5 x,
1
X4 x2
x3
Substituents X,-X5 on the phenyl ring can include hydrogen, fluorine,
chlorine, bromine, iodine, carboxyl, alkyl, alkene, alkyne, sulfonate,
amino, ammonium, amido, nitrite, alkoxy, where adjacent substituents
are taken together to form a ring, and combinations thereof.
In one embodiment, the donor dye is a member of the class of
dyes where Y, is amine, Y. is iminium, and X. and X5 are chlorine,
15. referred to herein as 4,7-dichlororhodamine dyes. Dyes falling within
the 4,7-dichlororhodamine class of dyes and their synthesis are
described herein.
As used here, alkyl denotes straight-chain and branched
hydrocarbon moieties, i.e., methyl, ethyl, propyl, isopropyl, tert-butyl,
isobutyl, sec-butyl, neopentyl, tert-pentyl, and the like. Substituted alkyl
denotes an alkyl moiety substituted with any one of a variety of
substituents, including, but not limited to hydroxy, amino, thio, cyano,
nitro, sulfo, and the like. Haloalkyl denotes a substituted alkyl with one
or more halogen atom substituents, usually fluoro, chloro, bromo, or
iodo. Alkene denotes a hydocarbon wherein one or more of the
carbon-carbon bonds are double bonds, and the non-double bonded
carbons are alkyl or substituted alkyl. Alkyne denotes a hydocarbon
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CA 02297589 2000-02-03
where one or more of the carbons are bonded with a triple bond and
where the non-triple bonded carbons are alkyl or substituted alkyl
moieties. Sulfonate refers to moieties including a sulfur atom bonded to
3 oxygen atoms, including mono- and di-salts thereof, e.g., sodium
sulfonate, potassium sulfonate, disodium sulfonate, and the like. Amino
refers to moieties including a nitrogen atom bonded to 2 hydrogen
atoms, alkyl moieties, or any combination thereof. Amido refers to
moieties including a carbon atom double bonded to an oxygen atom and
single bonded to an amino moiety. Nitrile refers to moieties including a
carbon atom triple bonded to a nitrogen atom. Alkoxy refers to a moiety
including an alkyl moiety single bonded to an oxygen atom. Aryl refers
to single or multiple phenyl or substituted phenyl, e.g., benzene,
naphthalene, anthracene, biphenyl, and the like.
Rõ-Rõ may also each independently be a linking moiety which
may be used to attach the energy transfer dye to a reagent, such as a
nucleotide, nucleoside or oligonucleotide. Examples of linking moieties
include isothiocyanate, sulfonyl chloride, 4,6-dichlorotriazinylamine,
succinimidyl ester, or other active carboxylate whenever the
complementary functionality is amine. Preferably the linking group is
maleimide, halo acetyl, or iodoacetamide whenever the complementary
functionality is sulfhydryl. S R. Haugland, Molecular Probes
Handbook of Fluorescent Probes and Research Chemicals, Molecular
probes, Inc. (1992). In a particularly preferred embodiment, as
illustrated in Figure 1, the linking group is an activated NHS ester
formed from a carboxyl group on either the donor or acceptor dye which
can be reacted with an aminohexyl-oligomer to form a dye labeled
oligonucleotide primer.
The energy transfer fluorescent dyes of this embodiment also
include an acceptor dye which is capable of absorbing the excitation
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CA 02297589 2000-02-03
energy emitted by the donor dye and fluorescing at a second
wavelength in response, and a linker which attaches the donor dye to
the acceptor dye. In the first class of energy transfer dyes, the linker is
a member of the class of linkers described in Section I and is attached
to the donor dye at the 4' position of the xanthene ring structure.
Energy transfer dyes of this first class exhibit enhanced
fluorescent strength as compared to the acceptor fluorophore itself and
energy transfer fluorescent dyes having the same donor - acceptor pair
where the linkage between the donor - acceptor pair is different.
The present invention also relates to a second class of energy
transfer fluorescent dyes in which the donor and acceptor dyes each
have the general structure
R,4
/ 0 /4 Y
R,= \ / / R,y
R,3 R,e
xs / x,
X \ 2
,
where Y,, Y2, Rõ-R16 and X,-X5 are as specified above.
Within this class of dyes, the linker is attached to the donor and
acceptor dyes by one of X3 and X, substituents of each of the donor and
acceptor dyes.
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CA 02297589 2000-02-03
R,1 R14
Y, / 0 / Y2
R12 R15
Ru Rte
X5 X
Xz
X3 orX
X 3' or X 4'
X2. LINKER
X1' I / X5'
Rta' R13'
R15'/ / . R12'
Y2. 0
Y1'
R 14' R11'
In a preferred embodiment of this class of dyes, the linker is
attached to the donor and acceptor dyes by the X3 substituent of each of
the donor and acceptor dyes.
Within this class of dyes, the linker is preferably short and/or rigid
as this has been found to enhance the transfer of energy between the
donor and acceptor dyes.
The present invention also relates to a third class of energy
transfer fluorescent dyes in which the acceptor dye is a member of the
4,7-dichlororhodamine class of dyes, i.e., dyes having the general
structure
RS RS
RZR1N o NR3R4
/4'
I
R6 Re
R7 Rio
X5 X1
6 5
X4 X2
X3
-22-

CA 02297589 2000-02-03
where
R,-R, are each independently hydrogen, alkyl or where R, and
R5, R2 and R5, R, and R8, R4 and R. are taken together to form a ring,
and combinations thereof;
R5-R,o are each independently hydrogen, fluorine, chlorine,
bromine, iodine, carboxyl, alkyl, alkene, alkyne, sulfonate, sulfone,
amino, ammonium, amido, nitrile, alkoxy, phenyl, or substituted phenyl,
or where adjacent substituents are taken together to form a ring, and
combinations thereof;
X,, X3 and X, are each independently hydrogen, fluorine, chlorine,
bromine, iodine, carboxyl, alkyl, alkene, alkyne, sulfonate, sulfone,
amino, ammonium, amido, nitrile, or alkoxy, or where adjacent
substituents are taken together to form a ring, and combinations thereof;
and
X. and X5 are chlorine.
With regard to R, - R10, X3 and X4, R, and R5, R. and R6, R3 and
R8, R4 and R9, and X3 and X4 may each independently be taken together
to form a 5, 6, or 7 membered ring.
The numbers (4', 5, 6) indicated in the ring structure indicate the
4, 5 and 6 ring positions on the rhodamine ring structure. As will be
discussed herein, the 4' and 5 ring positions are preferred sites for
attachment of the linker used in the energy transfer dyes of the present
invention which attaches the donor to the acceptor fluorophore. The 4',
5 and 6 ring positions are also preferred sites for attachment of a
biomolecule, such as a nucleotide or oligonucleotide to the energy
transfer dye.
Donor dyes within this class of energy transfer dyes may include
any dye which emits excitation energy which a 4,7-dichlororhoda mine
dye is capable of absorbing and producing an energy emission in
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CA 02297589 2000-02-03
response. In one embodiment, the donor dye has a xanthene ring
structure with a 4' ring position where the 4,7-dichlororhodamine
acceptor dye is attached to the donor dye by a linker which is attached
to the 4' ring position of the xanthene dye. The linker is preferably
attached to the 5 or 6 ring positions of the 4,7-dichlororhodamine
acceptor dye.
Energy transfer dyes according to this third class of dyes, i.e.,
where 4,7-dichlororhodamine is the acceptor dye, provide the advantage
of having a relatively narrow emission spectrum as compared to other
rhodamine dyes. This narrow emission spectrum enhances the spectral
resolution achievable by a set of these dyes, thereby facilitating
multicomponent analysis using these dyes.
The present invention also relates to a fourth class of energy
transfer fluorescent dyes in which the donor dye is a member of the
xanthene class of dyes, the acceptor dye is a member of the xanthene,
cyanine, phthalocyanine and squaraine classes of dyes, and the
acceptor has an emission maximum that is greater than about 600 nm
and/or preferably has an emission maximum that is at least about 100
nm greater than the absorbance maximum of the donor dye. Within this
class of dyes, the donor is preferably a member of the fluorescein class
of dyes.
The fourth class of energy transfer dyes of the present invention
exhibit unusually large Stoke shifts, as measured by the difference
between the absorbance of the donor and the emission of the acceptor.
In addition, these dyes exhibit efficient energy transfer in that minimal
donor fluorescence is observed.
Described herein in greater detail are the four classes of energy
transfer dyes of the present invention.
-24-

CA 02297589 2000-02-03
TABLE 1
H2N, 0 NH2 (CH2CH3)HN\ 0 NH(CH>CH3)
ci CO2H CI CO2H
CI CI
HN 0 HN 0
0- ol~~
NH NH
H 0 0 HO 0 0
CO2H CO2H
CO2H CO2H
5-CFB-OR110-2 5-CFB-OR6G-2
H2N NH2 (CH2CH3)HN I NH(CH2CH3)
C1 C02H CI CO2H
CI CI
HN 0 HN O 01T~
NH NH
0 HO 0 0
/ CO2H CO2H
HO2 2 HO2
8-CFB-OR110-2 6-CFB-DRGG-2
-25-

CA 02297589 2000-02-03
TABLE 1 (cont.)
(CH3)2N N(CH3)2 jN 0 N,_
Il ~ Il
CI Co2H C1 CO2H
CI CI
HN O HN'O
NH NH
HO p 0 HO O O
C02H C02H
CO2H CO2H
5-CFB-OTMR-2 5-CFB-OROX-2
(CH3)2N N(CH3)2 + N\ 0 N
CI C02H C1 C02H
I / Cl
HN 0 HN O
olr~ 0
NH NH
HO O O HO O O
C02H C02H
H02C H02C
6-CFB-OTMR-2 6-CFB-OROX-2
-26-

CA 02297589 2000-02-03
TABLE 1A
R5
R41 1
N \N
Rst
R51 I N....... M........ N
/ R42
N ` N
(CH&õ CYANINE N N
Oi ~R43 PHT4ALOCYANINE -
Rst \ \Rs,
O
Rst N
/ O Reg
1
(CH2)n SQUARAINE
OJ^RW
Rn R14
I
Y1 0 4 Y2
R72 R15
R13 R17 Ris
XANTHENE
-27-

CA 02297589 2000-02-03
A. First Class Of Energy Transfer Dyes
As described above, the first class of energy transfer dyes
according to the present invention includes a donor dye which is a
member of the xanthene class of dyes and hence has a xanthene ring
structure with a 4' ring position. Within this class of dyes, the acceptor
dye is a dye which is capable of absorbing the excitation energy emitted
by the donor dye and fluorescing at a second wavelength in response.
According to this embodiment, the donor may be a member of the
fluorescein, rhodamine or asymmetric benzoxanthene classes of dyes,
these dyes each being members of the broader xanthene class of dyes.
Illustrated below are the general structural formulas for these xanthene
dyes. The substituents illustrated on these dyes may be selected from
the wide variety of substituents which may be incorporated onto these
different classes of dyes since all dyes having the general xanthene,
fluorescein, rhodamine, and asymmetric benzoxanthene ring structures
are intended to fall within the scope of this invention.
R71 R14
Y Y2
I
4
R12 R15
R13 R17 R/6
XANTHENE
R11 R14 R11 R14 + R11 R14
H 4 O R26R25N 4 NR25R26 Y1 Y2
R12 R15 R12 R15 R12 R31
R13 RIO R13 RIO R13 R17
X1 X11 X1 X11 R34 R32
R33
X14 X12 X14 X12 ASYMMETRIC
X13 X13 DYES BENXANTHENE
FLUORESCEIN RHOOAMINE
-28-

CA 02297589 2000-02-03
Examples of classes of acceptor dyes which may be used in the
energy transfer fluorescent dye of this embodiment include, but are not
limited to, xanthene dyes, cyanine dyes, phthalocyanine dyes and
squaraine dyes. The general structures of these dyes are illustrated in
Table 1A. The substituents illustrated on these dyes may be selected
from the wide variety of substituents which may be incorporated onto
these different classes of dyes since all dyes having the general
xanthene, fluorescein, rhodamine, asymmetric benzoxanthene, cyanine,
phthalocyanine and squaraine ring structures are intended to fall within
the scope of this invention.
Examples of donor dyes which may be used in this embodiment
include, but are not limited to fluorescein, isomers of carboxyfluorescein
(e.g., 5 and 6 carboxy), isomers of carboxy-HEX (e.g., 5 and 6 carboxy),
NAN, Cl-FLAN, TET, JOE, ZOE, rhodamine, isomers of
carboxyrhodamine (e.g., 5 and 6 carboxy), isomers of carboxy R110
(e.g., 5 and 6 carboxy), isomers of carboxy R6G (e.g., 5 and 6 carboxy),
4,7-dichlorofluoresceins (See U.S. Patent No. 5,188,934), 4,7-
dichlororhodaminesf
asymmetric benzoxanthene dyes
and isomers of N,N,N',N'-
tetramethyl-carboxyrhodamine (TAMRA) (e.g., 5 and 6 carboxy).
Examples of acceptor dyes which may be used in this
embodiment include, but are not limited to isomers of carboxyfluorescein
(e.g., 5 and 6 carboxy), 4,7-dichlorofluoresceins,-4,7-
dichlororhodamines, fluoresceins, asymmetric benzoxanthene dyes,
isomers of carboxy-HEX (e.g., 5 and 6 carboxy), NAN, CI-FLAN, TET,
JOE, ZOE, rhodamine, isomers of carboxyrhodamine (e.g., 5 and 6
carboxy), isomers of carboxy R110 (e.g., 5 and 6 carboxy), isomers of
carboxy R6G (e.g., 5 and 6 carboxy), isomers of N,N,N',N'-tetramethyl
-29-

CA 02297589 2000-02-03
carboxyrhodamine (TAMRA) (e.g., 5 and 6 carboxy), isomers of
carboxy-X-rhodamine (ROX) (e.g., 5 and 6 carboxy) and Cy5.
Illustrated in Table 2 are the structures of these dyes.
In the first class of energy transfer dyes according to the present
invention, the linker is attached to the donor dye at the 4' position of the
xanthene ring structure. In one embodiment, the linker has the general
structure R21Z,C(O)R22R28, as illustrated below, where R21 is a C1.5 alkyl
which-is attached to the 4' ring position of the donor xanthene dye, Z, is
either NH, sulfur or oxygen, C(O) is a carbonyl group, R22 is a
substituent which includes an alkene, diene, alkyne, a five and six
membered ring having at least one unsaturated bond or a fused ring
structure which is attached to the carbonyl carbon, and R28 is a
functional group which attaches the linker to the acceptor dye.
ACCEPTOR
R 28
R220
ZIP
R11 R21
YJ O 4' Y2
/
R12 Res
Rv3 R.s
R17 25 Examples of five or six membered rings which may be used in R22
include, but are not limited to cyclopentene, cyclohexene,
cyclopentadiene, cyclohexadiene, furan, thiofuran, pyrrole, isopyrole,
isoazole, pyrazole, isoimidazole, pyran, pyrone, benzene, pyridine,
pyridazine, pyrimidine, pyrazine and oxazine. Examples of fused ring
-30-

CA 02297589 2000-02-03
structures include, but are not limited to indene, benzofuran,
thionaphthene, indole and naphthalene.
In one variation of this embodiment, illustrated below, the linker
has the general structure R21Z,C(O)R22R29Z2C(O) where R21 is a Ct.S
alkyl which is attached to the 4' ring position of the donor xanthene dye,
Z, and Z2 are each independently either NH, sulfur or oxygen, C(O) is a
carbonyl group, R22 is a substituent which includes an alkene, diene,
alkyne, a five and six membered ring having at least one unsaturated
bond or a fused ring structure which is attached to the carbonyl carbon,
R29 is a Ct.5 alkyl, and the terminal carbonyl group is attached to the ring
structure of the acceptor dye.
ACCEPTOR
O
Z2
R29
R22\/O
Z1~
R11 R21
Yt O 4 Y2
R12 R15
R13 Rts
R17
-31 -

CA 02297589 2000-02-03
A preferred embodiment of this linker is where R21 and R29 are
methylene, Z, and Z2 are NH, and R22 is benzene, as shown below.
ACCEPTOR *"~r O
HN~-CH2
O
HNNI
R11 CH2
Y1 O Y2
R12 R1s
13 R17 16
-32-

CA 02297589 2000-02-03
TABLE 2
HO 0 0 HO 0 0
/ CO2H CO2H
Fluorescein 5-carboxyfluorescein
CO2H
CI CI
HO 0 0 HO 0 0
CI \ i i Cl CI COZH
CI CO2H
CI 5-carboxy-HEX NAN
CO2H Cl
F. CO2H
HV0,11 0 HO 0 0
I Cl Cl
CI CO2H
FLAN HO2C CI TET
CO2H
HO Cl 0 Cl 0 HO CI O Cl
0
02C \ I / / CO2H CI \ I / / Cl
CO2H CO2H
HO2C \ JOE ZOE
CO2H
HO Z3 0 Z4 0 R2R1N R, 0 R4 NR3R4
/ /
Z2 Z1 Z6 R3 Z5 R2 \ I /R/ R
s
s
CI D, CI / I X,
HO2C \/ 1 CI X4 \ Cl
A X X3
4,7 Dichlorofluorescein 4,7 Dichlororhodamine
(See Pat No. 5,188,934)
-33-

CA 02297589 2000-02-03
TABLE 2 (cont.)
,N 0 / N+ -N 0 N+
-cl
CO2H C02H
Rhodamine 5-carboxyrhodamine
CO2H
.-N 0 N H2N 0 NH2
CI
CO2H CO2H
TAMRA R110
CH3 CO2H .CH3 CO2H
CHZ CHZ
H'N 0 N+H N 0 N+
H3C \ I i / CH3 \ I / /
CO2H CO2H
RG6 ROX
CO2H CO2H
-34-

CA 02297589 2000-02-03
TABLE 3
0
0
0
0
O
n
O
0 0
N
-35-

CA 02297589 2000-02-03
As illustrated in Example 4 and Figure 2, energy transfer dyes
such as 5-TMR-B-CF, which include a donor, acceptor and linker as
specified above exhibit enhanced fluorescence as compared to the
acceptor itself and energy transfer fluorescent dyes having the same
donor - acceptor pair where the linker between the donor - acceptor pair
is different. Without being bound by theory, the enhanced fluorescence
intensity observed is believed to be due to an improved energy transfer
orientation between the donor and acceptor dye which is achieved and
maintained by the relatively rigid R22 portion of the linker. As a result,
the energy transfer fluorescent dyes of the present invention exhibit
enhanced fluorescent strength as compared to the acceptor fluorophore
itself and energy transfer fluorescent dyes having the same donor -
acceptor pair where the linkage between the donor - acceptor pair is
different. The enhanced fluorescent strength of these dyes is
particularly evident in the presence of 8 M urea which serves to reduce
dye stacking.
In one variation of this embodiment, the acceptor is a member of
the xanthene class of dyes having the general structure
Rõ Ru
'' V3R YR ia
X,
where Y,, Y2, R11-R16 and X,-X6 are as specified above.
-36-

CA 02297589 2000-02-03
According to this variation, it is preferred that a linker, such as the
ones described above, is attached to the acceptor xanthene dye via the
X3. or X4 substituent of the acceptor xanthene dye. In a preferred
embodiment, as illustrated below, the linker is attached to the X3
substituent of the acceptor xanthene dye.
R11 Ru
Y1 0 Y2
ACCEPTOR
R12 R1S
R1] RIS
XS X1
X4
R11 UNKER
2
YI O 4' Y
1 R 2 R1s
R13 R1, DONOR
X5 X1
I
X4 2
X
Table 4 provides examples of the above-described energy
transfer dyes according to this embodiment of the invention. It is noted
that although the dyes illustrated in Table 4 include a 5-
carboxyfluorescein donor dye and a TAMRA acceptor dye, it should be
understood that a wide variety of other xanthene dyes can be readily
substituted as the donor dye. It should also be understood that a wide
variety of other xanthene dyes, as well as cyanine, phthalocyanine and
squaraine dyes can be readily substituted for the TAMRA acceptor dye,
-37-

CA 02297589 2000-02-03
as has been described above, all of these variations with regard to the
donor and acceptor dyes falling within the scope of the invention.
-38-

CA 02297589 2000-02-03
TABLE 4
(H3C)2N ( O I N(CH3)2 (H3C)2N 0 N(CH )2 (H3C)2N O N(CH3)2
CO2H CO,H CO2H
HN O HN O
HN' O
0 0 N
N
,NH NH NH
HO`s O. O HO.,, ~., O HO,,,,,,II,OO
i CO2H CO2H CO2H
J I
CO2H CO2H CO2H
5-TMR-B-CF 5-TMR-F-CF 5-TMR-P-CF
(H3C)2 TN N(CH3)2 (H3C)2N O N(CH3)2 (H3C)2N O N(CH3)2
H CO2H CO2H
HO HN HN
0 O O~
,NH NH NH
HOl~~ O. O HO, O HO~ O 0
CO2H CO2H CO2H
I I I
O2H CO2H CO2H
5-TMR-A-CF 5-TMR-D-CF 5-TMR-N-CF
-39-

CA 02297589 2000-02-03
TABLE 4 (cont.)
(H3C)2N N(CH3)2 (H3C)2N0_,N(CH3)2 (H3C)2N O~N(CH3)2
CI jl C02H Cl CO2H CI C02H
CI CI
CI
HN ... 0 HN HN0
~ O N
NH
NH
HO VC02H O HO, 0 O HO
CO2H yC02H
CO2H C02H C02H
5-DTMR-8-CF 5-DTMR-F-CF 5-DTMR-P-CF
(H3C)2NN(CH32 (H3C)2N O N(CH3)2 (H3C)2N 0 N(CH3)2
I T`
G C
CI C02H 02H CI I C02H
CI CI
CI
HN HN
HN ~ (J
NH aNH
,NH
HO O O H O
H ~ O O (
C02H I C02H C02H
O2H CO2H CO2H
C
5-DTMR-D-CF 5-OTMR-N-CF
5-DTMR-A-CF
-40-

CA 02297589 2000-02-03
B. Second Class Of Energy Transfer Dyes
The present invention also relates to a second class of energy
transfer fluorescent dyes, illustrated below, in which the donor dye and
acceptor each are members of the xanthene class of dyes having the
general structure
Rõ R,i
Y, 0 4' Y Z
1 Ra R15
Rn Rid
X5 X
X, Z
where Y1, Y2, R,,-R,6 and X,-X5 are as specified above.
According to this embodiment, the linker is attached to the X3 or
X4 substituent of both the donor and acceptor dyes, as illustrated below.
R11 R14
z
Y, VX4
R,z 15 DONOR25 XZ LINKER
X, x5 ACCEPTOR
R16 R13
R15 - - R12
1
Y2 0 Y,
R14 R11
-41 -

CA 02297589 2000-02-03
In this embodiment, the linker is preferably short and/or rigid.as this
has been found to enhance the transfer of energy between the donor
and acceptor dyes. For example, in one variation of this embodiment,
the linker preferably has a backbone attaching the donor to the acceptor
which is less than 9 atoms in length. In another variation of this
embodiment, the linker includes a functional group which gives the
linker some degree of structural rigidity, such as an alkene, diene, an
alkyne, a five and six membered ring having at least one unsaturated
bond or a fused ring structure. In yet another variation, the linker has
the general formula R25Z3C(0) or R25Z3C(O)R25Z4C(0) where R25 is
attached to the donor dye, C(0) is a carbonyl group and the terminal
carbonyl group is attached to the acceptor dye, R25 and Res are each
selected from the group of C1_4 alkyl, and Z3 and Z4 are each
independently either NH, 0 or S.
Examples of donor and acceptor dyes which may be used in this
embodiment include, but are not limited to fluorescein, 5 or 6
carboxyfluorescein, 5 or 6 carboxy-HEX, NAN, CI-FLAN, TET, JOE,
ZOE, 4,7-dichlorofluoresceins, asymmetric benzoxanthene dyes,
rhodamine, 5 or 6 carboxyrhodamine, 5 or 6 carboxy-R110, 5 or 6
carboxy-R6G, N, N, N', N'-tetramethyl (5 or 6)-carboxyrhodamine
(TAMRA), 5 or 6 carboxy-X-rhodamine (ROX) and 4,7-
dichiororhodamines. Illustrated in Table 2 are the structures of these
dyes.
In another variation of this embodiment, the linker includes a
R27Z5C(0) group where R27 is a Cl., alkyl attached to the donor dye, Z.
is either NH, sulfur or oxygen, and C(0) is a carbonyl group attached to
the acceptor dye.
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CA 02297589 2000-02-03
Table 5 provides examples of the second class of energy transfer
dyes according to the present invention. It is noted that although the
dyes illustrated in Table 5 include a 5-aminomethylfluorescein donor
dye, it should be understood that a wide variety of other xanthene dyes
can be readily substituted as the donor dye. It should also be
understood that a wide variety of other xanthene dyes, as well as
cyanine, phthalocyanine and squaraine dyes can be readily substituted
for the TAMRA acceptor dye, as has been described above, all of these
variations with regard to the donor and acceptor dyes falling within the
scope of the invention.
-43-

CA 02297589 2000-02-03
TABLE 5
H C N
( 3 )2 O N(CH3)2 (H3C)2N 0 I N(CH3)2
C02H CO2H
HN HN
OY
N
C02H
0
C02FH HO
HO O O
5TMR-gly-5AMF 5TMR-5AMF
-44-

CA 02297589 2000-02-03
TABLE 5 (cont.)
N2N ONH2 ~ N O NH 0 ' , CI CO2H CI C02H CI C02H
CI I
HN~O tHN HN 0
r-I rl
O 0
N
H02 H02 H02
O / OH O OH OH
N -,. N (CH3)2N N(CH3)2
\ I N(H3C)'Z N(CH3)2
C1 C02H CI C02H \ \ I /
CI C02H
CI I / Cl
HN 0
rJ O
HN
0
H02 H02 I / H02
LNOH N
O O O; ~OaOH O I OH
H
H2N NH2 '\-N NH (CH3)2 N(CH3)2
C C02H CI C02H cl CO2H
I I
CI CI
rt rH cl~ NH O)--j NH
N
Ij \
H02 HO2 HO2
00 OH 0 O OH O' OOH
-45-

CA 02297589 2000-02-03
TABLE 5 (cont.)
N N
(CH3)2N.. N(CH3)2 N(H3C)2 NCH
( 3)z
CI C0 2,H CI COZH CI COH
CI 1 / CI O I CI
NNH pH cl~ NH
HN
HOI HOC~
2C HO2C
/ I / I III j
O~ OH p ~ LOH O,6 'OH
H2N \ 0. C~1 NH,. ~,-N. NH (CH3)2N N(CH3)z
~~cl C02H CI CO2H CI C02H
I
CI CI
H0H02 H02
iO-OH NH H
1 O' OH O O OH
IAN N (CH3)2N 0 N(CH3)2
Z i I N(CH3)2
CI CO-2H C C02H CI C02H
CI CI 0
CI
NH H H
H02
H02 H02C 07 O / OH
O O OH O O OH
-46-

CA 02297589 2000-02-03
C. Third Class Of Energy Transfer Dyes
The third class of energy transfer fluorescent dyes include a 4,7-
dichlororhodamine dye as the acceptor dye and a dye which produces
an emission which the 4,7-dichlororhodamine dye can absorb as the
donor dye. These dyes exhibit enhanced fluorescence intensity as
compared to the acceptor dye alone. In addition, 4,7-
dichlororhodamine dyes exhibit a narrower emission spectrum than
other rhodamine dyes which facilitates their use in multiple component
analyses.
In a preferred embodiment, these energy transfer dyes include
those dyes according to the first and second classes of dyes in which
the acceptor is a 4,7-dichlororhodamine dye.
1. 4.7-Dichlororhodamine Dyes
4,7-dichlororhodamine dye compounds have the general structure
R5 R5
RAN O NR3R4
1 X41,
R6 R9
R7 Rio
X5 X,
6 5
X4 X2
x3
where:
R,-R4 are each independently hydrogen, alkyl or where R, and
R5, R, and R6, R. and R8, R4 and R. are taken together to form a ring,
and combinations thereof;
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CA 02297589 2000-02-03
R5-R,, are each independently hydrogen, fluorine, chlorine,
bromine, iodine, carboxyl, alkyl, alkene, alkyne, sulfonate, sulfone,
amino, ammonium, amido, nitrile, alkoxy, phenyl, or substituted phenyl,
or where adjacent substituents are taken together to form a ring, and
combinations thereof;
X1, X3 and X4 are each independently hydrogen, fluorine,
chlorine, bromine, iodine, carboxyl, alkyl, alkene, alkyne, sulfonate,
sulfone, amino, ammonium, amido, nitrile, or alkoxy, or where adjacent
substituents are taken together to form a ring, and combinations thereof;
and
X2 and X5 are chlorine.
With regard to R, - R4, alkyl substituents may include between
about 1 to 8 carbon atoms (i.e., methyl, ethyl, propyl, isopropyl, tert-
butyl, isobutyl, sec-butyl, neopentyl, tert-pentyl, and the like) and may
be straight-chain and branched hydrocarbon moieties. In a preferred
embodiment, R, - R4 are each independently either hydrogen, methyl,
or ethyl and more preferably either hydrogen or methyl.
With regard to R. - R,o, alkyl, alkene, alkyne and alkoxy -
substituents preferably include between about I to 8 carbon atoms (i.e.,
methyl, ethyl, propyl, isopropyl, tert-butyl, isobutyl, sec-butyl, neopentyl,
tert-pentyl, and the like) and may be straight-chain and branched
hydrocarbon moieties.
With regard to R, - RIO, R, and R5, R, and R,, R3 and R., R. and
R. may each independently be taken together to form a 5, 6, or 7
membered ring.
- 48 -

CA 02297589 2000-02-03
In one embodiment, R6 and R7 is benzo, and/or, R. and RIO is
benzo. In a preferred embodiment, R. - RIO are each independently
either hydrogen, methyl, or ethyl and more preferably either hydrogen or
methyl.
With regard to X,, X3 and X4, X1 is preferably a carboxylate and
one of X3 and X4 may include a substituent which is used to link the 4,7-
dichlororhodamine acceptor dye to a donor dye or to link a nucleotide or
an oligonucleotide to the energy transfer dye. The R. substituent at the
4' ring position may also be used to link the acceptor to either the donor
dye or to a biomolecule such as a nucleotide or oligonucleotide.
In one particularly preferred acceptor dye that may be used in the
present invention, referred to herein as DR1 10-2, R,-R,Q taken
separately are hydrogen, X, is carboxylate, and one of X3 and X4 is a
linking group (L), the other being hydrogen. The structure of DR1 10-2
is shown below.
H H H H
1 l
H-N 0 N-H
H H
11
LH DR110-2
In a second particularly preferred acceptor dye that may be used
in the present invention, referred to herein as DREG-2, one of R, and R,
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CA 02297589 2000-02-03
is ethyl, the other being hydrogen, one of R3 and R4 is ethyl, the other
being hydrogen, R. and R. taken separately are methyl, R6, R7, R9, and
R10 are hydrogen, X, is carboxylate, and one of X3 and X4 is a linking
group, the other being hydrogen. The structure of DREG-2 is shown
below.
H H H H
CH3CH2-N 0 / +1
11
CH3 / / CH3
H H
Cl / CO-
I I
0
LH Cl
DR6G-2
In a third particularly preferred acceptor dye that may be used in
the present invention, referred to herein as DTMR, R,-R6 taken
separately are hydrogen, Y1-Y4 taken separately are methyl, X, is
carboxylate, and one of X2 and X3 is linking group, the other being
hydrogen. The structure of DTMR is shown below.
-50-

CA 02297589 2000-02-03
CH3 H H + CH3
CH3-N 0 N-CH3
H H
H H
CI IO
0
CI
DTMR
In a fourth particularly preferred acceptor dye that may be used in
the present invention, referred to herein as DROX, R, and Rs are taken
together to form a six membered ring, R2 and R. are taken together to
form a six membered ring, R3 and R7 are taken together to form a six
membered ring, R4 and R. are taken together to form a six membered
ring, R5 and R6 are hydrogen, X, is carboxylate, and one of X3 and X4 is
a linking group, the other being hydrogen. The structure of DROX is
shown below.
N 0 -N
H H
/
CI CO
LH CI
CI
DROX
-51 -

CA 02297589 2000-02-03
Figures 3A and 3B show several additional preferred embodiments
of 4,7-dichlororhodamine dyes which can be used in the energy transfer dyes of
the present invention.
In compound 3A-A, one of R, and R2 is ethyl, the other being
hydrogen, R3 and R4 taken separately are hydrogen, R6 is methyl, R5 and R7-R,o
taken separately are hydrogen, X, is carboxylate , and one of X3 and X4 is a
linking group, the other being hydrogen.
In compound 3A-B, one of R, and R2 is ethyl, the other being
hydrogen, R3 and R4 taken separately are methyl, R5 is methyl, R6-R,o taken
separately are hydrogen, X, is carboxylate, and, one of X3 and X4 is the
linking
group, the other being hydrogen.
In compound 3A-C, R, and R2 taken separately are methyl, R3 and
R9 taken together form a six membered ring, R4 and R8 taken together form a
six
membered ring, R5, R6, R7, and RIO taken separately are hydrogen, X, is
carboxylate, and, one of X3 and X4 is a linking group, the other being
hydrogen.
In compound 3B-D, R, and R2 taken separately are hydrogen, R3
and R9 taken together form a six membered ring, R4 and R8 taken together form
a
six membered ring, R5i R6, R7, and Rio taken separately are hydrogen, X, is
carboxylate, and one of X3 and X4 is a linking group, the other being
hydrogen.
In compound 3B-E, one of R, and R2 is ethyl, the other being
hydrogen, R3 and R9 taken together form a six membered ring, R4 and R8 taken
together form a six membered ring, R5, R6, R7 and Rio taken separately are
hydrogen, X, is carboxylate, and, one of X3 and X4 is a linking group, the
other
being hydrogen.
In compound 3B-F, R, and R2 taken separately are hydrogen, R3 and
R4 taken separately are methyl, R5-R10 taken separately are hydrogen, X, is
carboxylate, and, one of X3 and X4 is a linking group, the other being
hydrogen.

CA 02297589 2000-02-03
Figures 4A and 4B show preferred generalized synthesis schemes
for the preparation of 4,7-dichlororhodamine dyes used in the energy transfer
dyes of this invention. The variable substituents indicated in each figure are
as
previously defined.
Figure 4A shows a generalized synthesis wherein the substituent X,
can be other than carboxylate. In this figure, X indicates moieties which are
precursors to X,. In the method illustrated in Figure 4A, two equivalents of a
3-
aminophenol derivative 4A-A/4A-B, such as 3-dimethylaminophenol, is reacted
with one equivalent of a dichlorobenzene derivative 4A-C, e.g., 4-carboxy-
3,6,dichloro-2-sulfobenzoic acid cyclic anhydride, i.e., where the X,'
moieties of
4A-C taken together are,
0 0 11
-C-O-S-
II
O
The reactants are then heated for 12 h in a strong acid, e.g.,
polyphosphoric acid or sulfuric acid, at 180 C. The crude dye 4A-D is
precipitated
by addition to water and isolated by centrifugation. To form a symmetrical
product,
the substituents of reactants 4A-A and 4A-B are the same, while to form an
asymmetrical product, the substituents are different.
Figure 4B shows a generalized synthesis wherein the substituent X,
is carboxylate. In the method of Figure 4B, two equivalents of a 3-aminophenol
derivative 4B-A/4B-B, such as 3-dimethylaminophenol, is reacted with one
equivalent of a phthalic annhydride derivative 4B-E, e.g.3,6-
dichlorotrimeliitic acid
anhydride. The reactants are then heated for 12 h in a strong acid, e.g.,
polyphosphoric acid or sulfuric acid, at 180 C. The crude dye 413-D is
precipitated
by addition to water and isolated by
53

CA 02297589 2000-02-03
centrifugation. To form a symmetrical product, the substituents of reactants
413-A
and 4B-B are the same, while to form an asymmetrical product, the substituents
are different.
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CA 02297589 2000-02-03
2. Energy Transfer Dyes With
4.7-Dichiororhodamine As The Acceptor
In general, the energy transfer dyes of the present invention
include a donor dye which absorbs light at a first wavelength and emits
excitation energy in response, a 4,7-dichlororhodamine acceptor dye
which is capable of absorbing the excitation energy emitted by the
donor dye and fluorescing at a second wavelength in response, and a
linker which attaches the donor dye to the acceptor dye. Prefered
examples of this class of dyes which use a 4,7-dichlororhodamine dye
as the acceptor dye is illustrated in Table 1.
Examples of acceptor dyes which may be used in this class of
dyes include, but are not limited to DR110-2, DREG-2, DTMR, DROX,
as illustrated above, as well as the dyes illustrated in Figures 3A-3B.
One subclass of these energy transfer fluorescent dyes are the
dyes according to the first class of dyes of the present invention in
which the acceptor dye is a 4,7-dichlororhodamine dye. The general
structure of these dyes is illustrated below.
RS Re
R2R,N 0 NR3R4
ACCEPTOR
Re Ro
Rr Rio
X5 X,
I
X. X2
LINKER
Rtt
t O Y
2
DONOR
R2 R,S
R,3 R17 Rte
-55-

CA 02297589 2000-02-03
Table 4 provides examples of the energy transfer dyes belonging
to the first class of dyes in which a 4,7 dichlororhodamine is used as the
acceptor dye. It is noted that although the dyes illustrated in Table 4
include a 5-carboxyfluorescein donor dye and a 5 or 6 carboxy DTMR
as the acceptor dye, it should be understood that a wide variety of other
xanthene dyes can be readily substituted as the donor dye and a wide
variety of other 4,7-dichlororhodamine dyes can be readily substituted
for the DTMR acceptor dye, all of these variations with regard to the
donor and acceptor dyes being intended to fall within the scope of the
invention.
Another subclass of these energy transfer fluorescent dyes are
the dyes according to the second class of dyes of the present invention
in which the acceptor dye is a 4,7-dichlororhodamine dye. The general
structure of these dyes where the donor xanthene dye and acceptor 4,7-
dichlororhodamine dye are linked to each other at either the five or six
ring positions of the donor and acceptor dyes is illustrated below.
RS Rd
RzR,N p t NR3R,
Re R9
R7 Rio
01 X, ACCEPTOR
6
X,3 o' ~ 5 1
Xiz
5 6 X3 or X~
Xi, XIS
Ris Rt3
R15 R1
YZo Y DONOR
Rõ Rõ
-56-

CA 02297589 2000-02-03
As described above, in this embodiment, the linker attaching the
donor to the acceptor dye is preferably short and/or rigid as this has
been found to enhance the transfer of energy between the donor and
acceptor dyes. The substituent labels shown above correspond to the
same groups of substituents as has been specified with regard to the
other dyes.
Table 5 provides examples of the second class of energy transfer
dyes according to the present invention in which 4,7 dichlororhodamine
is used as the acceptor dye. It is noted that although the dyes
illustrated in Table 5 include a 5-aminomethylfluorescein donor dye, it
should be understood that a wide variety of other xanthene dyes can be
readily substituted as the donor dye. It should also be understood that
a wide variety of other 4,7-dichlororhodamine dyes can be readily
substituted for the acceptor dye shown in Table 5 since, as has been
described above, all of these variations with regard to the donor and
acceptor dyes are intended to fall within the scope of the invention.
D. Fourth Class Of Energy Transfer Dyes
The present invention also relates to a fourth class of energy
transfer fluorescent dyes in which the donor dye is a member of the
xanthene class of dyes, and the acceptor dye is a member of the
xanthene, cyanine, phthalocyanine or squaraine classes of dyes.
Within this class of energy transfer dyes, it is preferred that the donor
be a member of the fluorescein class of dyes and the acceptor dye have
an emission maximum that is greater than about 600 nm and/or an
emission maximum that is at least about 100 nm greater than the
absorbance maximum of the donor dye.
The fourth class of dyes of the present invention exhibit
unusually large Stoke shifts, as measured by the difference between the
-57-

CA 02297589 2000-02-03
absorbance of the donor and the emission of the acceptor. In addition,
these dyes exhibit efficient energy transfer in that minimal donor
fluorescence is observed. Interestingly, energy is transfered from the
donor to the acceptor in some of the dyes belonging to this class even
though the absorbance spectrum of the acceptor dye does not overlap
with the emission spectrum of the donor dye.
Examples of acceptor dyes which may be used in this
embodiment include, but are not limited to 5-carboxy-X-rhodamine
(ROX) and Cy5.
The energy transfer dyes of this embodiment also include a linker
which attaches the donor to the acceptor. The linker used to attach the
donor to the acceptor dye may be any linker according to the first and
second classes of dyes. However, it is foreseen that alternate linkers
may be used in this class of dyes.
In one embodiment of this class of dyes, the linker is attached to
the 4' position of the donor dye's xanthene ring structure. The linker
preferably has a general structure R21Z1C(O)R22R28, as described above
where R21 is a Cl.,, alkyl which is attached to the 4' ring position of the
donor xanthene dye, Z, is either NH, sulfur or oxygen, C(O) is a
carbonyl group, R22 is a substituent which includes an alkene, diene,
alkyne, a five and six membered ring having at least one unsaturated
bond or a fused ring structure which is attached to the carbonyl carbon,
and R28 is a functional group which attaches the linker to the acceptor
dye. In cases where the acceptor dye is a member of the xanthene
class of dyes, the linker is preferably attached to acceptor at the 5
position of the xanthene ring structure.
Table 6 provides examples of the above-described energy
transfer dyes according to the present invention. It is noted that
although the dyes illustrated in Table 6 include a 5-carboxyfluorescein
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CA 02297589 2000-02-03
donor dye it should be understood that a wide variety of other xanthene
dyes can be readily substituted as the donor dye. It should also be
understood that a wide variety of other xanthene dyes, as well as
cyanine, phthalocyanine and squaraine dyes can be readily substituted
for the 5-carboxy ROX and Cy5 acceptor dyes, as has been described
above, all of these variations with regard to the donor and acceptor
dyes falling within the scope of the invention.
The energy transfer dyes of this embodiment exhibit unusually
large Stoke shifts which make these dyes particularly well suited for use
with dyes having smaller Stoke shifts in four dye DNA sequencing. For
example, Figures 5 and 6 illustrate two sets of four dyes which are
spectrally resolvable from each other. Within Figure 5, 5ROX-CF is a
dye falling within the scope of the fourth class of dyes described above.
Meanwhile, Figure 6 includes 5ROX-CF and Cy5-CF which both fall
within the scope of the fourth class of dyes described above.
As can be seen from the emission spectra of 5ROX-CF and Cy5-
CF illustrated in Figure 6, very little fluorescence from the donor dye (5-
carboxyfluorescein, 520 nm) is observed in these dyes. This is an
unexpected result in view of the large difference between the emission
maximum of the donor dye (fluorescein) and the absorbance maximum
of the acceptor dyes (ROX, 590 nm, Cy5, 640 nm).
-59-

CA 02297589 2000-02-03
TABLE 6
N 0 N\
C02H
o N
H000
/ COZH
L 5-ROX-CF
CO2H
-03S \ /
N* i N S03
OWN
HO / 0 O
/ CO2H
L CYS-CF
CO2H
-60-

CA 02297589 2000-02-03
II. Reagents Including Energy Transfer Dyes Of The Present Invention
The present invention also relates to fluorescent reagents which
incorporate an energy transfer fluorescent dye according to the present
invention. As described in greater detail in Section III, these reagents
may be used in a wide variety of methods for detecting the presence of
a component in a sample.
The fluorescent reagents of the present invention include any
molecule or material to which the energy transfer dyes of the invention
can be attached and used to detect the presence of the reagent based
on the fluorescence of the energy transfer dye. Types of molecules and
materials to which the dyes of the present invention may be attached to
form a reagent include, but are not limited to proteins, polypeptides,
polysaccharides, nucleotides, nucleosides, oligonucleotides,
oligonucleotide analogs (such as a peptide nucleic acid), lipids, solid
supports, organic and inorganic polymers, and combinations and
assemblages thereof, such as chromosomes, nuclei, living cells, such
as bacteria, other microorganisms, mammalian cells, and tissues.
Preferred classes of reagents of the present invention are
nucleotides, nucleosides, oligonucleotides and oligonucleotide analogs
which have been modified to include an energy transfer dye of the
invention. Examples of uses for nucleotide and nucleoside reagents
include, but are not limited to, labeling oligonucleotides formed by
enzymatic synthesis, e.g., nucleoside triphosphates used in the context
of PCR amplification, Sanger-type oligonucleotide sequencing, and
nick-translation reactions. Examples of uses for oligonucleotide
reagents include, but are not limited to, as DNA sequencing primers,
PCR primers, oligonucleotide hybridization probes, and the like.
One particular embodiment of the reagents are labeled
nucleosides (NTP), such as cytosine, adenosine, guanosine, and
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CA 02297589 2000-02-03
thymidine, labeled with an energy transfer fluorescent dye of the
present invention. These reagents may be used in a wide variety of
methods involving oligonucleotide synthesis. Another related
embodiment are labeled nucleotides, e.g., mono-, di- and triphosphate
nucleoside phosphate esters. These reagents include, in particular,
deoxynucleoside triphosphates (dNTP), such as deoxycytosine
triphosphate, deoxyadenosine triphosphate, deoxyguanosine
triphosphate, and deoxythymidine triphosphate, labeled with an energy
transfer fluorescent dye of the present invention. These reagents may
be used, for example, as polymerase substrates in the preparation of
dye labeled oligonucleotides. These reagents also include labeled
dideoxynucleoside triphosphates (ddNTP), such as dideoxycytosine
triphosphate, dideoxyadenosine triphosphate, dideoxyguanosine
triphosphate, and dideoxythymidine triphosphate, labeled with an
energy transfer fluorescent dye of the present invention. These
reagents may be used, for example, in dye termination sequencing.
Another embodiment of reagents are oligonucleotides which
includes an energy transfer fluorescent dye of the present invention.
These reagents may be used, for example, in dye primer sequencing.
As used herein, "nucleoside" refers to a compound consisting of
a purine, deazapurine, or pyrimidine nucleoside base, e.g., adenine,
guanine, cytosine, uracil, thymine, deazaadenine, deazaguanosine, and
the like, linked to a pentose at the 1' position, including 2'-deoxy and
2'-hydroxyl forms, e.g. as described in Kornberg and Baker, DNA
Replication, 2nd Ed. (Freeman, San Francisco, 1992). The term
"nucleotide" as used herein refers to a phosphate ester of a nucleoside,
e.g., mono, di and triphosphate esters, wherein the most common site of
esterification is the hydroxyl group attached to the C-5 position of the
pentose. "Analogs" in reference to nucleosides include synthetic
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CA 02297589 2000-02-03
nucleosides having modified base moieties and/or modified sugar
moieties, e.g. described generally by Scheit, Nucleotide Analogs (John
Wiley, New York, 1980). The terms "labeled nucleoside" and "labeled
nucleotide" refer to nucleosides and nucleotides which are covalently
attached to an energy transfer dye through a linkage.
As used herein, the term "oligonucleotide" refers to linear
polymers of natural or modified nucleoside monomers, including double
and single stranded deoxyribonucleosides, ribonucleosides, a-anomeric
forms thereof, and the like. Usually the nucleoside monomers are
linked by phosphodiester linkages, where as used herein, the term
"phosphodiester linkage" refers to phosphodiester bonds or analogs
thereof including phosphorothioate, phosphorodithioate,
phosphoroselenoate, phosphorodiselenoate, phosphoroanilothioate,
phosphoraniIidate, phosphoramidate, and the like, including associated
counterions, e.g., H, NH4, Na, and the like if such counterions are
present. The oligonucleotides range in size form a few monomeric
units, e.g. 8-40, to several thousands of monomeric units. Whenever an
oligonucleotide is represented by a sequence of letters, such as
"ATGCCTG," it will be understood that the nucleotides are in 5'->3'
order from left to right and that "A" denotes deoxyadenosine, "C"
denotes deoxycytidine, "G" denotes deoxyguanosine, and "T" denotes
thymidine, unless otherwise noted.
Nucleoside labeling can be accomplished using any of a large
number of known nucleoside labeling techniques using known linkages,
linking groups, and associated complementary functionalities. The
linkage linking the dye and nucleoside should (i) be stable to
oligonucleotide synthesis conditions, (ii) not interfere with
oligonucleotide-target hybridization, (iii) be compatible with relevant
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enzymes, e.g., polymerases, ligases, and the like, and (iv) not quench
the fluorescence of the dye.
Preferably, the dyes are covalently linked to the 5-carbon of
pyrimidine bases and to the 7-carbon of 7-deazapurine bases. Several
suitable base labeling procedures have been reported that can be
used with the invention, e.g. Gibson et al, Nucleic Acids Research,
6455-6467 (1987); Gebeyehu et al, Nucleic Acids Research, 15
4513-4535 (1987); Haralambidis et al, Nucleic Acids Research, 15
4856-4876 (1987); Nelson et al., Nucleosides and Nucleotides, 5(3)
10 233-241 (1986); Bergstrom, et al., JACS, 111 374-375 (1989); U.S.
Patent Nos. 4,855,225, 5,231,191, and 5,449,767.
Preferably, the linkages are acetylenic amido or alkenic amido
linkages, the linkage between the dye and the nucleotide base being
15 formed by reacting an activated N-hydroxysuccinimide (NHS) ester of
the dye with an alkynylamino-, alkynylethoxyamino- or alkenylamino-
derivatized base of a nucleotide. More preferably, the resulting
linkage is proargyl-1 -ethoxyamido (3-(amino)ethoxy-1 -propynyl), 3-
(carboxy)amino-1-propynyl or 3-amino-1 -propyn-1-yl.
Several preferred linkages for linking the dyes of the invention to
a nucleoside base are shown below.
R
C C-CH2 NH-C-
3-amino-l-propyn-1-yl
R Q
-C=C-CH2- NH-C-(CH-,)5- NHC-
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R Q
-C=CH-C- NH-(CH2)5- NH-C--
CH 20CH 2CH 2NR 1 R2
where R, and R2 taken separately are H, alkyl, a
protecting group or a fluorescent dye.
The synthesis of alkynylamino-derivatized nucleosides is taught
by Hobbs et al. in European Patent Application No. 87305844.0, and
Hobbs et al., J. Orq. .
hem, 54 3420 (1989),
Briefly, the alkynylamine-derivatized nucleotides
are formed by placing the appropriate halodideoxynucleoside
(usually 5-iodopyrimidine and 7-iodo-7-deazapurine
dideoxynucleosides as taught by Hobbs et al. (cited above)) and
Cu(I) in a flask, flushing with argon to remove air, adding dry DMF,
followed by addition of an alkynylamine, triethyl-amine and Pd(0). The
reaction mixture can be stirred for several hours, or until thin layer
chromatography indicates consumption of the halodideoxynucleoside.
When an unprotected alkynylamine is used, the alkynylamino-
nucleoside can be isolated by concentrating the reaction mixture
and chromatographing on silica gel using an eluting solvent which
contains ammonium hydroxide to neutralize the hydrohalide -
generated in the coupling reaction. When a protected alkynylamine is
used, methanol/methylene chloride can be added to the reaction
mixture, followed by the bicarbonate form of a strongly basic anion
exchange resin. The slurry can then be stirred for about 45 minutes,
filtered, and the resin rinsed with additional methanol/methylene
chloride. The combined filtrates can be concentrated and
purified by flash-chromatography on silica gel using a methanol-
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methylene chloride gradient. The triphosphates are obtained by
standard techniques.
The synthesis of oligonucleotides labeled with an energy transfer
dye of the present invention can be accomplished using any of a large
number of known oligonucleotide labeling techniques using known
linkages, linking groups, and associated complementary functionalities.
For example, labeled oligonucleotides may be synthesized
enzymatically, e.g., using a DNA polymerase or ligase, e.g., Stryer,
Biochemistry, Chapter 24, W.H. Freeman and Company (1981), or by
chemical synthesis, e.g., by a phosphoramidite method, a phosphite-
triester method, and the like, e.g., Gait, Oligonucleotide Synthesis, IRL
Press (1990). Labels may be introduced during enzymatic synthesis
utilizing labeled nucleoside triphosphate monomers, or introduced
during chemical synthesis using labeled non-nucleotide or nucleotide
phosphoramidites, or may be introduced subsequent to synthesis.
Generally, if the labeled oligonucleotide is made using enzymatic
synthesis, the following procedure may be used. A template DNA is
denatured and an oligonucleotide primer is annealed to the template
DNA. A mixture of deoxynucleoside triphosphates is added to the
reaction including dGTP, dATP, dCTP, and dTTP where at least a
fraction of one of the deoxynucleotides is labeled with a dye compound
of the invention as described above. Next, a polymerase enzyme is
added under conditions where the polymerase enzyme is active. A
labeled polynucleotide is formed by the incorporation of the labeled
deoxynucleotides during polymerase strand synthesis. In an alternative
enzymatic synthesis method, two primers are used instead of one, one
primer complementary to the + strand and the other complementary to
the - strand of the target, the polymerase is a thermostable polymerase,
and the reaction temperature is cycled between a denaturation
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temperature and an extension temperature, thereby exponentially
synthesizing a labeled complement to the target sequence by PCR,
e.g., PCP, Protocols, Innis et al. eds., Academic Press (1990).
Generally, if the labeled oligonucleotide is made using a
chemical synthesis, it is preferred that a phosphoramidite method be
used. Phosphoramidite compounds and the phosphoramidite method of
polynucleotide synthesis are preferred in synthesizing oligonucleotides
because of the efficient and rapid coupling and the stability of the
starting materials. The synthesis is performed with the growing
oligonucleotide chain attached to a solid support, so that excess
reagents, which are in the liquid phase, can be easily removed by
filtration, thereby eliminating the need for purification steps between
cycles.
In view of the utility of phosphoramidite reagents in labeling
nucleosides and oligonucleotides, the present invention also relates to
phosphoramidite compounds which include an energy transfer dye of
the present invention.
Detailed descriptions of the chemistry used to form
oligonucleotides by the phosphoramidite method are provided in
Caruthers et al., U.S. Pat. No. 4,458,066; Caruthers et al., U.S. Pat. No.
4,415,732; Caruthers et al., Genetic Engineering, 4 1-17 (1982); Users
Manual Model 392 and 394 Polynucleotide Synthesizers, pages -6-1
through 6-22, Applied Biosystems, Part No. 901237 (1991),
The following briefly describes the steps of a typical
oligonucleotide synthesis cycle using the phosphoramidite method.
First, a solid support including a protected nucleotide monomer is
treated with acid, e.g., trichloroacetic acid, to remove a 5'-hydroxyl
protecting group, freeing the hydroxyl for a subsequent coupling
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reaction. An activated intermediate is then formed by simultaneously
adding a protected phosphoramidite nucleoside monomer and a weak
acid, e.g., tetrazole, to the reaction. The weak acid protonates the
nitrogen of the phosphoramidite forming a reactive intermediate.
Nucleoside addition is complete within 30 s. Next, a capping step is
performed which terminates any polynucleotide chains that did not
undergo nucleoside addition. Capping is preferably done with acetic
anhydride and 1-methylimidazole. The internucleotide linkage is then
converted from the phosphite to the more stable phosphotriester by
oxidation using iodine as the preferred oxidizing agent and water as the
oxygen donor. After oxidation, the hydroxyl protecting group is removed
with a protic acid, e.g., trichloroacetic acid or dichloroacetic acid, and
the cycle is repeated until chain elongation is complete. After synthesis,
the polynucleotide chain is cleaved from the support using a base, e.g.,
ammonium hydroxide or t-butyl amine. The cleavage reaction also
removes any phosphate protecting groups, e.g., cyanoethyl. Finally, the
protecting groups on the exocyclic amines of the bases and the hydroxyl
protecting groups on the dyes are removed by treating the
polynucleotide solution in base at an elevated temperature, e.g., 55 C.
Any of the phosphoramidite nucleoside monomers may be dye-
labeled phosphoramidites. If the 5'-terminal position of the nucleotide is
labeled, a labeled non-nucleotidic phosphoramidite of the invention may
be used during the final condensation step. If an internal position of the
oligonucleotide is to be labeled, a labeled nucleotidic phosphoramidite
of the invention may be used during any of the condensation steps.
Subsequent to their synthesis, oligonucleotides may be labeled
at a number of positions including the 5'-terminus. See
Oligonucleotides and Analogs, Eckstein ed., Chapter 8, IRL Press
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(1991) and Orgel et al., Nucleic Acids Research 11(18) 6513 (1983);
U.S. Patent No. 5,118,800.
Oligonucleotides may also be labeled on their phosphodiester
backbone (Oligonucleotides and Analogs, Eckstein ed., Chapter 9) or at
the 3'-terminus (Nelson, Nucleic Acids Research 20(23) 6253-6259,
and U.S. Patent Nos. 5,401,837 and 5,141,813.).
For a review of oligonucleotide labeling
procedures see R. Haugland in Excited States of Biopolymers, Steiner
ed., Plenum Press, NY (1983).
In one preferred post-synthesis chemical labeling method an
oligonucleotide is labeled as follows. A dye including a carboxy linking
group is converted to the n-hydroxysuccinimide ester by reacting with
approximately 1 equivalent of 1,3-dicyclohexylcarbodiimide and
approximately 3 equivalents of n-hydroxysuccinimide in dry ethyl
acetate for 3 hours at room temperature. The reaction mixture is washed
with 5 % HCI, dried over magnesium sulfate, filtered, and concentrated
to a solid which is resuspended in DMSO. The DMSO dye stock is then
added in excess (10-20 x) to an aminohexyl derivatized oligonucleotide
in 0.25 M bicarbonate/carbonate buffer at pH 9.4 and allowed to react
for 6 hours, e.g., U.S. Patent No. 4,757,141. The dye labeled
oligonucleotide is separated from unreacted dye by passage through a
size-exclusion chromatography column eluting with buffer, e.g.,- 0.1
molar triethylamine acetate (TEAA). The fraction containing the crude
labeled oligonucleotide is further purified by reverse phase HPLC
employing gradient elution.
Ill. Methods Employing Dyes And Reagents Of The Present Invention
The energy transfer dyes and reagents of the present invention
may be used in a wide variety of methods for detecting the presence or
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a component in a sample by labeling the component in the sample with
a reagent containing the dye. In particular, the energy transfer dyes and
reagents of the present invention are well suited for use in methods
which combine separation and fluorescent detection techniques,
particularly methods requiring the simultaneous detection of multiple
spatially-overlapping analytes. For example, the dyes and reagents are
particularly well suited for identifying classes of oligonucleotides that
have been subjected to a biochemical separation procedure, such as
electrophoresis, where a series of bands or spots of target substances
having similar physiochemical properties, e.g. size, conformation,
charge, hydrophobicity, or the like, are present in a linear or planar
arrangement. As used herein, the term "bands" includes any spatial
grouping or aggregation of analytes on the basis of similar or
identical physiochemical properties. Usually bands arise in the
separation of dye-oligonucleotide conjugates by electrophoresis.
Classes of oligonucleotides can arise in a variety of contexts.
In a preferred category of methods referred to herein as "fragment
analysis" or "genetic analysis" methods, labeled oligonucleotide
fragments are generated through template-directed enzymatic synthesis
using labeled primers or nucleotides, e.g., by ligation or polymerase-
directed primer extension; the fragments are subjected to a size-
dependent separation process, e.g., electrophoresis or chromatography;
and, the separated fragments are detected subsequent to the
separation, e.g., by laser-induced fluorescence. In a particularly
preferred embodiment, multiple classes of oligonucleotides are
separated simultaneously and the different classes are distinguished by
spectrally resolvable labels.
One such fragment analysis method is amplified fragment length
polymorphisim detection (AmpFLP) and is based on amplified fragment
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length polymorphisms, i.e., restriction fragment length polymorphisms
that are amplified by FOR. These amplified fragments of varying size
serve as linked markers for following mutant genes through families.
The closer the amplified fragment is to the mutant gene on the
chromosome, the higher the linkage correlation. Because genes for
many genetic disorders have not been identified, these linkage markers
serve to help evaluate disease risk or paternity. In the AmpFLPs
technique, the polynucleotides may be labeled by using a labeled
oligonucleotide PCR primer, or by utilizing labeled nucleotide
triphosphates in the PCR.
Another fragment analysis method is nick translation. Nick
translation involves a reaction to replace unlabeled nucleotide
triphosphates in a double-stranded DNA molecule with labeled ones.
Free 3'-hydroxyl groups are created within the unlabeled DNA by "nicks"
caused by deoxyribonuclease I (DNAase I) treatment. DNA polymerase
I then catalyzes the addition of a labeled nucleotide to the 3'-hydroxyl
terminus of the nick. At the same time, the 5' to 3'-exonuclease activity
of this enzyme eliminates the nucleotide unit from the 5'-phosphoryl
terminus of the nick. A new nucleotide with a free 3'-OH group is
incorporated at the position of the original excised nucleotide, and the
nick is shifted along by one nucleotide unit in the 3' direction. This 3'
shift will result in the sequential addition of new labeled nucleotides to
the DNA with the removal of existing unlabeled nucleotides. The nick-
translated polynucleotide is then analyzed using a separation process,
e.g., electrophoresis.
Another exemplary fragment analysis method is based on
variable number of tandem repeats, or VNTRs. VNTRs are regions of
double-stranded DNA that contain adjacent multiple copies of a
particular sequence, with the number of repeating units being variable.
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Examples of VNTR loci are pYNZ22, pMCT118, and Apo B. A subset of
VNTR methods are those methods based on the detection of
microsatellite repeats, or short tandem repeats (STRs), i.e., tandem
repeats of DNA characterized by a short (2-4 bases) repeated
sequence. One of the most abundant interspersed repetitive DNA
families in humans is the (dC-dA)n--(dG-dT)n dinucleotide repeat family
(also called the (CA)n dinucleotide repeat family). There are thought to
be as many as 50,000 to 100,000 (CA)n repeat regions in the human
genome, typically with 15-30 repeats per block. Many of these repeat
regions are polymorphic in length and can therefore serve as useful
genetic markers. Preferably, in VNTR or STR methods, label is
introduced into the polynucleotide fragments by using a dye-labeled
PCR primer.
Another exemplary fragment analysis method is DNA
sequencing. In general, DNA sequencing involves an extension /
termination reaction of an oligonucleotide primer. Included in the
reaction mixture are deoxynucleoside triphosphates (dNTPs) which are
used to extend the primer. Also included in the reaction mixture is at
least one dideoxynucleoside triphosphate (ddNTP) which when
incorporated onto the extended primer prevents the further extension of
the primer. After the extension reaction has been terminated, the
different termination products that are formed are separated and
analyzed in order to determine the positioning of the different
nucleosides.
Fluorescent DNA sequencing may generally be divided into two
categories, "dye primer sequencing" and "dye terminator sequencing".
In dye primer sequencing, a fluorescent dye is incorporated onto the
primer being extended. Four separate extension / termination reactions
are then run in parallel, each extension reaction containing a different
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dideoxynudeoside triphosphate (ddNTP) to terminate the extension
reaction. After termination, the reaction products are separated by gel
electrophoresis and analyzed. See, for example, Ansorge et al., Nucleic
Acids Res. 15 4593-4602 (1987).
In one variation of dye primer sequencing, different primers are
used in the four separate extension / termination reactions, each primer
containing a different spectrally resolvable dye. After termination, the
reaction products from the four extension / termination reactions are
pooled, electrophoretically separated, and detected in a single lane.
wee, for example, Smith et al., Nature 21 674-679 (1986). Thus, in this
variation of dye primer sequencing, by using primers containing a set of
spectrally resolvable dyes, products from more than one extension /
termination reactions can be simultaneously detected.
In dye terminator sequencing, a fluorescent dye is attached to
each of the dideoxynucleoside triphosphates. An extension /
termination reaction is then conducted where a primer is extended using
deoxynucleoside triphosphates until the labeled dideoxynucleoside
triphosphate is incorporated into the extended primer to prevent further
extension of the primer. Once terminated, the reaction products for
each dideoxynucleoside triphosphate are separated and detected. In
one embodiment, separate extension /termination reactions are
conducted for each of the four dideoxynucleoside triphosphates. In
another embodiment, a single extension/termination reaction is
conducted which contains the four dideoxynucleoside triphosphates,
each labeled with a different, spectrally resolvable fluorescent dye.
Thus according to one aspect of the invention, a method is
provided for conducting dye primer sequencing using one or more
oligonucleotide reagents of the present invention. According to this
method, a mixture of extended labeled primers are formed by
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hybridizing a nucleic acid sequence with a fluorescently labeled
oligonucleotide primer in the presence of deoxynucleoside
triphosphates, at least one dideoxynucleoside triphosphate and a DNA
polymerase. The fluorescently labeled oligonucleotide primer includes
an oligonucleotide sequence complementary to a portion of the nucleic
acid sequence being sequenced, and an energy transfer fluorescent dye
attached to the oligonucleotide.
According to the method, the DNA polymerase extends the
primer with the deoxynucleoside triphosphates until a dideoxynucleoside
triphosphate is incorporated which terminates extension of the primer.
After termination, the mixture of extended primers are separated. The
sequence of the nucleic acid sequence is then determined by
fluorescently detecting the mixture of extended primers formed.
In a further embodiment of this method, four dye primer
sequencing reactions are run, each primer sequencing reaction
including a different fluorescently labeled oligonucleotide primer and a
different dideoxynucleoside triphosphate (ddATP, ddCTP, ddGTP and
ddTTP). After the four dye primer sequencing reactions are run, the
resulting mixtures of extended primers may be pooled. The mixture of
extended primers may then be separated, for example by
electrophoresis and the fluorescent signal from each of the four different
fluorescently labeled oligonucleotide primers detected in order to
determine the sequence of the nucleic acid sequence.
According to a further aspect of the invention, a method is
provided for conducting dye terminator sequencing using one or more
dideoxynucleoside triphosphates labeled with an energy transfer dye of
the present invention. According to this method, a mixture of extended
primers are formed by hybridizing a nucleic acid sequence with an
oligonucleotide primer in the presence of deoxynucleoside
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triphosphates, at least one fluorescently labeled dideoxynucleotide
triphosphate and a DNA polymerase. The fluorescently labeled
dideoxynucleotide triphosphate includes a dideoxynucleoside
triphosphate labeled with an energy transfer fluorescent dye of the
present invention.
According to this method, the DNA polymerase extends the
primer with the deoxynucleoside triphosphates until a fluorescently
labeled dideoxynucleoside triphosphate is incorporated into the
extended primer. After termination, the mixture of extended primers are
separated. The sequence of the nucleic acid sequence is then
determined by detecting the fluorescently labeled dideoxynucleoside
attached to the extended primer.
In a further embodiment of this method,. the step of forming a
mixture of extended primers includes hybridizing the nucleic acid
sequence with four different fluorescently labeled dideoxynucleoside
triphosphates, i.e., a fluorescently labeled dideoxycytosine triphosphate,
a fluorescently labeled dideoxyadenosine triphosphate, a fluorescently
labeled dideoxyguanosine triphosphate, and a fluorescently labeled
dideoxythymidine triphosphate.
In each of the above-described fragment analysis methods, the
labeled oligonucleotides are preferably separated by electrophoretic
procedures, e.g. Gould and Matthews, cited above; Rickwood and
Hames, Eds., Gel Electrophoresis of Nucleic Acids: A Practical
Approach, (IRL Press Limited, London, 1981); or Osterman, Methods
of Protein and Nucleic Acid Research, Vol. 1 Springer-Verlag, Berlin,
1984). Preferably the type of electrophoretic matrix is crosslinked
or uncrosslinked polyacrylamide having a concentration (weight to
volume) of between about 2-20 weight percent. More preferably, the
polyacrylamide concentration is between about 4-8 percent. Preferably
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in the context of DNA sequencing in particular, the electrophoresis
matrix includes a strand separating, or denaturing, agent, e.g., urea,
formamide, and the like. Detailed procedures for constructing such
matrices are given by Maniatis et al., "Fractionation of Low Molecular
Weight DNA and RNA in Polyacrylamide Gels Containing 98%
Formamide or 7 M Urea," in Methods in Enzymology, 65 299-305
(1980); Maniatis et al., "Chain Length Determination of Small Double-
and Single-Stranded DNA Molecules by Polyacrylamide Gel
Electrophoresis," Biochemistry, 14 3787-3794 (1975); Maniatis et al.,
Molecular Cloning: A Laboratory Manual (Cold Spring Harbor
Laboratory, New York, 1982), pgs. 179-185; and ABI PRISMTM 377 DNA
Sequencer User's Manual, Rev. A, January 1995, Chapter 2 (p/n
903433, The Perkin-Elmer Corporation, Foster City, CA).
The optimal polymer concentration, pH,
temperature, concentration of denaturing agent, etc. employed in a
particular separation depends on many factors, including the size
range of the nucleic acids to be separated, their base compositions,
whether they are single stranded or double stranded, and the nature of
the classes for which information is sought by electrophoresis.
Accordingly application of the invention may require standard
preliminary testing to optimize conditions for particular separations.
By way of example, oligonucleotides having sizes in the range df
between about 20-300 bases have been separated and detected in
accordance with the invention in the following matrix: 6 percent
polyacrylamide made from 19 parts to 1 part acrylamide to bis-
acrylamide, formed in a Tris-borate EDTA buffer at pH 8.3.
After electrophoretic separation, the dye-oligonucleotide
conjugates are detected by measuring the fluorescence emission from
the dye labeled polynucleotides. To perform such detection, the labeled
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polynucleotides are illuminated by standard means, e.g. high intensity
mercury vapor lamps, lasers, or the like. Preferably the illumination
means is a laser having an illumination beam at a wavelength between
488 and 550 nm. More preferably, the dye-polynucleotides are
illuminated by laser light generated by an argon ion laser,
particularly the 488 and 514 nm emission lines of an argon ion laser,
or an the 532 emission line of a neodymium solid-state YAG laser.
Several argon ion lasers are available commercially which lase
simultaneously at these lines, e.g. Cyonics, Ltd. (Sunnyvale, Calif.)
10, Model 2001, or the like. The fluorescence is then detected by a light-
sensitive detector, e.g., a photomultiplier tube, a charged coupled
device, or the like.
IV. Kits Incorporating The Energy Transfer Dyes
The present invention also relates to kits having combinations of
energy transfer fluorescent dyes and/or reagents. In one embodiment,
the kit includes at least two spectrally resolvable energy transfer dyes
according to the present invention. In this kit, the energy transfer dyes
preferably include the same donor dye so that a single light source is
needed to excite the dyes.
In another embodiment, the kit includes dideoxycytosine
triphosphate, dideoxyadenosine triphosphate, dideoxyguanosine
triphosphate, and dideoxythymidine triphosphate, each
dideoxynucleotide triphosphate labeled with an energy transfer dye
according to the present invention. In one embodiment, each energy
transfer dye is spectrally resolvable from the other energy transfer dyes
attached to the other dideoxynucleotide triphosphates. In this kit, the
energy transfer dyes preferably include the same first xanthene dye.
In yet another embodiment, the kit includes at least two
oligonucleotides, each oligonucleotide including an energy transfer dye
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according to the present invention. In one embodiment, each
oligonucleotide contains an energy transfer dye which is spectrally
resolvable from the energy transfer dyes attached to the other
oligonucleotides. In another embodiment, the kit includes at least four
oligonucleotides which each contain a spectrally resolvable energy
transfer dye.
The energy transfer fluorescent dyes and their use in DNA
sequencing is illustrated by the following examples. Further objectives
and advantages other than those set forth above will become apparent
from the examples.
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Examples
1. Synthesis of 5TMR-B-CF
()q3g2N O N(CH,3)2
'C02H
HN
NH
0
HO JC02~H
C02H
5TMR-B-CF was synthesized from 5-TMR NHS and
4'-aminomethyl-5-carboxyfluorescein according to the reaction
sequences described in Examples 1A-C. 5TMR-B-CF was then
converted to 5TMR-B-CF-NHS according to the reaction sequence
described in 1 D so that the dye could be coupled to a nucleoside,
nucleotide or oligonucleotide primer.
A. Synthesis of 5-TMR-6
+ (H3C)2N 0 N(CHJ2
(H3C)2N 0 N(CH3)2
NH2 COZH
C02H ..._~. 1
0 C02H 0 NH
O N
O
C02H
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A mixture of 4-aminomethylbenzoic acid (3 mg, 19 mol), 5-TMR
NHS (5 mg, 9 mol) and triethylamine (20 L) was suspended in
dimethylformamide (DMF, 200 L) in a 1.5-mL eppendorf*tube. The
mixture was heated to 60 C for 10 minutes. Reaction progress was
monitored by thin layer chromatography (TLC) on silica gel with elution
with a 400/30/10 mixture of dichloromethane, methanol and acetic acid.
The insoluble 4-aminomethylbenzoic acid was separated by
centrifugation and the DMF solution was decanted into 5% HCI (1 mL).
The insoluble 5TMR-B was separated by centrifugation, washed with
5% HCl (2x1 mL) and dried in a vacuum centrifuge. The product was
dissolved in DMF (200 L) and used to prepare 5TMR-B-NHS.
B. Synthesis of 5-TMR-B-NHS
(H3C)2N O N(CH3)2 (H3C)2N O N(CH
CO2F-i Ca2H
O O O
O NH + O O NH
O O O
CO2H 0 0-N
O
A solution of 5TMR-B in DMF (125 L), diisopropylethylamine
(10 L) and disuccinimidylcarbonate (10 mg) was combined in a 1.5-mL
eppendorf tube and heated to 60 C. The reaction progress was
monitored by TLC on silica gel with elution with a 600/60/16 mixture of
dichloromethane, methanol and acetic acid. After five minutes, the
reaction appeared to be complete. The solution was diluted into
methylene chloride (3 mL) and washed with 250 mM
carbonate/bicarbonate buffer (pH 9, 4x1 mL), dried (NaSO4) and
concentrated to dryness on a vacuum centrifuge. The solid was
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dissolved in DMF (100uL). The yield was determined by diluting an
aliquot into pH 9 buffer and measuring the absorbance at 552 nm.
Using an extinction coefficient of 50,000 cm" W, the concentration of
5TMR-B-NHS was 4.8 mM. Yield from 5TMR NHS was 8%.
C. Synthesis of 5TMR-B-CF
+ NH2 +
(H3C)2N - ' 0 _ N(CH2)2 HO O O (H3C)2N , I O - N(CH3)2
C02H C02H C02H
O NH C02H _i HN
+
O NH
' .
O
O-N HO O O
C02H
C02H
A solution of 5TMR-B-NHS (1,umol in 250 4L DMF) was
combined with a solution of 4'-aminomethyl-5-carboxyfluorescein (CF,
2.2 mol in 100 /2L DMSO) and triethylamine (20 uL) in a 1.5-mL
eppendorf tube. The reaction was monitored by HPLC using a C8
reverse-phase column with a gradient elution of 15% to 35% acetonitrile
vs. 0.1 M triethylammonium acetate. HPLC analysis indicated the
5TMR-B-NHS was consumed, leaving the excess, unreacted CF. The
reaction was diluted with 5% HCI (1mL) and the product separated by
centrifugation, leaving the unreacted CF in the aqueous phase. The
solid was washed with 5% HCI (4x1 mL), dried in a vacuum centrifuge
and taken up in DMF (300 /L). The yield was quantitative.
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D. Synthesis of 5-TMR-B-CF-NHS
+ (H3C)27V 0 N(CH3)2
(H3C)2N p N(CH3)2
CO2H
CO2H
HN HN 0
O lTl C'N NH(CH NH
O. 0
NH + Cl- HO V"'O.
HD ~ O O O I t~ 2-1
~ ' CO2H HO=N1 O
C~H O
A solution of 5TMR-B-CF (0.6 mol in 100,uL DMF), 1-(3-
dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride (DEC, 2 mg)
and N-hydroxysuccinimide (4 mg) were combined in a 1.5-mL eppendorf
tube. The mixture was sonicated briefly and heated to 60 C. The
reaction was monitored by TLC on silica gel with elution with a
600/60/16 mixture of dichloromethane, methanol and acetic acid. The
reaction was complete in 30 minutes and diluted with 5% HCI. The
product was separated by centrifugation and dried in a vacuum
centrifuge. The activated dye was dissolved in DMF (201 L).
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CA 02297589 2000-02-03
2. Synthesis of 5ROX-CF
NH2 YO VO HO O 0 / CO-
~l
-O NH
CO2H
HO O O
0
C02H
COZH
15.
A solution of 5ROX NHS (2 Amol in 100 /1L DMSO) was mixed
with CF (2,umol in 100 ,uL DMSO) and triethylamine (10 /.4L). The
reaction was followed by HPLC on a C8 reverse phase column using a
gradient elution of 20% to 40% acetonitrile vs. 0.1 M TEAA. The
reaction was diluted into 5% HCI (1 ml-) and the product collected by
centrifugation, washed with 5% HCI (1x1 ml-) and dried in a vacuum
centrifuge. The product was taken up in DMF (200 ML).
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CA 02297589 2000-02-03
3. Synthesis of Cy5-CF
S4r
SO? NHZ ' N+ N
`I N~. HO O O
O + COZY-I
NH
O,N ~ I
p COZH HO 1 0 0
CC2H
I
CO2H
A solution of CF (0.4,umol in 20 /2L CMSO) and triethylamine (2
4L) was added to monoCy5 NHS (approximately 0.3 j. mol). The
reaction was followed by HPLC on a C8 reverse phase column using a
gradient elution of 10% to 30% acetonitrile vs. 0.1 M TEAA. The
reaction was diluted into 5% HCI (1 ml-) and the product collected by
centrifugation, washed with 5% HCI (1x1 ml-) and dried in a vacuum
centrifuge. The product was taken up in DMF (100 ,4L).
4. Comparison Of Fluorescence Strength of Energy Transfer Dyes
The following example compares the fluorescence emission
strength of a series of energy transfer dyes according to the present
invention. Dye solutions of 5TMR, 6TMR-CF, 5TMR-gly-CF, 5TMR-CF,
5TMR-B-CF, 5TMR-gly-5AMF, 5TMR-5AMF and 5TMR-lys-5FAM were
measured in 1xTBE/8M urea. Each dye solution had an optical density
of 0.1 at 560 nm and was excited at 488 nm.
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CA 02297589 2000-02-03
TABLE 7
cK,cs,r+ o rv~-, cK,cz,+~ fco-o C:~M c~++
0
STMR O O O
I r++
o
cam ON
6TMR-CF
CGr4
07H
STMR-96-CF
0 *CH h
O 1UC~h C0,01
COIN
0 mm
0 O
0 0
C,OjM
CORM
STM14Cf corm
5T1-&
a ty ~,yar+ 0 mtct . 0 Nl h
ayc.'}iN
COQ COIN C02H
HN 0 HN O
O 1
NH I O MF1
HO=C o-+
I o I I
ca + O ~~ I 0
0 0 5WR-SAME
BAR-lys-SEAM
5TMR-91y-SAMF
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CA 02297589 2000-02-03
The structures of each of these dyes is illustrated in Table 7.
Figure 2 provides a bar graph of the relative fluorescence of each of
these dyes.
As can be seen from Figure 2, energy transfer dyes where the
linker is attached to the acceptor at the 5 ring position (5TMR-CF and 5-
TMR-B-CF were found to exhibit significantly stronger fluorescence than
the acceptor dye itself or when the acceptor dye is linked at the 6 ring
position (6TMR-CF). As also can be seen from Figure 2, energy transfer
dyes where the linker has the formula R,XC(O)R2 where R2 is benzene
(5TMR-B-CF) were found to have significantly enhanced fluorescence
as compared to the dye where the linker has the formula -CH2NHCO-
(5TMR-CF) or -CH2NHCOCH2NHCO- (5TMR-gly-5AMF).
As can also be seen from Figure 2, energy transfer dyes where
the linker is attached to both the donor and acceptor at the 5 ring
position (5TMR-5AMF and 5TMR-gly-5AMF) were found to have
significant fluorescence. Interestingly, the use of a lysine linker was
found not to result in appreciable energy transfer between the donor and
acceptor.
5. Dye Primer Sequencing Using Energy Transfer Dye
In this example, dye primer sequencing was performed on M13
(SEQ. ID. NO.: 1) in order to compare the relative brightness of 5TMR-
CF and 5TMR-B-CF labeled oligonucelotides. In this example, dye
primer sequencing was performed according to the ABI PR/SMTM 377
DNA Sequencer User's Manual, Rev. B, January 1995, Chapter 2 (p/n
402114, The Perkin-Elmer Corporation, Foster City, CA). 5TMR-CF and
5TMR-B-CF were each attached to the 5' end of M13-21 primer (SEQ.
ID. NO.:2). Equimolar solutions of each primer were mixed with the M13
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CA 02297589 2000-02-03
(SEQ. ID. NO.: 1) and sequenced with a single dideoxy nucleotide
mixture (ddA/dNTP) and Taq FS. A plot of the resulting mixture of
oligonucleotides that were detected using 5TMR-CF and 5TMR-B-CF
labeled primers is presented in Figure 7. As can be seen from Figure 7,
oligonucleotides labeled with 5TMR-B-CF are brighter than
oligonucleotides labeled with 5TMR-CF. As can also be seen from
Figure 7, the mobility of oligonucleotides labeled with 5TMR-B-CF are
about one nucleotide slower than the oligonucleotides labeled with
5TMR-CF.
10-
6. Dye Primer Sequencing Using Four Dyes
Dye primer sequencing was performed on the M13 (SEQ. ID.
NO.: 1) using a set of four dyes attached to the M13-21 primer (SEQ. ID.
NO. 2) as described in Example 5. Figure 8 is a four color plot of the
dye labeled oligonucleotides produced from the sequencing. The peak
for cytosine corresponds to the fluorescence of 5-carboxy-R110. The
peak for adenosine corresponds to the fluorescence of 5-carboxy-R6G.
The peak for guanosine corresponds to the fluorescence of TMR-B-CF.
The peak for thymidine corresponds to the fluorescence of ROX-CF.
As can be seen from Figure 8, each of the dye labeled
oligonucleotides exhibit significant fluorescence intensity. In addition,
the different dye labeled oligonucleotides exhibit sufficiently similar
mobility so that good resolution of the series of peaks is achieved.
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CA 02297589 2000-02-03
7. Synthesis of 6-CFB-DTMR-2-NHS
.N 0 N-
CI CO2H
CI
HN 0
o 1
ITI
NH
6-CFB-DTMR-2-NHS
0
C
02H
HO %0--,C
O
No
6-CFB-DTMR-2 was synthesized from DTMR-2 and 6-CFB
according to the reaction sequences described in Examples 1A-B. 6-
CFB-DTMR-2 was then converted to 6-CFB-DTMR-2-NHS according to
the reaction sequence described in 1 C so that the dye could be coupled
to a nucleoside, nucleotide or oligonucleotide primer.
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CA 02297589 2000-02-03
A. Synthesis of DTMR-2-NHS
* 1 I
N\ 0 N-- 0 I N~
/ N HO
11
CI I COZH C O~N r CI I CO2H
N //
DTMR-2
/ CI + CI
H 0 -N 0 0 DTMR-2-NHS
OWN Ir O
A solution of DTMR-2 in DMF, N-hydroxysuccinimide and 1-(3-
dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride were combined
in an eppendorf tube and heated to 60 C. The reaction progress was
monitored by TLC on silica gel. After the reaction appeared to be
complete, the solution was diluted into methylene chloride and washed
with 250 mM carbonate/bicarbonate buffer (pH 9, 4x1 mL), and then
with an HCI solution (5%, 1x1 mL), dried (Na2SO4) and concentrated to
dryness on a vacuum centrifuge.
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B. Synthesis of 6-CF-B-DTMR-2
NH2
CI C02H NH CIY C02H
HO 0 / 0
cl CI
0 0 HN 0
C02H
CO2H
DTMR-2-NHS NH
6-CF-B 6-CF-B-DTMR-2
HO 0 / O
C02H
CO2H
A solution of 6-CFB in dimethylsulfoxide (100 pL, 11 mM) was
combined with a solution of DTMR-2 succidimidyl ester in
dimethylformamide (100 pL, 22 mM) and triethylamine (20 pL). The
reaction was added to a solution of hydrochloric acid (5%, 1 ml-) and the
solid separated by centrifugation. The red solid was dissolved in
carbonate/bicarbonate buffer (250 mM, pH 9, 100 pL) and reprecipitated
with dilute HCI.. The solid was dried in a vacuum centrifuge and
dissolved in dimethylformamide (200 pL). The concentration of the dye
solution was determined by diluting an aliquot into 40% acetonitrile / 0.1
M triethylammonium acetate buffer (pH 7). Assuming an extinction
coefficient of 80,000 cm-'m-' for fluorescein, the 6-CF-B-DTMR-2
solution was found to be 4mM (70% yield).
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CA 02297589 2000-02-03
C. Synthesis of 6-CF-B-DTMR-NHS
N TH" C CO2H NH
6-CF-B-DTMR-2 CI H p _N HO
NH NH
H 0 H p 6-CFB-OTMR-NHS
COIN COZH
COZH
0_~~ 0
A solution of 6-CF-B-DTMR-2 in dimethylformamide (200 pL, 4
mM) was added N-hydroxysuccinimide (10 mg) and 1-(3-
dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride (5 pg).
Additional N-hydroxysuccinimide (10 mg) was added. The reaction
progress was monitored by thin-layer chromatography on silica gel with
elution with dichloromethane : methanol : acetic acid in a 600:60:16
mixture. When the reaction was complete, dilute HCI (5%, 1 mL) was
added and the product separated by centrifugation. The solid was dried
in a vacuum centrifuge and dissolved in dimethylformamide (100 pL).
The concentration of the dye solution was determined by diluting an
aliquot into 40% acetonitrile / 0.1 M triethylammonium acetate buffer (pH
7). Assuming an extinction coefficient of 80,000 cm-'m-1 for fluorescein,
the 6-CF-B-DTMR-NHS solution was found to be 5.4 mM (68% yield).
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CA 02297589 2000-02-03
8. Comparison Of Fluorescence Strength of Dyes
The following example compares the fluorescence emission
strength of a series of energy transfer dyes according to the present
invention to the corresponding acceptor dye. According to this example,
each dye was attached to a 21 primer sequence
(5'-TGTAAAACGACGGCCAGT) (SEQ. ID. NO.: 1) with an aminohexyl
linkage at the 5' end. The oligonucleotides were quantitated based on
the absorbance at 260 nm, assuming an extinction coefficient of
180,000 cm-' M-1. Spectra were obtained at a primer concentration of
0.4 pM in 8M urea, 1X Tris/Borate/EDTA (TBE) buffer with 488nm
excitation. Figure 9A provides the overlaid spectra of 5-CFB-DR110-2
and DR110-2. Figure 9B provides the overlaid spectra of 5-CFB-DR6G-
2 and DREG-2. Figure 9C provides the overlaid spectra of 6-CFB-
DTMR-2 and DTMR-2. Figure 9D provides the overlaid spectra of 6-
CFB-DROX-2 and DROX-2.
The structures of each of these dyes is illustrated in Table 1. As
can be seen from Figures 9A-D, energy transfer dyes were found to
exhibit significantly stronger fluorescence than the acceptor dye itself.
Figure 10 shows the normalized fluorescence emission spectra of
four dye-labeled oligonucleotides. Spectra were obtained at a primer
concentration of 0.4 pM in 8M urea, 1X Tris/Borate/EDTA (TBE) buffer
with 488nm excitation. The dyes shown in Figure 10 include 5-CFB-
DR110-2, 5-CFB-DR6G-2, 6-CFB-DTMR-2, and 6-CFB-DROX-2. As
can be seen from Figure 10, all four energy transfer dyes are well
resolved relative to each other.
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CA 02297589 2000-02-03
g. Dye Primer Sequencing Using Energy Transfer Dye
In this example, dye primer sequencing was performed on M13
(SEQ. ID. NO.:1) using 5-CF-TMR-2, 5-CF-B-TMR-2, 6-CF-B-DTMR-2 and
DTMR-2 labeled primers. In this example, dye primer sequencing was performed
according to the ABI PR/SMTM' 377 DNA Sequencer User's Manual, Rev. B,
January 1995, Chapter 2(p/n 402114, The Perkin-Elmer Corporation, Foster City,
CA). The dye was attached to the 5' end of M13-21 primer (SEQ. ID. NO.:2).
Equimolar solutions of each primer were mixed with the M13 (SEQ. ID. N0.:1)
and
sequenced with a single dideoxy nucleotide mixture (ddA/dNTP) and Taq FS.
Plots of the resulting mixtures of oligonucleotides that were detected using 5-
CF-
TMR-2 and 5-CF-B-TMR-2 labeled primers are presented in Figure 11. As can be
seen from this figure, 5-CF-B-TMR-2 provides a significantly stronger signal
than
5-CF-TMR-2, showing the fluorescence enhancement provided by the linker used
in 5-CF-B-TMR-2.
Plots of the resulting mixtures of oligonucleotides that were detected
using 6-CF-B-DTMR-2 and DTMR-2 labeled primers are presented in Figure 12.
As can be seen from this figure, 6-CF-B-DTMR-2 provides a significantly
stronger
signal than DTMR-2, showing the fluorescence enhancement provided by the
energy transfer dye.
10. Dye Primer Sequencing Using Four Dyes --
Dye primer sequencing was performed on the M13 (SEQ. ID. NO.:1)
using a set of four dyes attached to the M13-21 primer (SEQ. ID. NO.:2) as
described in Example 5. Figure 13 is a four color plot of the dye labeled
oligonucleotides produced from the sequencing. The peak for cytosine
corresponds to the fluorescence of 5-CFB-DR110-2. The peak for adenosine
corresponds to the fluorescence of 6-CFB-DR6g-2. The peak for guanosine
corresponds to the fluorescence of 5-CFB-
93 -

CA 02297589 2000-02-03
DTMR-2. The peak for thymidine corresponds to the fluorescence of 5-
CFB-DROX-2.
As can be seen from Figure 13, each of the dye labeled
oligonucleotides exhibit significant fluorescence intensity. In addition,
the different dye labeled oligonucleotides exhibit sufficiently similar
mobility so that good resolution of the series of peaks is achieved.
The foregoing description of preferred embodiments of the
invention has been presented for purposes of illustration and
description. It is not intended to be exhaustive or to limit the invention to
the precise forms disclosed. Obviously, many modifications and
variations will be apparent to practitioners skilled in this art and are
intended to fall within the scope of the invention.
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CA 02297589 2000-02-03
SEQUENCE LISTING
(1) GENERAL INFORMATION:
(i) APPLICANT: Perkin-Elmer Corporation,
Applied Biosystems Division
(ii) TITLE OF INVENTION: ENERGY TRANSFER DYES
WITH ENHANCED FLUORESCENCE
(iii) NUMBER OF SEQUENCES: 2
(iv) CORRESPONDENCE ADDRESS:
(A) ADDRESSEE: David J. Weitz, Wilson
Sonsini Goodrich & Rosati
(B) STREET: 650 Page Mill Road
(C) CITY: Palo Alto
(D) STATE: California
(E) COUNTRY: USA
(F) ZIP: 94304-1050
(v) COMPUTER READABLE FORM:
(A) MEDIUM TYPE: 3.5 inch diskette
(B) COMPUTER: IBM compatible
(C) OPERATING SYSTEM: Microsoft Windows
3.1/DOS 5.0
(D) SOFTWARE: Wordperfect for windows 6.0,
ASCII (DOS) TEXT format
(vi) CURRENT APPLICATION DATA:
(A) APPLICATION NUMBER:
(B) FILING DATE:
(C) CLASSIFICATION:
-95-

CA 02297589 2000-02-03
(vii) PRIOR APPLICATION DATA:
(A) APPLICATION NUMBER: 08/642,330
(B) FILING DATE: May 3, 1996
(vii) PRIOR APPLICATION DATA:
(A) APPLICATION NUMBER: 08/672,196
(B) FILING DATE: June 27, 1996
(viii) ATTORNEY/AGENT INFORMATION:
(A) NAME: David J. Weitz
(B) REGISTRATION NUMBER: 38,362
(C) REFERENCE/DOCKET NUMBER: PELM4304.
(ix) TELECOMMUNICATION INFORMATION:
(A) TELEPHONE: (415) 493-9300
(B) TELEFAX: (415) 493-6811
(2) INFORMATION FOR SEQ ID NO: 1:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 1217 nucleotides
(B) TYPE: nucleic acid
(C) STRANDEDNESS: single
(D) TOPOLOGY: linear
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 1:
GCCAAGCTTG CATGCCTGCA GGTCGACTCT AGAGGATCCC 40
CGGGTACCGA GCTCGAATTC GTAATCATGG TCATAGCTGT 80
TTCCTGTGTG AAATTGTTAT CCGCTCACAA TTCCACACAA 120
CATACGAGCC GGAAGCATAA AGTGTAAAGC CTGGGGTGCC 160
TAATGAGTGA GCTAACTCAC ATTAATTGCG TTGCGCTCAC 200
-96-

CA 02297589 2004-11-19
CA 02203494 1997-04-23
TGCCCGCTTT CCAGTCGGGA AACCTGTCGT GCCAGCTGCA 240
TTAATGAATC GGCCAACGCG CGGGGAGAGG CGGTTTGCGT 280
ATTGGGCGCC AGGGTGGTTT TTCTTTTCAC CAGTGAGACG 320
GGCAACAGCT GATTGCCCTT CACCGCCTGG CCCTGAGAGA 360
GTTGCAGCAA GCGGTCCACG CTGGTTTGCC CCAGCAGGCG 400
AAAATCCTGT TTGATGGTGG TTCCGAAATC GGCAAAATCC 440
CTTATAAATC AAAAGAATAG CCCGAGATAG GGTTGAGTGT 480
TGTTCCAGTT TGGAACAAGA GTCCACTATT AAAGAACGTG 520
GACTCCAACG TCAAAGGGCG AAAAACCGTC TATCAGGGCG 560
10, ATGGCCCACT ACGTGAACCA TCACCCAAAT CAAGTTTTTT 600
GGGGTCGAGG TGCCGTAAAG CACTAAATCG GAACCCTAAA 640
GGGAGCCCCC GATTTAGAGC TTGACGGGGA AAGCCGGCGA 680
ACGTGGCGAG AAAGGAAGGG AAGAAAGCGA AAGGAGCGGG 720
CGCTAGGGCG CTGGCAAGTG TAGCGGTCAC GCTGCGCGTA 760
ACCACCACAC CCGCCGCGCT TAATGCGCCG CTACAGGGCG 800
CGTACTATGG TTGCTTTGAC GAGCACGTAT AACGTGCTTT 840
CCTCGTTGGA ATCAGAGCGG GAGCTAAACA GGAGGCCGAT 880
TAAAGGGATT TTAGACAGGA ACGGTACGCC AGAATCTTGA 920
GAAGTGTTTT TATAATCAGT GAGGCCACCG AGTAAAAGAG 960
TCTGTCCATC ACGCAAATTA ACCGTTGTAG CAATACTTCT 1000
TTGATTAGTA ATAACATCAC TTGCCTGAGT AGAAGAACTC 1040
AAACTATCGG CCTTGCTGGT AATATCCAGA ACAATATTAC 1080
CGCCAGCCAT TGCAACAGGA AAAACGCTCA TGGAAATACC 1120
TACATTTTGA CGCTCAATCG TCTGAAATGG ATTATTTACA 1160
TTGGCAGATT CACCAGTCAC ACGACCAGTA ATAAAAGGGA 1200
CATTCTGGCC AACAGAG 1217
(2) INFORMATION FOR SEQ ID NO: 2:
(i) SEQUENCE CHARACTERISTICS:
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CA 02297589 2000-02-03
(A) LENGTH: 18 nucleotides
(B) TYPE: nucleic acid
(C) STRANDEDNESS: single
(D) TOPOLOGY: linear
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 2:
TGTAAAACGA CGGCCAGT 18
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Dessin représentatif