Note: Descriptions are shown in the official language in which they were submitted.
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ELUTING REAGENTS, METHODS AND KITS FOR ISOLATING
DNA
Background of The Invention
Nucleic acids such as DNA, are used extensively in the field of molecular
biology for research and clinical analyses. Common methods for analyzing DNA
are
Southern blotting, amplification through methods such as polymerase chain
reaction (PCR),
and sequencing. Using these methods, differences in DNA sequence are
determined to aid in
gene identification, population screening, pathogen identification and
diagnostic testing. All
of these analyses require purified DNA samples as the basis for consistent and
valid results.
There are numerous nucleic acid purification methods that fall into two
general categories, liquid phase and solid phase purification. In liquid phase
purification, the
DNA remains in the liquid phase while impurities are removed by precipitation
and/or
centrifugation. In solid phase purification, the DNA is bound to a solid
support while
impurities are selectively eluted. Both purification strategies utilize
conventional methods,
which require many steps and often hazardous reagents, as well as more rapid
methods,
which require fewer steps and usually less hazardous reagents.
Using conventional liquid phase methods, DNA is most commonly isolated
using density gradient centrifugation, organic solvent extraction, or salt
precipitation.
Protocols describing these purification methods are given in Sambrook et al.,
Molecular
Cloning: A Laboratory Manual, 2nd ed., 7.19-7.25, 9.16-9.19, Cold Spring
Harbor Press,
Cold Spring Harbor, NY (1989) and Ausubel, et al., Current Protocols in
Molecular Biology,
4.4.2-4.4.4 (1987). Briefly stated, the liquid phase purification methods of
density gradient
centrifugation, phenol-chloroform extraction, and salt precipitation generally
require four
main steps: lysing the cells to release the DNA from cellular and nuclear
membranes;
removing impurities (such as proteins, lipids and carbohydrates);
concentrating by alcohol
precipitation; and then rehydrating the DNA in a hydration solution. The major
differences
among these three methods occur during the second step, where impurities are
removed from
the DNA by density differentiation, organic-aqueous phase partitioning, or
selective salt
precipitation.
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A conventional liquid phase purification method for purifying blood dried on
specimen collection cards (Guthrie cards) is described by McCabe et al., Human
Genetics,
75, 213-216 (1987). The method follows closely a procedure for liquid blood
described in
Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd ed., 9.16-9.19,
Cold Spring
Harbor Press, Cold Spring Harbor, NY (1989). In this phenol extraction method,
dried white
cells are removed from the collection paper by rehydrating with a saline
solution. The white
cells are incubated in a buffer to lyse the cells. Then, three phenol
extractions are performed
to remove protein impurities followed by three ether extractions to remove the
phenol. The
DNA is concentrated by sodium acetate-ethanol precipitation, washed with 70%
ethanol and
then rehydrated in a standard DNA hydration solution. Several reagents (ten),
two of which
are hazardous (phenol and ether), are typically required for this method.
Although these
conventional methods typically yield highly purified DNA preparations, they
are laborious
and hazardous.
As with liquid phase purification, conventional solid phase methods have been
developed to generate highly purified DNA. Generally these methods require
four general
steps: lysing cells to release DNA from cellular and nuclear membranes;
binding the released
DNA to a solid support; washing away impurities; and then eluting the purified
DNA. The
first two steps, lysing the cells and binding the released DNA, usually
require hazardous
reagents at high concentration.
For solid phase DNA purification, many solid supports have been used
including membrane filters, magnetic beads, metal oxides, and latex particles.
Probably the
most widely used solid supports are silica-based particles (see, e.g., U.S.
Pat. No. 5,234,809
(Boom et al.); International Publication No. WO 95/01359 (Colpan et al.); U.S.
Pat. No.
5,405,951 (Woodard); International Publication No. WO 95/02049 (Jones); WO
92/07863
(Qiagen GmbH). For example, the method disclosed in U.S. Pat. No. 5,234,809
(Boom et
al.) uses a high concentration chaotropic solution to bind DNA to silica
particles and requires
six centrifugation steps and five reagents to purify DNA from whole blood.
Disadvantages of
this method are the use of a particulate suspension, the use of many
centrifugation steps, and
the use of hazardous reagents, such as guanidinium isothiocyanate and acetone.
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One means for simplifying the conventional solid phase purification
procedures is to eliminate the elution step and use the DNA while it is bound
to a solid
support for subsequent analyses, such as amplification. Thus, by using
immobilized DNA,
usually at least one reagent and one step is omitted. For example, U.S. Pat.
No. 5,234,809
(Boom et al.) describes such a method for purifying DNA, although it is not
present in a
complex mixture such as blood. Using the method described above, but omitting
the elution
step, reduces the number of reagents and steps by one.
In another example, U.S. Pat. No. 5,496,562 (Burgoyne) describes a method of
purifying cellulose filter paper containing dried blood that uses four
reagents during four
phenol washes and five isopropanol washes. After drying, a small piece of the
filter paper is
cut from the square and used directly as a substrate for PCR amplification.
Despite the use of
bound DNA for analysis, these methods still require many steps and hazardous
reagents.
Recently, there has been a trend toward developing more rapid and simple
methods for both liquid and solid phase purification. This has been driven in
part by the
development of DNA amplification assays which reduce the time necessary for
analysis. As
the number of DNA-based assays has increased in the field, there is a need for
more rapid
means of processing the biological samples. Also, using simpler methods
reduces the risk of
sample cross-contamination by reducing the number of sample handling steps. In
addition,
the simpler the method, the more readily the process may be automated.
One rapid liquid phase method for DNA purification uses a chelating resin to
remove metal impurities from liquid blood or blood stains (Walsh et al.,
BioTechniques, 10,
506-513 (1991)). Using this method, blood cells are first washed with
deionized water and
then incubated with a suspension of the chelating resin and deionized water at
56 C for 15-30
minutes. This incubation is followed by vortexing, incubating at 100 C for 8
minutes,
vortexing again, and removing the impurities by centrifugation. This method is
rapid
(completed in 45-75 minutes) and simple (requires only two reagents).
Another simple and rapid method for liquid phase DNA purification is
described by Nordvag et al., BioTechniques, 12, 490-492 (1992). Starting with
whole human
blood, the blood cells are washed twice with a solution of 10 mM EDTA and 10
mM NaCl
and collected by microcentrifugation after each wash. Then the cells are
resuspended in 50
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mM Tris(hydroxymethyl)aminomethanehydrochloric acid (Tris-HCI) buffer (pH 8.0)
and
boiled for 3 minutes prior to PCR amplification. For this purification method,
only two
reagents are required, both of which are generally nonhazardous. Furthermore,
the method
requires only approximately 15 minutes.
An even simpler single reagent method is described by Carducci et al.,
BioTechnigues, 13, 735-737 (1992). Using this procedure, a 3 mm diameter blood
spot is
autoclaved for 3 minutes and then boiled for 5 minutes or sonicated for 10
minutes in a PCR-
compatible buffer (10 mM Tris-HCI pH 8.3, 50 mM KCI, 3 mM MgC12 and 0.001
gelatin).
The impurities remain bound to the disk following autoclaving while the DNA is
recovered in
the buffer.
All three of these liquid phase methods for DNA purification use low
concentrations, nonhazardous reagents, and simplified methods. However, these
three
methods (Walsh et al., Nordvag et al., and Carducci, et al.) could be
simplified further by
eliminating the use of resins (which must be uniformly suspended prior to
use), eliminating
the repetitive washing of cells, or eliminating the cumbersome autoclaving of
blood spots.
Rapid and simple methods for solid phase DNA purification have also been
developed. The procedure of Berlin et al., Human Mutation, 1, 260-261 (1992)
describes
washing dried blood spots successively with a nonionic detergent-containing
buffer. To elute
the DNA from the filter paper, each sample is incubated at 65 C for one hour
with another
nonionic detergent-containing buffer containing a proteinase K solution. A
final incubation
at greater than 95 C for 10 minutes is necessary to inactivate the proteinase
K. This method
reduces the number of reagents required to three, but has the disadvantages of
using an
enzyme, a long incubation time, and a high incubation temperature (i.e.,
greater than 95 C).
A rapid method using a membrane filter as a means of trapping DNA is
disclosed in U.S. Pat. No. 5,234,824 (Mullis). Typically, this method requires
a high
concentration lysing reagent to lyse cells present in whole blood. Then, the
lysate is applied
to a filter and washed successively with a second lysing reagent and then
either buffer or
water to further purify the DNA. The. DNA is eluted from the membrane by
boiling for 15
minutes in water or in a buffered reagent containing magnesium chloride.
Disadvantages of
this solid phase purification method include the absence of a chelating agent
in the
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purification and elution reagents, which can increase the probability of DNA
damage (e.g.,
due to nucleases). In addition, there is a requirement for a cumbersome high
temperature
incubation (i.e., about 100 C).
In another example, W.O. Pat. No. 96/18731 (Deggerdal) describes a method
5 of purifying DNA from cells by mixing the cells with a detergent and a solid
phase made up
of magnetic beads. In this method, cells may be pre-lysed by the detergent to
release the
DNA which is subsequently bound to the solid phase. Alternatively, detergent
may be added
to a suspension made up of the cells and the solid phase, or the cells,
detergent, and solid
phase may be suspended together to allow the detergent to lyse the cells in
the liquid phase
and subsequently bind the DNA to the solid phase. However, this method
involves multiple
steps of adding or removing the liquid phase (i.e., detergent or the cell
debris-detergent
suspension) from the solid phase.
A very simple method is presented by Makowski et al., Nucleic Acids
Research, 23, 3788-3789 (1995) in which 3 mm diameter disks punched from blood
samples
dried on cellulose collection paper are washed with deionized water (two 30
minute washes)
and used directly for PCR amplification. As discussed in the above analysis of
the `824
Patent, a major disadvantage of using -deionized water as a purification
reagent is that the
absence of a chelating agent increases the probability of DNA damage (e.g.,
due to
nucleases). In addition, the absence of a detergent reduces the efficiency
with which
impurities are solubilized.
Nucleic Acids may be detected and quantitated by several means. Commonly,
UV absorbance at a wavelength of 260 nm is used. A wavelength of 320 nm is
used to
determine background absorbance. Also, fluorimetry in the presence of Hoechst
33258 dye
(e.g., Hoefer; DyNA Quant Fluorimeter, Pharmacia Biotech, Piscataway, NJ),
antibody
detection strips (DNA Dipstick, Invitrogen, Carlsbad, CA), branched signal
amplification
(Chiron Corporation, Emeryville, CA), and quantitative PCR amplification
(e.g., Applied
Biosystems 7700, Perkin Elmer Applied Biosystems Division, Foster City, CA)
are used to
detect and quantitate nucleic acids.
As generally known and practiced, the purity of the DNA may be ascertained
by measuring the absorbance at various wavelengths. The presence of impurities
such as
* Trade-mark
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proteins, lipids, carbohydrates, cellular debris, etc. can increase the
measured absorbance. In
contrast, pure nucleic acids, especially DNA used in PCR amplification, have a
substantially
lower absorbance at established wavelengths.
Currently, there are numerous nucleic acid amplification systems available.
While the most commonly used amplification methods are Polymerase Chain
Reaction
(PCR), other target amplification technologies include Ligase Chain Reaction
(LCR), Nucleic
Acid Sequence Based Amplification (NASBA), Self-sustained Sequence Replication
(SSR or
3SR), Strand Displacement Amplification (SDA), and Transcription Mediated
Amplification
(TMA).
PCR is used routinely to amplify one or more targeted nucleic acid sequences
within a sample or mixture of nucleic acids. This process is disclosed in U.S.
Pat. No.
4,965,188 (Mullis). For each target nucleic acid sequence to be amplified in
this process,
separate complementary strands of nucleic acid are treated with two primers
selected to be
substantially complementary to portions of the target nucleic acid within the
two strands. A
thermostable enzyme (a polymerase) is generally used to extend the primers to
form
complementary primer extension products. When these are separated into their
complementary strands, they serve as templates to extend the complementary
primer into the
target nucleic acid sequence. When separated, these in turn act as templates
for synthesis of
additional nucleic acid sequences. The PCR amplification process involves a
series of simple
steps. These include temperature cycling to cause hybridization of primers and
templates,
polymerase mediated synthesis of the primer extension products, and separation
and
subsequent annealing of the strands of template strands and the synthesized
target nucleic
acid sequences. Thus, there is an exponential increase in the amount of
targeted nucleic acid
sequences synthesized. PCR amplification is a very sensitive process.
Therefore, a very high
purity of starting sample is necessary.
LCR is another diagnostic technique that is often utilized in conjunction with
a
primary PCR amplification. LCR employs a thermostable ligase and allows the
discrimination of DNA sequences differing in only a single base pair. LCR
depends on
highly pure NA templates due to its sensitivity.
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Purified nucleic acids can be further analyzed by Southern hybridization, or
Southern blotting as it is more commonly known. Southern blotting is the
capillary transfer
of DNA fragments from gels to various types of filter paper. It allows the
researcher to detect
rare sequences in a complex population of restriction fragments and is useful
in gene cloning,
reverse genetics, and the analysis of restriction-fragment-length-
polymorphisms (RFLP's) for
human genetic disease diagnosis. Southern blotting involves the digestion of
DNA with one
or more restriction enzymes, followed by a size separation by electrophoresis
on an agarose
gel. The DNA is then denatured in situ and transferred from the gel to a
membrane (e.g.,
nitrocellulose or nylon). The DNA attached to the membrane is then hybridized
to
radiolabelled DNA or RNA, and autoradiography is used to locate the positions
of bands
complementary to the probe. Southern blotting is highly sensitive. A sequence
of 1000 base
pairs (bp) that occurs only once in the mammalian genome (i.e., 1 part in 3
million) can be
detected in an overnight exposure if 10 gg of genomic DNA is transferred to
the filter and
hybridized to a probe several hundred nucleotides in length.
To advance the field of DNA sample preparation there is a need for solid
phase DNA purification strategies. There is also a need for reagents and
methods that are
adaptable to solid phase purification strategies are not only simple and rapid
but general in
scope to maximize adaptability for automation. There is a need for reagents
that are of
generally low concentration, stable at room temperature (i.e., 20-25 C), less
hazardous (i.e.,
less corrosive, flammable or toxic), nonparticulate to eliminate the need for
mixing, and
protective of DNA quality. There is also a need for methods with few steps
that can be
performed using a variety of biological starting materials, whether hydrated
or dried,
especially as applied to routine testing as found in clinical laboratories.
The reagents must
not inhibit subsequent DNA analysis procedures by interfering with the
buffering capacity of
PCR buffers, or cause degradation of polymerase, primers or oligonucleotides
used in DNA
amplification. There is also a need for methods with few steps that can be
performed using a
variety of biological starting materials, whether hydrated or dried,
especially as applied to
routine testing as found in clinical laboratories.
The reagents and methods used in the solid phase purification strategy must
also not interfere with standard methods for nucleic acid quantification,
restriction enzyme
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digestion, DNA sequencing, hybridization technologies, such as Southern
Blotting, etc., and
amplification methods such as Polymerase Chain Reaction (PCR), include Ligase
Chain
Reaction (LCR), Nucleic Acid Sequence Based Amplification (NASBA), Self-
sustained
Sequence Replication (SSR or 3SR), Strand Displacement Amplification (SDA),
and
Transcription Mediated Amplification (TMA), or other DNA analysis.
Summary of the Invention
The present invention provides reagents, methods, and kits that incorporate a
solid support for purifying, amplifying, and characterizing DNA from liquid
and dried
biological samples. The purified DNA is suitable for use in subsequent widely
used
techniques such as amplification and restriction enzyme digestion.
The reagents of the present invention generally contain low concentrations of
buffers, salts, acids, bases, chelating agents, and/or detergents so that they
are not
significantly inhibitory to subsequent DNA analyses. In conventional systems,
reagents
containing high concentrations of one or more of these components are
typically used for
DNA purification. By using these low concentration reagents, the number of
steps required
for DNA purification is reduced making the method more rapid and simple. These
reagents
are also generally less hazardous than those used for conventional DNA
purification. The
solid phase purification methods described typically require only two main
steps (e.g.,
washing and drying). If removal of DNA from a solid support (or solid support
matrix) is
required, another step (elution) is used.
A commercially available DNA purifying reagent is used in the present
invention to solubilize and/or rupture cell or protein coat membranes
facilitating the release
of DNA and/or to solubilize impurities facilitating their removal. The
composition of the
DNA purifying reagent should render it compatible with (i.e., not
significantly inhibitory to)
subsequent DNA analyses, such as PCR amplification. For example, the molarity
of the
DNA purifying reagent should be low.
A DNA eluting reagent may be used to remove purified DNA from a solid
support following solid phase purification. The DNA eluting reagent includes:
a buffer to
maintain the pH at least about 7 (preferably, at least about 8, more
preferably, at least about 9,
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and most preferably, at least about 10); a base to adjust the reagent pH; a
chelating agent; and
deionized and substantially nuclease-free water. The buffer preferably has a
pKa of at least
about 8. A preferred buffer is Tris. The base is preferably one that can raise
the pH of the
reagent to no less than 7. The base is preferably an alkaline metal hydroxide.
Such alkaline
metal hydroxides include sodium hydroxide, potassium hydroxide, and lithium
hydroxide.
The chelating agent is preferably ethylenediamine-tetraacetatic acid (EDTA) or
cyclohexanediamine-tetraacetatic acid (CDTA). However, any chelating agent
capable of
reducing nuclease activity is suitable for use. The combined amount of buffer,
base, and
chelating agent is of low concentration (typically, no greater than about 20
mM), rendering it
generally compatible with (i.e., not significantly inhibitory to) subsequent
DNA analyses,
such as PCR amplification or restriction enzyme digestion.
Suitable solid supports include cellulose, cellulose acetate, glass fiber,
nitrocellulose, nylon, polyester, polyethersulfone, polyolefm, polyvinylidene
fluoride, and
combinations thereof. A preferred solid support is composed of cellulose such
as that used
commonly for specimen collection.
Where tissues, cell membranes, cell walls or viral protein coats are resistant
to
lysis by desiccation or treatment with a DNA purifying reagent containing a
non-ionic
detergent, the solid support may be treated with a lysing reagent to assist in
lysis and
subsequent purification. In conventional methods, this lysing step is
performed typically
prior to contacting the biological material with the solid support. However,
by adding a
lysing reagent to the solid support, a step is eliminated and the method is
simplified.
Preferably, the lysing reagent is applied to the solid support and then dried
on the solid
support before contacting the biological material with the treated solid
support, although this
is not a necessary requirement.
The lysing reagent is used preferably for the purification of DNA and can be
composed of an amount of a detergent effective to lyse cells or protein coats
sufficiently to
release DNA; a chelating agent to reduce DNA damage; water; and optionally, a
buffer
effective to provide a pH of greater than about 2. The detergent is preferably
anionic.
Examples of anionic detergents include N-lauroyl sarcosine or a dodecylsulfate
salt. Sodium
dodecylsulfate is a particularly preferred anionic detergent. The buffer is
preferably effective
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to provide a pH of greater than about 6. Tris is a particularly preferred
buffer. The chelating
agent is preferably EDTA or CDTA.
Optionally, the lysing reagent can include an RNA digesting enzyme, such as
RNase A, for the purpose of degrading RNA present in the biological sample.
Including an
5 RNA digesting enzyme eliminates the need for a separate RNase digestion
step, as is typically
required in conventional methods.
This invention also provides methods for purifying DNA from biological
samples. The biological samples include, for example, cell or virus
suspensions, body fluids,
whole blood, bone marrow, buffy coat, plasma, cultured cells, all suspensions
(e.g., bacteria,
10 tissue homogenates) and environmental samples. The environmental samples
include, for
example, air, water or soil. For solid phase purification, the methods of the
present invention
involve contacting the biological sample with a solid support. A DNA purifying
reagent is
added to the solid support containing the biological sample to facilitate
solubilization of
impurities, lysis of cell walls, release of DNA from the cells and DNA binding
to the solid
support. Washing of the solid support with a DNA purifying reagent
(preferably, at least
twice) causes impurities to be removed from the solid support. The solid
support containing
the bound and purified DNA may be used directly in amplification or other
analyses.
Alternatively, the DNA may be removed using the DNA eluting reagent. To elute
DNA from
the solid support, the DNA eluting reagent is contacted with the solid
support, incubated, and
then removed.
Another aspect of this invention involves the combination of a DNA purifying
reagent and/or the DNA eluting reagent with one or more optional ancillary
reagents. The
first ancillary reagent, an RBC lysis reagent, is used to lyse red blood cells
and facilitate
subsequent purification of NAs from the white blood cells contained in
mammalian whole
blood. The second and third ancillary reagents, a cell suspension reagent and
lytic enzyme
reagent, are used together to digest cell walls in yeast and Gram-positive
bacteria prior to
DNA purification. The fourth ancillary reagent, a protein digesting reagent is
used to digest
contaminating proteins. A fifth ancillary reagent, an isotonic solution is
used to suspend
DNA and/or cells as needed.
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A further embodiment of the present invention is a method for purifying DNA
from yeast and Gram-positive bacteria. The method involves combining the
biological sample
with a cell suspension reagent. The cell suspension reagent includes a buffer,
a chelating agent,
and a cell suspending agent to form a cell suspension. To the cell suspension
is added a lytic
enzyme reagent. The lytic enzyme reagent includes an enzyme to digest cell
walls, a buffer, an
acid to adjust the pH of the reagent, and two stabilizing agents. The digested
cells may be used
for liquid or solid phase purification described above.
The present invention also provides kits for purifying DNA comprising
instruction means for preparing substantially pure DNA from a biological
sample and one or all
of the following: a DNA purifying reagent, a DNA eluting reagent, a lysing
reagent, an RBC
lysis reagent, a cell suspension reagent, a lytic enzyme reagent, an isotonic
solution or any
combination thereof. The kit can also include a solid support, either
untreated or treated with a
lysing reagent. In addition, the kit can include a vessel to contain the solid
support.
Substantially pure nucleic acids are those that are suitable for use in
subsequent analyses
known to those with skill in the art, for example, DNA amplification, reverse
transcription, and
restriction enzyme digestion.
In another aspect, the present invention provides a method for isolating DNA,
the
method comprising: (a) contacting a biological material that contains DNA with
a solid
support; (b) treating the biological material that contains DNA with a DNA
purifying reagent
which solubilizes impurities, lyses cell walls, releases DNA from the cells,
binds DNA to the
solid support, and/or removes impurities from the solid support; (c) purifying
the DNA from
the remainder of the biological material; and (d) eluting the DNA from the
solid support with
a DNA eluting reagent comprising incubating the support for at least 10
minutes at a
temperature of at least 60 C, wherein the DNA eluting reagent comprises: (i)
0.001 to 1 mM
Tris; (ii) 1 to 10 mM of a base; (iii) 0.0001 to 0.1 mM of a chelating agent;
and (iv) water,
wherein all amounts are based on the total volume of the DNA eluting reagent.
Detailed Description of the Invention
The present invention provides reagents, methods and kits for incorporating a
solid support purifying, amplifying, and characterizing DNA from biological
samples. Such
biological samples include biological material, typically in an aqueous
mixture or dried, that
contains nucleic with (NAs) like DNA, including complex biological mixtures of
prokaryotic
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lla
or eukaryotic cells. Typically, the biological material also contains
carbohydrates, proteins, and
lipids. Biological materials include the following: body fluids such as whole
blood, bone
marrow, blood spots, blood serum, blood plasma, bully coat preparations,
saliva and
cerebrospinal fluid, buccal swabs, cultured cells, cell suspensions of
bacteria or tissue
homogenates, solid animal tissues such as heart, liver and brain, body waste
products, such as
feces and urine, environmental samples taken from air, water, sediment or
soil, plant tissues,
yeasts, bacteria, viruses, mycoplasmas, fungi, protozoa, rickettsia, and other
small microbial
cells. Lysates or homogenates of these biological materials may also be used.
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Preferably, the reagents, methods and kits incorporating a solid support of
the
present invention provide substantially pure DNA in any form. The DNA may be
composed
of, for example, chromosomal or genomic DNA, extrachromosomal DNA (such as
mitochondrial and plasmid DNA), single stranded DNA, and viral DNA.
Using these reagents, methods, and kits incorporating a solid support, DNA of
substantially high purity can be obtained. The purity of the DNA is determined
by the
substantial reduction of impurities, such as proteins, that could interfere
with subsequent
analyses, such as the sensitive RT-PCR and/or PCR assays. As used herein,
"pure" means
substantially free of carbohydrate, protein, and lipid impurities, such that
the purified DNA
can be used in subsequent analyses known to those with skill in the art. Thus,
the isolated
and purified DNA obtained according to the present invention is suitable for
use in
subsequent analyses. Preferably, the methods and kits of the present invention
purify a wide
range of DNA, all of which can be recovered over a wide molecular weight
range.
This invention describes methods for using a low concentration reagent for
purification of DNA. These methods are generally more rapid and simple than
those used
typically for DNA purification. The purified DNA obtained from these
purification steps can
be-evaluated for purity, yield, size, amplification ability, etc.
The biological samples include, for example, cell or virus suspensions, body
fluids, and tissue homogenates. If the biological sample consists of cells or
viruses, the cells
or viruses may be enumerated prior to this step. The enumeration may be
conducted using
standard cell counting methods such as an electronic cell counter (e.g., CBC5
Coulter
Counter, Coulter Corp., Hialeah, FL) or a visual counter (e.g., a
hemacytometer, Bright Line,
American Optical, Buffalo, NY).
The process for solid phase DNA purification consists of applying a biological
sample to a solid support which may be treated with a lysing reagent. Contact
with the solid
support causes the cell and nuclear membranes to solubilize and/or rupture,
thereby releasing
the DNA which then binds to the solid support. The solid support may be heated
to facilitate
solubilization and rupture of the cell and nuclear membranes. The released DNA
binds to the
solid support allowing impurities to be removed by the addition of a first
reagent. This first
reagent may be a commercially available purifying reagent for DNA. Impurities
are
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solubilized in the first reagent and are removed by suitable means such as
centrifugation,
pipetting, pressure, or vacuum leaving DNA is left bound to the solid support.
Thus, the
process uses only one reagent and two main steps (i.e., washing and the
removal of excess
aqueous solution). If DNA is removed from the solid support, an additional
reagent, a DNA
eluting reagent, is added and another step (eluting) is carried out.
For solid phase DNA purification, it may be necessary to remove the purified
DNA from the solid support prior to analysis. The present invention also
includes a low
concentration DNA elution reagent for eluting DNA from a solid support. The
composition
of the low concentration DNA elution reagent may vary, but the total
concentration is
typically less than 20 mM for all compositions.
The low concentration DNA elution reagent, herein referred to as the "DNA
Eluting Reagent," is capable of removing DNA from a solid support. It contains
a base, a
buffer, a chelating agent, and water in combination to maintain a pH of at
least about 7,
preferably, at least about 8, more preferably, at least about 9, and most
preferably, at least
about 10.
The DNA Eluting Reagent contains a buffer to maintain the pH at least about
7 and preferably has a pKa of at least about 8. Suitable buffers include, but
are not limited to,
N,N-bis[2-hydroxyethyl]glycine (available under the trade designation "BICINE"
from Sigma
Chemical Company, St. Louis, MO), 3-[cyclohexylamino]-2-hydroxy-l-
propanesulfonic acid
(available under the trade designation "CAPSO" from Sigma Chemical Company),
and Tris.
The buffer is used in an amount that is not significantly inhibitory to
subsequent DNA
analyses, such as PCR amplification. Thus, it is typically used in an amount
of no greater
than about 20 mM. Preferably, the buffer is Tris and is used in an amount of
about 0.001-20
mM, more preferably, about 0.01-15 mM and most preferably, about 1-10 mM,
based on the
total volume of the reagent.
In addition to the buffer, the DNA Eluting Reagent contains a base to adjust
the reagent pH. The base is used in an amount that is not significantly
inhibitory to
subsequent DNA analyses, such as PCR amplification. Thus, the base is
typically used in an
amount of no greater than about 20 mM. Such bases include, but are not limited
to,
potassium hydroxide and sodium hydroxide. Preferably, the base is an alkaline
metal
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WO 99/39010 PCT/US99/02190
14
hydroxide like sodium hydroxide, potassium hydroxide, or lithium hydroxide and
is used in
an amount of about 0.2-20 mM, more preferably, about 0.5-15 mM, and most
preferably,
about 1-5 mM, based on the total volume of the reagent.
In addition to a buffer and a base, the DNA Eluting Reagent includes a
chelating agent. A chelating agent is used in an amount effective to reduce
DNA damage
(e.g., by nuclease activity) during and following removal from the solid
support so that the
DNA is suitable for subsequent analyses. Suitable chelating agents are those
capable of
chelating divalent cations in aqueous media. Such chelating agents include,
but are not
limited to, ethylene diamine tetraacetate (EDTA) and cyclohexane diamine
tetraacetate
(CDTA). Preferably, the chelating agent is EDTA. In addition, the chelating
agent is used in
an amount that is not significantly inhibitory to subsequent DNA analyses,
such as PCR
amplification. Thus, it is typically used in an amount of no greater than
about 0.1 mM.
Preferably, the chelating agent is used in an amount of about 0.0001-0.1 mM,
more
preferably, about 0.005-0.05 mM, and most preferably, about 0.0015-0.015 mM,
based on the
total volume of the reagent.
The buffer, base and chelating agent are combined with water to form the
DNA Eluting Reagent. The water is preferably deionized and nuclease free. The
combined
amount of buffer, base, and chelating agent is of low concentration
(typically, no greater than
about 20 mM), rendering it generally compatible with (i.e., not significantly
inhibitory to)
subsequent DNA analyses, such as PCR amplification or restriction enzyme
digestion.
All the reagents used in purifying DNA from the source biological material
have been formulated to be compatible with amplification and other analyses.
The reagents
have low concentrations of buffer, salt, detergent, and chelating agents that
make them
compatible with amplification analyses. The final purified nucleic acids are
suspended in the
DNA Eluting Reagent for solid phase nucleic acid extractions. Therefore, these
reagents have
been optimized for use in downstream DNA analyses. Such DNA analyses might
include,
but are not limited to, RT-PCR and PCR.
Currently available PCR amplification reactions from 3 manufacturers, Perkin
Elmer, Promega, and Roche Molecular Biochemicals, are conducted in a 1 X
buffered
CA 02319691 2007-12-20
r,
solution that typically has the concentrations of Tris buffer, salt, and
nonionic detergent at a
basic pH between 8-10 as shown in Table 1.
TABLE 1
PERKIN ELMER PROMEGA ROCHE
MOLECULAR
BIOCHEMICALS
5 Tris (mM) 10 10 10
KC1(mM) 50 50 50
Triton X-100 (%) - 0.1 -
Gelatin (%) 0.001 - -
MgCl2 (mM) - 1.5 -1.5 -1.5
10 H 8.3 9.0 8.3
The lysing reagents and eluting reagents have Tris buffer concentrations that
are either of the same order of magnitude or significantly lower than the
concentrations found
in PCR systems. Concentrations of Tris buffer in the eluting reagent typically
range from 1-
15 10 mM and will not inhibit or significantly interfere with the
amplification process.
Another aspect of this invention involves the combination of the DNA
purifying reagent and/or the DNA Eluting Reagent with one or more optional
ancillary
reagents. These ancillary reagents include reagents known to one of skill in
the art for nucleic
acid purification. The methods and kits of the present invention, however, are
not limited to
the use of these specific ancillary reagents, as one of skill in the art may
use other reagents
and/or techniques to achieve the same purpose. Also, the DNA purifying reagent
and/or the
DNA Eluting Reagent can be used with other reagents and/or techniques if
desired.
The first ancillary reagent is a red blood cell lysing reagent used to lyse
red
blood cells and facilitate subsequent purification of DNA from the white blood
cells
contained in mammalian whole blood. This reagent is referred to herein as the
"RBC Lysis
Reagent" and contains ammonium chloride, sodium bicarbonate, and EDTA.
Preferably, the
ammonium chloride is used in the RBC Lysis Reagent at a concentration of about
140-150
mM, and more preferably, about 142-146 mM, based on the total volume of the
reagent.
* Trade-mark
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16
Preferably, the sodium bicarbonate is used at a concentration of about 0.5-5
mM, and more
preferably, about 0.5-2 mM, based on the total volume of the reagent.
Preferably, the EDTA
is used at a concentration of about 0.5-10 mM, and more preferably, about 0.75-
1.25, based
on the total volume of the reagent. RBC Lysis Reagent contains water,
preferably of the
purity described above. RBC Lysis Reagent is contacted with mammalian whole
blood in an
amount of 3 volumes of RBC Lysis Reagent to 1 volume of blood. The sample
incubates
about 1-30 minutes, preferably about 10 minutes, and white cells are separated
from the
sample by centrifuging at 15,000 for 20 seconds. All but about 1-3% of the
supernatant
fraction is discarded leaving the white cells available for DNA purification.
When combined with mammalian whole blood, the RBC Lysis Reagent forms
a red cell lysate containing substantially intact white blood cells. It can
also contain viruses
with substantially intact protein coats. The white blood cells (and any cell-
associated viruses
that may be present) are then separated from the red cell lysate. The white
blood cells can be
combined with a nucleic acid purifying reagent directly or following
application to a solid
support.
The second and third ancillary reagents are used together to digest cell walls
from yeast and Gram-positive bacteria prior to DNA purification. The reagents
are referred
to herein as "Cell Suspension Reagent" and "Lytic Enzyme Reagent." They are
used in the
first steps of the DNA purification procedure to digest cell walls that may be
resistant to lysis
by a nucleic acid purifying reagent. The Cell Suspension Reagent is combined
with a
biological sample to form a cell suspension. The Lytic Enzyme Reagent is
combined with the
cell suspension to form a mixture containing digested cells. These digested
cells are then
separated from the mixture by centrifugation, for example, and then contacted
with the
nucleic acid purifying reagent directly or following application to a solid
support.
The Cell Suspension Reagent keeps cells intact while their cell walls are
being
digested by lytic enzymes. This reagent contains a buffer, preferably Tris, to
maintain the
reagent pH at about 7-8.5, and more preferably, about 7.5-8Ø The buffer is
used preferably
at a concentration of about 0.05-0.15 M, and more preferably, about 0.08-0.12
M, based on
the total volume of the reagent. The Cell Suspension Reagent also contains a
chelating agent,
preferably EDTA, to reduce DNA damage. The chelating agent is used, preferably
at a
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17
concentration of about 0.05-0.15 M, and more preferably, at about 0.08-0.12 M,
based on the
total volume of the reagent. The preferred molar ratio of buffer to chelating
agent is about
1:1. This reagent also contains agents such as sorbitol, to keep cells intact
while their cell
walls are being digested. This agent is used preferably at a concentration of
about 0.8-1.0 M,
and more preferably, about 0.85-0.95 M, based on the total volume of the
reagent. The
buffer, chelating agent and cell suspending agent are combined with water. The
water is
preferably deionized and substantially nuclease-free.
The Lytic Enzyme Reagent contains a lytic enzyme that digests beta-1,3-
glucose polymers that are contained in yeast cell walls. A purified form of
this enzyme is
readily available from commercial sources, such as Sigma Chemical Company, St.
Louis,
MO. The activity of this enzyme is preferably at least about 200 units per mg,
more
preferably, at least about 1000 units per mg, and most preferably, at least
about 5,000 units
per mg. In addition to the enzyme, the Lytic Enzyme Reagent contains a buffer,
preferably
Tris, to maintain the reagent pH. Tris is used preferably at a concentration
of about 1-20 mM,
more preferably, about 5-15 mM, and most preferably, about 8-12 mM, based on
the total
volume of the reagent. The pH of the lytic enzyme reagent is adjusted to a pH
of about 7.5-
8.2 using an acid, such as hydrochloric acid. In addition, the Lytic Enzyme
Reagent contains
two stabilizing agents. The first is preferably glycerol. Glycerol is used
preferably in an
amount of about 20-50% glycerol (volume/volume), more preferably, about 24-40%
glycerol,
and most preferably, about 28-32% glycerol. The second stabilizing agent is
preferably
calcium chloride. Calcium chloride is used preferably at a concentration of
about 0.5-5 mM,
and more preferably, at about 0.75-1.25 mM, based on the total volume of the
reagent. The
enzyme, buffer, acid, and two stabilizing agents are combined with water. The
water is
preferably U. water. Preferably, the reagent is purified by passing through a
filter of about
0.2 /,iM pore size.
Typically, to digest cell walls of yeast, for example, with the second and
third
ancillary reagents, 300 Ail Cell Suspension Reagent are added to a 10-20 /.cl
suspension of
about 100 million yeast cells along with 1.5 Al Lytic Enzyme Reagent and
incubated at 37 C
for 30 minutes. After centrifuging at 15,000 x g for 1 minute, the supernatant
fraction is
removed leaving the digested cells available for DNA purification.
CA 02319691 2007-12-20
18
A fourth ancillary reagent, the protein digesting reagent, herein referred to
as
the "Protein Digesting Reagent," is used to digest contaminating protein,
especially in solid
tissue samples. A purified form of this enzyme, Proteinase K, is readily
available from
commercial sources such as Sigma Chemical Company and is used at a
concentration of
about 0.1 mg/mL. Heating at greater than 36 C accelerates the activity of this
enzyme.
A fifth ancillary reagent, an Isotonic Solution, is typically used to make
cell or
DNA suspensions. Suitable isotonic solutions are salt-based, often buffered
with tris, citrate
or phosphate. An example is phosphate buffered saline (PBS).
For solid phase purification, suitable solid supports include, but are not
limited
to, cellulose, cellulose acetate, glass fiber, nitrocellulose, nylon,
polyethersulfone, polyester,
polyolefin, polyvinylidene fluoride, and combinations thereof. A preferable
solid support is
composed of cellulose fibers such as found in the specimen collection paper
903 available
from Schleicher and Schuell (Keene, NH) or BFC 180 available from Whatman
International
Ltd. (Springfield Mill, Kent, England). Another preferable solid support is
polyolefin.
Polyolefin is herein defined as any olefin based copolymer or homopolymer
including
modified polymers such as graft copolymers. Acceptable polyolefins include
low, medium,
and high density polyolefins and linear, low density polyethylene,
polypropylene and
polybutylene. Preferably, the polyolefin solid support is hydrophilic and
composed of a
mixture of low density polyethylene and polypropylene fibers such as those
found in the
Filtrona polyolefin available from American Filtrona, Inc. (Richmond, VA).
Most
preferably, the solid support is directionally porous giving uniform flow
characteristics and
low back pressure, is composed of fibers that are interlaced and bonded to
each other, is
resilient to allow for easy packing into a spin tube, well, cartridge, or
another vessel, has a
void volume of about 50-90% and is composed of fibers having a diameter of
about 20-30
,um.
The size of the solid support suitable for use with the reagents of this
invention
may vary according to the volume of biological material. For example, when
Schleicher and
Schuell 903 paper, which has a thickness of 0.5 mm, is used for the solid
support, a 3 mm
diameter disk will hold about 3 l blood and an 8 mm diameter disk will hold
about 25 E.cl
* Trade-mark
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WO 99/39010 PCT/US99/02190
19
blood. As the volume of the biological material increases, the thickness
and/or diameter may
increase accordingly.
The shape of the solid support suitable for use with the reagents of this
invention may vary according to the type of biological material. For example,
when buccal,
nasopharyngeal, vaginal, urethral, and rectal samples are obtained, a swab is
an appropriate
collection device. When body fluids such as blood or saliva samples are
obtained, the solid
support may be, for example, a sheet, a precut disk or a cylinder. If
necessary, the solid
support is contained in an appropriate vessel, e.g., a paper form (such as a
Guthrie card), a
microcentrifuge tube, a spin tube, a 96-well plate, a chamber, or a cartridge.
The solid support may be treated with a lysing reagent to assist in lysis and
subsequent purification. Preferably, the volume of the lysing reagent used to
treat the solid
support is at least one-tenth of the total volume of the solid support. More
preferably, the
volume of the lysing reagent is at least half the total volume of the solid
support, and most
preferably, the volume of the lysing reagent corresponds to the total volume
of the solid
support. The total volume of the solid support refers to the volume defined by
the external
boundaries of the solid support. The resulting product is a lysing matrix for
isolation of
nucleic acids such as DNA, herein referred to as the "Lysing Matrix." By
combining a lysing
reagent with a solid support, the DNA purification method is simplified by
removing a
separate lysing step. Preferably, the lysing reagent is applied to the solid
support and then
dried on the solid support before contact with the biological material. In
contrast,
conventional systems typically contact the biological material with the lysing
reagent as a step
prior to contact with the solid support, or the biological material is
suspended with the solid
support after which the lysis reagent is added to the resulting suspension.
Optionally, the lysing reagent can include an RNA digesting enzyme if it is
necessary to digest RNA present in a biological sample. By combining an RNA
digesting
enzyme with a solid support, the DNA purification method is simplified by
removing a
separate digestion step. A preferred RNA digesting enzyme is RNase A. A
purified form of
this enzyme is readily available from commercial sources such as Sigma
Chemical Company,
St. Louis, MO. Preferably, RNase A is added to the Lysing Reagent in an amount
of about
0.005-1 mg per ml and more preferably, about 0.01-0.1 mg per ml. The activity
of this
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WO 99/39010 PCT/US99/02190
enzyme is preferably at least about 50 units per mg and more preferably, at
least about 100
units per mg.
In a preferred embodiment, the lysing reagent includes the anionic detergent
and the RNA digesting enzyme, but does not include a chelating agent or a
buffer. Suitable
5 anionic detergents are capable of lysing cells and/or solubilizing proteins
and lipids. Such
anionic detergents include, but are not limited to, salts (e.g., sodium,
potassium, lithium salts)
of dodecyl sulfate as well as N-lauroyl sarcosine or a dodecylsulfate salt.
Preferably, the
anionic detergent is a dodecyl sulfate salt. Preferably, it is used in an
amount of about 0.1-
10%, more preferably, 0.2-1.6%, and most preferably, about 1.0-1.2%
weight/volume, based
10 on the total volume of the reagent. For biological samples with a high RNA
content, such as
cell culture suspensions, an RNA digesting enzyme is necessary. A preferred
RNA digesting
enzyme is RNase A. For biological samples with a high RNA content,
commercially
available RNase A, (e.g., Puregene RNase A available at a concentration of 4
mg/mL,
Gentra Systems Inc., Minneapolis, MN) is added to the anionic detergent
solution in an
15 amount of about 0.005 - 1 mg per mL and more preferably, about 0.01-0.1 mg
per mL. The
activity of this enzyme is preferably at least about 50 units per mg and more
preferably, at
least about 100 units per mg.
In yet another preferred embodiment, the lysing reagent includes only the
anionic detergent, but does not include a chelating agent, buffer, or the RNA
digesting
20 enzyme. Anionic detergents are used as described above.
This invention also provides methods for purifying DNA from biological
samples. For solid phase purification, the methods of the present invention
typically use only
one reagent and two main steps (e.g., washing and drying). The method involves
contacting
the biological sample with a solid support to lyse the cells thereby releasing
the DNA which
then binds to the solid support. A commercially available DNA purifying
reagent is added to
the solid support to facilitate solubilization and removal of impurities.
Sequential washing of
the solid support with this reagent causes impurities to be removed from the
solid support.
Prior to use in subsequent analysis, excess aqueous solution may be removed
from the solid
support containing thepurified DNA by methods such as evaporation or
centrifugation as
described in examples 1, 2, and 3.
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21
As an alternative to using the solid support containing the purified DNA in
subsequent analyses, the DNA may be removed from the solid support. An
additional reagent
and an additional step (eluting) are used if the DNA is removed from the solid
support.
Preferable, the DNA Eluting Reagent is used to remove, DNA from the solid
support. This is
illustrated in Examples 4, 5, 7, 8, 9, 10, 11, and 13.
Preferably, the method involves contacting the solid support containing the
DNA with the DNA Eluting Reagent and incubating. Preferably, the amount of DNA
Eluting
Reagent is about 0.25 volumes DNA Eluting Reagent to about 1 volume solid
support, more
preferably, the volume is about 1 volume reagent to about 1 volume solid
support, and most
preferably, the volume is about 4 volumes reagent to about 1 volume solid
support.
The temperature of the incubation is, preferably, at least about 30 C, more
preferably, at least about 80 C, and most preferably, at least about 100 C.
The duration of
the incubation is preferably, at least about 2 minutes, more preferably, at
least about 5
minutes and most preferably, at least about 10 minutes. The DNA is removed
from the solid
support by standard methods, such as centrifugation, vacuum or pressure.
In a preferred embodiment, the solid support is treated with the Lysing
Reagent such that the Lysing Reagent is bound to the solid support. The Lysing
Reagent may
be bound covalently, non-covalently, by being trapped within the interstitial
spaces of the
solid support, or by being deposited on the material (e.g., fibers, beads,
etc.) of the solid
support. The resulting product is a Lysing Matrix. Preferably, the Lysing
Reagent is allowed
to dry on the solid support.
The Lysing Reagent is added to the solid suppport, preferably at a volume
corresponding to at least one-tenth of the total volume of the solid support,
more preferably at
a volume corresponding to at least half of the total volume of the solid
support, and most
preferably at a volume corresponding to at least the total volume of the solid
support.
In another embodiment of the invention, the Lysing Reagent may be added
directly to the material (e.g., fibers, beads, etc.) used in making the solid
support and
preferably allowed to dry before it is made into the final user-ready form
(e.g., paper, swab,
disk, plug, column, etc.). In yet another embodiment, the solid support may be
treated with a
crystalline or powder form of the lysing reagent and allowed to bind to the
solid support.
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22
DNA is isolated by allowing the sample of biological material (cultured cells,
whole blood, etc.) to contact the Lysing Matrix. Although the sample may be
treated with a
lysing reagent before contact with the Lysing Matrix, the efficiency of
purification and the
DNA yield are greatly improved when the biological material is not pre-lysed.
Thus,
preferably, the biological material is added directly to the Lysing Matrix
which lyses the cells
and solubilizes protein coats and lipids. The efficiency of lysis may be
improved by heating
at greater than at least 30 C, more preferably at greater than at least 50 C,
and most
preferably at greater than at least 80 C. After at least 1 minute of
incubating the sample
within the Lysing Matrix, it is washed with the DNA purifying reagent.
Sequential washing
of the Lysing Matrix with the DNA purifying reagent causes impurities to be
removed from
the Lysing Matrix. Preferably, the amount of DNA purifying reagent used for
DNA
purification is about 0.5 volume DNA purifying reagent to about 1 volume of
biological
material, more preferably, about 2 volumes of DNA purifying reagent to about 1
volume of
biological material, and most preferably, about 5 volumes of DNA purifying
reagent to about
1 volume of biological material. Preferably, the number of washes with the DNA
purifying
reagent is at least two and more preferably, at least 3. This method is
illustrated in Examples
7, 8, 9, 10, 12, and 13.
A further embodiment of the present invention is a method for purifying
nucleic acids, like DNA, from yeast and Gram-positive bacteria. These
biological materials
are typically more resistant to lysis. The method involves combining the
biological sample
with a first ancillary reagent, i.e., a Cell Suspension Reagent (e.g., Cell
Suspension Solution,
Gentra Systems, Inc., Minneapolis, MN). The Cell Suspension Reagent includes a
buffer, a
chelating agent and a cell suspending agent to form a cell suspension. To the
cell suspension
is added a second ancillary reagent, i.e., a Lytic Enzyme Reagent (e.g., Lytic
Enzyme
Solution, Gentra Systems, Inc., Minneapolis, MN). The Lytic Enzyme Reagent
includes an
enzyme to digest cell walls, a buffer, an acid to adjust the pH of the reagent
and two
stabilizing agents. The digested cells may be used for liquid or solid phase
purification
described above.
As another aspect of this invention, a kit is provided that includes specific
protocols, which in combination with the reagents and optionally the solid
supports described
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WO 99/39010 PCTIUS99/02190
23
herein, may be used for purifying DNA from biological materials according to
the methods of
the invention. The kit includes instruction means. Depending on the
application, the kit may
also include any combination of a DNA purifying reagent, DNA Eluting Reagent,
RBC Lysis
Reagent, Cell Suspension Reagent, Lytic Enzyme Reagent, Protein Digesting
Reagent,
Isotonic Solution, solid supports, solid supports treated with Lysing Reagent
and/or RNA
digesting enzyme, vessels to contain the solid supports, vessels to contain
the waste liquids,
and vessels to contain any eluted DNA. Two preferred DNA Purification Kits are
described
below.
A kit for purifying DNA using solid phase purification contains: a DNA
purifying reagent (e.g., GENERATION DNA Purification Solution, Gentra
Systems, Inc.,
Minneapolis, MN), instruction means, a Lysing Matrix, and a vessel to hold the
Lysing
Matrix. In this kit the purified DNA remains bound to the solid support for
subsequent
analysis. Methods to illustrate the use of this kit are given in Examples 5
and 28.
A kit for purifying DNA using solid phase purification and subsequent elution
contains: a DNA purifying reagent, instruction means, the DNA Eluting Reagent,
a solid
support or a Lysing Matrix, a vessel to hold the solid support or the Lysing
Matrix, one or
more vessels to collect the waste, and a vessel to collect the purified DNA.
Methods to
illustrate the use of this kit are given in Examples 4, 5, 7, 8, 9, 10, and
25.
In order that the invention may be better understood, specific embodiments for
vessels that contain the solid support will now be described in more detail.
In one preferred embodiment of this invention, the vessel is a cartridge
equipped with two inlet ports at the top. The inlet ports are attached to
vessels upstream
containing the sample or reagents through a connector, such as a female Luer-
Lock. One
inlet, the sample port, is used for the application of the biological sample
to the solid support.
An optional feature on the sample port is a self-sealing mechanism that seals
the sample port
after sample has been transferred through it. The second inlet serves as a
reagent port. An
optional feature on both inlet ports is a protective breakaway seal.
Furthermore, the inlet
ports, breakaway seals and diffuser may be housed in an optional screw-cap. At
the bottom
of the solid support is an optional diffuser with a pore size suitable for the
passage of cellular
debris, proteins and lipid molecules. The diffuser allows for a uniform
traversal of biological
CA 02319691 2008-09-29
24
material across the cross section of the cartridge, and prevents unequal
buildup of biological
material anywhere below the solid support. The outlet of the cartridge comes
equipped with a
protective cap that fits neatly over the tapered barrel. The purified DNA is
collected in a collection
tube that consists of a conical tube with a snap cap for easy and
contamination-free storage. The
entire vessel can be scaled in size depending on the size of the samples to be
processed and the
yields needed for subsequent analysis.
In another preferred embodiment of this invention, the vessel consists of a
spin tube
designed to hold an insert into which the solid support is packed. The solid
support may be
cellulose, cellulose acetate, glass fiber, nitrocellulose, nylon, polyester,
polyethersulfone,
polyolefm, polyvinylidene fluoride, and combinations thereof. The insert
consists of a flanged
top to hold it in the spin tube and a perforated bottom to allow fluids to
pass through while
supporting the solid support. A cap tethered to the spin tube was used to
cover the insert.
Examples of a commercially available spin tube are given in Examples 2, 4, 7,
8, 9, and 10. The
biological material passes through the perforated bottom and is collected at
the
bottom of the spin tube. When used, the biological material is applied to the
solid support. The
requisite volume of reagent, whether a nucleic acid purifying reagent or
eluting reagent, is then
added to the solid support. The spin tube is then placed in a centrifuge and
subjected to
centrifugal forces that draw out the biological material, the purifying
reagent and the purified
DNA through the solid support during the purification process.
In yet another embodiment, the vessel may be multiple well plates, for
example, 6, 12,
24, 48 or 96 well plates where a solid support is packed into each well. The
bottom of each well
has an exit port through which waste and debris can pass.
In another aspect, the present invention provides a DNA eluting composition
for
removing DNA from a solid support comprising: (a) a buffer; (b) a base; (c) a
chelating agent; and
(d) water, wherein the chelating agent is present in an amount of 0.0001 mM to
no greater than 0.1
mM based on the total volume of the DNA eluting composition; wherein the base
is present in an
amount between 5 to 8 mM; wherein the pH of the DNA eluting composition is at
least 9.0; and
wherein the combined amount of buffer, base, and chelating agent is present in
an amount no greater
than 20 mM based on the total volume of the DNA eluting composition.
In another aspect, the present invention provides a method for isolating DNA,
the method
comprising: (a) contacting a biological material that contains DNA with a
solid support; (b)
releasing the DNA from the biological material, wherein the DNA binds to the
solid support;
CA 02319691 2012-01-27
24a
(c) treating the biological material with a DNA purifying composition to
purify the DNA from
the remainder of the biological material; and (d) eluting the DNA from the
solid support with
the DNA eluting composition as defined in claim 1, wherein eluting comprises
incubating the
solid support containing the DNA with the DNA eluting composition at a
temperature of at least
60 C .
This invention will be further described by reference to the following
detailed
examples. These examples are offered to further illustrate the various
specific and illustrative
embodiments and techniques.
All of the raw materials mentioned below are readily available from commercial
sources such as Sigma Chemical Company, St. Louis, MO. All percentages are in
volume per
volume, based on the total volume of the reagent, unless specified otherwise.
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WO 99/39010 25 PCT/US99/02190
Examples
Example 1. Evaluation of Solid Supports For DNA Purification
Several solid supports, which were cut into small pieces with surface area of
about 3 mm diameter or 2 mm square, were evaluated as substrates for DNA
purification. A
1 l volume of whole blood was pipetted onto each solid support, held in a 0.6
ml tube or the
well of a 96-well plate, and allowed to dry. To purify the DNA, 200 l DNA
purifying
reagent (GENERATION' DNA Purification Solution, Gentra Systems, Inc.,
Minneapolis,
MN) were added and incubated for 15 minutes. After pipetting up and down three
times to
mix, the DNA purifying reagent (containing eluted impurities) was discarded.
This washing
procedure was repeated twice more for a total of three washes. During this
three-step
washing procedure, impurities were selectively removed leaving the purified
DNA bound to
the solid support. Although the solid supports could be dried by evaporation
at room
temperature to about 80 C, an optional alcohol washing step was used to
accelerate the
drying process. A volume of 200 ul 100% ethanol was pipetted onto each solid
support,
incubated for 1 minute and then removed. Isopropanol (2-propanol) at 100% was
also found
to be a-suitable alcohol to accelerate drying. The ethanol rinse was repeated
once more for a
total of two rinses and then the disks were allowed to dry at room temperature
for at least two
hours.
To evaluate the solid supports in a DNA amplification assay, each was
transferred to a 0.6 ml tube. Each amplification reaction contained 1X
amplification buffer
(Promega, Madison, WI), 1.5 mM MgCl2, 200 M each deoxynucleotide, 2.5 units
Taq DNA
Polymerase (Promega, Madison, WI), and primers each at 1 M specific to the D
1 S80 locus.
The primers were shortened from those given by Budowle et al., Am. J. Hum.
Genet., 48,
137-144 (1991) with the oligonucleotide sequences as follows: sense 5' GAA-ACT-
GGC-
CTC-CAA-ACA-CTG-CCC 3' (SEQ ID NO:1) and antisense 5' GTC-TTG-TTG-GAG-
ATG-CAC-GTG-CCC 3' (SEQ ID NO:2). The samples were amplified using 35 cycles
of
94 C for 1 minute, 70 C for 1 minute, and 72 C for 2 minutes.
The results showed the presence of D 1 S80 amplification products using
several solid supports. The solid supports that were found to be suitable for
DNA
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WO 99/39010 26 PCT/US99/02190
purification are listed below. The best results (i.e., the greatest amount of
amplification
product) were observed using the cellulose paper solid supports.
Brand Name Substrate Tune Manufacturer
S&S 903 cellulose paper Schleicher and
Schuell,
Keene, NH
Ahlstrom 238 cellulose paper Ahlstrom,
Mt. Holly
Springs, PA
BCF180 cellulose paper Whatman
International Ltd.
Springfield
Mill, England
3MM cellulose paper Whatman
International Ltd.
Springfield
Mill, England
Durapore polyvinylidene fluoride Millipore
Corporation,
Bedford, MA
BiodyneA charged nylon Pall Corporation,
Port Washington,
NY
NC/Bind nitrocellulose Poretics
Corporation,
Livermore, CA
UnifloPlus glass fiber Schleicher and
Schuell,
Keene, NH
UnifloPlus cellulose acetate Schleicher and
Schuell,
Keene, NH
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WO 99/39010 27 PCTIUS99/02190
Pur-Wrap Dacron swab Hardwood
Products,
Guilford, ME
BiodynePlus charged nylon Pall Corporation,
Port Washington,
NY
PES Filter polyethersulfone Poretics
Corporation,
Livermore, CA
Filtrona polyolefin American
Filtrona,
Richmond, VA
Leukosorb polyester Pall Corporation,
Port Washington,
NY
Example 2. Rapid Solid Phase Purification of DNA from Whole Blood
To evaluate a rapid solid phase purification method, two blood samples were
collected from each of three individuals, one was used fresh and the other was
stored frozen
at -80 C for 3 months and then thawed before use. A volume of 3 l whole blood
was
pipetted onto a 3 mm diameter disk of S&S 903 paper, which was contained in
the insert of a
2 ml spin tube (Spin-X, Catalog No. 9424, Coming Costar, Cambridge, MA). A
volume of
200 ,ul nucleic acid DNA purifying reagent (GENERATION DNA Purification
Reagent,
Gentra Systems, Inc., Minneapolis, MN) was pipetted into the insert and the
sample
incubated for 1 minute. The DNA purifying reagent was removed by
centrifugation at 15,000
x g for 10 seconds to collect the eluted impurities in the spin tube. A second
and third wash
with a DNA purifying reagent was performed in the same way for a total of
three washes.
Each disk containing purified DNA was transferred to a 0.6 ml siliconized tube
for
amplification analysis. The waste collected in the spin tube was discarded.
To evaluate the purified DNA samples in an amplification assay, 50 l PCR
amplification solution was added to each disk. Each amplification reaction
contained 1X
amplification buffer (Promega, Madison, WI), 1.5 mM MgCl2, 200 M each
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28
deoxynucleotide, 2.5 units Taq DNA Polymerase (Promega, Madison, WI), and 1 aM
each
primer. Oligonucleotide primers given by Ridker et al., New Engl. J. Med.,
332, 912-917
(1995) were used to amplify a factor V gene sequence during 35 cycles, where a
cycle was
defined as 94 C for 1 minute, 58 C for 1 minute, and 72 C for 1 minute. A 10
,ul aliquot
from each DNA sample was electrophoresed through a 2% agarose gel at 80 volts
for 45
minutes to determine amplification results. The gel and running buffer
contained 0.125 ,ug
per ml ethidium bromide to allow visualization of the amplified DNA on a
transiluminator.
A factor V amplification product of 223 base pairs was observed for each of
the six samples following gel electrophoresis. The amplification results
showed that the
rapid solid phase DNA purification method, which was performed in about 5
minutes, gave
substantially pure DNA from fresh or frozen whole blood.
Example 3. Solid Phase Purification of DNA from Several Biological Samples
At least two DNA samples were prepared from the following biological
materials (human source except where noted): whole blood, bone marrow, saliva,
buccal
cells, cultured K562 lymphoblast cells, Drosophila melanogaster (D.
melanogaster) fruit
flies, alfalfa leaves and Escherichia coli (E. coli) bacteria. Samples of
whole blood, bone
marrow, saliva and buccal cell scrapes were applied to S&S 903 paper, dried
and then
sampled by punching a 3 mm diameter disk with a hole punch. Samples of plant
or animal
tissues were prepared by pressing adult D. melanogaster flies or alfalfa first
leaves
(cotyledons) onto S&S 903 paper. The samples were placed between the
collection paper and
a piece of PARAFILM "M" (American National Can, Greenwich, CT) and pressed
with
thumb pressure. Cultured cell suspensions were prepared in standard growth
medium
suitable for either K562 human cells or E. coli bacterial cells. A volume of 1
l medium
containing around 10,000 K562 cells or a volume of 5 l containing around 3
million E. coli
cells was pipetted onto a 3 mm diameter disk and dried. Then each disk was
purified as .
described in Example 1.
To evaluate the purified DNA samples in an amplification assay, a 50111
volume of PCR amplification solution was added directly to each tube
containing a disk with
CA 02319691 2007-12-20
29
bound DNA. The PCR solution was as described in Example 2 above except for the
primers,
which are given below. Whole blood, bone marrow, saliva, buccal cells, D.
melanogaster
tissue, and K562 cells were amplified using primers specific to glyceraldehyde
3-phosphate
dehydrogenase (GAPDH) gene sequences given in the mRNA Capture Kit (United
States
Biochemical Corporation, Cleveland, OH). The amplification program used to
amplify
GAPDH was 30 cycles of 94 C for 1 minute, 55 C for 1 minute, and 72 C for 1
minute.
DNA samples from whole blood were also tested for the presence of
extrachromosomal DNA
by using the mitochondrial primers MT-1 and MT-2 described by Wang et al.,
BioTechnigues
17, 76-82 (1994) and the amplification program described above for GAPDH.
Alfalfa and E.
coli DNA samples were tested by using primers specific for 16s-like ribosomal
DNA
described by Schmidt et al., BioTechnigues, 11, 176-177 (1991). The
amplification program
was 30 cycles of 94 C for 1 minute, 50 C for 1 minute and 72 C for 2 minutes.
After
amplification, 10 /l of the 50 l reaction were analyzed by agarose gel
electrophoresis as
described in Example 2.
The results showed that each sample gave the expected amplification product
indicating the presence of substantially pure DNA. Amplification of DNA
purified from
whole blood, bone marrow, saliva, buccal cells, D. melanogaster and K562 cells
gave an
amplification product of about 300 base pairs for GAPDH. Also amplification of
DNA
purified from whole blood gave an amplification product of about 394 base
pairs using
primers specific for mitochondrial DNA; this showed that extrachromosal DNA
was retained
on the solid support disk. From alfalfa and E. coli DNA, an amplification
product of about
400 base pairs was observed, derived from 16s-like ribosomal DNA
amplification.
Example 4. Solid Phase Purification and Elution of DNA from Whole Blood and
Buccal Swab Samples
To test both wet and dry samples of whole blood and buccal swabs, three
samples of each type were collected from three individuals, giving a total of
12 samples. For
liquid whole blood samples, a volume of 25 l was pipetted onto an 8 mm
diameter disk of
S&S 903 collection paper that had been placed into the insert of a 2 ml spin
tube (Spin-X*
Catalog No. 9424, Corning Costar, Cambridge, MA). For dry whole blood samples,
an 8 mm
* Trade-mark
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WO 99/39010 PCT/US99/02190
disk was punched from a 300 l dried blood spot and inserted into the insert
of a 2 ml spin
tube. Buccal swabs were obtained by swabbing the inner cheek surface 20 times
with a
sterile cotton-tipped swab (Pur-Wraps , Hardwood Products, Gilford, ME). The
cotton end
of the swab was cut off and placed into the insert of a 2 ml spin tube within
two hours of
5 collection for the wet samples and after drying 24 hours for the dry
samples. To purify the
samples, 200 /il DNA purifying reagent (GENERATION DNA Purification Solution,
Gentra
Systems, Inc., Minneapolis, MN) were pipetted into each insert and incubated 1
minute for
wet samples and 15 minutes for dry samples. The DNA purifying reagent was
removed by
centrifugation at 15,000 x g for 10 seconds to collect the eluted impurities
in the 2 ml spin
10 tube. A second and third wash with DNA purifying reagent was performed in
the same way
for a total of three washes. To elute the purified DNA bound to the solid
support, each insert
was transferred to a clean 2 ml receiver tube. Then 100 l DNA Eluting Reagent
were
pipetted into the insert containing the solid support and heated for 15
minutes at 80 C in a
dry block heater (e.g., VWR Scientific Products Catalog No. 13259-007) fitted
with an
15 aluminium block containing 12 mm diameter wells. The DNA Eluting Reagent
contained 10
mM Tris, 1 mM NaOH and 0.1 mM EDTA, pH 10.9. After heating, each sample was
centrifuged for 20 seconds at 15,000 x g to collect the purified DNA.
To evaluate the purified DNA samples in an amplification assay, a 5 ml aliquot
was tested from each sample. The amplification procedure described in Example
2 was used.
20 A factor V amplification product of about 223 base pairs was observed for
each of the 12 samples. The results showed that the solid phase purification
method gave
substantially pure DNA from both wet and dry blood and buccal cell samples
using cellulose
collection paper and cotton swabs for the solid supports.
25 Example 5. Purification of DNA in Whole Blood and Cultured Cells Using a
Cartridge
A cartridge was constructed using a standard 1 ml polypropylene syringe
(Catalog Number 309602, Beckton Dickinson, Franklin Lakes, NJ) into which was
inserted a
solid support. The solid support was comprised of cellulose acetate (Filtrona
, American
Filtrona, Richmond, VA) of dimensions about 5 mm diameter x 27 mm long. The
solid
30 support had been treated previously with 500 l Lysing Reagent and RNase A
and allowed to
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31
dry at room temperature for 24 hours. The Lysing Reagent contained 0.5% SDS,
0.1 M Tris,
0.1 M EDTA to which was added 0.04 mg/ml RNase A (about 100 units RNase A per
mg).
Two whole blood samples and two K562 cultured cells samples each containing
about 2
million cells in a 300,u1 volume were each pipetted into a cartridge supported
in a vertical
position. After incubating for 15 minutes at room temperature to allow the
cells to lyse and
the RNase to digest RNA present in the samples, a 300,u1 volume of DNA
purifying reagent
(GENERATION* DNA Purification Solution, Gentra Systems, Inc., Minneapolis, MN)
was
introduced via 2.5 nun W. silicon tubing using a 60 rpm peristaltic pump
(Catalog No.
MC13003, Markson Science, Hillsboro, OR). After a 1 minute incubation, air was
pumped
through the cartridge to expel the cartridge contents into a waste container.
Then, a second
300,41 volume of DNA purification reagent was pumped into the cartridge and
incubated 1
minute. This washing step was repeated once more for a total of three washes
with DNA
purifying reagent. The solid support in the cartridge was rinsed by pumping
300 ,ul of DNA
Eluting Reagent through it. To remove the purified DNA from the solid support,
300 ,ul of
DNA Eluting Reagent was pumped into the cartridge. The cartridge was plugged
at both
ends and incubated at 60 C for 30 minutes in a gravity convection oven.
Alternately, an
appropriate microwave oven may be used. The cartridge may be heated for 25
minutes at
30% power in a 1100 W Sharp microwave oven. Then the DNA Eluting Reagent,
which
contained the purified DNA, was pumped out of the cartridge and into a 1.5 ml
microcentrifuge tube. Alternately, the DNA eluting reagent can be heated to a
temperature
greater than 60 C and then pumped onto the cartridge.
To evaluate the purified DNA samples in an amplification assay, a 5 ,ul
aliquot
was tested from each sample. The amplification procedure described in Example
2 was used.
A factor V amplification product of about 223 base pairs was observed for
each of the 4 samples. The results showed that the solid phase purification
method in a
cartridge format gave substantially pure DNA from both whole blood or cultured
cell
samples.
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WO 99/39010 32 PCT/US99/02190
Examale 6. Purification and Restriction Enzyme Digestion of DNA Bound To A
Solid
Suaaort
To further test the quality of DNA purified using a DNA purifying reagent
(GENERATION DNA Purification Solution, Gentra Systems, Inc., Minneapolis, MN)
while
bound to a solid support, seven restriction enzymes were used to test their
ability to digest the
purified DNA. A volume of 300 1 whole blood from a single individual was
pipetted onto
S&S 903 paper and dried at room temperature. Then seven 5 mm diameter disks
were
punched out and each placed into a 0.6 ml tube. A volume of 200,41 DNA
purifying reagent
was added to each tube and incubated for 15 minutes. After pipetting up and
down three
times to mix, the DNA purifying reagent was discarded. This washing procedure
was
repeated twice for a total of three washes. During this three-step washing
procedure,
impurities were selectively removed leaving the purified DNA bound to the
disk. A volume
of 200 l 100% isopropanol (2-propanol) was pipetted onto each disk, incubated
for 1 minute
and then removed. This was repeated once for a total of two alcohol rinses.
The disks
containing the purified DNA were allowed to dry at room temperature for two
hours.
To test the quality of the DNA bound to each disk, a 25 l volume of
restriction enzyme solution was added directly to each tube. Each restriction
enzyme solution
contained the appropriate buffer supplied by the manufacturer (New England
Biolabs,
Beverly, MA) and 2.5 mM spermidine (Sigma Chemical Company). The following
enzymes
were tested with the units added to each reaction specified: Pst I (12 units),
Hind III (20
units), Eco RI (20 units), Msp I (20 units), Bam HI (20 units), Hpa I (5
units), and Hae III (10
units). The samples were digested at 37 C for 4 hours during which time the
digested DNA
fragments were released from the solid support into the digestion solution. To
collect the
restriction fragments, each sample tube was pierced with a 27 gauge needle and
placed into a
clean 0.6 ml tube. The digestion solution was collected by centrifuging at
2,000 x g for 2
minutes. To determine whether the purified DNA was digested, a 20 l volume was
removed
from each sample and electrophoresed through a I% agarose gel for 12 hours at
22 volts.
The results showed the presence of a characteristic smear of DNA restriction
fragments, ranging from high to low molecular weight for each of the seven
enzymes tested.
CA 02319691 2007-12-20
33
This demonstrated that the DNA samples were substantially pure and suitable
for restriction
enzyme digestion. '
Example 7. Evaluation of Detergents on Solid Support Treatment
Different detergents were tested to determine the best type of detergent
needed
to optimize DNA yields. The following types of detergents were tested:
ANIONIC Sodium Dodecyl Sulfate (SDS)
Sarkosyl*
CATIONIC Dodecyltrimethylam-monium bromide
NONIONIC Tween -20
Triton X-100
Controls were set up with no detergent and with no added sample.
Each of the polysulfone solid supports used had a circumference of 25.31 nun
and a height of 9.73 mm (Filtrona , Lot # 18475, American Filtrona, Richmond,
VA). A
volume of 360 l of a 1% detergent solution was applied to each solid support
to saturate it at
room temperature for at least 16 hours. Duplicate solid supports were prepared
for each
treatment. The solid supports were placed into the insert of a 2 ml spin tube
(Spin-X, Catalog
No. 9424, Corning Costar, Cambridge, MA). A whole blood sample containing
about 2
million cells in 300,ul was applied to each solid support and allowed to
incubate for at least 1
minute at room temperature to allow the cells to lyse. A 200 l volume of DNA
purifying
reagent (GENERATION DNA Purification Solution, Gentra Systems, Inc.,
Minneapolis,
MN) was then added. After a 1 minute incubation, the DNA purifying reagent was
removed
by centrifugation at 15,000 x g for 10 seconds to collect impurities in the 2
ml collection tube.
This was repeated twice for a total of 3 washes. The waste solution was
removed from the
receiving tube in between the second and the third wash. The solid support was
then rinsed
by adding 200 l of DNA Eluting Reagent (1 mM Tris, 0.001 mM EDTA, 5mM NaOH)
and
centrifuging at 15,000 x g for 10 seconds. To remove the purified DNA from the
support, the
insert containing the solid support was transferred to a clean receiver tube
and 200 l of DNA
Eluting Reagent was added to it. The solid support was then incubated at 80 C
for 10
minutes in a dry block heater (e.g., VWR Scientific Products Catalog No. 13259-
007) and the
* Trade-mark
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34
DNA Eluting Reagent which contained the purified DNA, was removed by
centrifugation at
15,000 x g for 20 seconds.
Genomic DNA yields and PCR amplification yields were measured to evaluate
the purified DNA. To determine relative genomic DNA yields, a volume of 10 ,ul
purified
DNA was mixed with 1 l lOX standard tracking dye and loaded into a 0.7%
agarose gel
containing 0.125 jig/ml ethidium bromide in the gel and running buffer. The
DNA was
electrophoresed for 15 minutes at 80 volts and the bands examined visually for
band intensity
on a UV transilluminator.
The PCR amplification assays was conducted by adding 2.5 l purified DNA
sample directly to a 22.5 PCR amplification mix for a total amplification
volume of 25 Al.
Each amplification reaction contained 1X amplification buffer (Promega,
Madison, WI), 1.5
mM MgC12, 200 tM each deoxynucleotide, 1.25 units Taq DNA Polymerase (Promega,
Madison, WI), and 1,uM each primer. Primers were sequences specific to the
human
betaglobin gene: sense 5' CCT-GGC-TCA-CCT-GGA-CAA-CCT-CAA 3' (SEQ ID NO:3)
and antisense 5'TAG-CCA-CAC-CAG-CCA-CCA-CTT-TCT 3' (SEQ ID NO:4). The
samples were amplified using 35 cycles of 94 C for 1 minute, 70 C for 1
minute, and 72 C
for 2 minutes. Then 10 121 of the amplified DNA were loaded into a 2% agarose
gel
containing 0.125 ,ug/ml ethidium bromide in the gel and running buffer. The
samples were
electrophoresed at 80 volts for 45 minutes and the 1.1 kb DNA bands were
visualized on a
UV transilluminator. The detergents were evaluated by visual ranking of the
band intensity
for both genomic and amplified DNA as shown in Table 2.
TABLE 2
Genomic DNA Yield PCR Yield
Anionic Sodium Dodecyl Sulfate (SDS) 4 3
Sarkosyl 3 2
Cationic Dodecyltrimethylammonium bromide 2 1
Nonlonic Tween-20 I I
Triton X-100 I 1
No 1 1
Detergent
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WO 99/39010 PCT/US99/02190
No Blood 0 0
Non ionic detergents showed no substantial improvement in DNA yield over the
controls.
The cationic detergent used showed approximately a two fold increase in
genomic DNA
5 yield. The two anionic detergents gave the best yield for genomic and
amplified DNA.
Example 8. Effects of NaOH concentration Detergent Type and Solid Support
Density on DNA Amplification
The effects of NaOH concentration and detergent type, whether anionic or
10 zwitterionic, were examined with two solid support densities. Four
solutions were prepared
containing 0 or 5 mM NaOH and 1 % sodium dodecyl sulfate or 1 % CHAPS. CHAPS
is a
commercially available zwitterionic detergent. A volume of 360 js1 of each of
these solutions
was added to the solid supports as described in Example 7. The two polyolefin
solid support
densities examined were 0.113 grams fibers/cc (low density) and 0.184 grams
fibers/cc (high
15 density) (Filtrona , American Filtrona, Richmond, VA). A 300 Al whole blood
sample was
added to each solid support, washed and eluted as described in Example 7,
except using a 150
/.cl volume of DNA purifying reagent (GENERATION' DNA Purification Solution,
Gentra
Systems, Inc., Minneapolis, MN). The purified DNA was analyzed by PCR
amplification and
UV spectrophotometry. The PCR protocol used was identical to that described in
Example 7.
20 Genomic DNA yields were examined by UV spectrophotometry and by 0.7%
agarose gel
electrophoresis. To quantitate DNA by UV spectrophotometry, 50 l of purified
DNA was
first added to 950 Al deionized water. The UV absorbance was then measured at
wavelengths
of 320 (background) nm, 260 nm and 280 nm. The yield was calculated as A2. x
50 x
dilution factor x elution volume.
25 The results showed that there was no detectable difference in DNA yields
for
solid support treatments carried out using no NaOH and 5 mM NaOH. There was a
2.8 fold
increase in DNA yields using SDS over CHAPS. A 75% increase using the high
density solid
support over the low density solid support was observed.
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36
Example 9. Effects of Chelating Agents. Salts and Detergents on Solid Support
Treatment
To determine the effects of chelating agents, salts and detergents on solid
support treatment, the polyolefin solid supports were treated with 8 solutions
containing 0.5%
or 2.0% sodium dodecyl sulfate, 0 or 50 mM EDTA, and 0 or 100 mM NaCl. A 200
Ml
whole blood sample was added to each solid support, washed, and eluted as
described in
Example 7. The purified DNA was collected and the genomic DNA yield examined
by UV
spectrophotometry as described in Example 8. The relative yields were further
visualized by
agarose gel electrophoresing the purified DNA samples on a 0.7% agarose gel,
as described in
Example 7. No differences in DNA yields were observed between 0 and 50 mM
NaCl.
Similarly, no differences in DNA yields were observed between 0 and 50 mM
EDTA.
However, there was a 3 fold improvement in the yield when 0.5% SDS was used as
compared
to 2% SDS.
Example 10. Determination of the Optimal Anionic Detergent Concentration
Optimal anionic detergent concentrations were estimated by treating the
polyolefin solid support with solutions of sodium dodecyl sulfate (SDS)
ranging from 0.2 -
1.6%. Solid supports were treated with 8 solutions containing 0.2, 0.4, 0.6,
0.8, 1.0, 1.2, 1.4,
1.6% SDS as described in Example 7. A 200 l whole blood sample was added to
each solid
support, washed, and eluted as described in Example 7. The purified DNA was
collected, and
the genomic DNA yield visualized by agarose gel electrophoreses as described
in Example 7.
Visual estimation of the band intensity on the 0.7% agarose gel showed that
all
concentrations of SDS showed good genomic DNA yields although the two highest
yields
were observed at SDS concentrations of 1.0 and 1.2%.
Example 11. The Effect of Varvin2 Time and Temperature on DNA Elution
The effect of time and temperature on DNA yield was tested using polyolefin
solid supports as described in Example 7. DNA from 200 tl blood samples was
purified
using two 400 ,ul washes with DNA purification reagent (GENERATION' DNA
Purification
Solution, Gentra Systems, Inc., Minneapolis, MN) and one wash with DNA Eluting
Reagent.
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37
After adding another volume of 200 /l DNA Eluting Reagent, the samples were
incubated for
minutes at four elution temperatures in a dry block heater (e.g., VWR
Scientific Products
Catalog No. 13259-007). The average of three samples for each of the
incubation
temperatures is given in Table 3.
5 TABLE 3
Temperature ( C) DNA Yield (ua)
24 0.0
60 0.8
80 1.5
10 100 6.9
An incubation temperature of 100 C gave the highest DNA yield. Additional
tests at 120 C do not indicate a substantial improvement.
The effect of incubation time at 99 C during the elution step was examined
using a second whole blood sample. The same purification protocol described
above was
followed except that a different dry block heater (Robbins Scientific,
TruTemprm, Sunnyvale,
CA) was used. Results are shown in Table 4.
TABLE 4
Time (minutes) 1 2 3 4 5 6 7 8 9 10
DNA Yield JjW 0 0 0 0.8 1.0 2.7 3.0 2.6 4.3 4.0
An incubation time of at least 9 minutes at 99 C was found to give the
optimum DNA yield.
Example 12. Design of Vessels to contain the Solid Support
A cartridge was constructed using a standard 1 ml polypropylene syringe
(Catalog Number 309602, Beckton Dickinson, Franklin Lakes, NJ) into which was
inserted a
solid support. The solid support was comprised of cellulose acetate (F ltrona
, American
Filtrona, Richmond, VA) of dimensions about 5 mm diameter x 27 mm long.
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38
In a second design, the cartridge is equipped with two inlet ports at the top.
One inlet, the sample port, is used for the application of the biological
sample to the solid
support. An optional feature on the sample port is a self-sealing mechanism
that seals the
sample port off after sample has been transferred through it. The second inlet
serves as a
reagent port. An optional feature on both inlet ports is a protective
breakaway seal. At the
bottom of the solid support is an optional diffuser with a pore size suitable
for the passage of
cellular debris, proteins and lipid molecules. The diffuser allows for an
equitable dispersal of
biological material across the cross section of the cartridge, and prevents
unequal buildup of
biological material anywhere below the solid support. The outlet of the
cartridge comes
equipped with a protective cap. The purified DNA is collected in a collection
tube that
consists of a 0.5 ml conical tube with a snap cap for easy and contamination
free storage.
In another vessel design, a spin tube (Spin-X, Conning Costar No. 9424,
Cambridge, MA) was used with an insert into which was placed a solid support.
The solid
support used was a polyolefin plug (American Filtrona, Richmond, VA) which was
placed
into the insert. The insert consists of a flanged top to hold it in the spin
tube and a perforated
bottom to allow fluids to pass through while supporting the solid support. A
cap tethered to
the-spin tube was used to cover the insert. An example of a commercially
available spin tube
is given in Example 1. The biological material passes through the perforated
bottom and is
collected at the bottom of the spin tube. When used, the biological material
is applied to the
solid support. The requisite volume of reagent, whether DNA purifying reagent
or DNA
Eluting Reagent, is then added to the solid support. The spin tube is then
placed in a
centrifuge and subjected to centrifugal forces that draw out the biological
material, the
purifying reagent and the purified DNA through the solid support during the
purification
process.
Example 13. Testing the use of Polvolefin Solid Supports in a 96-well Plate
System.
To test the efficacy of DNA purification in a high throughput system,
hydrophilic polyolefin solid supports (R- 18495, American Filtrona Company,
Richmond,
VA) were inserted into wells in a 96-well plate with a well capacity of 800 Al
(Unifilter plate
manufactured without a filter by Polyfiltronics, Rockland, MA). The solid
supports were
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cylindrical in size and had a circumference of 16.7 mm and a length of 10 mm.
The
aforementioned 96-well sample processing plate was placed on top of another 96
well plate
with a 2 ml well capacity which served as a waste collection plate. A volume
of 100,41
whole blood was applied to each solid support and allowed to incubate for 1
minute. The
solid supports were then subsequently washed twice by adding a volume of 200
l DNA
purifying reagent (GENERATION DNA Purification Solution, Gentra Systems,
Inc.,
Minneapolis, MN) to the well and incubating for 1 minute. The waste material
was
subsequently removed by centrifuging for 1 minute at 1500 x g in a Jouan C412
centrifuge
with an M4 rotor fitted with a microplate carrier (Jouan, Winchester, VA). The
solid
supports were then washed with 100 l DNA Eluting Reagent and centrifuged as
above
without incubation. To elute the purified DNA from the washed solid supports,
the
processing plate was transferred to a clean standard polystyrene 96-well plate
and a volume of
100 l of DNA Eluting Reagent was added to each well. The stacked processing
plate and
sample collection plate were placed into a convection oven (BioOven I, St.
John's Associates,
Beltsville, MD) set at 80 C and incubated for 30 minutes. The DNA was
subsequently eluted
from the solid support by centrifugation at 1500 x g for 1 minute. Eight 10 l
sample eluates
were analyzed for the presence of DNA by electrophoreses in a I% agarose gel
for 15
minutes at 80 volts. Each of the eight samples contained DNA as visualized by
examination
on a UV transilluminator.
Example 14. The Effect of treating a Solid Support with RNase A
A 300 ,uL volume of Lysing Reagent (0.5% SDS, 0.1 M Tris base, 0.1 M
EDTA disodium salt) was applied to a cellulose acetate solid support (American
Filtrona,
Richmond, VA) and allowed to dry at room temperature. A second solid support
was treated
with Lysing Reagent which also contained 0.04 mg/ml RNase A (at 4 mg/ml from
Gentra
Systems, Inc., Minneapolis, MN) and allowed to dry at room temperature. The
solid supports
had a diameter of 8 mm and a length of 6.75 mm. The two treated solid supports
were then
placed into the insert of a spin tube (as described in Example 8), and a
volume of 150 ul of E.
coli overnight bacterial culture added directly to each solid support. E. coli
bacterial cultures
contain large amounts of RNA and serve as a useful model to test the efficacy
of immobilized
CA 02319691 2007-12-20
RNA Digesting Enzyme. The samples were then incubated at 37 C for 12 minutes
to enable
RNA digestion. They were subsequently washed three times with a volume of 150
/u1 DNA
purifying reagent (GENERATION DNA Purification Reagent, Gentra Systems, Inc.,
Minneapolis, MN). Then 150 l of Basic Eluting Reagent (10 mM Tris, 0.1 M EDTA
and 1
5 mM NaOH) was added to the solid support for 20 minutes at room temperature.
The nucleic
acids were eluted by centrifuging for 10 seconds at 15,000 x g. A volume of 10
1 was
analyzed for the presence of DNA by electrophoreses through a 1% agarose gel
for 60
minutes at 80 V. Examination of the gel on a UV transilluminator showed
clearly the
presence of a prominent low molecular weight smear (approximately 0.1 - 1.4
kb)
10 corresponding to RNA in the sample purified using the solid support with
the solid support
treated with Lysing Reagent. In contrast, the sample purified with the Lysing
Reagent plus
RNase lacked the low molecular weight RNA smear showing that the presence of
RNase was
effective in removing contaminating RNA.
15 Example 15. DNA Eluting Reagent Optimization for DNA Amplification
The eluting reagent was optimized so as to offer the best DNA yields from the
solid support and produce high PCR yields without interfering with the PCR
buffering
system. Optimal concentrations of base, either NaOH or KOH, Tris buffer and
chelating
agent (EDTA) were tested on DNA amplification yields using PCR.
20 Conditions were tested by adding a 25 l blood sample to a cellulose solid
support contained in a spin tube. The cellulose solid support was subsequently
washed 3
times with 200 Al DNA purifying reagent (GENERATION DNA Purification
Solution,
Gentra Systems, Inc., Minneapolis, MN) and 2 times with DNA Eluting Reagent.
The
samples were all treated identically except for the concentration of base in
the DNA Eluting
25 Reagent. Concentrations of 1-8 mM NaOH in the DNA Eluting Reagent were
tested.
A TagMan 7700 Quantitative PCR system, using a B-actin amplification target
was used for DNA amplification, as per the manufacturer's recommendation
(Perkin Elmer,
Applied Biosystems Division, Foster City, CA). To test for amplification
inhibition, a
dilution series was prepared for each test sample and the starting quantity of
DNA computed
30 for each. All test samples were compared to the DNA sample at the highest
dilution since
* Trade-mark
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inhibitors would also be maximally diluted at the highest dilution. If a
diluted DNA test
sample gave a similar yield to the DNA sample at maximum dilution, (after
adjusting by the
dilution factor), then no amplification inhibition in that test sample was
assumed.
The best PCR yields were obtained at 5-8 mM NaOH. Similar experiments
with KOH showed no differences in PCR yields using NaOH or KOH.
Tris buffer concentrations and concentrations of EDTA were tested to
determine which concentrations optimized high PCR yields and low amplification
inhibition.
It was observed that lowering the concentration of Tris buffer from 1 mM to
0.1 mM, and
lowering the concentration of EDTA from 0.1 mM to 0.001 mM significantly
reduced
amplification inhibition.
Example 16. Optimization of Wash and Elution Procedures
Various combinations of wash and elution procedures were tested to determine
which combination provided optimal DNA yields and low % amplification
inhibition using a
TaqMan 7700 Quantitative PCR Instrumentation. The PCR procedures are as
described in
Example 4.
A volume of 25,41 of blood was applied to a cellulose solid support contained
in a spin tube (Spin-X, Corning Costar No. 9424, Cambridge, MA) and allowed to
absorb for
5 minutes. Each wash with a DNA purifying reagent (GENERATION DNA Purification
Solution, Gentra Systems, Inc., Minneapolis, MN) took 2 minutes. DNA Elution
Reagent is
applied to the solid support for 20 minutes at 80 C. Various purification and
elution
procedures were tested including the ones listed below. Each procedure was
tested in
triplicate.
(1) 3 x 150 pl NA purifying reagent + 1 x 150 l DNA Eluting Reagent
(2) 4 x 200 l NA purifying reagent + 1 x 200 Al DNA Eluting Reagent
(3) 3 x 200 kl NA purifying reagent + 2 x 200 l DNA Eluting Reagent
Results are shown in Table 5.
TABLE 5
Human Li-Actin DNA Yield (,ug)
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Procedure (1) 0.509
Procedure(2) 1.09
Procedure (3 1.09
Both Procedures (2) and (3) gave good purity and yields.
Example 17. Optimization of Solid Support Treatments
Cellulose solid supports were treated with Lysing Reagents having different
compositions for comparison to the untreated solid support. The first
composition was
composed of 0.5% SDS, 0.1 M Tris and 0.1 mM EDTA, while the second composition
was
composed of 1% SDS, 10 mM Tris and 0.1 mM EDTA. Cellulose paper was inserted
into a
spin tube (Spin-X, Corning Costar No. 9424, Cambridge, MA) and treated with
the two
aforementioned compositions. The treated cellulose papers were then allowed to
dry for at
least 16 hours at room temperature. Untreated cellulose paper was also used as
a comparison
to the treated samples. A volume of 25 1.41 of blood was applied to each
cellulose solid
support and allowed to incubate for 5 minutes. An optimal purification
procedure
incorporating 3 washes with a DNA purifying reagent (GENERATION* DNA
Purification
Solution, Gentra Systems, Inc., Minneapolis, MN) and 2 washes with DNA Eluting
Reagent
was conducted. The DNA was collected and analyzed using TaqMan 7700
Quantitative PCR
Instrumentation, where a Li-actin amplification target was used for DNA
amplification, as per
the manufacturer's recommendation (Perkin Elmer, Applied Biosystems Division,
Foster
City, CA).
The treatment with 1% SDS gave the best DNA yields. There were no
significant detectable differences in DNA yield and % amplification when the
level of SDS
was reduced to 0.5% from 1.0%. However, the absence of SDS reduced DNA yields
by over
50% and increased inhibition from 10% to over 40%.
Examine 18. Analysis of DNA Purification: Measurement of DNA Purity.
A sample of whole blood was drawn into a vacutainer tube containing EDTA
(B-D16852, Becton Dickinson & Co., Franklin Lakes, NJ) and mixed well. A small
aliquot
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of whole blood was removed and the total number of white cells counted on a
CBC5 Cell
Counter (Coulter Electronics, Hialeah, FL) according to the manufacturer's
instructions. This
was determined to be 7.25 x 106 cells/ml. The remainder of the blood was then
frozen at -
80 C in 1 ml aliquots until needed for further purification.
Frozen blood was thawed rapidly in a 37 C water bath and kept on ice until
use. Seven 200 j4 samples of blood were aliquoted and added to each of seven 2
ml spin
tubes (Spin-X, Catalog No. 9424, Corning Costar, Cambridge, MA) containing a
lysing
matrix housed in an insert, and a waste collection tube. The lysing matrix
comprised of a
cylindrical polyolefin solid support matrix with a diameter of 8 mm, and a
height of 8 mm
(Filtrona , Catalog No. 18475, American Filtrona, Richmond, VA). The
polyolefin solid
support matrix had been previously saturated with a solution containing 1% SDS
and 20
Ecg/ml RNase A and was subsequently dried.
After the samples were allowed to absorb to the matrix for at least 1 minute,
400 /.cl DNA purifying reagent (GENERATION DNA Purification Solution, Gentra
Systems, Inc., Minneapolis, MN) were added to the sample and allowed to
incubate for 1
minute at room temperature. Impurities were collected in the 2 ml spin tube by
centrifuging
the spin tube at 12,000 x g for 10 minutes. The insert containing the solid
support was
transferred to a second spin tube and the first spin tube was discarded.
Another 400 ml DNA
purifying reagent was added to the solid support, incubated for 1 minute at
room temperature,
and the spin tube centrifuged at 12,000 x g for 10 minutes. A 200 Ml volume of
DNA Eluting
Reagent was added to the solid support and centrifuged without incubation.
Each solid
support containing the purified DNA was then transferred to a clean 2 ml spin
tube and 200
jul DNA Eluting Reagent added. The tubes were incubated for 10 minutes at 99
C, and the
purified DNA was eluted from the solid support by centrifuging at 12,000 x g
for 20 seconds.
Impurities such as heme are a major contaminant in DNA purification
processes involving blood. The presence of heme can be determined using an
automated
EL311 Microplate Reader (Bio-Tek Instruments, Inc., Winooski, VT). Samples
were diluted
1:50 in deionized water and a 200 ,ul volume placed in a 96-well plate. The
absorbance was
measured at 405 nm. If the absorbance at 405 nm is less than 0.01 nm, the
purity of the
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sample is established. The average visible absorption at 405 nm was 0.004 for
the seven
samples, indicating a high degree of purity.
Another estimate of DNA purity is the absorbance ratio at 260 nm and 280
nm, A2w/Ano. If the value of this ratio is between 1.7 - 2.0, the sample is
considered
relatively free of proteins and other contaminants. This ratio is calculated
as follows:
(A260 - A320) / (A280 - A320)
The average A260SA ratio for the seven samples was found to be 1.95, which
indicates substantially pure DNA.
Example 19. Analysis of DNA Purification: Measurement of DNA Concentration and
Yield.
The seven purified samples from example 18 were further analyzed for
concentration and yield. A 1:50 dilution of each sample was prepared in
deionized water
along with a blank containing DNA Eluting Reagent. Absorbances at 320 rim
(background),
260 nm, and 280 nm were read using a Beckman DU64 Spectrophotometer (Beckman
Instruments, Inc., Fullerton, CA). The DNA concentration was calculated as
follows:
(A260 - A320) X 50 (DNA Extinction Coefficient) X 50 (Dilution Factor)
The average for the seven samples was found to be 41 ug/ml. This
concentration was then multiplied by the volume of the sample (200 /.cl) to
give an average
yield of 8.2 ,ug for each of the seven samples.
The theoretical maximum yield was determined from the white cell count
assuming that each human diploid cell has 6 pg DNA. Therefore, based on the
following
calculation, a theoretical maximum yield of 8.7,ug DNA is obtained.
(7.25 x 1(6 cells/ml) X (0.2 ml) X (6 x 10' ,ug) = 8.7 ,ug
To calculate the percentage yield, the average yield of 8.2,4g DNA was
divided by the theoretical maximum yield of 8.7 ,ug. This calculation resulted
in a percentage
yield of 94%.
Following quantitation, the DNA concentration may be adjusted by dilution or
concentration as needed. If the DNA is too concentrated, it may be diluted in
a diluent such
as deionized water. If the DNA is too dilute, it may be concentrated by using
a standard
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alcohol salt precipitation method. In this method, sodium chloride is added to
100 mM with
two volumes (relative to DNA sample volume) of 100% ethanol. The sample is
mixed by
inverting the tube and is centrifuged at 15,000 x g for 5 minutes to pellet
out the DNA. The
DNA pellet is washed by adding 3 volumes of 70% ethanol, inverting the tube
and
5 centrifuging at 15,000 x g for 1 minute. After discarding the supernatant,
the pellet is
allowed to air dry for 15 minutes. Then a hydration solution such as deionized
water is added
to prepare the desired, more concentrated solution.
However, no concentration adjustment of these samples was needed prior to
PCR amplification.
Example 20. Analysis of DNA Size
DNA size for each of the seven samples of Example 18 was determined by
comparison to the 23.1 kb band of lambda DNA digested with Hind M. A volume of
10 Id
from each of the seven 200,41 DNA samples was mixed with tracking dye and
loaded into a
1 % agarose gel. The samples were electrophoresed at 80 volts for 1 hour in I
X TAE running
buffer. Both gel and running buffer contained 0.125 Mg/ml ethidium bromide so
that DNA
could be visualized on a transilluminator. Comparison of DNA samples with the
marker
lanes showed that greater than 95% of the DNA exceeded the 23.1 kb marker
indicating that
the DNA was of substantially high molecular weight.
Example 21. Testing the Suitability of Purified DNA for PCR Amplification and
Subsequent Restriction Enzyme Digestion.
Each of the seven samples from Example 17 were tested to see if they were
suitable for analysis by PCR. A 2.5 ml volume from each of these seven samples
was added
to a 22.5 PCR amplification mix for a total amplification volume of 25 1.
Each
amplification reaction contained I X amplification buffer (Promega, Madison,
WI), 1.5 mM
Mg C12, 200 /zM each deoxynucleotide, 1.25 units Taq DNA Polymerase (Promega,
Madison,
WI), and 1 FuM each primer. Primers were sequences specific to a region of the
HLA-H gene
used for hereditary hemochromatosis genetic screening, 5'-TGG-CAA-GGG-TAA-ACA-
GAT-CC-3' (SEQ ID NO:5) and 5'-CTC-AGG-CAC-TCC-TCT-CAA-CC-3' (SEQ ID
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NO:6) (Feder et al. , 1995, Nature Genetics 13: 399-408). The samples were
amplified using
35 cycles of 94 C for 1 minute, 58 C for 1 minute, and 72 C for 1 minute.
To determine whether the DNA samples were suitable amplification
templates, the 7 samples were examined for both the presence and the correct
size (388 bp) of
an amplification product. A volume of 10 l from each of the 7 reactions was
loaded into a
2% agarose gel containing 0.125 g/ml ethidium bromide in the gel and running
buffer. The
samples were electrophoresed at 80 volts for 45 minutes and the DNA bands
visualized on a
transilluminator. Each of the 7 samples gave a large band of the expected 388
bp size
showing that the DNA was of a purity suitable for PCR amplification.
The amplified DNA samples were then tested for their ability to be digested by
the restriction enzyme Rsa I. This enzyme is used in clinical laboratories to
detect a DNA
point mutation associated with the genetic disease hereditary hemochromatosis.
A 10 Al
volume of the amplification reaction was mixed with 5 l of the Rsa I
restriction enzyme mix
containing 3.3 mg bovine serum albumin, 3.3 units Rsa I, and 1.5 l lOX
restriction enzyme
buffer (all components from New England BioLabs, Beverley, MA). The samples
were
incubated at 37 C for 30 minutes to allow the restriction enzyme to digest the
amplified
DNA.
A 15 l reaction volume of each of the seven samples was electrophoresed in a
2% agarose gel run at 85 volts for 60 minutes. Ethidium bromide was present at
0.125 g/ml
in the gel and running buffer to allow visualization of the bands on a
transilluminator.
Examination of the gel showed that all seven samples were cut efficiently at
the Rsa I
restriction site such that the 388 bp band was absent. In each of the 7 lanes,
two bands were
visible of approximately 250 and 140 bp in size.
Example 22. Restriction Enzyme Digestion and Southern blotting Analysis of DNA
purified using DNA Purifying Reagents.
DNA from seven 5 mm diameter dried blood spots was purified, digested and
electrophoresed as described in Example 6. Following electrophoreses, the
restriction
fragments were transferred over a 7 hour period to a nylon membrane
(Biotrans+1 "s, ICN
Biomedicals, Inc., Irvine, CA) by Southern blotting using a transfer solution
containing 0.4 N
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NaOH and 0.6 M NaCl. The nylon blot was hybridized for 14 hours at 65 C in HYB-
9
Hybridization Solution (Gentra Systems, Inc., Minneapolis, MN) and then washed
according
to the manufacturer's instructions. The probe was prepared from an amplified
300 bp region
of the glyceraldehyde 3-phosphate dehydrogenase labeled with 32P-labeled dCTP
using a
random priming kit (Amersham Life Science, Inc., Arlington Heights, IL). The
membrane
was placed against X-ray film (XARS, Eastman Kodak Company, Rochester, NY)
between
two intensifying screens at -80 C for 14 hours. The resulting autoradiogram
showed bands in
each of the lanes corresponding to digested DNA complementary to GAPDH
sequences in the
genome.
Example 23. Evaluation of Potential Cross-Contamination in DNA Purification
Methods.
= Test materials: Whole blood (Memorial Blood Center of Minneapolis), 8E5
cultured cells (Folk, et al., 1986, Guenthner et al., 1998), or phosphate-
buffered saline (PBS) were loaded on lysing matrix contained in two different
vessel formats (Capture P1ateTM, Gentra Systems Inc., Minneapolis, MN and
Capture ColumnTl, Gentra Systems Inc., Minneapolis, MN). The Capture
ColumnTM consists of a lysing matrix enclosed in an insert which is placed in
a
centrifuge tube. The Capture PlateTM consists of 96 flow-through wells each
enclosing a lysing matrix. The bottom of each well has a tapered exit port.
= Experimental Set-up: A 200 l sample volume of blood or PBS was added to
the Capture ColumnTM tubes or Capture ColumnTM wells using aerosol
resistant tips.
= Purification Method: Samples were purified by washing twice with 400 l
DNA purifying reagent, (DNA Purification SolutionTM, Gentra Systems Inc.,
Minneapolis, MN) and 1 wash with 200 l volume of a DNA eluting reagent
(DNA Elution Solution Gentra Systems Inc., Minneapolis, MN). Capture
ColumnsTM were centrifuged between washes for 10 seconds at 13,000 x g and
Capture PlatesTM were centrifuged for 3 minutes at 2000 x g. Fresh sealing
film was applied to each plate between washes to prevent contamination.
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Sample elution was performed by adding 200 Al DNA Elution SolutionTM to
each well. Capture ColumnsTM were heated at 99 C for 10 minutes in a block
heater and Capture PlatesTM were heated for 25 minutes at 30% power in a
1100W Sharp microwave oven. Following centrifugation the eluates were
ready for amplification.
= Amplification: A 2 l sample of each eluate was amplified to detect
contaminating DNA in the samples without DNA (PBS). HLA-H primers
(Feder et al., 1996) were used for experiments using blood and HIV-1 (gag)
primers (Guenthner et al., 1998) were used for 8E5 cultured cells. The cycling
conditions used were: 40 cycles of: 94 C for 30 seconds, 58 C for 30
seconds, and 72 C for 30 seconds in a PE2400 or 9700 thermal cycler.
= Detection: For gel analysis of Capture ColumnT'" amplification products, 5
ul
of the 25 p1 reaction were loaded onto a 2% gel and electrophoresed at 80
volts for 45 minutes. For gel analysis of Capture PlateTM amplification
products, a 96-well format minigel (2% agarose) was used at 80 volts for 5
minutes. For TaqMan detection on a PE7200 Sequence Detection System,
fluorescent probes for HLA-H and HIV were synthesized by PE Applied
Biosystems.
24. Samale Collection and Handline for DNA Purification on a Solid Suaaort.
DNA is purified from whole blood, bone marrow, buffy coat, body fluids,
cultured cells and solid tissue on a lysing matrix (Capture ColumnTM, Gentra
Systems Inc.,
Minneapolis, MN). Prior to purification on the Capture ColumnTM, samples were
processed
as follows:
i. Whole Blood and Bone Marrow
Whole blood and bone marrow were collected in EDTA to reduce
DNA degradation. However, other anticoagulants such as ACD
(citrate) and heparin may be used successfully. Samples may be either
fresh or frozen. However, improved yields may be observed using
frozen samples. Frozen samples are stable at -80 C for at least two
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years. Before use, the samples are thawed quickly in a 37 C water
bath and kept on ice until use. If the blood or bone marrow is not
frozen, it is recommended that it be stored at 4 C. A 200,01 volume of
blood or bone marrow may be used for DNA purification. If it is
necessary to purify DNA from a larger volume, a buffy coat sample
may be prepared.
ii. Bufft Coat
Whole blood was collected in EDTA to reduce DNA degradation.
However, other anticoagulants such as ACD (citrate) and heparin may
be used successfully. The fresh samples were stored at 4 C. White
blood cells were isolated rapidly using an adequate lysing reagent
(Lysis SolutionTM, Gentra Systems Inc., Minneapolis, MN).
Alternatively, buffy coat may be prepared from up to 5 ml whole blood
by centrifuging the sample at 800 x g for 10 minutes at room
temperature. Alternatively, the tube containing blood may be placed in
a vertical position at 4 C overnight to allow cells to settle. A thin layer
of white blood cells (buffy coat) should be visible between the upper
plasma layer and the lower red blood cell layer. The upper plasma
layer is removed and the the buffy coat is carefully collected with a
pipet, and kept on ice until use. DNA may be purified from up to 200
l buffy coat preparation containing a maximum of 10 million white
blood cells.
iii. Body Fluids
(Examples include saliva, synovial fluid, cerebrospinal fluid, urine,
amniotic fluid, plasma and serum.)
Body fluid samples are collected and stored at 4 C and used as quickly
as possible. Alternatively, they may be stored frozen at -80 C. For
body fluids with low cell numbers, it is preferable to concentrate
samples by centrifugation. Cells from a 3-40 ml volume of body fluid
were pelleted by centrifuging at 2,000 x g for 10 minutes. The
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supernatant was removed leaving behind 200 /1 to 1 ml residual fluid.
The pellet in the residual fluid was thoroughly suspended by pipetting
up and down 10 times and kept on ice or stored frozen at -80 C.
iv. Cultured Cells
5 Fresh samples and those stored frozen at -80 C were used. The
suspended cultured cells were collected and place on ice until use. Cell
counts were obtained using a hemacytometer or other cell counter. A
200 l suspension containing up to 10 million cultured cells was added
directly to the Capture ColumnTM.
10 v. Solid Tissue
Fresh samples and those stored frozen at -80 C were used. The
samples were kept on ice at all times to reduce DNase activity. 20 mg
tissue was added to a 1.5 ml microfuge tube containing 30 Al cold
PBS1' (preferably containing 1 mM EDTA to reduce Dnase activity)
15 and was quickly homogenized with a microfuge tube pestle. The
sample was placed on ice to allow cell clumps to settle for 2 to 10
minutes. The upper 200 l cell suspension was then removed
excluding any cell clumps.
vi. Gram-negative Bacteria
20 Fresh samples and those stored frozen at -80 C were used. The
samples were kept on ice. Typically, an overnight culture contains 1-3
billion cells per ml. However, due to the smaller genome size of
Gram-negative bacteria, up to 3 billion cells were applied to the
column for DNA purification. The culture was centrifuged, washed,
25 resuspended and applied to the column.
PBS with EDTA: 8 gm NaCl, 0.2 gm KCI, 2.72 gm Na2HP04.7H20, 0.24 gm
KH2PO4, 0.372 gm EDTA disodium salt dissolved in ultrapure water, brought
up to a volume of 1,000 ml and autoclaved.
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Example 25. DNA Purification on a Lysins Matrix.
The samples from Example 24 were purified on a lysing matrix (Capture
ColumnTM Gentra Systems, Minneapolis, MN) as follows:
i. Sample Purification
1. A volume of 200 l of a well-mixed sample was added to the
Capture ColumnTM and allowed to absorb at room temperature
for at least 1 minute or up to 1 hour.
2. A volume of 400 /.d of a DNA purifying reagent (DNA
Purification SolutionTM, Gentra Systems, Minneapolis, MN)
was added and allowed to incubate for 1 minute at room
temperature.
3. The Capture ColumnTM was centrifuged for 10 seconds at
2,000-12,000 x g. A waste volume of 6001d was collected in
the waste collection tube.
4. A volume of 400 /.cl DNA Purification SolutionTM was added
again to the Capture ColumnTM and allowed to incubate for 1
minute at room temperature.
5. The Capture ColumnTM was then centrifuged for 10 seconds at
2,000-12,000 x g and the waste volume was collected.
6. A volume of 200 Al DNA Elution SolutionTM was then added.
The Capture ColumnTM was centrifuged as described above.
7. The Capture ColumnTM was transferred to a DNA collection
tube and the waste was discarded.
8. A volume of 200 l DNA Elution SolutionTM was added and
allowed to incubate for 10 minutes in a dry block heater pre-
heated to 99 C. The Capture ColumnTM was then centrifuged
as previously described to release DNA from the lysing matrix.
9. The purified DNA was then ready for analysis.
ii. DNA Storage
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The purified DNA is stable for at least 3 months at 4 C. For long term
storage, it can be stored at -20 C.
Example 26. DNA Quantification Uslne UV Spectronhotometric Analysis.
Water is often used for diluting DNA for UV spectrophotometric analysis.
However,
there can be significant variability in both the A26dA2ao ratio and the yield
determined
when water is used as a diluent. Commercial buffers such as Tris-based or
phosphate
based buffers may be used to overcome these problems. Consistent results are
obtained by diluting DNA samples in TE BufferTM (10 mM Tris, 11 mM EDTA pH
8.0) (Gentra Systems, Minneapolis, MN) as described below. Additional
consistency
is obtained by using a masked quartz cuvette (e.g., Beckman Instruments, Inc.
Semi-
Microcell Masked Cuvette Cat. No. 533041).
ii. Sample Preparation and UV Snectrophotometric Analysis
1. Purified DNA samples are gently vortexed for 5 seconds.
2. Dilution tubes were prepared by adding 190 Al TE BufferTM to
0.6 ml microfuge tubes.
3. A blank solution was prepared by diluting a volume of 10 Al
DNA Eluting reagent (DNA Elution SolutionTM, Gentra
Systems, Minneapolis, MN) with 190 l TE BufferTM in a 0.6
ml microfuge tube.
4. 10 l DNA was removed from each sample and mixed with TE
BufferTM to make a total volume of 200 l, giving a 1:20
dilution.
5. The diluted samples were then vortexed at high speed for 5
seconds.
6. A volume of 200 l diluted sample was used to determine yield
and purity using a UV spectrophotometer by determining
absorbances at 26 nm, 280 nm and 320 nm.
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iii. DNA Yield and Purity Calculations
1. To calculate the DNA concentration of each sample: (A260-
A320) x 50 x dilution factor (e.g., 200/10) = DNA concentration
in g/ml. Note: A320 measures background scatter.
2. To calculate the DNA yield: DNA concentration( g/ml) x
volume of Elution Solution (0.2 ml) = DNA yield (ug).
3. To calculate DNA purity: (A260-A320)/A2so-A320) = purity of the
DNA. The A26anao ratio should be at least 1.5, however, this
ratio may not be an accurate measure of DNA purity (see
references 1, 2, 3). This ratio was first used to detect nucleic
acid contamination in protein preparations and as such, is a
poor indicator of DNA quality. DNA quality can be better
assessed by simply analyzing the DNA by agarose gel
electrophoresis or by evaluating performance (e.g., by PCR
amplification).
27. DNA Purification on a Flat Solid Support
Fresh or frozen biological samples were collected and processed as described
in Example 24. Large sample volumes (e.g. 300 jil) were pipetted onto a flat
solid
support ( Collection Cards TM, Gentra Systems, Minneapolis, MN), dried and
then
sampled by punching out a disk prior to DNA purification. Samples may be
stored on
the Collection Cards at room temperature for at least 9 months or at -20 C for
long
term storage.
The following samples were collected and allowed to dry on the Collection
Card in a horizontal position at room temperature for two hours.
i. Whole Blood (obtained via skin puncture or venipuncture)
ii. Buccal Cells (epithelial cells from inner cheek)
iii. Body Fluids (saliva, urine, plasma, serum)
iv. Cultured Cells
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DNA Purification
The sample was removed from the Collection Card by punching a 3 mm disk with a
clean hole punch, and then purified in a 96-well plate, a 0.2 ml or 0.6 ml
microfuge
tube. The 3 mm disk was placed in a well of a 96-well plate and the plate was
positioned in a robotic workstation. (Alternatively, the samples may be
processed
manually in a 96-well plate using a multichannel pipet or in a 0.2 or 0.6 ml
tube using
a micropipet). A volume of 200 l of DNA purifying reagent (DNA Purification
Solution, Gentra Systems, Minneapolis, MN) was added and allowed to incubate
for
minutes at room temperature causing the DNA to remain bound to the disk while
10 the contaminants were released. The solution was mixed by pipetting and
then
removed. This process was repeated twice. A volume of 200 l 100% isopropanol
or
100% ethanol was then added and allowed to incubate for 1 minute at room
temperature. The alcohol was removed, and the alcohol wash repeated. The disk
was
then dried at room temperature for at least 1-16 hours to evaporate the
alcohol. After
15 drying, the sample disks were light orange to white in color. The purified
disks are
stable for at least 9 months at room temperature or at -20 C for long term
storage.
DNA Amplification
1. If the disk was purified in a 0.2 or 0.6 ml amplification tube, at least 50
l amplification solution was added directly to the tube. If the disk
was purified in a 96-well flat bottom plate, the purified DNA sample
disk was transferred to an amplification tube at least 50 l
amplification solution was then added. The disk was completely
submerged in the amplification solution. The sample was then
amplified using standard conditions.
2. The disk may be stored in amplification solution for at least 4 months
at room temperature.
Re-Use for DNA Sample Disks
The purified DNA disks may be washed and re-used at least 5 times.
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1. The disk is removed from the amplification tube and subsequently
transferred to a filter insert contained within a 2 ml receiver centrifuge
tube..
2. 200 l DNA purifying reagent (DNA Purification Solution, Gentra
5 Systems, Minneapolis, MN) is pipetted into the filter insert and
centrifuged at 13,000-16,000 x g for 5 seconds to wash the disk. This
wash is repeated once more for a total of 2 washes.
3. The wash solution in the receiver tube is discarded and the washed disk
is transferred to a new amplification tube. The amplification solution
10 is added and amplified as described above.
Example 28. Purification of DNA from Biological Samules on a Losing Matrix
Disk and
Subsequent Amplification
DNA was purified from five biological samples on lysing matrix disks
15 (Capture Disk, Gentra Systems, Minneapolis, MN). The quality of the DNA was
ascertained
using PCR amplification.
Biological samples were collected and prepared as follows: human whole
blood and bone marrow were collected in tubes containing EDTA (Becton
Dickinson No.
6457); a buffy coat was isolated from 0.2 ml whole blood collected in EDTA; a
0.5 ml urine
20 sediment was prepared by centrifuging a 40 ml urine sample at 800 x g for
10 minutes; and 1
million K562 cells were suspended in 0.3 ml culture medium. DNA was purified
from 3 Al
of each prepared sample as described in the following sections. Each 3 mm disk
containing
purified DNA was amplified in a 50 ,ul reaction using primers specific of the
HLA-H locus
(used for hereditary hemochromatosis screening). A 388 base pair amplification
product was
25 expected.
Sample Collection and Handling
i. Buffo Coat Preparation
Whole blood or bone marrow was collected in EDTA to reduce DNA
degradation. However, other anticoagulants such as ACD (citrate) and heparin
30 may be used successfully. White blood cells were isolated from the red
blood
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cells in the sample by using an RBC lysis reagent (PUREGENE RBC Lysis
Solution, Gentra Systems, Minneapolis, MN). Alternatively, the buffy coat
may be prepared by centrifuging the sample at 800 x g for 10 minutes at room
temperature. A thin layer of white blood cells (buffy coat) should be visible
between the upper plasma layer and the lower red blood cell layer. The upper
plasma layer was removed and the buffy coat collected with a pipet and kept
on ice. A 3 l suspension of buffy coat containing at least 2,100 white blood
cells was then added to the Capture Disk.
ii. Body Fluids
Examples of body fluids include saliva, synovial fluid, cerebrospinal fluid,
urine, amniotic fluid, plasma and serum. For body fluids with low cell
numbers, samples are concentrated by centrifugation. Cells from a 3-40 ml
volume of body fluid are pelleted by centrifuging at 800 x g for 10 minutes.
The supernatant is removed and the pellet is suspended in the residual fluid
and kept on ice.
iii. Cultured Cells
The number of cells was determined using a hemacytometer or other cell
counter. A 3,41 suspension containing at least 2,100 cultured cells was added
to the lysing matrix disk.
iv. Gram-negative Bacteria
A 3 l suspension containing at least 600,000 bacterial cells was added to the
lysing matrix Disk. Typically, an overnight culture of bacteria contains 1-3
billion cells per ml. Thus, the culture can be used directly, or if necessary,
concentrated by centrifugation.
v. Mouse Saliva
A mouse was restrained in a vertical position, and 3-5 /,cl saliva was removed
from underneath the tongue of the mouse using a micropipettor.
vi. Whole Blood or Bone Marrow
Whole blood or bone marrow was collected in EDTA to reduce DNA
degradation. However, other anticoagulants such as ACD (citrate) and heparin
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may be used successfully. A 3 l volume of blood or bone marrow was used
for DNA purification.
DNA Purification
The above samples are purified as follows:
1. A volume of 3 l well-mixed sample was pipetted onto a 3 mm lysing
matrix disk in the insert of a 2 ml spin tube. The sample was allowed
to absorb at room temperature for at least 1 minute or up to 2 hours.
2. A volume of 200 l of DNA purifying reagent (DNA Purification
Solution, Gentra Systems, Minneapolis, MN) was added to the insert
and allowed to incubate for 1 minute at room temperature.
3. The spin tube was centrifuged at 2,000-16,000 x g for 10 seconds to
collect the wash solution in the receiver tube.
4. The incubation with the DNA purifying reagent and the centrifugation
was repeated twice. The lysing matrix disk containing the immobilized
purified DNA was white or off-white in color. The immobilized DNA
was then ready for DNA amplification.
DNA Amplification
The disk was placed directly into an amplification tube. A volume of 25-50 l
amplification master mix was added to the tube, and the DNA was amplified
using
standard conditions. The disk was stored in the amplification solution for at
least 4
months at room temperature.
Sample Re-Use
The disk may be re-used for further amplification. The protocol is as follows:
The disk is washed twice with 200 l of DNA Purification Solution and
centrifuged at
2,000-16,000 x g for 5 seconds before amplification.
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1
SEQUENCE LISTING
<110> HEATH, ELLEN M.
SHUMAN, RUTH
<120> ELUTING REAGENTS, METHODS AND KITS FOR ISOLATING DNA
<130> Gentra 5252.01
<140> UNASSIGNED
<141> 1999-02-02
<150> PROV. NO. UNKNOWNN
<151> 1998-02-02
<160> 6
<170> Patentln Ver. 2.0
<210> 1
<211> 24
<212> DNA
<213> Artificial Sequence
<220>
<223> Description of Artificial Sequence:
Oligonucleotide primer sequence
<400> 1
gaaactggcc tccaaacact gccc 24
<210> 2
<211> 24
<212> DNA
<213> Artificial Sequence
<220>
<223> Description of Artificial Sequence:
oligonucleotide primer sequence
<400> 2
gtcttgttgg agatgcacgt gccc 24
<210> 3
<211> 24
<212> DNA
<213> Artificial Sequence
SUBSTITUTE SHEET (RULE 26)
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<220>
<223> Description of Artificial Sequence: Primer having
sequence specific to the human betaglobin gene
(sense strand).
<400> 3
cctggctcac ctggacaacc tcaa 24
<210> 4
<211> 24
<212> DNA
<213> Artificial Sequence
<220>
<223> Description of Artificial Sequence: Primer with
sequence specific to the human betaglobin gene
(anti-sense strand).
<400> 4
tagccacacc agccaccact ttct 24
<210> 5
<211> 20
<212> DNA
<213> Artificial Sequence
<220>
<223> Description of Artificial Sequence
<220>
<223> Description of Artificial Sequence: Primer
specific to a sequence of the HLA-H gene used for
hereditary hemochromatosis genetic screening
<400> 5
tggcaagggt aaacagatcc 20
<210> 6
<211> 20
<212> DNA
<213> Artificial Sequence
<220>
<223> Description of Artificial Sequence: Primer
specific to a region of the HLA-H gene used for
hereditary hemochromatosis genetic screening.
<400> 6
SUBSTITUTE SHEET (RULE 26)
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WO 99/39010 PCT/US99/02190
3
ctcaggcact cctctcaacc 20
SUBSTITUTE SHEET (RULE 26)
