U.S. patent application number 11/741596 was filed with the patent office on 2008-06-05 for method for rapid amplification of dna.
This patent application is currently assigned to Invitrogen Corporation. Invention is credited to Scott Davis, Keqin Gregg, Wan Ji, Jon Kemppainen, Bonnie Reus, Kristen Taylor.
Application Number | 20080131886 11/741596 |
Document ID | / |
Family ID | 25378729 |
Filed Date | 2008-06-05 |
United States Patent
Application |
20080131886 |
Kind Code |
A1 |
Ji; Wan ; et al. |
June 5, 2008 |
METHOD FOR RAPID AMPLIFICATION OF DNA
Abstract
The present disclosure relates to methods of DNA amplification
with a first primer that has a random sequence of nucleotides at
its 3' end and a generic sequence 5' of the random nucleotides, as
well as a second primer with the generic sequence of the first
primer. The disclosure further relates to a method of precipitating
DNA on a solid medium to improve DNA amplification. In a preferred
embodiment, the presently disclosed methods are used for
high-throughput genotyping of DNA samples, such as bloodstains or
trace amounts of DNA.
Inventors: |
Ji; Wan; (Austin, TX)
; Gregg; Keqin; (Austin, TX) ; Reus; Bonnie;
(Cedar Park, TX) ; Kemppainen; Jon; (Austin,
TX) ; Taylor; Kristen; (Austin, TX) ; Davis;
Scott; (Bertram, TX) |
Correspondence
Address: |
INVITROGEN CORPORATION;C/O INTELLEVATE
P.O. BOX 52050
MINNEAPOLIS
MN
55402
US
|
Assignee: |
Invitrogen Corporation
Carlsbad
CA
|
Family ID: |
25378729 |
Appl. No.: |
11/741596 |
Filed: |
April 27, 2007 |
Related U.S. Patent Documents
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Application
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Patent Number |
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11483855 |
Jul 10, 2006 |
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11741596 |
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10672104 |
Sep 26, 2003 |
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11483855 |
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09881565 |
Jun 13, 2001 |
6638722 |
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10672104 |
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Current U.S.
Class: |
435/6.11 ;
435/6.1 |
Current CPC
Class: |
C12Q 1/686 20130101;
C12Q 1/6858 20130101; C12Q 1/6846 20130101; C12Q 1/6858 20130101;
C12Q 2525/179 20130101; C12Q 2525/179 20130101; C12Q 1/686
20130101; C12Q 2525/155 20130101 |
Class at
Publication: |
435/6 |
International
Class: |
C12Q 1/68 20060101
C12Q001/68 |
Claims
1-31. (canceled)
32. A method of identifying a polymorphism, the method comprising:
(a) providing a single reaction mixture comprising: (i) a DNA
sample; (ii) a first primer comprising a random sequence of
nucleotides at its 3' end and a generic sequence 5' of the random
nucleotides; and (iii) a second primer comprising the generic
sequence of the first primer and lacking the random sequence of the
first primer; (b) subjecting the DNA sample to DNA amplification by
a first DNA polymerase wherein the first primer anneals to the DNA
to allow the first DNA polymerase to produce a DNA product; (c)
subjecting the DNA product of step (b) to DNA amplification by
heat-stable DNA polymerase wherein the second primer anneals to the
DNA product to allow the heat-stable DNA polymerase to produce
amplified DNA products; and (d) analyzing the amplified DNA
products of step (c) to identify a polymorphism.
33. The method of claim 32, wherein the polymorphism is a single
nucleotide polymorphism (SNP).
34. The method of claim 33, wherein the SNP is identified by
Oligonucleotide Ligation Assay (OLA), Doublecode OLA, sequencing,
Single Base Extension Assay, allele specific primer extension, or
mismatch hybridization.
35-46. (canceled)
Description
STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
[0001] Not applicable.
REFERENCE TO A "MICROFICHE APPENDIX"
[0002] Not applicable.
BACKGROUND OF THE INVENTION
[0003] 1. Field of the Invention
[0004] The present disclosure relates generally to the field of DNA
amplification and more particularly to the field of amplifying any
stretch of DNA in a sequence-independent manner.
[0005] 2. Description of Related Art
[0006] The following description includes information that may be
useful in understanding the present disclosure. It is not an
admission that any of the information provided herein is prior art,
or relevant, to the presently claimed inventions, or that any
publication specifically or implicitly referenced is prior art.
[0007] It is well known that there is often an association between
genetic variation and phenotype manifestation. Genetic variations
and their associated phenotypes are studied using various methods
of genotyping genomic DNA. A Single Nucleotide Polymorphism (SNP)
is a single nucleotide variation at a specific location in the
genome of different individuals. SNPs are stable genetic variations
frequently found in genes, and contribute to the wide range of
phenotypic variations found in organisms. SNP genotyping is useful
in developing detailed genetic and physical maps of chromosomes.
Genotyping densely distributed SNP markers across the different
chromosomes of an individual can help reveal statistically
significant correlations between chromosomal loci and phenotypic
expression. Extensive genotyping, however, requires not only a
simple and rapid way for obtaining, shipping, storing, and sorting
large amounts of genetic material, but also convenient and
high-throughput methods for extracting large quantities of DNA from
these samples.
[0008] There are a variety of available methods for obtaining and
storing tissue and/or blood samples. These alternatives allow
tissue and blood samples to be stored and transported in a form
suitable for the recovery of genomic DNA from the samples for
genotype analysis. DNA samples can be collected and stored on a
variety of solid mediums, including Whatmann.RTM. paper, Guthrie
cards, tubes, swabs, filter paper, slides, or other containers.
When whole blood is collected on filter paper, for example, it can
be dried and stored at room temperature.
[0009] One known and more frequently used method for securing and
storing DNA is described in U.S. Pat. No. 5,496,562. This method
involves storing dried animal blood samples on chemically treated
filter paper, called FTA paper, that protects genomic DNA from
degrading (commercially available as FTA.TM. paper by
Whatman.RTM.). FTA paper is light weight and easy to store, which
makes it a popular choice for collecting genetic material and
samples. Samples on FTA paper are conveniently stored and shipped
at room temperature.
[0010] All of the materials available to those of skill in the art
for storing blood or other tissues containing DNA have limitations.
For example, the amount of tissue or blood collected may be very
limited, which makes wide-scale and high-throughput genotyping
impractical and expensive. For example, despite the widespread use
of FTA paper, its usefulness is limited because the stored
bloodstains contain only a small amount of genomic DNA. A 6.0
cm.sup.2 piece of FTA paper only preserves approximately 100 .mu.l
of blood, equivalent to approximately 1.0 .mu.g of DNA. While it is
possible to extract genomic DNA from a larger piece of FTA paper,
the size of the paper makes it cumbersome to manipulate in the
small wells of a 96-well plate or a 384-well plate, both of which
are important tools for high-throughput screening of large numbers
of DNA samples. Therefore, the usefulness of a tool like FTA paper
has been restricted to low-volume genotyping.
[0011] The limited amount of DNA stored on FTA paper also makes it
impractical for genotyping multiple polymorphisms and genetic loci
in a single organism. The FTA paper sample can be cut into smaller
pieces for genotyping multiple SNPs; a small circle of 1.0-2.0
mm.sup.2 diameter of the sample contains about 1-5 ng of genomic
DNA, which is sufficient for one polymerase chain reaction (PCR).
But this approach is undesirable because it requires repetitive
cutting, sorting, and extracting of the FTA paper, which is not
only tedious but also prone to human error. For a genomic scan of
hundreds or thousands of SNPs, the task of cutting and analyzing
DNA samples stored on FTA paper is an insurmountable barrier for
researchers.
[0012] Additionally, the strong adherence between DNA and FTA paper
makes DNA extraction for analysis difficult. Although proteinase K
and endonuclease digestion can facilitate DNA release as suggested
by the manufacturer, this approach is too complicated and expensive
for high-throughput operations. The commercially available FTA
Purification Reagent, which can be used to prepare DNA stored on
FTA paper for analysis by PCR.TM. yields inconsistent results. For
example, often no specific DNA amplification is achieved after the
DNA sample is processed using this reagent, which is unacceptable
in a high-throughput operation. The manufacturer also suggests that
the strong adhesion of DNA to FTA paper allows for repeated
genotyping of DNA stored on FTA paper. Notwithstanding the fact
that PCR efficacy for "recycled" FTA paper has not been fully
tested, cleaning the tiny FTA papers between consecutive SNP PCRs
is impractical for high-throughput processing. The small pieces of
floating filter paper are difficult to wash by conventional
aspiration, and they tend to clog aspiration needles or pipette
tips. Further small pieces are easily lost during the cleaning
process. Finally, repeated pipetting of PCR products has an
associated risk of cross contamination among different wells.
[0013] The shortcomings associated with small samples of blood or
tissue from an organism are overcome by efficient methods of whole
genomic DNA amplification. For example, whole genomic DNA amplified
from the small amounts of DNA sample stored on FTA paper could be
used in multiple PCR reactions to extensively genotype various
polymorphisms such as SNPs found in a single organism in a
high-throughput screening process. Nevertheless, while several
methods for whole genome amplification have been proposed and
successfully used for various applications in the past, these
methods are generally inefficient, complex, and expensive.
Therefore, the need exists for a simple and cost effective way of
amplifying genomic DNA from small samples of blood or tissue.
[0014] One of the first methods for amplifying DNA was the linker
adaptor-mediated PCR (LAM-PCR) approach, which has been applied to
microdissected chromosomes (Zhou et al., Bio Techniques 28:766-774,
2000; Albani et al., Plant J 4(5):899-903, November 1993), yeast
artificial chromosome (YAC) DNA (Sutcliffe et al., Genomics
13(4):1303-6, 1992), and genomic DNA (Kinzler et al., Nucleic Acids
Res 25:17(10):3645-53, May 1989). In this approach, the starting
DNA is first digested with a restriction enzyme, usually an enzyme
with a four base recognition sequence. After inactivation of the
restriction enzyme, a known sequence (either an adaptor or a
synthetic linker) is ligated to the ends of the DNA fragments
generated by the restriction-enzyme digest, providing primer
binding sites for PCR amplification. The DNA can then be amplified
by PCR using primers that are complementary to the sequence of the
adaptor or linker.
[0015] Unfortunately, the usefulness of LAM-PCR is limited because
it involves multiple steps, including DNA fragmentation, adaptor or
linker ligation, and PCR amplification. These steps make this
process both laborious and expensive for high-throughput
genotyping. An additional shortcoming of this method is that
sequences that do not contain the recognition sequence of the
restriction enzyme used at appropriately spaced intervals will not
be amplified by PCR because the regions will be too long to
amplify. This method is also time-consuming and cumbersome because
of the extensive manipulations of DNA necessary to attach the known
sequences to both ends of the fragments, especially when applied to
small quantities of DNA, such as microdissected chromosomal pieces,
or DNA found in bloodstains or small samples of tissue.
[0016] Another more restrictive method available for amplifying
genomic DNA uses inter-ALU PCR (more generally known as
inter-repetitive element PCR), which relies on the presence of
appropriately spaced and oriented ALU repetitive elements or other
repeated sequences. Inconsistent results are obtained, however,
with low complexity DNA sources such as YACs, cosmids, or phage,
because of the low incidence of these repeat sequences. Other
inconsistencies arise because repeated sequences do not occur
uniformly throughout the genome, and thus a sequence of interest
occurring in an area in which the necessary repeated sequences are
rare or absent will not be amplified. Another major limitation of
this method is that it is species specific. For example, the use of
this method is restricted to DNA of the species from which the
repetitive elements are derived and for which the PCR primers were
constructed.
[0017] A method called degenerated oligonucleotide-primed PCR
(DOP-PCR) utilizes partially degenerated sequence (6 out of 21) and
repeated thermocycling Telenius, et al., Genomics 13(3):718-25,
1992. In the DOP-PCR method, the first rounds of PCR amplification
have a low primer annealing temperature of around 30.degree. C. The
primer used consists of a random hexamer that is flanked on the 3'
side by a defined hexamer and on the 5' side by a defined sequence.
Because the 3' end of the primer has a defined hexamer, the target
sequence must match this hexamer in order to amplify. Therefore,
the number of sequences that will be amplified by this method are
limited. The inadequacy of the DOP-PCR method is further
demonstrated when it is applied to DNA sources of limited
complexity such as YACs, cosmids, or phage inserts. The resulting
product is not a smear on a ethidium bromide stained agarose gel
(as occurs with randomly amplified DNA), but rather distinct bands,
indicating that hybridization occurs at relatively few sites and
thus sequence independent amplification is not achieved.
[0018] Another attempt to amplify genomic DNA was a method termed
primer-extension preamplification (PEP) (Zhang et al., Proc. Natl.
Acad. Sci. USA 89:5847-5851, 1992). The PEP method utilizes 15 base
pair (bp) random oligonucleotides and repeated thermocycling to
randomly prime multiple sites in the genomic DNA for PCR. A method
utilizing 6 base pair (bp) random oligonucleotides and PCR has also
been reported (Peng et al., Clin Pathol 47:605-608, 1994). Although
both PEP and DOP-PCR have been employed in several specific
applications, they are consistently hampered by their relatively
low amplification efficiency (Wells et al., Nucleic Acids Res
27:1214-1218, 1999). A possible explanation for this low efficiency
is that because the primers contain random nucleotides and
therefore form a large spectrum of different oligonucleotides, the
effective concentration of any specific primer is very low, which
may limit the exponential amplification of PCR. Additionally, the
non-specific binding of the random oligonucleotides tends to
initiate DNA synthesis within the PCR products of previous rounds.
Therefore, the size of the PCR products decreases constantly with
each additional round of PCR amplification, which renders the final
PCR products very small, especially when a large number of PCR
cycles are performed. These small PCR products are not as useful as
larger pieces of amplified DNA for the subsequent genetic analysis
of the DNA or genotype analysis.
[0019] Another method of genomic DNA amplification, termed tagged
random PCR, was described by Grothues et al. (Nucleic Acids Res
21:1321-1322, 1993) and Wong et al. (Nucleic Acids Res 24:3778-83,
1996). This method attempts to overcome the shortcomings associated
with PEP and DOP-PCR by separating random priming and PCR
amplification into two steps and amplifying whole genomic DNA with
a single PCR primer. In the first amplification step, tagged random
primers consisting of a random 6 bp or 9 to 15 bp 3' tail and a
constant 17 to 22 bp 5' head indiscriminately prime the genomic
DNA. Next, unincorporated tagged primers are removed by gel
filtration using a Biogel P100 spin column or a Centricon-100 spin
column. In the second amplification step, the DNA molecules fitted
with the 5' constant head and its reverse complement at both ends
are amplified by PCR. Although the scheme can amplify whole genomic
DNA, its multiple steps of reaction and purification are too
complex and expensive for high-throughput screening.
[0020] The construction of libraries from microdissected
chromosomal bands is an elegant way to obtain DNA probes from
genomic regions of particular interest. The applicability of this
approach has been restricted by the time consuming and technically
difficult process of amplifying DNA from microdissected material.
Traditionally, DNA from 20 to 30 microdissected chromosomal bands
is collected in a small droplet. The DNA is then subjected to
various manipulations before it is used for PCR amplification.
These manipulations include phenol/chloroform extractions,
restriction enzyme digestion and ligation to a vector or linker
(LAM-PCR). These steps must be performed in very small volumes on
the stage of a microscope with specialized equipment (Kao et al.,
Proc Natl Acad Sci USA 1:88(5):1984-8, 1991), which severely limits
the usefulness of this technique.
[0021] Yeast artificial chromosomes (YACs) are ideal vectors for
the detailed mapping of large stretches of DNA. One of the main
disadvantages of the YAC cloning system is that there have been no
methods available to purify YAC DNA in large quantities. High
molecular weight DNA can be prepared from yeast clones carrying
YACs and the YACs can be isolated on a pulsed field gel. This
approach, however, yields only very small amounts of pure YAC DNA.
This is a major disadvantage because many important uses of these
large inserts, e.g. screening of cDNA libraries or Fluorescent in
situ hybridization (FISH) analysis, require larger amounts of
purified YAC DNA.
[0022] Thus, a need exists for a more efficient and inexpensive
method for amplifying DNA samples that is compatible with
high-throughput screening, is sequence independent, applicable to
any type of DNA, useful for amplifying DNA from any species, and
most important, capable of amplifying extremely limited amounts of
DNA. There is also a need for an amplification process that is
simple (to avoid the problem of PCR contamination), has high
fidelity in reproducing genetic material, and has a low rate of
distortion of amplified sequences.
BRIEF SUMMARY OF THE INVENTION
[0023] The present disclosure seeks to overcome the drawbacks
inherent in other methods of DNA amplification by providing a
simple and direct method for amplifying DNA. The method of the
present disclosure preferably amplifies DNA in a
sequence-independent manner using a single reaction mixture and a
single programmable thermocycling reaction. This method can be used
to amplify trace amounts of DNA, including genomic DNA from small
tissue or blood samples, such as fine needle aspirates or single
tissue sections, or even from a single cell. The single reaction
mixture used in this method also greatly reduces the risk of sample
contamination and facilitates high-throughput screening, and in a
preferred embodiment a single heat-stable DNA polymerase is
included to amplify all DNA in the single reaction mixture. This
method allows DNA to be amplified from any species or organism. It
is understood that the present disclosure encompasses sequence
independent amplification of DNA from any source, including but not
limited to human, animal, plant, yeast, viral, eukaryotic, and
prokaryotic DNA.
[0024] The present disclosure also offers an improved method for
processing DNA samples on a solid medium. Other known methods of
preparing DNA samples stored on a solid medium for genetic analysis
or DNA amplification are inefficient and inconsistent, thereby
limiting the usefulness of the information obtained from the DNA
samples. The method of the present disclosure seeks to overcome the
drawbacks inherent in these other methods by greatly simplifying
the preparation of DNA samples and improving the DNA for subsequent
analysis. The method of the present disclosure precipitates the DNA
sample on a solid medium using methods well known to those of skill
in the art. In a preferred embodiment, the DNA sample is a
bloodstain on a solid medium. The DNA processed according to the
presently disclosed method can be subsequently subjected to DNA
amplification using the presently disclosed methods and/or genetic
analysis. This disclosed precipitation method produces more
consistent results, reduces the cost of high-throughput operations,
and improves the quality of DNA amplified from the DNA sample.
[0025] The present disclosure includes methods of amplifying DNA
from a DNA sample. In a preferred embodiment, the method of
amplifying DNA uses a reaction mixture that contains a DNA sample;
a first primer with a random sequence of nucleotides at its 3' end
and a generic sequence 5' of the random nucleotides; and a second
primer that has the generic sequence of the first primer but lacks
the random sequence of the first primer. In a preferred embodiment,
a single reaction mixture is used. An example of a first primer is
the sequence designated SEQ ID NO:1, and an example of the second
primer is the sequence designated SEQ ID NO:2. Preferably, the
reaction mixture contains other components that are necessary for
DNA amplification, which are well known to those of skill in the
art.
[0026] The DNA sample in the reaction mixture is subjected to DNA
amplification by a first DNA polymerase, wherein the first primer
anneals to the DNA to allow the first DNA polymerase to synthesize
a complementary DNA strand from the 3'end of the first primer to
produce a DNA product. The steps for DNA amplification by the first
DNA polymerase are denaturing the DNA product; annealing the first
primer with the DNA to allow the formation of a DNA-primer hybrid;
and incubating the DNA-primer hybrid to allow the first DNA
polymerase to extend the primer and synthesize the DNA product.
Preferably, these DNA amplification steps are repeated at least one
time. In a preferred embodiment, the annealing temperature and the
incubating temperature are the same. In another preferred
embodiment, the DNA product produced by the DNA amplification is
flanked by the generic sequence and reverse complement of the
generic sequence.
[0027] This DNA product is then subjected to DNA amplification by a
heat-stable DNA polymerase, wherein the second primer anneals to
the DNA product and the heat-stable DNA polymerase synthesizes a
complementary DNA strand from the 3' end of the second primer to
produce a second DNA product. The steps for DNA amplification by
the heat-stable DNA polymerase are denaturing the DNA product;
annealing the second primer with the DNA product to allow the
formation of a DNA-primer hybrid; and incubating the DNA-primer
hybrid to allow the heat-stable DNA polymerase to synthesize the
second DNA product. Preferably, these DNA amplification steps are
repeated about 30 to about 35 times, and more preferably about 40
times. In a preferred embodiment, the second DNA product is flanked
by the generic sequence and the reverse complement of the generic
sequence. In another preferred embodiment; the annealing
temperature is higher than the optimal annealing temperature of the
random sequence of nucleotides at the 3' end of the first
primer.
[0028] In a preferred embodiment, the first DNA polymerase has 5'
to 3' exonuclease activity or primer displacement activity. The
first DNA polymerase is preferably E. coli DNA polymerase I, and
the heat-stable DNA polymerase is preferably Taq DNA polymerase. In
another preferred embodiment, the first DNA polymerase and the
heat-stable DNA polymerase are the same DNA polymerase, and that
DNA polymerase is Taq DNA polymerase.
[0029] In another preferred embodiment, the first primer has about
4 to about 8 random nucleotides at its 3' end. In a more preferred
embodiment, the first primer has about 6 random nucleotides at its
3-end. Preferably the generic sequence of the first primer is about
15 to about 28 nucleotides in length, or more preferably about 20
to about 25 nucleotides in length. The random nucleotides of the
first primer may also be G:C rich or A:T rich, to preferably
amplify certain regions of the DNA sample. Finally, the generic
sequence of the first primer preferably will have a single or
multiple restriction enzyme recognition site, which will facilitate
subcloning of the amplified DNA products.
[0030] In a preferred embodiment, the DNA sample is genomic DNA,
microdissected chromosome DNA, yeast artificial chromosome (YAC)
DNA, cosmid DNA, phage DNA, P1 derived artificial chromosome (PAC)
DNA, or bacterial artificial chromosome (BAC) DNA. In another
preferred embodiment, the DNA sample is mammalian DNA, plant DNA,
yeast DNA, viral DNA, or prokaryotic DNA. In yet another preferred
embodiment, the DNA sample is obtained from a human, bovine,
porcine, ovine, equine, rodent, avian, fish, shrimp, plant, yeast,
virus, or bacteria. Preferably the DNA sample is genomic DNA,
wherein the method of amplifying DNA includes DNA amplification
with a fluorescent label. In another preferred embodiment, the DNA
sample is bovine DNA. Preferably, the DNA sample is tissue on a
solid medium, wherein the tissue is blood, preferably in the form
of a bloodstain. In a preferred embodiment, the solid medium is
filter paper, wherein the filter paper is chemically treated, for
example FTA.TM. paper. In a preferred embodiment the bloodstain is
from a mammal, and the mammal is preferably human, bovine, or
porcine. The DNA sample may be obtained from many sources well
known to those of skill in the art, including but not limited to a
buccal swab, a nose swab, blood, cord blood, amniotic fluid,
embryonic tissue, hair, endothelial cells, hoof clippings, or
fingernail clipping.
[0031] In another preferred embodiment, the method of amplifying
DNA further includes genotype analysis of the amplified DNA
product. Alternatively, the method of amplifying DNA preferably
further includes identifying a single nucleotide polymorphism (SNP)
in the amplified DNA product. In preferred embodiments, a SNP may
be identified in the DNA of an organism by a number of methods well
known to those of skill in the art, including but not limited to
identifying the SNP by DNA sequencing, by amplifying a PCR product
and sequencing the PCR product, by Oligonucleotide Ligation Assay
(OLA), by Doublecode OLA, by Single Base Extension Assay, by allele
specific primer extension, or by mismatch hybridization. Preferably
the identified SNP is associated with a phenotype, including
disease phenotypes and desirable phenotypic traits. The amplified
DNA generated by using the disclosed method of DNA amplification
may also preferably be used to generate a DNA library, including
but not limited to genomic DNA libraries, microdissected chromosome
DNA libraries, BAC libraries, YAC libraries, PAC libraries, cDNA
libraries, phage libraries, and cosmid libraries.
[0032] Another aspect of the present disclosure is a preferred
method of amplifying DNA that uses a reaction mixture with a DNA
sample; a first primer with a random sequence of nucleotides at its
3' end and a generic sequence 5' of the random nucleotides; a
second primer with the generic sequence of the first primer and
lacking the random sequence of the first primer; and a heat-stable
DNA polymerase. In a preferred embodiment, a single reaction
mixture is used. Preferably, the reaction mixture also contains
other components that are necessary for DNA amplification, which
are well known to those of skill in the art. In a preferred
embodiment, the heat-stable DNA polymerase is Taq DNA polymerase,
the DNA sample is a bloodstain on a solid medium, and the DNA
sample is preferably dehydrated on the solid medium.
[0033] The DNA sample in the reaction mixture is subjected to DNA
amplification wherein the first primer anneals to the DNA to allow
the heat-stable DNA polymerase to synthesize a complementary DNA
strand from the 3' end of the first primer to produce a DNA
product. The steps for DNA amplification by the heat-stable DNA
polymerase are denaturing the DNA product; annealing the first
primer with the DNA to allow the formation of a DNA-primer hybrid;
and incubating the DNA-primer hybrid to allow the heat-stable DNA
polymerase to synthesize the DNA product. Preferably, these DNA
amplification steps are repeated at least one time. In a preferred
embodiment, the annealing temperature and the incubating
temperature are the same. In another preferred embodiment, the DNA
product produced by the DNA amplification is flanked by the generic
sequence and reverse complement of the generic sequence.
[0034] This DNA product is then subjected to DNA amplification by
the heat-stable DNA polymerase, wherein the second primer anneals
to the DNA product and the heat-stable DNA polymerase synthesizes a
complementary DNA strand from the 3' end of the second primer to
produce a second DNA product. The steps for DNA amplification by
the heat-stable DNA polymerase are denaturing the DNA product;
annealing the second primer with the DNA product to allow the
formation of a DNA-primer hybrid; and incubating the DNA-primer
hybrid to allow the heat-stable DNA polymerase to synthesize the
second DNA product. Preferably, these DNA amplification steps are
repeated about 30 to about 35 times, and more preferably about 40
times. In a preferred embodiment, the second DNA product is flanked
by the generic sequence and reverse complement of the generic
sequence. In another preferred embodiment, the annealing
temperature is higher than the optimal annealing temperature of the
random sequence of the first primer.
[0035] In another preferred method of amplifying DNA, a reaction
mixture is provided that has a DNA sample, wherein the DNA sample
is a tissue on a solid medium; a first primer with a random
sequence of nucleotides at its 3' end and a generic sequence 5' of
the random nucleotides; a second primer with the generic sequence
of the first primer and lacking the random sequence of the first
primer; and a heat-stable DNA polymerase. In a preferred
embodiment, a single reaction mixture is used. In a preferred
embodiment, the tissue on the solid medium is blood. In another
preferred embodiment the solid medium is filter paper, and the
filter paper is chemically treated. The DNA sample is preferably
dehydrated on the filter paper. Preferably, the reaction mixture
also contains other components that are necessary for DNA
amplification, which are well known to those of skill in the art.
In a preferred embodiment, the heat-stable DNA polymerase is Taq
DNA polymerase, the DNA sample is a bloodstain on a solid medium,
and the DNA sample is preferably dehydrated on the solid
medium.
[0036] The DNA sample in the reaction mixture is subjected to DNA
amplification by a heat-stable DNA polymerase, wherein the first
primer anneals to the DNA to allow the heat-stable DNA polymerase
to synthesize a complementary DNA strand from the 3' end of the
first primer to produce a DNA product. The steps for DNA
amplification by the heat-stable DNA polymerase are denaturing the
DNA product; annealing the first primer with the DNA to allow the
formation of a DNA-primer hybrid; and incubating the DNA-primer
hybrid to allow the heat-stable DNA polymerase to synthesize the
DNA product. Preferably, these DNA amplification steps are repeated
at least one time. In a preferred embodiment, the annealing
temperature and the incubating temperature are the same. In another
preferred embodiment, the DNA product produced by the DNA
amplification is flanked by the generic sequence and reverse
complement of the generic sequence.
[0037] This DNA product is then subjected to DNA amplification by
the heat-stable DNA polymerase, wherein the second primer anneals
to the DNA product and the heat-stable DNA polymerase synthesizes a
complementary DNA strand from the 3' end of the second primer to
produce a second DNA product. The steps for DNA amplification by
the heat-stable DNA polymerase are denaturing the DNA product;
annealing the second primer with the DNA product to allow the
formation of a DNA-primer hybrid; and incubating the DNA-primer
hybrid to allow the heat-stable DNA polymerase to synthesize the
second DNA product. Preferably, these DNA amplification steps are
repeated about 30 to about 35 times, and more preferably about 40
times. In a preferred embodiment, the second DNA product is flanked
by the generic sequence and reverse complement of the generic
sequence. In another preferred embodiment, the annealing
temperature is higher than the optimal annealing temperature of the
random sequence of nucleotides at the 3' end of the first
primer.
[0038] Another aspect of the present disclosure is a preferred
method of identifying a polymorphism, which uses a reaction mixture
with a DNA sample; a first primer with a random sequence of
nucleotides at its 3' end and a generic sequence 5' of the random
nucleotides; and a second primer with the generic sequence of the
first primer and lacking the random sequence of the first primer.
In a preferred embodiment, a single reaction mixture is used.
Preferably, the reaction mixture also contains other components
that are necessary for DNA amplification, which are well known to
those of skill in the art. In a preferred embodiment, the amplified
DNA products are analyzed to identify a polymorphism, and
preferably the polymorphism is a single nucleotide polymorphism
(SNP). The methods of identifying SNPs are well known to those of
skill in the art. In a preferred embodiment of identifying a SNP,
the SNP is identified by DNA sequencing, Oligonucleotide Ligation
Assay (OLA), Doublecode OLA, Single Base Extension Assay, allele
specific primer extension, or mismatch hybridization.
[0039] The DNA sample in the reaction mixture is subjected to DNA
amplification by a first DNA polymerase, wherein the first primer
anneals to the DNA to allow the first DNA polymerase to synthesize
a complementary DNA strand from the 3' end of the first primer to
produce a DNA product. The steps for DNA amplification by the first
DNA polymerase are denaturing the DNA product; annealing the first
primer with the DNA to allow the formation of a DNA-primer hybrid;
and incubating the DNA-primer hybrid to allow the first DNA
polymerase to synthesize the DNA product. Preferably, these DNA
amplification steps are repeated at least one time. In a preferred
embodiment, the DNA product produced by the DNA amplification is
flanked by the generic sequence and reverse complement of the
generic sequence.
[0040] This DNA product is then subjected to DNA amplification by a
heat-stable DNA polymerase, wherein the second primer anneals to
the DNA product to allow the heat-stable DNA polymerase to produce
amplified DNA products. The amplified DNA products are produced
when the heat-stable DNA polymerase synthesizes a complementary DNA
strand from the 3' end of the second primer annealed to the DNA
product. The steps for DNA amplification by the heat-stable DNA
polymerase are denaturing the DNA product; annealing the second
primer with the DNA product to allow the formation of a DNA-primer
hybrid; and incubating the DNA-primer hybrid to allow the
heat-stable DNA polymerase to synthesize the amplified DNA
products. The amplified DNA products are then preferably analyzed
to identify a polymorphism. Preferably, these DNA amplification
steps are repeated about 30 to about 35 times, and more preferably
about 40 times. In a preferred embodiment, the amplified DNA
products are flanked by the generic sequence and reverse complement
of the generic sequence. In another preferred embodiment, the
annealing temperature is higher than the optimal annealing
temperature of the random sequence of nucleotides at the 3' end of
the first primer.
[0041] Another aspect of the present disclosure is a preferred
method of amplifying DNA that uses a reaction mixture with a DNA
sample to be amplified; a first primer with a random sequence of
nucleotides at its 3' end and a generic sequence 5' of the random
nucleotides; and a second primer with the generic sequence of the
first primer and lacking the random sequence of the first primer.
Preferably, the reaction mixture also contains other components
that are necessary for DNA amplification, which are well known to
those of skill in the art. In a preferred embodiment, the DNA
sample is tissue on a solid medium, and the DNA sample is
preferably dehydrated on the solid medium.
[0042] The DNA sample in the reaction mixture is heated to a
temperature that denatures the DNA to be amplified, cooled to a
temperature that allows the random sequence of the first primer to
hybridize to its complement DNA, and incubated to allow synthesis
of a DNA product by a DNA polymerase. In a preferred embodiment the
DNA polymerase is Taq DNA polymerase. Preferably, the steps of
heating, cooling, and incubating the reaction mixture are repeated
at least one time. In another preferred embodiment, the DNA product
is flanked by the generic sequence and reverse complement of the
generic sequence.
[0043] A series of DNA amplification reactions are performed with
the DNA product, wherein the annealing step is at a temperature
that selects for the generic sequence of the second primer
hybridizing to complement DNA in the DNA product over the random
sequence of the first primer hybridizing to complement DNA in the
DNA product. Preferably, the DNA amplification reactions involve a
heat-stable DNA polymerase synthesizing a complementary DNA strand
from the 3' end of the second primer to produce amplified DNA
products. The steps for DNA amplification by the heat-stable DNA
polymerase are denaturing the DNA product; annealing the second
primer with the DNA product to allow the formation of a DNA-primer
hybrid; and incubating the DNA-primer hybrid to allow the
heat-stable DNA polymerase to synthesize amplified DNA products.
Preferably, the series of DNA amplification reactions includes
about 30 to about 35 reactions, and more preferably about 40
reactions. In a preferred embodiment, the products of the DNA
amplification reactions are flanked by the generic sequence and
reverse complement of the generic sequence.
[0044] A preferred embodiment of the present disclosure is a method
of amplifying a DNA sample on a solid medium that involves
precipitating the DNA sample on the solid medium and subjecting the
precipitated DNA to DNA amplification to produce amplified DNA
products. Preferably the solid medium is filter paper, and the
filter paper is chemically treated. In a preferred embodiment, the
DNA sample is dehydrated on the filter paper. In another preferred
embodiment, the DNA sample is tissue, and the tissue is blood.
[0045] The DNA sample on a solid medium is preferably precipitated
with salt and alcohol, and rinsed with alcohol. Preferably, the
salt used to precipitated the DNA is sodium acetate, potassium
acetate, ammonium acetate, sodium chloride, or potassium chloride;
preferably the alcohol used is ethanol or isopropanol. In preferred
embodiments, the produced amplified DNA products are subjected to
genotype analysis, or a polymorphism is identified in the DNA
products, preferably a single nucleotide polymorphism (SNP). The
SNP may be identified by a number of techniques well known to those
of skill in the art, including preferably DNA sequencing,
Oligonucleotide Ligation Assay (OLA), Doublecode OLA, Single Base
Extension Assay, allele specific primer extension, or mismatch
hybridization.
[0046] Another aspect of the present disclosure is a preferred
method of identifying a polymorphism, which precipitates a DNA
sample on a solid medium, and uses a reaction mixture with the
precipitated DNA sample; a first primer with a random sequence of
nucleotides at its 3' end and a generic sequence 5' of the random
nucleotides; and a second primer with the generic sequence of the
first primer and lacking the random sequence of the first primer.
In a preferred embodiment, a single reaction mixture is used.
Preferably, the reaction mixture also contains other components
that are necessary for DNA amplification, which are well known to
those of skill in the art. In a preferred embodiment, the amplified
DNA products are analyzed to identify a polymorphism, and
preferably the polymorphism is a single nucleotide polymorphism
(SNP). The methods of identifying SNPs are well known to those of
skill in the art. In a preferred embodiment of identifying a SNP,
the SNP is identified by DNA-sequencing, Oligonucleotide Ligation
Assay (OLA), Doublecode OLA, Single Base Extension Assay, allele
specific primer extension, or mismatch hybridization.
[0047] The DNA sample in the reaction mixture is subjected to DNA
amplification by a first DNA polymerase, wherein the first primer
anneals to the DNA to allow the first DNA polymerase to synthesize
a complementary DNA strand from the 3' end of the first primer to
produce a DNA product. The steps for DNA amplification by the first
DNA polymerase are denaturing the DNA product; annealing the first
primer with the DNA to allow the formation of a DNA-primer hybrid;
and incubating the DNA-primer hybrid to allow the first DNA
polymerase to synthesize the DNA product. Preferably, these DNA
amplification steps are repeated at least one time. In a preferred
embodiment, the DNA product produced by the DNA amplification is
flanked by the generic sequence and reverse complement of the
generic sequence.
[0048] This DNA product is then subjected to DNA amplification by a
heat-stable DNA polymerase, wherein the second primer anneals to
the DNA product to allow the heat-stable DNA polymerase to produce
a second DNA product. The second DNA product is produced when the
heat-stable DNA polymerase synthesizes a complementary DNA strand
from the 3' end of the second primer annealed to the DNA product.
The steps for DNA amplification by the heat-stable DNA polymerase
are denaturing the DNA product; annealing the second primer with
the DNA product to allow the formation of a DNA-primer hybrid; and
incubating the DNA-primer hybrid to allow the heat-stable DNA
polymerase to synthesize the second DNA product. The amplified DNA
product is then preferably analyzed to identify a polymorphism.
Preferably, these DNA amplification steps are repeated about 30 to
about 35 times, and more preferably about 40 times. In a preferred
embodiment, the second DNA product is flanked by the generic
sequence and reverse complement of the generic sequence. In another
preferred embodiment, the annealing temperature is higher than the
optimal annealing temperature of the random sequence of nucleotides
at the 3' end of the first primer.
[0049] In a preferred embodiment, the solid medium is filter paper,
and the filter paper is chemically treated. In another preferred
embodiment, the DNA sample is dehydrated on the filter paper.
Preferably, the DNA sample is tissue, and the tissue is blood. The
DNA sample on a solid medium is preferably precipitated with salt
and alcohol, and rinsed with alcohol. Preferably, the salt used to
precipitated the DNA is sodium acetate, potassium acetate, ammonium
acetate, sodium chloride, or potassium chloride; preferably the
alcohol used is ethanol or isopropanol.
[0050] The DNA amplification methods of the present disclosure will
be useful for amplifying small amounts of DNA, which will allow
multiple sites in the DNA sample to be genotyped for
high-throughput screening. Additionally, the present method will
allow for the rapid construction of band specific painting probes
for any chromosomal region, and can also be used to microdissect
and amplify unidentifiable chromosomal regions or marker
chromosomes in abnormal karyotypes. The presently disclosed method
will also allow for the rapid cloning of amplified DNA for
sequencing or generating DNA libraries. Thus, the method will not
only be a valuable tool for genotype analysis and high-throughput
screening, it should also be a valuable tool in cytogenetic
diagnosis.
BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS
[0051] The following drawings form part of the present
specification and are included to further demonstrate certain
aspects of the present disclosure. The disclosure may be better
understood by reference to one or more of these drawings in
combination with the detailed description of specific embodiments
presented herein.
[0052] FIG. 1. Diagram to illustrate the first set of reactions of
the DNA amplification method. As demonstrated, during the first
cycle of DNA amplification the sample DNA is denatured and the
first primers randomly prime the single-stranded DNA for DNA
synthesis. The specific generic DNA sequence at the 5' end of the
first primer does not randomly anneal to the DNA strand. Next, Taq
DNA polymerase synthesizes the complementary DNA strand from the 3'
end of the randomly annealed first primers. In a second cycle of
DNA amplification in the first set of reactions, the newly
synthesized DNA strand with the generic sequence at its 5' end is
denatured from the sample DNA strand. Next, the first primers again
randomly prime the newly synthesized DNA strand, and Taq DNA
polymerase synthesizes the complementary DNA strand from the 3' end
of the randomly annealed first primers. This results in a final
product of a DNA strand flanked by the generic sequence at its 5'
end and the reverse complement of the generic sequence at its 3'
end. This DNA product will be amplified in a second set of
reactions of DNA amplification using a second primer that
hybridizes to the generic sequences flanking the DNA products.
[0053] FIG. 2. PCR amplification of DNA samples (bloodstains)
stored on FTA paper. The efficiency of PCR amplification of samples
processed using the commercial FTA Purification Reagent is compared
to samples processed using a preferred method of the present
disclosure. Identical punches obtained from the same bovine
bloodstains on FTA paper were treated using either the commercial
FTA Purification Reagent or the precipitation method of the present
disclosure. After the DNA samples were treated, the samples were
subjected to PCR amplification as described in Example 1. Lane 1,
DNA molecular size marker; lanes 2-5, direct PCR products of 4
bloodstain samples processed with commercial FTA Purification
Reagent; lanes 7-10, direct PCR products of the identical 4
bloodstain samples as lanes 2-5, respectively, first processed with
the precipitation method of the present disclosure. It is apparent
that DNA samples processed using the precipitation method of the
present disclosure are more consistently and optimally amplified by
PCR than samples treated with FTA Purification Reagent.
[0054] FIG. 3. PCR products of bloodstains on FTA paper processed
with the precipitation method of the present disclosure were
compared with PCR products of amplified genomic DNA generated from
bloodstains on FTA paper using the precipitation method and the DNA
amplification method of the present disclosure. Upper panel:
Agarose gel electrophoresis of bovine PCR products generated
directly from bloodstains on FTA paper that were processed with the
precipitation method of the present disclosure. Lane 1, DNA
molecular size marker; lanes 2-14, direct PCR products from the
bloodstain samples of 13 individual animals. Lower panel: Agarose
gel electrophoresis of bovine PCR products generated using genomic
DNA amplified with the disclosed DNA amplification method using as
DNA samples bloodstains on FTA paper that were processed with the
disclosed precipitation method. Lane 1, DNA molecular size marker;
lanes 2-14, direct PCR products of DNA amplified from genomic DNA
samples of 13 individual animals. It is apparent that DNA amplified
by the method of the present disclosure can be used to accurately
characterize DNA samples by PCR.
[0055] FIG. 4. Genomic DNA amplification from bloodstains on FTA
paper, comparing the commercial FTA Purification Reagent system
with the precipitation method of the present disclosure. Identical
sets of DNA samples were first processed using the commercial FTA
Purification Reagent system or the presently disclosed
precipitation method, and then the DNA samples were amplified using
the DNA amplification method of the present disclosure. Lane 1, DNA
molecular size marker; lanes 2-7, genomic DNA amplification of 6
bloodstains on FTA paper processed using the commercial FTA
Purification Reagent; lanes 8-13, genomic DNA amplification of 6
bloodstains on FTA paper processed using the precipitation method
of the present disclosure. It is readily apparent that the
disclosed method of DNA amplification yields far more amplified
genomic DNA products when the disclosed precipitation method is
used to process DNA samples on FTA paper than when the FTA
Purification Reagent is used.
[0056] FIG. 5. Genomic DNA amplification of bloodstains stored on
FTA paper using the presently disclosed DNA amplification method.
The efficiency of a series of generic DNA sequences used to
generate a first primer and a second primer for amplifying genomic
DNA were compared. In each of the reaction mixtures for DNA
amplification with the second primers listed below, the first
primer used contained the same generic sequence as the second
primer with 6 additional random nucleotides at the 3' end. Lane 1,
DNA molecular size marker; lane 2, genomic DNA amplification with a
second primer having the sequence of SEQ ID NO:3; lane 3, genomic
DNA amplification with a second primer having the sequence of SEQ
ID NO:4; lane 4, genomic DNA amplification with a second primer
having the sequence of SEQ ID NO:5; lane 5, genomic DNA
amplification with a second primer having the sequence of SEQ ID
NO:6; lane 6, genomic DNA amplification with a second primer having
the sequence of SEQ ID NO:7; lane 7, genomic DNA amplification with
a second primer having the sequence of SEQ ID NO:8; lane 8, genomic
DNA amplification with a second primer having the sequence of SEQ
ID NO:9; lane 9, genomic DNA amplification with a second primer
having the sequence of SEQ ID NO:10; lane 10, genomic DNA
amplification with a second primer having the sequence of SEQ ID
NO:11; and lane 11, genomic DNA amplification with a second primer
having the sequence of SEQ ID NO:12. The general ability of generic
sequences designed according to the present disclosure to amplify
DNA using the DNA amplification method is demonstrated by the
uniform DNA amplification demonstrated in lanes 2-11.
[0057] FIG. 6. Diagram to illustrate the Doublecode OLA
(oligonucleotide ligation assay) reaction to detect SNP variations
in a DNA sample. The upper diagram illustrates one option for
performing OLA using a labeled Reporter oligonucleotide. The
disadvantage of this technique is that a Reporter oligonucleotide
specific to a single SNP must be individually labeled by a fluor.
Since a new labeled Reporter oligonucleotide must be generated for
each SNP genotyped, this method is an expensive option for
large-scale genotyping. The lower diagram illustrates the
Doublecode OLA reaction, which offers a significant improvement
over the above method because it uses a labeled generic
AntiSignalcode oligonucleotide that can be produced in large
quantities and utilized for detecting any SNP. This AntiSignalcode
oligonucleotide is used with a Reporter oligonucleotide that
contains the reverse complement of the AntiSignalcode (Signalcode
sequence), as well as a region complementary to a single SNP. Thus,
this technique provides a less expensive option for detecting SNPs
than the technique illustrated in the upper panel.
DETAILED DESCRIPTION OF THE INVENTION
[0058] Genetic analysis of limited quantities of genomic DNA often
occurs in the areas of DNA forensics, paleoarcheology, genetic
disease diagnosis, genetic linkage analysis, and genetic diversity
analysis. Analysis and research in each of these areas will be
greatly improved if an efficient and inexpensive method for
amplifying genomic DNA and other types of DNA samples in a
sequence-independent matter is available. More extensive genetic
analysis of small DNA samples using amplified genomic DNA offers a
wide range of benefits in each of the above areas. Additionally, a
method that could amplify genomic DNA from a single cell, either
haploid or diploid, would allow for a more complete genetic
analysis of an individual cell from, for example, a
pre-implantation embryo, fetal cells in the peripheral blood of
pregnant women, sperm, or oocytes. The methods of DNA amplification
set forth in the present disclosure can be utilized in any of the
above areas to amplify DNA from limited starting materials, thereby
allowing for more complete genetic analyses of a large range of DNA
samples. Additionally, these methods are practical for wide-scale,
high-throughput screening of DNA samples.
[0059] Those of skill in the art understand that the basic steps in
DNA amplification are heat denaturation, annealing of
oligonucleotide primers, and extension of complementary DNA by a
DNA polymerase. The steps of denaturation, annealing, and extension
make up a single cycle of DNA amplification. In the heat
denaturation step, the temperature is raised to a temperature
sufficient to cause double-stranded DNA to denature into
single-stranded DNA. Next, during the annealing step, the
temperature is lowered to a temperature that facilitates the
annealing of the oligonucleotide primers to the single-stranded
DNA. Finally, during extension, the incubation temperature allows
the DNA polymerase to synthesize complementary DNA from the 3' end
of the annealed primer. In the presently disclosed methods for DNA
amplification, the sample DNA, a first primer having random
nucleotides at its 3' end and a generic sequence at its 5' end, and
a second primer with the generic sequence of the first primer are
placed together in a single reaction mixture. The sample DNA is
then amplified using a first set of reactions and a second set of
reactions, each of which includes the steps of denaturation,
annealing, and extension.
[0060] The first set of reactions of DNA amplification begins by
denaturing the double-stranded DNA sample to a single-stranded
condition, which allows primers to anneal to the DNA. Next, the
reaction temperature is lowered to a temperature that allows the
random nucleotides at the 3' end of the first primer to anneal to
the DNA to form hybrid duplexes. After the hybrid duplexes form,
DNA polymerase present in the reaction mixture extends the
complementary DNA strand from the 3' end of the first primer during
an incubation period. The DNA polymerase will preferably have 5' to
3' exonuclease activity so that it will be able to remove other
first primers anneal further downstream on the same DNA strand,
thus allowing longer complementary DNA strands to be synthesized
during the first set of reactions. Alternatively, the DNA
polymerase can have primer displacement activity, which will
achieve a similar result. Primer displacement activity means that
when the DNA polymerase is moving along the DNA strand synthesizing
complementary DNA and it encounters another primer annealed to the
DNA, the primer will be displaced and the polymerase reaction will
proceed. This activity also results in longer polymerization
products. While the annealing and incubation steps are preferably
performed at different temperatures, both the annealing and
incubation steps may occur at the same temperature if the DNA
polymerase is active at that temperature in the first set of
reactions.
[0061] After the first cycle of DNA amplification described above,
the newly synthesized complementary DNA strand will have the
generic sequence of the first primer at its 5' end, which was
incorporated into the strand when the 3' end of the first primer
was used as the starting point for synthesizing the complementary
DNA strand (see FIG. 1.). The above steps of denaturation,
annealing, and extension can be repeated, and generally should be
repeated at least once during the first set of reactions. The
denaturation step of the second cycle of the first set of reactions
separates the new first cycle DNA strands with the 5' generic
sequence from the original DNA strands. After denaturation, the new
first cycle DNA strands are available to the first primer present
in the reaction mixture for another round of annealing and
extension.
[0062] During the second cycle of the first set of reactions, the
first primer anneals to the first cycle DNA strand, DNA polymerase
extends a complementary strand from the 3' end of the first primer,
and the newly synthesized complementary DNA once again incorporates
the 5' end of the first primer into its sequence. This new second
cycle DNA fragment will also have the reverse complement of the
generic sequence on its 3' end, because DNA polymerase will
synthesize the full-length complementary DNA product of the first
cycle DNA strand, which has the generic sequence at its 5' end.
Thus, the DNA fragments amplified during the first set of reactions
have the generic sequence at one end of the fragment and its
reverse complement at the other. These DNA products of the first
set of reactions flanked with the generic sequence and its reverse
complement can now be readily amplified during a second set of
reactions with a second primer. The second primer has the same
generic DNA sequence as the first primer, but without the random
nucleotides at its 3' end.
[0063] The DNA products of the first set of reactions are
subsequently amplified using the second primer present in the
single reaction mixture. After these DNA products are denatured,
the temperature of the reaction is lowered so that the second
primer will anneal to the generic sequence at the ends of the DNA
products. The annealing temperature used for the second set of
reactions will generally be higher than the annealing temperature
used in the first set of reactions. The annealing temperature used
in the second set of reactions should be higher than the optimal
annealing temperature of the random sequence of the nucleotides of
the first primer. The higher temperature will minimize or prevent
random riming by the first primer through its random nucleotide
sequence located at its 3' end in the second set of reactions. This
characteristic eliminates the need to remove any remaining first
primer from the single reaction mixture during the second set of
reactions.
[0064] After the second primer anneals to the ends of the DNA
products, a heat-stable DNA polymerase extends the complementary
DNA strand from the 3' end of the second primer. The second set of
reactions involves repeating the above steps of denaturation,
annealing, and extension to achieve exponential amplification of
the DNA products, preferably using a total of about 30 to about 40
cycles. The final amplified DNA is ready for extensive analysis
using a variety of techniques, such as utilizing the amplified DNA
to genotype multiple sites in the DNA, including polymorphisms such
as SNPs, single tandem repeats (STRs), restriction fragment length
polymorphisms (RFLPs), variable number of tandem repeats (VNTRs),
complex tandem repeats (CTRs), microsatellites, deletions,
substitutions, or insertions. Alternatively, the amplified DNA may
be used to generate DNA libraries from a variety of sources.
[0065] Any type of DNA sample may be amplified using the methods of
the present disclosure because it is a sequence-independent method
of DNA amplification that can amplify even trace amounts of DNA. In
one preferred embodiment, the DNA sample is genomic DNA,
microdissected chromosome DNA, yeast artificial chromosome (YAC)
DNA, P1 derived artificial chromosome (PAC) DNA, cosmid DNA, phage
DNA, or bacterial artificial chromosome (BAC) DNA. In another
preferred embodiment, the DNA sample is tissue, blood, or a single
cell. Preferably the DNA sample is readily and easily obtained from
an organism, and is easy to store. The DNA sample can be obtained
from any species or organism, including but not limited to human,
mammal, bovine, porcine, ovine, equine, rodent, avian, fish,
zebrafish, shrimp, plants, yeast, virus, or bacteria.
[0066] DNA samples of tissue or blood containing genomic DNA
suitable for DNA amplification by the disclosed method may be
conveniently obtained from, for example, buccal swab, nose swab,
hair, mouthwash, cord blood, amniotic fluid, embryonic tissue,
endothelial cells, hoof clippings, or fingernail clipping. Genomic
DNA in paraffin-embedded tissue may also be amplified using the
disclosed method. The DNA amplification methods of the present
disclosure can amplify genomic DNA from a single cell, including
but not limited to a single cell isolated from a pre-implantation
embryo, fetal cells in the peripheral blood of pregnant women,
sperm, or oocytes, or a single cell from any tissue. A single cell
may be isolated using a variety of methods, including flow
cytometry (Herzenberg et al., Proc Natl Acad Sci USA 76:1453-55,
1979; Iverson et al., Prenatal Diagnosis 1:61-73, 1981; Bianchi et
al., Prenatal Diagnosis 11:523-28, 1991), which can utilize
fluorescent activation cell sorting (FACS), magnetic-activated cell
sorting (MACS, Ganshirt-Ahlert et al., Am J Obstet Gynecol
166:1350, 1992), or a combination of both procedures. Additionally,
a combination of gradient centrifugation and flow cytometry methods
can also be used to increase isolation or sorting efficiency. In
one preferred embodiment, the DNA sample does not have to be
purified or treated with proteinase K before DNA amplification
using the disclosed method.
[0067] The first primer used in the DNA amplification methods of
the present disclosure preferably has about 4 to about 9 random
nucleotides at its 3' end. In a preferred embodiment, the first
primer has 5, 6, 7, or 8 random nucleotides at its 3' end. The
first primer also has from about 10 to about 30 and preferably from
about 15 to about 25 nucleotides of a generic sequence at its 5'
end. In a preferred embodiment the first primer has 16, 17, 18, 19,
20, 21, 22, 23, or 24 nucleotides of a generic sequence at its 5'
end. The random sequence of nucleotides and the generic sequence 5'
of the random nucleotides may be adjacent in the first primer.
Alternatively, one or more nucleotides may be inserted between the
random sequence of nucleotides and the generic sequence 5' of the
random nucleotides in the first primer. The first primer may also
have additional nucleotides 5' of the generic sequence. An example
of a first primer is the sequence designated SEQ ID NO:1, in which
N designates a random nucleotide. The random sequence of
nucleotides can be composed of any of the nucleotides, for example
G, A, T, or C, in any order. It is understood that these letter
designations represent G for guanine, A for adenine, T for thymine,
and C for cytosine nucleotides. The random nucleotides can also
include nucleotide analogs, and other modified nucleotides that are
well known to those of skill in the art.
[0068] The first primer theoretically may contain all combinations
of these nucleotides in every position of the random portion of the
primer. Thus, the random nucleotides at the 3' end of the first
primer will be complementary to random sites throughout the target
DNA segments. It is understood by those of skill in the art that
the longer the random sequence of nucleotides is in the first
primer the less often the target sequence will occur in the genome,
and therefore the less often the first primer will anneal to the
target DNA segments. Additionally, the random sequence of the first
primer can be designed to be rich in the nucleotides A and T or
alternatively in the nucleotides G and C to allow for preferential
amplification of particular regions in the sample DNA, such as A:T
rich regions or G:C rich regions. It is well within the skill of
those in the art to use any ratio of the 4 nucleotides to generate
the random sequence of nucleotides.
[0069] As an example, if the 3' end of the first primer has 5
random nucleotides, there would be 4.sup.5 or 1,024 different
sequences in the random segment of the first primer for that
particular amplification. The complements of these sequences occur
in both orientations at random throughout the denatured DNA
segments of the DNA sample. By both orientations it is meant that
priming would occur on both strands of the melted DNA duplex that
is to be amplified.
[0070] As used herein, the term "generic sequence" refers to any
DNA sequence that would be a useful DNA amplification primer. An
example of the second primer is the sequence designated SEQ ID
NO:2. Thus, the generic sequence will preferably not have any
obvious self-homologies, nor runs of the same nucleotide, and the
generic sequence is preferably not overly G:C or A:T rich. A primer
that contains self-homologies or sequences in one region that are
complementary to sequences in another region of the primer will
form internal hairpin duplexes and thus would be unavailable to
hybridize with the sample DNA. Also, since G:C pairing involves 3
hydrogen bonds and A:T pairing involves 2 hydrogen bonds, a primer
with a disproportionately high content of the nucleotides G or C,
singly or in combination, will have a higher melting temperature
than a primer that was comprised of a higher content of A and T.
One of skill in the art can use this characteristic to manipulate
the annealing temperatures of the first and second primers to a
higher or lower temperature in the disclosed DNA amplification
method. Within the limits mentioned above, any generic sequence
that can be used to amplify DNA using the disclosed method is
contemplated to be within the scope of the present disclosure.
[0071] The sequence of the second primer used in the second set of
reactions is the same as the generic nucleotide sequence 5' of the
random nucleotide sequence of the first primer. While the second
primer may have additional nucleotides at its 5' end, this will
affect the annealing temperature of the DNA amplification reaction.
The second primer may also have additional nucleotides at its 3'
end, but these may interfere with the ability of the primer to
uniformly amplify DNA products during the second set of reactions
of DNA amplification by reducing the ability of the second primer
to universally bind and amplify the DNA products of the first set
of reactions. Therefore, the second primer will preferably have no
additional nucleotides on its 3' end.
[0072] In the first set of reactions of the disclosed method as
described in the paragraphs above, lower temperatures for the
annealing reaction are used because the first primer anneals to the
sample DNA through a short sequence of random nucleotides at its 3'
end. The incubation temperature preferably will allow for DNA
polymerase to successfully synthesize the complementary DNA strand
from the 3' end of the annealed primer. If Taq DNA polymerase is
used in the first set of reactions, an extension temperature that
allows Taq to have polymerase activity should be used. The DNA
products of this first set of reactions are flanked by the generic
sequence of the first primer and its reverse complement.
[0073] During the second set of reactions of DNA amplification, the
second primer will hybridize to these flanking sequences. Because
the generic DNA sequence is longer than the stretch of random
nucleotides at the 3' end of the first primer, the annealing
temperature in the second set of reactions will generally be at a
higher temperature. The higher annealing temperature will generally
minimize or prevent any remaining first primers that were not
incorporated into DNA products of the first set of reactions but
are still present in the reaction mixture from annealing to the DNA
products and randomly initiating DNA synthesis. Higher temperatures
generally require the use of a polymerase that is heat-stable,
which means that the polymerase can synthesize DNA at high
temperatures. One well-known example of a heat-stable DNA
polymerase is Taq DNA polymerase. A number of heat-stable or
thermostable DNA polymerases are commercially available, including
recombinant Taq DNA polymerases and native Taq DNA polymerases (see
Table 2). Another option is to use long-range PCR to generate
longer DNA products with, for example, TaqPlus DNA Polymerase.
Long-range PCR can be used in either the first set of reactions,
the second set of reactions, or both sets of reactions. In one
embodiment, Tub DNA polymerase can be used to amplify long DNA
sequences in the presently disclosed DNA amplification method.
Protocols for using Tub DNA polymerase and amplifying long regions
of DNA are found in Forrester and Redford (Methods Mol. Biol.
67:31-38, 1997), incorporated herein by reference.
[0074] In the presently disclosed method, the DNA to be amplified
in the first set of reactions is first denatured by heating the
reaction mixture to between about 90.degree. C. and about
100.degree. C., and preferably to about 95.degree. C. for about one
to about five minutes and preferably for about two minutes. During
this step, both the first and second primers are present in the
reaction mixture. Alternatively, the second primer may be added to
the reaction mixture after the first set of reactions but before
the second set of reactions. The first and second primers can be
added to the reaction mixture containing the DNA sample to be
amplified before heat denaturation or at any time during the
denaturation step of the first cycle of the first set of reactions.
In the preferred embodiment, the first and second primers are added
to the single reaction mixture in equal molar ratios. The molar
ratios of the two primers, however, may also vary in relation to
each other to optimize DNA amplification. The molar ratios of the
DNA to be amplified and the first and second primers can be varied
by one of skill in the art to optimize DNA amplification.
[0075] Next, the temperature of the reaction mixture is lowered to
a temperature that allows the first primer to anneal to the
single-stranded DNA. The second primer present in the reaction
mixture will not generally anneal to the single-stranded DNA in the
first set of reactions because the reverse complement of the longer
generic DNA sequence necessary for annealing the primer will
rarely, if at all, be present in the single-stranded DNA. The
annealing temperature of the random sequence of nucleotides of the
first primer preferably should be between about 37.degree. C. and
about 50.degree. C., preferably between about 42.degree. C. and
about 45.degree. C. Preferably, a different temperature from the
annealing temperature may be used during the incubation period for
extension of the complementary DNA strand that allows the DNA
polymerase to synthesize DNA from the 3' end of the first primer.
If the DNA polymerase functions at the annealing temperature, then
this temperature may be maintained during the incubation period.
The incubation period is preferably about 2 minutes to about 7
minutes, more preferably about 5 minutes.
[0076] These steps of the first set of reactions should be repeated
at least once, so that preferably two cycles of these initial DNA
amplification steps are performed, although more than two cycles of
DNA amplification in this first set of reactions is contemplated.
For example, 3 or 4 cycles may be performed in the first set of
reactions. But for every additional cycle of denaturation,
annealing, and extension, the DNA products available for the second
set of reactions of DNA amplification will generally be shortened.
This is because each successive round of random priming by the
first primer further shortens the previously amplified DNA
products. This effect is overcome during the second set of
reactions of DNA amplification because the second primers anneal to
the ends of the DNA products flanked by the generic sequence and
the reverse complement of the generic sequence produced in the
first set of reactions.
[0077] The DNA products of the first set of reactions, which are
flanked by the generic sequence and its reverse complement are
subsequently exponentially amplified in the second set of reactions
of DNA amplification in the disclosed method. In the second set of
reactions, the DNA products of the first set of reactions are first
denatured by heating the reaction mixture to between about
90.degree. C. and about 100.degree. C., and preferably to about
95.degree. C. for about 15 seconds to about 2 minutes, preferably
for about 30 seconds to about 1 minute. Next, the temperature of
the reaction mixture is decreased to a temperature that allows the
second primer to anneal to the single stranded DNA products. The
annealing temperature of the second primer is preferably between
about 55.degree. C. and about 68.degree. C., preferably between
about 60.degree. C. and about 65.degree. C. The annealing
temperature of the second primer must be stringent enough to
minimize or prevent random priming by the unincorporated first
primers remaining in the reaction mixture. Therefore, it is not
necessary to remove the first primers from the reaction mixture
during the second set of reactions, which increases the efficiency
of the disclosed method. This also greatly simplifies the present
DNA amplification method for high-throughput screening as compared
to other known methods.
[0078] While the incubation temperature may be the same as the
annealing temperature in the second set of reactions if the DNA
polymerase is active at that temperature, preferably the
temperature of the incubation step is raised to a more optimal
temperature for the heat-stable DNA polymerase to synthesize DNA.
The optimal temperature for the extension step will be dependent on
the DNA polymerase used in the second set of reactions. For
example, during the incubation step of the second set of reactions,
the temperature is increased to about 68.degree. C. to about
75.degree. C., and preferably to about 70.degree. C. to about
72.degree. C., and held for about 30 seconds to about 10 minutes,
and preferably for about 4 minutes to about 6 minutes. The
denaturation, annealing, and extension steps of the second set of
reactions are repeated about 30 to about 40 times, and preferably
about 33 to about 35 times. The reaction can then be held at about
72.degree. C. for about 7 minutes to about 10 minutes to complete
any nascent polymerizations. It is not necessary to add fresh
enzyme after each denaturation step if a heat-stable DNA polymerase
such as the Taq DNA polymerase is used because Taq is not
completely denatured by the denaturation step, and functions
optimally at higher temperatures. Although a non-heat-stable DNA
polymerase could also be used in the second set of reactions if it
were added after each denaturation step of every cycle, this
inefficient method would be impractical for high-throughput
screening.
[0079] It is well known to those of skill in the art that the
optimal temperatures for each step of the first set of reactions
and the second set of reactions are determined (usually
empirically) by the size of the sample DNA to be amplified and by
the size and sequence of the primers. For example, simple formulas
for determining the melting temperature of a perfectly matched
duplex based on the G:C content of the primer are well known in the
art. The optimal annealing temperature of a primer can be
calculated by one of skill in the art by using a variety of
available computer software programs, such as Oligo Analyzer, which
is available at the website www.idtdna.com. It is also well known
to one of skill in the art that the temperatures between any of the
steps in the first set of reactions and/or the second set of
reactions may be increased or decreased gradually over about a 1 to
about an 8 minute period of time, and preferably over about a 3
minute period of time.
[0080] One of skill in the art may also desire to incorporate one
or more restriction enzyme sites in the generic sequence for
subsequent cloning of the amplified products. Restriction enzymes
sites are DNA sequences that are recognized and cleaved at a
specific point by a restriction endonuclease enzyme. The use of
particular restriction enzymes is well known in the art (see Table
1), and a particular restriction enzyme compatible with the vector
of choice for cloning the amplified DNA may be chosen. The number
of available vectors are too numerous to list, and are well known
to those of skill in the art. Popular vectors such as pBR322, or
the pGem or PUC series of plasmids, contain certain specific
restriction enzyme recognition sites in their polyclonal regions.
The generic sequence can be designed so that one or more
recognition sequences are included in the generic primer that are
compatible with sites in the chosen cloning vector.
[0081] In a certain embodiment, the present disclosure encompasses
a first primer and a second primer for use in DNA amplification.
The first primer preferably has a region of about 4 to about 8
random nucleotides at its 3' end and about 15 to about 25 bp of a
generic DNA 5' of the random nucleotide sequence. This first primer
is further characterized by the ability of its random sequence of
nucleotides to hybridize to DNA sequences at a temperature of
between about 37.degree. C. and about 42.degree. C. The second
primer is preferably between about 15 and about 25 bp in length,
and has the same sequence as the generic sequence 5' of the random
sequence of nucleotides in the first primer. The second primer may
also have additional nucleotides to facilitate the method of DNA
amplification, particularly in relation to the high stringency
annealing step in the second set of reactions. The second primer
can further contain a restriction enzyme recognition site to
facilitate the subcloning of the amplified DNA products into a
vector of choice or a stretch of CUA repeats to facilitate cloning,
for example by the "Clone Amp" protocol (BRL).
[0082] In a preferred embodiment, the DNA polymerase used to
amplify the DNA in the first set of reactions is the same as the
heat-stable DNA polymerase used in the second set of reactions.
Using the same DNA polymerase for both the first and second set of
reactions greatly simplifies the disclosed method of DNA
amplification because only one reaction mixture is prepared with
the single heat-stable DNA polymerase, which greatly facilitates
high-throughput screening. Using the same DNA polymerase means that
the enzyme is simply added to the initial reaction mixture, and no
additional enzyme must be added during the first or second set of
reactions of DNA amplification.
[0083] It is also contemplated, however, that one DNA polymerase
may be used in the first set of reactions and a second heat-stable
DNA polymerase used in the second set of reactions. During the
first set of reactions, if a heat-stable DNA polymerase is not
used, fresh enzyme must be added to the reaction mixture after each
denaturation step, because the DNA polymerase will be destroyed by
the heat necessary to denature the DNA. The DNA amplification steps
of the first set of reactions are repeated one to three times,
preferably one time as discussed above, again with fresh enzyme
added after each denaturation step. A heat-stable DNA polymerase
must then be added for the second set of reactions of DNA
amplification, either before, during or after the first
denaturation step of the second set of reactions.
[0084] The preferred DNA polymerase used in the presently disclosed
method is a heat-stable enzyme with 5' to 3' exonuclease activity,
or alternatively primer displacement activity. For example, Taq DNA
polymerase can be added to the initial reaction mixture to amplify
the DNA in both the first set of reactions and the second set of
reactions of the disclosed method. Taq DNA polymerase possesses
intrinsic 5' to 3' exonuclease activity, which allows Taq to digest
oligonucleotide primers that it encounters downstream while
synthesizing complementary DNA (Longley et al., Nucleic Acids Res
18(24):7317-22, 1990). DNA polymerases that may be used in the
first set of reactions include any polymerase with 5' to 3'
exonuclease activity, or alternatively primer displacement activity
with or without exonuclease activity. Enzymes that may be used in
the first set of reactions include but are not limited to, Taq DNA
polymerase, modified Taq DNA polymerase such as for example
Amplitaq Gold, E. coli DNA Polymerase I, Tub DNA Polymerase, and
DNA Polymerase I (see Table 2).
[0085] If the DNA polymerase used in the first set of reactions
differs from the heat-stable DNA polymerase used in the second set
of reactions, the final DNA products of the first set of reactions
may have to be diluted into buffer that allows the heat-stable DNA
polymerase to perform optimally. The first set of reactions may be
performed in relatively low volume, particularly when the sample
DNA is present in small amounts as in microdissected chromosomes
and in YACs isolated from pulsed field gels, or from small tissue
or blood samples, or single cells. It is contemplated that the
volume of the first set of reactions and the second set of
reactions may vary widely depending on the particular application
and that higher or lower reaction volumes are encompassed by the
present disclosure. Although a small aliquot of the first set of
reactions may be used with a heat-stable DNA polymerase and its
buffer in the second set of reactions, preferably the reaction
volume for both the first set of reactions and second set of
reactions is the same, particularly if the same DNA polymerase is
utilized for both sets of reactions.
[0086] It is contemplated that when DNA polymerase and its buffer
are added to the single reaction mixture of the present method,
other components necessary for DNA amplification are present in the
reaction mixture. The necessary reaction components for DNA
amplification are well known to those of skill in the art and may
include, but are not limited to, bovine serum albumin, MgCl.sub.2
in a concentration of about 1.5 mM to about 5 mM final
concentration, the four deoxynucleotide bases (DATP, dGTP, dTTP,
and dCTP), and purified water, for example distilled, deionized or
ultrafiltered water. The buffers employed may contain components
such as Tris HCl at a pH of about 7.0 to about 9.0, MgCl.sub.2,
NaCl, and DTT (dithiothreitol). Buffers may also include KCl and
gelatin. The composition of buffers for PCR and DNA amplification
are well known to those of skill in the art, and the concentration
of certain components such as MgCl.sub.2 for example, can easily be
determined empirically for each reaction.
[0087] It is also understood by those of skill in the art that the
temperatures, incubation periods, and ramp times of the DNA
amplification steps may vary considerably without significantly
altering the efficiency of DNA amplification and other results.
Alternatively, those of skill in the art may alter these parameters
to optimize the DNA amplification reactions. These minor variations
in reaction conditions and parameters are included within the scope
of the present disclosure. The DNA products of the above reactions
may be visualized by running them on an agarose or acrylamide
electrophoresis gel, preferably on a 1.5% to 2.0% agarose gel.
After staining the gel with ethidium bromide, the products of the
random, sequence independent amplification will preferably appear
as a smear.
[0088] In one embodiment, the present disclosure encompasses a
method for amplifying DNA, independent of the sequence of the DNA,
that includes the steps of: [0089] (a) adding to the DNA sample in
a single reaction mixture, 10 mM Tris HCl (pH 8.3), 5 mM
MgCl.sub.2, 50 mM KCl, 0.001% gelatin, 300 .mu.M dNTP (dATP, dGTP,
dCTP, and dTTP), 300 nM of the first primer having the sequence of
SEQ ID NO:1, 300 nM of the second primer having the sequence of SEQ
ID NO:2, and 1.25 unit Taq DNA polymerase, for a total volume of
about 50 .mu.M; [0090] (b) denaturing the DNA by heating the
reaction mixture to a temperature of about 95.degree. C. for about
5 minutes; [0091] (c) denaturing the DNA by heating the reaction
mixture to a temperature of about 95.degree. C. for about 1 minute,
and then cooling the reaction mixture to a temperature of about
42.degree. C. for about 5 minutes, thereby allowing the first
primer to anneal to the denatured DNA to form a DNA-primer hybrid
and the Taq DNA polymerase to synthesize the complementary strand
of DNA from the 3' end of the first primer; [0092] (d) repeating
step (c) one time; [0093] (e) denaturing the DNA products by
heating the reaction mixture to a temperature of about 95.degree.
C. for about 15 seconds, cooling the reaction mixture to a
temperature of about 65.degree. C., thereby allowing the second
primer to anneal to the denatured DNA to form a DNA-primer hybrid;
and raising the reaction mixture to a temperature of about
68.degree. C., thereby allowing the Taq DNA polymerase to
synthesize the complementary strand of DNA from the 3' end of the
second primer; [0094] (f) repeating step (e) about 39 times.
[0095] An example of the first primer is the sequence
5'-TAGCAGTGGTAACAACGCAGAGANNNNN-3' (SEQ ID NO:1). An example of the
second primer is the sequence 5'-TAGCAGTGGTAACAACGCAGAGA-3' (SEQ ID
NO:2). Additional examples of the generic sequence that may be used
as a second primer in the presently disclosed method to amplify DNA
include, but are not limited to:
TABLE-US-00001 5'-ACAACGCAGAGTAAGCAGTGGTA-3',; SEQ ID NO: 3
5'-ACAACGGTAGCAGAGTAAGCAGT-3',; SEQ ID NO: 4
5'-GAGTAAGCAGTACAACGGTAGCA-3',; SEQ ID NO: 5
5'-GAGGCATAAGCAGTACAACGGTA-3',; SEQ ID NO: 6
5'-CAACGGTAGAGGCATAAGCAGTA-3',; SEQ ID NO: 7
5'-GGCATAAGCAGTACAACGGTAGA-3',; SEQ ID NO: 8
5'-AACGGTAGAGGCATAAGCAGTAC-3',; SEQ ID NO: 9
5'-AGTACAACGGTAGAGGCATAAGC-3',; SEQ ID NO: 10
5'-AAGCAGTACAACGGTAGAGGCAT-3',; SEQ ID NO: 11
5'-CGGTAGAGGCATAAGCAGTACAA-3',. SEQ ID NO: 12
[0096] The first primer used in the same reaction mixture for DNA
amplification with each of the above second primers will contain
the same generic sequence with an additional random sequence of
nucleotides at its 3' end. The optimal annealing temperatures of
the first set of reactions and the second set of reactions of DNA
amplification can be determined by one of skill in the art based on
the generic DNA sequence and the number of random nucleotides at
the 3' end of the first primer. Preferably, the optimal annealing
temperature of each set of reactions will be such that second
primer annealing is minimized or prevented in the first set of
reactions and first primer annealing through its random sequence of
nucleotides is minimized or prevented in the second set of
reactions.
[0097] When DNA samples utilized in the presently disclosed DNA
amplification methods are stored on a solid medium, preparing the
DNA sample for amplification and/or genetic analysis can be not
only inefficient, but also can yield inconsistent results, thereby
limiting the information that is obtained from the DNA sample. The
present disclosure seeks to overcome the drawbacks inherent in
other methods of preparing DNA samples stored on solid mediums for
DNA amplification and/or genetic analysis. The presently disclosed
method, also termed the precipitation method, greatly simplifies
the preparation of DNA samples stored on a solid medium by
eliminating the unnecessary steps of DNA purification. In the
disclosed method, the DNA sample on a solid medium is precipitated
by methods well known to those of skill in the art, and then
directly subjected to DNA amplification and/or genetic analysis.
This method produces more consistent results, reduces the cost of
high-throughput operations, and improves the quality of DNA
amplified from the DNA sample.
[0098] The present disclosure includes the variety of solid mediums
well known to those of skill in the art for storing DNA, including
as tissue and blood samples. Preferably, the solid medium is dry,
and has a solid matrix or solid support, such as preferably an
absorbent cellulose-based paper (such as filter paper), or a
micromesh of synthetic plastics materials. The solid matrix may
also be in the form of a tablet or pellet. Preferably the solid
medium will protect against the degradation of the DNA sample
incorporated or absorbed on the matrix or support. A solid medium
allows DNA samples to be stored and transported in a form suitable
for the recovery of the DNA in the sample for genotype analysis.
DNA samples can be collected and stored for example on FTA.TM.
paper, Whatmann.RTM. paper, Gibson paper, Guthrie cards, swabs, and
filter paper. In a preferred embodiment the DNA sample is stored on
FTA paper. Blood or tissue collected on filter paper can be dried
and stored at room temperature.
[0099] Methods of precipitating DNA using a salt and alcohol
solution are well known to those of skill in the art, and are
included within the scope of the present disclosure. In a preferred
embodiment, the precipitation method of the present disclosure
begins by washing the DNA sample on the solid medium with water,
for example distilled, deionized, or ultrafiltered water, to remove
any chemicals that might interfere with subsequent DNA
amplification reactions. In a preferred embodiment, the DNA sample
is repeatedly washed with water. Next, the solid medium is treated
with a solution that includes salt and alcohol, which precipitates
the DNA in the sample. After the precipitation step the DNA is
fixed on the solid support. In a preferred embodiment, the salt
used to precipitate the DNA is sodium acetate, potassium acetate,
or ammonium acetate, preferably at a concentration of about 0.1 to
about 0.5 M, more preferably about 0.2 to about 0.3 M. In another
preferred embodiment, the alcohol used to precipitate the DNA is
isopropanol, ethanol, or other similar water-miscible solvents such
as n-propanol, preferably at a purity level of about 70% to about
100%, more preferably about 95%. It is well within the skill of
those in the art to determine the appropriate ratio of salt to
alcohol in the precipitation solution to precipitate the DNA. In a
preferred embodiment, the ratio is 50/50 v/v.
[0100] After the DNA is precipitated, it is washed with alcohol to
dissolve any salts remaining in the sample from the precipitation
step. This step can also accelerate dehydration of the sample. In a
preferred embodiment, the alcohol used to wash the precipitated DNA
is isopropanol, ethanol, or other similar water-miscible solvents
such as n-propanol, preferably at a purity level of about 80% to
about 95%, more preferably about 70%. Interestingly, when DNA
samples on FTA paper are processed using the disclosed
precipitation method, the final DNA-paper can remain the red-brown
color of blood. Nevertheless, the processed DNA on the FTA paper
now can be efficiently and predictably amplified by any one of many
methods of DNA amplification known by those of skill in the art,
including but not limited to the DNA amplification method of the
present disclosure, as well as PCR.TM.. Thus, the presently
disclosed methods greatly reduce the variation of DNA amplification
efficiency found when DNA samples stored on solid supports are
processed using commercially available reagents.
[0101] Additionally, the solutions used in the presently disclosed
precipitation method, which include water, alcohol, and salts, are
inexpensive and easy to make. The disclosed precipitation method
thus also greatly reduces the cost of high-throughput operations,
particularly when compared to other commercially available
reagents. For example, the ethanol wash can reduce the time for FTA
paper dehydration by at least 50% when compared to the water-based
FTA Purification Reagent protocol. Additionally, the presently
disclosed methods for precipitation and DNA amplification to
analyze DNA samples stored on FTA paper can all be conducted in
96-well or 384-well plates, which greatly facilitates
high-throughput operations.
[0102] Genotype analysis of sample DNA on a solid support,
processed using the disclosed precipitation and/or DNA
amplification methods, or genotype analysis of DNA amplified by the
preferred methods of the present disclosure, may be performed using
a variety of methods and techniques that are well known to those of
skill in the art. The advantages offered by the disclosed methods
of DNA amplification for high-throughput screening are that the
genotypes of large numbers of organisms can be rapidly screened for
diagnostic or research purposes. The term "genotype analysis"
refers to any type of genetic typing, genotyping, fingerprinting,
haplotyping, DNA typing, or any similar phrase. The term includes
the use of any methods or protocols known to those of skill in the
art for determining an individual's genotype at one or more genetic
loci, including identifying haplotypes. Techniques that are nucleic
acid based include but are not limited to size fractionation, SNP
analysis, allele specific oligonucleotide (ASO) hybridization,
sequencing, RFLP analysis, denaturation temperature analysis, and
mass spectrometry analysis. Methodologies available to those of
skill in the art are numerous and continually developing, and
cannot be detailed herein. Many types of polymorphisms may be
detected using amplified DNA, including but not limited to SNPs,
RFLPs, VNTRs, STRs, CTRs, and microsatellites.
[0103] Single nucleotide polymorphisms (SNPs) are nucleotide
sequence variants that are of predictive value in identifying many
genetic diseases, as well as phenotypic characteristics that may be
desirable, which are often caused by a limited number of different
mutations in a population. SNPs are found in both coding and
non-coding regions of genomic DNA. In spite of the paucity of
scorable phenotypes, SNPs are found in large numbers throughout the
human genome (Cooper et al., Hum Genet 69:201-205, 1985). Certain
SNPs result in disease-causing mutations such as, for example,
heritable breast cancer (Cannon-Albright and Skolnick, Semin Oncol
23:1-5, 1996). It is specifically contemplated that DNA amplified
by the disclosed methods may be useful in the detection of SNPs or
other polymorphisms in an individual. Current methods of screening
for polymorphisms are known (see for example U.S. Pat. Nos.
6,221,592 and 5,679,524). A limitation of these techniques,
however, is the inability to provide multiple copies of genomic DNA
to enhance signals and facilitate detection. The disclosed methods
overcome this problem by facilitating rapid, high-throughput DNA
amplification of randomly primed nucleic acid sequences throughout
the full length of, for example, an individual's genome. Since
multiple copies of each region including a SNP or other
polymorphism would be present in a sample following DNA
amplification using the disclosed methods, the likelihood of
producing a detectable signal utilizing standard SNP detection
methods increases.
[0104] A SNP may be identified in the DNA of an organism by a
number of methods well known to those of skill in the art,
including but not limited to identifying the SNP by PCR.TM. or DNA
amplification, Oligonucleotide Ligation Assay (OLA) (Landegren et
al., Science 241:1077, 1988), Doublecode OLA, mismatch
hybridization, mass spectrometry, Single Base Extension Assay, RFLP
detection based on allele-specific restriction-endonuclease
cleavage (Kan and Dozy, Lancet ii:910-912, 1978), hybridization
with allele-specific oligonucleotide probes (Wallace et al., Nucl
Acids Res 6:3543-3557, 1978), including immobilized
oligonucleotides (Saiki et al., Proc Natl Acad Sci USA
86:6230-6234, 1989) or oligonucleotide arrays (Maskos and Southern,
Nucl Acids Res 21:2269-2270, 1993), allele-specific PCR.TM. (Newton
et al., Nucl Acids Res 17:2503-16, 1989), mismatch-repair detection
(MRD) (Faham and Cox, Genome Res 5: 474-482, 1995), binding of MutS
protein (Wagner et al., Nucl Acids Res 23:3944-3948, 1995),
single-strand-conformation-polymorphism detection (Orita et al.,
Genomics 5:874-879, 1983), RNAase cleavage at mismatched
base-pairs-(Myers et al., Science 230:1242, 1985), chemical (Cotton
et al., Proc Natl Acad Sci USA 85:4397-4401, 1988) or enzymatic
(Youil et al., Proc Natl Acad Sci USA 92:87-91, 1995) cleavage of
heteroduplex DNA, methods based on allele specific primer extension
(Syvanen et al., Genomics 8:684-692, 1990), genetic bit analysis
(GBA) (Nildforov et al., Nuci Acids Res 22:4167-4175, 1994), and
radioactive and/or fluorescent DNA sequencing using standard
procedures well known in the art.
[0105] Preferably the identified SNP is linked to a phenotype,
including disease phenotypes and desirable phenotypic traits. The
amplified DNA products of the disclosed methods may also be used to
generate a DNA library, including genomic DNA libraries,
particularly if the generic sequence of the first and second
primers include a restriction enzyme site to facilitate cloning of
the DNA products. Additionally, the presently disclosed methods
allow for the rapid construction of band specific painting probes
for any chromosomal region, and can also be used to microdissect
and amplify unidentifiable chromosomal regions or marker
chromosomes in abnormal karyotypes. Thus, the disclosed methods are
not only a valuable tool for genotype analysis and high-throughput
screening, but also a valuable tool in cytogenetic diagnosis.
[0106] A Single Base Extension Assay is performed by annealing an
oligonucleotide primer to a complementary nucleic acid, and
extending the 3' end of the annealed primer with a chain
terminating nucleotide that is added in a template directed
reaction catalyzed by a DNA polymerase. The selectivity and
sensitivity of a single base primer extension reaction are affected
by the length of the oligonucleotide primer and the reaction
conditions (e.g. annealing temperature, salt concentration). The
selectivity of a primer extension reaction reflects the amount of
exact complementary hybridization between an oligonucleotide primer
and a nucleic acid in a sample. A highly selective reaction
promotes primer hybridization only to nucleic acids with an exact
complementary sequence (i.e. there are no base mismatches between
the hybridized primer and nucleic acid). In contrast, in a non
selective reaction, the primer also hybridizes to nucleic acids
with a partial complementary sequence (i.e. there are base
mismatches between the hybridized primer and nucleic acid). In
general, parameters which favor selective primer hybridization (for
example shorter primers and higher annealing temperatures) result
in a lower level of hybridized primer. Therefore, parameters which
favor a selective single base primer extension assay result in
decreased sensitivity of the assay.
[0107] Additionally, cycled Single Base Extension Reactions may be
performed by annealing a nucleic acid primer immediately 5' to a
region containing a single base to be detected. Two separate
reactions are conducted. In the first reaction, a primer is
annealed to the complementary nucleic acid, and labeled nucleic
acids complementary to non-wild-type variants at the single base to
be detected, and unlabeled dideoxy nucleic acids complementary to
the wild-type base, are combined. Primer extension is stopped the
first time a base is added to the primer. Presence of label in the
extended primer is indicative of the presence of a non-wild-type
variant. A DNA polymerase, such as Sequenase.TM. (Amersham), is
used for primer extension. In a preferred embodiment, a
thermostable polymerase, such as Taq or thermal sequenase is used
to allow more efficient cycling. Once an extension reaction is
completed, the first and second probes bound to target nucleic
acids are dissociated by heating the reaction mixture above the
melting temperature of the hybrids. The reaction mixture is then
cooled below the melting temperature of the hybrids and additional
primer is permitted to associate with target nucleic acids for
another round of extension reactions. After completion of all
cycles, extension products are isolated and analyzed.
Alternatively, chain-terminating methods other than dideoxy
nucleotides may be used. For example, chain termination occurs when
no additional bases are available for incorporation at the next
available nucleotide on the primer.
[0108] A particularly powerful means of analyzing genetic
information from DNA amplified using the disclosed methods is DNA
chip technology. DNA chips and microarrays comprising arrays of
oligonucleotide or polynucleotide probes can be used to determine
whether a target nucleic acid has a nucleotide sequence identical
to or different from a specific reference sequence. The basic chip
or microarray encompasses an array of oligonucleotide or
polynucleotide probes immobilized on a solid support. Chips for
screening and detection are designed to contain probes exhibiting
complementarity to one or more selected sequences whose sequence is
known. Chips are used to read a target sequence comprising either
the reference sequence itself or variants of that sequence. Target
sequences may differ from the reference sequence at one or more
positions but show a high overall degree of sequence identity with
the reference sequence (e.g., at least 75, 90, 95, 99, 99.9, or
99.99%). Hybridization of a target sequence to an immobilized probe
results in a detectable signal. Signal can be delivered for example
by conformational changes occurring in the probe, quenching or
excitation of a label incorporated into the bound probe, or by
quenching or excitation of a label incorporated into the target.
Signal delivery may be read manually, mechanically, or digitally. A
number of patents, herein incorporated by reference, disclose the
preparation and use of DNA chips and microarrays including: U.S.
Pat. Nos. 5,837,832, 6,156,501, 6,174,683, and 5,985,567.
Additionally, allele specific primer extension can be combined with
primer arrays for high-throughput genotyping of SNPs (see Pastinen
et al., Genome Res 10(7):1031-42, 2000, incorporated herein by
reference).
[0109] In the context of the present disclosure, it is specifically
contemplated that the DNA amplification products of the disclosed
methods may be analyzed using DNA chips or microarrays in order to
detect specific genetic sequences, including genetic polymorphisms
or mutations, such as for example SNPs. In one embodiment, it is
envisioned that genomic DNA will be amplified utilizing the methods
of the present disclosure in order to produce a library of DNA
sequences theoretically encompassing the entire genomic sequence.
The amplified DNA products may then be passed over a DNA chip or
microarray encompassing oligonucleotide or polynucleotide probes.
The ability or inability of the amplified DNA to hybridize to the
microarray or DNA chip will facilitate the characterization of the
specific sequences and their polymorphisms present in the DNA
sample.
[0110] One embodiment of the present disclosure involves
fluorescence in situ hybridization (FISH) analysis of chromosomes.
First, a chromosomal DNA sample of interest is obtained. This
sample may be a YAC chromosomal insert, a sample of microdissected
chromosome, a cosmid DNA insert, a PAC DNA insert, a plasmid
insert, or a phage insert, for example lambda phage. For example
YAC DNA may be isolated from the other yeast chromosomes on a
pulsed field electrophoresis gel. Once obtained, the DNA is
amplified by the disclosed method. The amplified DNA can then be
labeled by a further PCR that contains a labeled nucleotide base
which will be incorporated into the amplified product. Using PCR to
label DNA is well known to those of skill in the art. The label may
include, but is not limited to, biotin, Spectrum-Orange, or
Spectrum-Green. Using the disclosed method for amplifying DNA, no
prior purification of the DNA is required, and the method results
in a substantial improvement in the speed of probe preparation and
in the quality of the FISH signal over other DNA amplification
strategies. The ability to obtain such reliable FISH signals will
allow new ways of screening for the presence of common
translocations in a variety of human tumors.
[0111] Additionally, labeled amplified DNA can be hybridized to a
chromosome preparation such as interphase or, preferably, metaphase
spreads. In metaphase spreads, the chromosomes are shortened and
thickened and are more easily visualized and identified.
Hybridization with the labeled probe allows one to determine the
particular chromosome and the position on the chromosome from which
the amplified probe was derived. Amplified, labeled DNA may also be
hybridized to interphase nuclei in order to determine the number of
hybridization sites in the nucleus. The hybridized probes that are
labeled with biotin can be visualized with
fluorescein-isothiocyanate conjugated avidin under a fluorescence
microscope. Probes labeled with Spectrum-Orange or Spectrum-Green
are directly visualized by fluorescence microscopy.
[0112] The methods and preferred embodiments of the present
disclosure have been described above. Many techniques and methods
are well known to those of skill in the art and may be used to
assist practitioners in carrying out the methods of the present
disclosure. The following is a general description of some of these
techniques.
[0113] Nucleic Acids:
[0114] Genes are sequences of DNA in an organism's genome encoding
information that is converted into various products making up a
whole cell. They are expressed by the process of transcription,
which involves copying the sequence of DNA into RNA. Most genes
encode information to make proteins, but some encode RNAs involved
in other processes. If a gene encodes a protein, its transcription
product is called mRNA ("messenger" RNA). After transcription in
the nucleus (where DNA is located), the mRNA is transported into
the cytoplasm for the process of translation, which converts the
code of the mRNA into a sequence of amino acids to form protein. In
order to direct transport of mRNA into the cytoplasm, the 3' ends
of mRNA molecules are post-transcriptionally modified by the
addition of several adenylate residues to form the "polyA" tail.
This characteristic modification distinguishes gene expression
products destined to make protein from other molecules in the cell,
and thereby provides one means for detecting and monitoring the
gene expression activities of a cell.
[0115] 1. Oligonucleotide Probes and Primers:
[0116] Nucleic acid sequences that are "complementary" are those
that are capable of base-pairing according to the standard
Watson-Crick complementary rules. That is, the larger purines will
base pair with the smaller pyrimidines to form combinations of
guanine paired with cytosine (G:C) and adenine paired with either
thymine (A:T) in the case of DNA, or adenine paired with uracil
(A:U) in the case of RNA. Inclusion of less common bases such as
inosine, 5-methylcytosine, 6-methyladenine, hypoxanthine and others
in hybridizing sequences does not interfere with pairing. As used
herein, the term "complementary" sequences means nucleic acid
sequences that are substantially complementary, as may be assessed
by the same nucleotide comparison set forth above, or as defined as
being capable of annealing to the nucleic acid segment being
described under relatively stringent conditions such as those
described herein.
[0117] The term-primer, as defined herein, is meant to encompass
any nucleic acid that is capable of priming the synthesis of a
nascent nucleic acid in a template-dependent process. Sequence
specific primers should be of sufficient length to provide specific
annealing to the targeted RNA or DNA sequence. The use of a primer
of between about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52,
53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69,
70, 75, 80, 85, 90, 95, and 100 or more nucleotides in length
allows the formation of a duplex molecule that is both stable and
selective, although shorter and longer primers are specifically
contemplated in the context of the present disclosure. For initial
DNA amplification steps, hybridization of as few as 5 to 9
nucleotide bases is contemplated. Complementary sequences over
stretches greater than 20 bases in length are generally preferred
for subsequent amplification steps, in order to increase stability
and selectivity of the hybrid, and thereby improve the quality and
degree of particular hybrid molecules obtained.
[0118] Although shorter primers are easier to make and increase in
vivo accessibility, numerous other factors are involved in
determining the specificity of hybridization. Both binding affinity
and sequence specificity of a primer to its complementary target
increases with increasing length. It is contemplated that exemplary
primers of 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36,
37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53,
54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70,
75, 80, 85, 90, 95, and 100 or more nucleotide base pairs will be
used, although others are contemplated as well. Accordingly,
nucleotide sequences may be selected for their ability to
selectively form duplex molecules with complementary stretches of
genes, DNA, or RNAs, or more specifically to provide primers for
amplification of DNA or RNA preparations including DNA or RNA
directly or indirectly derived from cells, cell lysates, and
tissues. Probes and primers of the present disclosure are used to
amplify DNA, as well as detect genes, changes in gene expression,
gene polymorphisms, single nucleotide polymorphisms, and changes in
mRNA expression where one could be detecting virtually any gene or
genes of interest from any species. The target polynucleotide will
be RNA molecules, mRNA, cDNA, DNA, or amplified DNA. By varying the
stringency of annealing, and the region of the primer, different
targets may be discovered.
[0119] Primers may be chemically synthesized by methods well known
within the art. Chemical synthesis methods allow for the placement
of detectable labels such as fluorescent labels, radioactive
labels, etc. to be placed virtually anywhere within the polynucleic
acid sequence. Solid phase methods as well as other methods of
oligonucleotide or polynucleotide synthesis known to one of
ordinary skill may used within the context of the disclosure.
[0120] It is specifically contemplated that a wide variety of
appropriate detection or recognition means are known in the art and
may be incorporated into the primers. Such labels may include, but
are not limited to: fluorescent labels, radioactive labels, mass
labels, affinity labels, chromophores, dyes, electroluminescence,
chemiluminescence, enzymatic tags, or other ligands, such as
avidin/biotin, or antibodies, which are capable of being detected
and are described below.
[0121] 2. DNA Amplification:
[0122] One of the best known amplification methods is PCR.TM.,
which is described in detail in U.S. Pat. Nos. 4,683,195, 4,683,202
and 4,800,159, each incorporated herein by reference. While PCR.TM.
is considered to be an acceptable means of carrying out DNA
amplification, it is specifically contemplated that the methods of
the present disclosure may be carried out using alternate
amplification techniques which would be well known to one of
ordinary skill and are briefly discussed below. In PCR.TM., pairs
of primers that selectively hybridize to nucleic acids are used
under conditions that permit selective hybridization. The term
primer, as used herein, encompasses any nucleic acid that is
capable of priming the synthesis of a nascent nucleic acid in a
template-dependent process. Primers may be provided in
double-stranded or single-stranded form, although the
single-stranded form is preferred. The primers are used in any one
of a number of template dependent processes to amplify the
target-gene sequences present in a given template sample.
[0123] The nucleic acid target for the disclosed DNA amplification
method is generally considered to be any nucleic acid or nucleic
acid analog capable of being amplified by techniques well known in
the art. By way of example, target nucleic acids specifically
contemplated in the context of the disclosure, may include, but is
not limited to: genomic DNA, cDNA, RNA, mRNA, cosmid DNA, BAC DNA,
PAC DNA, YAC DNA, and synthetic DNA. In a contemplated embodiment,
genomic DNA is from a prokaryotic or eukaryotic cell or tissue and
utilized as the sample DNA in the disclosed DNA amplification
method. In other embodiments, poly-A mRNA is isolated and reverse
transcribed (referred to as RT) to obtain cDNA, which is then used
as the sample DNA for DNA amplification using the presently
disclosed method. In other contemplated embodiments, cDNA may be
obtained and used as the sample DNA to be amplified. In still
another embodiment, RNA or mRNA is directly amplified using the
disclosed DNA amplification method, wherein the starting material
is an RNA sample rather than a DNA sample.
[0124] i. PCR.TM.
[0125] In PCR.TM. two primer sequences are prepared which are
complementary to regions on opposite complementary strands of the
target-gene(s) sequence. The primers will hybridize to form a
DNA:primer hybrid if the target-gene(s) sequence is present in a
sample. An excess of deoxyribonucleoside triphosphates are added to
a reaction mixture along with a DNA polymerase, e.g., Taq
polymerase, that facilitates template-dependent nucleic acid
synthesis.
[0126] If the DNA:primer hybrid is formed, the polymerase will
cause the primers to be extended along the target-gene(s) sequence
by adding on nucleotides. By raising and lowering the temperature
of the reaction mixture, the extended primers will dissociate from
the target-gene(s) to form reaction products, excess primers will
bind to the target-gene(s) and to the reaction products and the
process is repeated. These multiple rounds of amplification,
referred to as "cycles," are conducted until a sufficient amount of
amplification product is produced.
[0127] Next, the amplification product is detected. In certain
applications, the detection may be performed by visual means.
Alternatively, the detection may involve indirect identification of
the product via fluorescent labels, chemiluminescence, radioactive
scintigraphy of incorporated radiolabel or incorporation of labeled
nucleotides, mass labels or even via a system using electrical or
thermal impulse signals.
[0128] ii LCR
[0129] Another method for amplification is the ligase chain
reaction ("LCR"), disclosed in European Patent Application No.
320,308, incorporated herein by reference. In LCR, two
complementary probe pairs are prepared, and in the presence of the
target sequence, each pair will bind to opposite complementary
strands of the target such that they abut. In the presence of a
ligase, the two probe pairs will link to form a single unit. By
temperature cycling, as in PCR, bound ligated units dissociate from
the target and then serve as "target sequences" for ligation of
excess probe pairs. U.S. Pat. No. 4,883,750, incorporated herein by
reference, describes a method similar to LCR for binding probe
pairs to a target sequence.
[0130] iii. Qbeta Replicase
[0131] Qbeta Replicase, described in PCT Patent Application No.
PCT/US87/00880, also may be used as still another amplification
method in the present disclosure. In this method, a replicative
sequence of RNA which has a region complementary to that of a
target is added to a sample in the presence of an RNA polymerase.
The polymerase will copy the replicative sequence which can then be
detected.
[0132] iv. Isothermal Amplification
[0133] An isothermal amplification method, in which restriction
endonucleases and ligases are used to achieve the amplification of
target molecules that contain nucleotide
5'-[.alpha.-thio]-triphosphates in one stand of a restriction site
also may be useful in the DNA amplification. Such an amplification
method is described by Walker et al. (Nucleic Acids Res
20(7):1691-6, 1992), incorporated herein by reference.
[0134] v. Strand Displacement Amplification
[0135] Strand Displacement Amplification (SDA) is another method of
carrying out isothermal amplification of nucleic acids which
involves multiple rounds of strand displacement and synthesis,
i.e., nick translation. The SDA technique is described in U.S. Pat.
Nos. 5,712,124, 5,648,211 and 5,455,166, herein incorporated by
reference. A similar method, called Repair Chain Reaction (RCR),
involves annealing several probes throughout a region targeted for
amplification, followed by a repair reaction in which only two of
the four bases are present. The other two bases can be added as
biotinylated derivatives for easy detection. A similar approach is
used in SDA.
[0136] vi. Cyclic Probe Reaction
[0137] Target specific sequences can also be detected using a
cyclic probe reaction (CPR). In CPR, a probe having 3' and 5'
sequences of non-specific DNA and a middle sequence of specific RNA
is hybridized to DNA that is present in a sample. Upon
hybridization, the reaction is treated with RNase H, and the
products of the probe identified as distinctive products are
released after digestion. The original template is annealed to
another cycling probe and the reaction is repeated.
[0138] vii. Transcription-Based Amplification
[0139] Other nucleic acid amplification procedures specifically
contemplated in the context of the present disclosure include
transcription-based amplification systems (rAS), including nucleic
acid sequence based amplification (NASBA) and 3SR, Kwoh et al.,
Proc Natl Acad Sci USA, 86:1173-77, 1989; PCT Patent Application WO
88/10315 et al., 1989 (each incorporated herein by reference).
[0140] In NASBA, the nucleic acids can be prepared for
amplification by standard phenol/chloroform extraction, heat
denaturation of a clinical sample, treatment with lysis buffer, and
minispin columns for isolation of DNA and RNA or guanidinium
chloride extraction of RNA. These amplification techniques involve
annealing a primer which has target specific sequences. Following
polymerization, DNA/RNA hybrids are digested with RNase H while
double stranded DNA molecules are heat denatured again. In either
case the single stranded DNA is made fully double stranded by
addition of second target specific primer, followed by
polymerization. The double-stranded DNA molecules are then multiply
transcribed by a polymerase such as T7 or SP6. In an isothermal
cyclic reaction, the RNAs are reverse transcribed into double
stranded DNA, and transcribed once again with a polymerase such as
T7 or SP6. The resulting products, whether truncated or complete,
indicate target specific sequences.
[0141] viii. Other Amplification Methods
[0142] Other amplification methods, as described in British Patent
Application No. GB 2,202,328, and in PCT Patent Application No.
PCT/US89/01025, each incorporated herein by reference, may be used
in accordance with the present disclosure. In the former
application, "modified" primers are used in a PCR.TM.-like template
and enzyme dependent synthesis. The primers may be modified by
labeling with a capture moiety (e.g., biotin) and/or a detector
moiety (e.g., enzyme). In the latter application, an excess of
labeled probes are added to a sample. In the presence of the target
sequence, the probe binds and is cleaved catalytically. After
cleavage, the target sequence is released intact to be bound by
excess probe. Cleavage of the labeled probe signals the presence of
the target sequence.
[0143] Davey et al., European Patent Application No. 329,822
(incorporated herein by reference) disclose a nucleic acid
amplification process involving cyclically synthesizing
single-stranded RNA ("ssRNA"), ssDNA, and double-stranded DNA
(dsDNA), which may be used in accordance with the present
disclosure. The ssRNA is a first template for a first primer
oligonucleotide, which is elongated by reverse transcriptase
(RNA-dependent DNA polymerase). The RNA is then removed from the
resulting DNA:RNA duplex by the action of ribonuclease H(RNase H,
an RNase specific for RNA in duplex with either DNA or RNA). The
resultant ssDNA is a second template for a second primer, which
also includes the sequences of an RNA polymerase promoter
(exemplified by T7 RNA polymerase) 5' of its homology to the
template. This primer is then extended by DNA polymerase
(exemplified by the large "Klenow" fragment of E. coli DNA
polymerase I), resulting in a double-stranded DNA molecule, having
a sequence identical to that of the original RNA between the
primers and having additionally, at one end, a promoter sequence.
This promoter sequence can be used by the appropriate RNA
polymerase to make many RNA copies of the DNA. These copies can
then reenter the cycle leading to very swift amplification. With
proper choice of enzymes, this amplification can be done
isothermally without adding enzymes at each cycle. Because of the
cyclical nature of this process, the starting nucleic acid sequence
can be either DNA or RNA.
[0144] Miller et al., PCT Patent Application WO 89/06700
(incorporated herein by reference), disclose a nucleic acid
sequence amplification scheme based on the hybridization of a
promoter/primer sequence to a target single-stranded DNA followed
by transcription of many RNA copies of the sequence. This scheme is
not cyclic, i.e., new templates are not produced from the resultant
RNA transcripts.
[0145] Other suitable amplification methods include "race and
"one-sided PCR.TM." (Frohman, In: PCR Protocols: A Guide To Methods
And Applications, Academic Press, N.Y., 1990, each herein
incorporated by reference). Methods based on ligation of two (or
more) oligonucleotides in the presence of nucleic acid having the
sequence of the resulting "di-oligonucleotide," thereby amplifying
the di-oligonucleotide, also may be used to amplify DNA in
accordance with the present disclosure (Wu et al., Genomics
4:560-569, 1989, incorporated herein by reference).
[0146] 3. Restriction Enzymes
[0147] Restriction enzymes recognize specific short DNA sequences
four to eight nucleotides long (see Table 1), and cleave DNA at a
site within this sequence. In the context of the present
disclosure, restriction enzymes may be used to cleave DNA molecules
at sites corresponding to various restriction-enzyme recognition
sites prior to or subsequent to the amplification reaction.
[0148] Since the sequence of the recognition site for a variety of
restriction enzymes is well known in the art (e.g., see Table 1
below), primers can be designed that contain nucleotides
corresponding to the recognition sequences. Primer sets can have in
addition to the restriction recognition sequence degenerate
sequences corresponding to different combinations of nucleotide
sequences. Table 1 below exemplifies restriction enzymes and their
cleavage sites that may be useful in the present disclosure.
TABLE-US-00002 TABLE 1 RESTRICTION ENZYMES Enzyme Name Recognition
Sequence AatII GACGTC Acc65 I GGTACC Acc I GTMKAC Aci I CCGC Acl I
AACGTT Afe I AGCGCT Afl II CTTAAG Afl III ACRYGT Age I ACCGGT Ahd I
GACNNNNNGTC Alu I AGCT Alw I GGATC AlwN I CAGNNNCTG Apa I GGGCCC
ApaL I GTGCAC Apo I RAATTY Asc I GGCGCGCC Ase I ATTAAT Ava I CYCGRG
Ava II GGWCC Avr II CCTAGG Bae I NACNNNNGTAPyCN BamH I GGATCC Ban I
GGYRCC Ban II GRGCYC Bbs I GAAGAC Bbv I GCAGC BbvC I CCTCAGC Bcg I
CGANNNNNNTGC BciV I GTATCC Bcl I TGATCA Bfa I CTAG Bgl I
GCCNNNNNGGC Bgl II AGATCT Blp I GCTNAGC Bmr I ACTGGG Bpm I CTGGAG
BsaA I YACGTR BsaB I GATNNNNATC BsaH I GRCGYC Bsa I GGTCTC BsaJ I
CCNNGG BsaW I WCCGGW BseR I GAGGAG Bsg I GTGCAG BsiE I CGRYCG
BsiHKA I GWGCWC BsiW I CGTACG Bsl I CCNNNNNNNGG BsmA I GTCTC BsmB I
CGTCTC BsmF I GGGAC Bsm I GAATGC BsoB I CYCGRG Bsp1286 I GDGCHC
BspD I ATCGAT BspE I TCCGGA BspH I TCATGA BspM I ACCTGC BsrB I
CCGCTC BsrD I GCAATG BsrF I RCCGGY BsrG I TGTACA Bsr I ACTGG BssH
II GCGCGC BssK I CCNGG Bst4C I ACNGT BssS I CACGAG BstAP I
GCANNNNNTGC BstB I TTCGAA BstE II GGTNACC BstF5 I GGATGNN BstN I
CCWGG BstU I CGCG BstX I CCANNNNNNTGG BstY I RGATCY BstZ17 I GTATAC
Bsu36 I CCTNAGG Btg I CCPuPyGG Btr I CACGTG Cac8 I GCNNGC Cla I
ATCGAT Dde I CTNAG Dpn I GATC Dpn II GATC Dra I TTTAAA Dra III
CACNNNGTG Drd I GACNNNNNNGTC Eae I YGGCCR Eag I CGGCCG Ear I CTCTTC
Eci I GGCGGA EcoN I CCTNNNNNAGG EcoO109 I RGGNCCY EcoR I GAATTC
EcoR V GATATC Fau I CCCGCNNNN Fnu4H I GCNGC Fok I GGATG Fse I
GGCCGGCC Fsp I TGCGCA Hae II RGCGCY Hae III GGCC Hga I GACGC Hha I
GCGC Hinc II GTYRAC Hind III AAGCTT Hinf I GANTC HinPl I GCGC Hpa I
GTTAAC Hpa II CCGG Hph I GGTGA Kas I GGCGCC Kpn I GGTACC Mbo I GATC
Mbo II GAAGA Mfe I CAATTG Mlu I ACGCGT Mly I GAGTCNNNNN Mnl I CCTC
Msc I TGGCCA Mse I TTAA Msl I CAYNNNNRTG
MspAl I CMGCKG Msp I CCGG Mwo I GCNNNNNNNGC Nae I GCCGGC Nar I
GGCGCC Nci I CCSGG Nco I CCATGG Nde I CATATG NgoMI V GCCGGC Nhe I
GCTAGC Nla III CATG Nla IV GGNNCC Not I GCGGCCGC Nru I TCGCGA Nsi I
ATGCAT Nsp I RCATGY Pac I TTAATTAA PaeR7 I CTCGAG Pci I ACATGT PflF
I GACNNNGTC Pf1M I CCANNNNNTGG Ple I GAGTC Pme I GTTTAAAC Pml I
CACGTG PpuM I RGGWCCY PshA I GACNNNNGTC Psi I TTATAA PspG I CCWGG
PspOM I GGGCCC Pst I CTGCAG Pvu I CGATCG Pvu II CAGCTG Rsa I GTAC
Rsr II CGGWCCG Sac I GAGCTC Sac II CCGCGG Sal I GTCGAC Sap I
GCTCTTC Sau3A I GATC Sau96 I GGNCC Sbf I CCTGCAGG Sca I AGTACT ScrF
I CCNGG SexA I ACCWGGT SfaN I GCATC Sfc I CTRYAG Sfi I
GGCCNNNNNGGCC Sfo I GGCGCC SgrA I CRCCGGYG Sma I CCCGGG Sml I
CTYRAG SnaB I TACGTA Spe I ACTAGT Sph I GCATGC Ssp I AATATT Stu I
AGGCCT Sty I CCWWGG Swa I ATTTAAAT Taq I TCGA Tfi I GAWTC Tli I
CTCGAG Tse I GCWGC Tsp45 I GTSAC Tsp5O9 I AATT TspR I CAGTG Tthlll
I GACNNNGTC Xba I TCTAGA Xcm I CCANNNNNNNNNTGG Xho I CTCGAG Xma I
CCCGGG Xmn I GAANNNNTTC
[0149] 4. Other Enzymes
[0150] A polymerase is an enzyme that catalyses the synthesis of
nucleic acids on preexisting nucleic acid templates, assembling RNA
from ribonucleotides or DNA from deoxyribonucleotides. Polymerases
specifically contemplated in the context of the present disclosure
may be naturally isolated, modified, or synthetic. While it is
generally contemplated that the polymerase employed will be
thermostable, non-thermostable polymerases may also be employed in
the context of the present disclosure. Tables 2 and 3 set forth
exemplary polymerases and nucleic acid modifying enzymes that may
be used in the context of the disclosure.
TABLE-US-00003 TABLE 2 POLYMERASES Thermostable DNA Polymerases:
OmniBase .TM. Sequencing Enzyme Pfu DNA Polymerase Taq DNA
Polymerase Taq DNA Polymerase, Sequencing Grade TaqBead .TM. Hot
Start Polymerase AmpliTaq Gold Vent DNA Polymerase Tub DNA
Polymerase TaqPlus DNA Polymerase Tfl DNA Polymerase Tli DNA
Polymerase Tth DNA Polymerase DNA Polymerases: DNA Polymerase I,
Klenow Fragment, Exonuclease Minus DNA Polymerase I DNA Polymerase
I Large (Klenow) Fragment Terminal Deoxynucleotidyl Transferase T7
DNA Polymerase T4 DNA Polymerase REVERSE TRANSCRIPTASES AMV Reverse
Transcriptase M-MLV Reverse Transcriptase
TABLE-US-00004 TABLE 3 DNA/RNA MODIFYING ENZYMES Ligases: T4 DNA
Ligase Kinases: T4 Polynucleotide Kinase
[0151] 5. Labels
[0152] Recognition moieties incorporated into primers, incorporated
into the amplified product during amplification, or attached to
probes are useful in identification of the amplified molecules. A
number of different labels may be used for this purpose such as,
for example: fluorophores, chromophores, radio-isotopes, enzymatic
tags, antibodies, chemiluminescence, electroluminescence, affinity
labels, etc. One of skill in the art will recognize that these and
other fluorophores not mentioned herein can also be used with
success in this disclosure.
[0153] Examples of affinity labels include but are not limited to
the following: an antibody, an antibody fragment, a receptor
protein, a hormone, biotin, DNP, or any polypeptide/protein
molecule that binds to an affinity label and may be used for
separation of the amplified gene.
[0154] Examples of enzyme tags include enzymes such as urease,
alkaline phosphatase, or peroxidase. Additionally, colorimetric
indicator substrates can be employed to provide a detection means
visible to the human eye or spectrophotometrically, to identify
specific hybridization with complementary nucleic acid-containing
samples. All these examples are generally known in the art and the
skilled artisan will recognize that the present disclosure is not
limited to the examples described above.
[0155] The following fluorophores are specifically contemplated to
be useful in the present disclosure: Alexa 350, Alexa 430, AMCA,
BODIPY 630/650, BODIPY 650/665, BODIPY-FL, BODIPY-R6G, BODIPY-TMR,
BODIPY-TRX, Cascade Blue, Cy2, Cy3, Cy5, 6-FAM, Fluorescein, HEX,
6-JOE, Oregon Green 488, Oregon Green 500, Oregon Green 514,
Pacific Blue, REG, Rhodamine Green, Rhodamine Red, ROX, TAMRA, TET,
Tetramethylrhodamine, and Texas Red.
[0156] 6. Separation and Quantitation Methods
[0157] Following amplification, it may be desirable to separate the
amplification products of several different lengths from each
other, from the template, and from excess primers for the purpose
of analysis or more specifically for determining whether specific
amplification has occurred.
[0158] i Gel Electrophoresis
[0159] In one embodiment, amplification products are separated by
agarose, agarose-acrylamide or polyacrylamide gel electrophoresis
using standard methods (Sambrook et al., "Molecular Cloning," A
Laboratory Manual, 2d Ed, Cold Spring Harbor Laboratory Press, New
York, 13.7-13.9:1989). Gel electrophoresis techniques are well
known in the art.
[0160] ii. Chromatographic Techniques
[0161] Alternatively, chromatographic techniques may be employed to
effect separation. There are many kinds of chromatography which may
be used in the present disclosure: adsorption, partition,
ion-exchange, and molecular sieve, as well as many specialized
techniques for using them including column, paper, thin-layer and
gas chromatography (Freifelder, Physical Biochemistry Applications
to Biochemistry and Molecular Biology, 2nd ed. Wm. Freeman and Co.,
New York, N.Y., 1982). Yet another alternative is to capture
nucleic acid products labeled with, for example, biotin or antigen
with beads bearing avidin or antibody, respectively.
[0162] iii. Microfluidic Techniques
[0163] Microfluidic techniques include separation on a platform
such as microcapillaries, including by way of example those
designed by ACLARA BioSciences Inc., or the LabChip.TM. by Caliper
Technologies Inc. These microfluidic platforms require only
nanoliter volumes of sample, in contrast to the microliter volumes
required by other separation technologies. Miniaturizing some of
the processes involved in genetic analysis has been achieved using
microfluidic devices. For example, published PCT Application No. WO
94/05414, to Northrup and White, incorporated herein by reference,
reports an integrated micro-PCR.TM. apparatus for collection and
amplification of nucleic acids from a specimen. U.S. Pat. Nos.
5,304,487, 5,296,375, and 5,856,174 describe apparatus and methods
incorporating the various processing and analytical operations
involved in nucleic acid analysis and are incorporated herein by
reference.
[0164] iv. Capillary Electrophoresis
[0165] In some embodiments, it may be desirable to provide an
additional, or alternative means for analyzing the amplified DNA.
In these embodiments, microcapillary arrays are contemplated to be
used for the analysis. Microcapillary array electrophoresis
generally involves the use of a thin capillary or channel that may
or may not be filled with a particular separation medium.
Electrophoresis of a sample through the capillary provides a size
based separation profile for the sample. Microcapillary array
electrophoresis generally provides a rapid method for size-based
sequencing, PCR.TM. product analysis, and restriction fragment
sizing. The high surface to volume ratio of these capillaries
allows for the application of higher electric fields across the
capillary without substantial thermal variation across the
capillary, consequently allowing for more rapid separations.
Furthermore, when combined with confocal imaging methods, these
methods provide sensitivity in the range of attomoles, which is
comparable to the sensitivity of radioactive sequencing methods.
Microfabrication of microfluidic devices including microcapillary
electrophoretic devices has been discussed in detail in, for
example, Jacobson et al., Anal Chem, 66:1107-1113, 1994;
Effenhauser et al., Anal Chem, 66:2949-2953, 1994; Harrison et al.,
Science, 261:895-897, 1993; Effenhauser et al., Anal Chem,
65:2637-2642, 1993; Manz et al., J. Chromatogr 593:253-258, 1992;
and U.S. Pat. No. 5,904,824, incorporated herein by reference.
Typically, these methods comprise photolithographic etching of
micron scale channels on a silica, silicon, or other crystalline
substrate or chip, and can be readily adapted for use in the
present disclosure.
[0166] Tsuda et al. (Anal Chem, 62:2149-2152, 1990) describes
rectangular capillaries, an alternative to the cylindrical
capillary glass tubes. Some advantages of these systems are their
efficient heat dissipation due to the large height-to-width ratio
and, hence, their high surface-to-volume ratio and their high
detection sensitivity for optical on-column detection modes. These
flat separation channels have the ability to perform
two-dimensional separations, with one force being applied across
the separation channel, and with the sample zones detected by the
use of a multi-channel array detector.
[0167] In many capillary electrophoresis methods, the capillaries,
e.g., fused silica capillaries or channels etched, machined, or
molded into planar substrates, are filled with an appropriate
separation/sieving matrix. Typically, a variety of sieving matrices
known in the art may be used in the microcapillary arrays. Examples
of such matrices include, e.g., hydroxyethyl-cellulose,
polyacrylamide, agarose, and the like. Generally, the specific gel
matrix, running buffers, and running conditions are selected to
maximize the separation characteristics of the particular
application, e.g., the size of the nucleic acid fragments, the
required resolution, and the presence of native or undenatured
nucleic acid molecules. For example, running buffers may include
denaturants, chaotropic agents such as urea to denature nucleic
acids in the sample.
[0168] v. Mass Spectroscopy
[0169] Mass spectrometry provides a means of "weighing" individual
molecules by ionizing the molecules in vacuo and making them "fly"
by volatilization. Under the influence of combinations of electric
and magnetic fields, the ions follow trajectories depending on
their individual mass (m) and charge (z). For low molecular weight
molecules, mass spectrometry has been part of the routine
physical-organic repertoire for analysis and characterization of
organic molecules by the determination of the mass of the parent
molecular ion. In addition, by arranging collisions of this parent
molecular ion with other particles (e.g., argon atoms), the
molecular ion is fragmented forming secondary ions by the so-called
collision induced dissociation (CID). The fragmentation
pattern/pathway very often allows the derivation of detailed
structural information. Other applications of mass spectrometric
methods in the art are summarized in Methods in Enzymology, Vol.
193: "Mass Spectrometry" (J. A. McCloskey, editor), 1990, Academic
Press, New York.
[0170] Due to the apparent analytical advantages of mass
spectrometry in providing high detection sensitivity, accuracy of
mass measurements, detailed structural information by CID in
conjunction with an MS/MS configuration and speed, as well as
on-line data transfer to a computer, there has been considerable
interest in the use of mass spectrometry for the structural
analysis of nucleic acids. Reviews summarizing this field include
(Schram, Methods Biochem Anal, 34:203-287, 1990) and (Crain, Mass
Spectrometry Reviews, 9:505-554, 1990), here incorporated herein by
reference. The biggest hurdle to applying mass spectrometry to
nucleic acids is the difficulty of volatilizing these very polar
biopolymers. Therefore, "sequencing" had been limited to low
molecular weight synthetic oligonucleotides by determining the mass
of the parent molecular ion and through this, confirming the
already known sequence, or alternatively, confirming the known
sequence through the generation of secondary ions (fragment ions)
via CID in an MS/MS configuration utilizing, in particular, for the
ionization and volatilization, the method of fast atomic
bombardment (FAB mass spectrometry) or plasma desorption (PD mass
spectrometry). As an example, the application of FAB to the
analysis of protected dimeric blocks for chemical synthesis of
oligodeoxynucleotides has been described (Koster et al., Biomedical
Environmental Mass Spectrometry 14:111-116, 1987).
[0171] Two ionization/desorption techniques are
electrospray/ionspray (ES) and matrix-assisted laser
desorption/ionization (MALDI). ES mass spectrometry was introduced
by Fenn et al., J. Phys. Chem. 88; 4451-59, 1984; PCT Application
No. WO 90/14148 and its applications are summarized in review
articles, for example, Smith et al., Anal Chem 62:882-89, 1990, and
Ardrey, Electrospray Mass Spectrometry, Spectroscopy Europe,
4:10-18, 1992. As a mass analyzer, a quadrupole is most frequently
used. The determination of molecular weights in femtomole amounts
of sample is very accurate due to the presence of multiple ion
peaks that can be used for the mass calculation.
[0172] MALDI mass spectrometry, in contrast, can be particularly
attractive when a time-of-flight (TOF) configuration is used as a
mass analyzer. The MALDI-TOF mass spectometry was introduced by
(Hillenkamp et al., Biological Mass Spectrometry eds. Burlingame
and McCloskey, Elsevier Science Publishers, Amsterdam, pp. 49-60,
1990). Since, in most cases, no multiple molecular ion peaks are
produced with this technique, the mass spectra, in principle, look
simpler compared to ES mass spectrometry. DNA molecules up to a
molecular weight of 410,000 daltons could be desorbed and
volatilized (Williams et al., Science, 246:1585-87, 1989). More
recently, the use of infrared lasers (IR) in this technique (as
opposed to UV-lasers) has been shown to provide mass spectra of
larger nucleic acids such as synthetic DNA, restriction enzyme
fragments of plasmid DNA, and RNA transcripts up to a size of 2180
nucleotides (Berkenkamp et al., Science, 281:260-2, 1998).
Berkenkamp also describes how DNA and RNA samples can be analyzed
by limited sample purification using MALDI-TOF IR.
[0173] In Japanese Patent No. 59-131909, an instrument is described
that detects nucleic acid fragments separated either by
electrophoresis, liquid chromatography or high speed gel
filtration. Mass spectrometric detection is achieved by
incorporating into the nucleic acids atoms that normally do not
occur in DNA such as S, Br, I or Ag, Au, Pt, Os, Hg.
[0174] vii. Energy Transfer
[0175] Labeling hybridization oligonucleotide probes with
fluorescent labels is a well known technique in the art and is a
sensitive, nonradioactive method for facilitating detection of
probe hybridization. More recently developed detection methods
employ the process of fluorescence energy transfer (FET) rather
than direct detection of fluorescence intensity for detection of
probe hybridization. FET occurs between a donor fluorophore and an
acceptor dye (which may or may not be a fluorophore) when the
absorption spectrum of one (the acceptor) overlaps the emission
spectrum of the other (the donor) and the two dyes are in close
proximity. Dyes with these properties are referred to as
donor/acceptor dye pairs or energy transfer dye pairs. The
excited-state energy of the donor fluorophore is transferred by a
resonance dipole-induced dipole interaction to the neighboring
acceptor. This results in quenching of donor fluorescence. In some
cases, if the acceptor is also a fluorophore, the intensity of its
fluorescence may be enhanced. The efficiency of energy transfer is
highly dependent on the distance between the donor and acceptor,
and equations predicting these relationships have been developed by
Forster, Ann Phys 2:55-75, 1948. The distance between donor and
acceptor dyes at which energy transfer efficiency is 50% is
referred to as the Forster distance (Ro). Other mechanisms of
fluorescence quenching are also known in the art including, for
example, charge transfer and collisional quenching.
[0176] Energy transfer and other mechanisms that rely on the
interaction of two dyes in close proximity to produce quenching are
an attractive means for detecting or identifying nucleotide
sequences, as such assays may be conducted in homogeneous formats.
Homogeneous assay formats differ from conventional probe
hybridization assays that rely on the detection of the fluorescence
of a single fluorophore label because heterogeneous assays
generally require additional steps to separate hybridized label
from free label. Several formats for FET hybridization assays are
reviewed in Nonisotopic DNA Probe Techniques (Academic Press, Inc.,
pgs. 311-352, 1992).
[0177] Homogeneous methods employing energy transfer or other
mechanisms of fluorescence quenching for detection of nucleic acid
amplification have also been described. Higuchi et al.
(Biotechnology 10:413-417, 1992), discloses methods for detecting
DNA amplification in real-time by monitoring increased fluorescence
of ethidium bromide as it binds to double-stranded DNA. The
sensitivity of this method is limited because binding of the
ethidium bromide is not target specific and background
amplification products are also detected. Lee et al. (Nucleic Acids
Res 21:3761-3766, 1993), discloses a real-time detection method in
which a doubly-labeled detector probe is cleaved in a target
amplification-specific manner during PCR.TM.. The detector probe is
hybridized downstream of the amplification primer so that the 5'-3'
exonuclease activity of Taq polymerase digests the detector probe,
separating two fluorescent dyes, which then form an energy transfer
pair. Fluorescence intensity increases as the probe is cleaved.
Published PCT application WO 96/21144 discloses continuous
fluorometric assays in which enzyme-mediated cleavage of nucleic
acids results in increased fluorescence. Fluorescence energy
transfer is suggested for use, but only in the context of a method
employing a single fluorescent label that is quenched by
hybridization to the target.
[0178] Signal primers or detector probes that hybridize to the
target sequence downstream of the hybridization site of the
amplification primers have been described for use in detection of
nucleic acid amplification (U.S. Pat. No. 5,547,861). The signal
primer is extended by the polymerase in a manner similar to
extension of the amplification primers. Extension of the
amplification primer displaces the extension product of the signal
primer in a target amplification-dependent manner, producing a
double-stranded secondary amplification product that may be
detected as an indication of target amplification. The secondary
amplification products generated from signal primers may be
detected by means of a variety of labels and reporter groups,
restriction sites in the signal primer that are cleaved to produce
fragments of a characteristic size, capture groups, and structural
features such as triple helices and recognition sites for
double-stranded DNA binding proteins.
[0179] Many donor/acceptor dye pairs are known in the art and may
be used in the present disclosure. These include but are not
limited to: fluorescein isothiocyanate (FITC)/tetramethylrhodamine
isothiocyanate (TALIC), FITC/Texas Red.TM. Molecular Probes,
FITC/N-hydroxysuccmirmidyl 1-pyrenebutyrate (PYB), FITC/eosin
isothiocyanate (EITC), N-hydroxysuccinimidyl 1-pyrenesulfonate
(PYS)/FITC, FITC/Rhodamine X, FITC/tetramethylrhodamine (TAMRA),
and others. The selection of a particular donor/acceptor
fluorophore pair is not critical. For energy transfer quenching
mechanisms it is only necessary that the emission wavelengths of
the donor fluorophore overlap the excitation wavelengths of the
acceptor, i.e., there must be sufficient spectral overlap between
the two dyes to allow efficient energy transfer, charge transfer,
or fluorescence quenching. P-(dimethyl aminophenylazo) benzoic acid
(DABCYL) is a non-fluorescent acceptor dye which effectively
quenches fluorescence from an adjacent fluorophore, e.g.,
fluorescein or 5-(2'-aminoethyl) aminonaphthalene (EDANS). Any dye
pairs that produce fluorescence quenching in the detector nucleic
acids are suitable for use in the methods of the disclosure,
regardless of the mechanism by which quenching occurs. Terminal and
internal labeling methods are both known in the art and may be
routinely used to link the donor and acceptor dyes at their
respective sites in the detector nucleic acid.
[0180] viii. Microarrays and Chip Technologies
[0181] Specifically contemplated in the present disclosure is the
use or analysis of amplified products by microarrays and/or
chip-based DNA technologies such as those described by (Hacia et
al., Nature Genet, 14:441-449, 1996) and (Shoemaker et al., Nature
Genetics, 14:450-456, 1996). These techniques involve quantitative
methods for analyzing large numbers of genes rapidly and
accurately. By tagging genes with oligonucleotides or using fixed
probe arrays, chip technology can be employed to segregate target
molecules as high density arrays and screen these molecules on the
basis of hybridization (Pease et al., Proc Natl Acad Sci USA,
91:5022-5026, 1994; Fodor et al, Nature, 364:555-556, 1993).
[0182] ix. OIA.
[0183] Also contemplated is the use of BioStar's OIA technology to
quantitate amplified products. OIA uses the mirror-like surface of
a silicon wafer as a substrate. A thin film optical coating and
capture antibody is attached to the silicon wafer. White light
reflected through the coating appears as a golden background color.
This color does not change until the thickness of the optical
molecular thin film is changed.
[0184] When a positive sample is applied to the wafer, binding
occurs between the ligand and the antibody. When substrate is added
to complete the mass enhancement, a corresponding change in color
from gold to purple/blue results from the increased thickness in
the molecular thin film. The technique is described in U.S. Pat.
No. 5,541,057, herein incorporated by reference.
[0185] x. Real Time PCR
[0186] Amplified RNA or DNA may be quantitated using the Real-Time
PCR technique (Higuchi et al., Biotechnology 10:413-417, 1992). By
determining the concentration of the amplified products that have
completed the same number of cycles and are in their linear ranges,
it is possible to determine the relative concentrations of the
specific target sequence in the original DNA mixture. For example,
if the DNA mixtures are cDNAs synthesized from RNAs isolated from
different tissues or cells, the relative abundance of the specific
mRNA from which the target sequence was derived can be determined
for the respective tissues or cells. This direct proportionality
between the concentration of the amplification products and the
relative mRNA abundance is only true in the linear range of the
amplification reaction.
[0187] The final concentration of the target DNA in the plateau
portion of the curve is determined by the availability of reagents
in the reaction mixture and is independent of the original
concentration of target DNA. Therefore, the first condition that
must be met before the relative abundance of a RNA or DNA species
can be determined by Real-Time PCR for a collection of RNA or DNA
populations is that the concentrations of the amplified products
must be sampled when the reaction products are in the linear
portion of their curves. The second condition that must be met for
an RT-PCR experiment to successfully determine the relative
abundance of a particular mRNA species is that relative
concentrations of the amplifiable cDNAs must be normalized to some
independent standard. The goal of a Real-Time PCR experiment is to
determine the abundance of a particular RNA or DNA species relative
to the average abundance of all RNA or DNA species in the
sample.
[0188] xi. Luminex
[0189] The Luminex technology allows the quantitation of nucleic
acid products immobilized on color coded microspheres. The
magnitude of the biomolecular reaction is measured using a second
molecule called a reporter. The reporter molecule signals the
extent of the reaction by attaching to the molecules on the
microspheres. As both the microspheres and the reporter molecules
are color coded, digital signal processing allows the translation
of signals into real-time, quantitative data for each reaction. The
standard technique is described in U.S. Pat. Nos. 5,736,303 and
6,057,107, herein incorporated by reference.
[0190] 8. Identification Methods
[0191] Amplification products must be visualized in order to
confirm amplification of the target-gene(s) sequences. One typical
visualization method involves staining of a gel with a fluorescent
dye, such as ethidium bromide or Vistra Green, and visualization
under UV light. Alternatively, if the amplification products are
integrally labeled with radio- or fluorometrically-labeled
nucleotides, the amplification products can be exposed to x-ray
film or visualized under the appropriate stimulating spectra
following separation.
[0192] In one embodiment, visualization is achieved indirectly,
using a nucleic acid probe. Following separation of amplification
products, a labeled, nucleic acid probe is brought into contact
with the amplified products. The probe preferably is conjugated to
a chromophore but may be radiolabeled. In another embodiment, the
probe is conjugated to a binding partner, such as an antibody or
biotin, where the other member of the binding pair carries a
detectable moiety. In other embodiments, the probe incorporates a
fluorescent dye or label. In yet other embodiments, the probe has a
mass label that can be used to detect the molecule amplified. Other
embodiments also contemplate the use of Taqman.TM. and Molecular
Beacon.TM. probes. In still other embodiments, solid-phase capture
methods combined with a standard probe may be used.
[0193] The type of label incorporated in DNA amplification products
is dictated by the method used for analysis. When using capillary
electrophoresis, microfluidic electrophoresis, HPLC, or LC
separations, either incorporated or intercalated fluorescent dyes
are used to label and detect the amplification products. Samples
are detected dynamically, in that fluorescence is quantitated as a
labeled species moves past the detector. If any electrophoretic
method, HPLC, or LC is used for separation, products can be
detected by absorption of UV light, a property inherent to DNA and
therefore not requiring addition of a label. If polyacrylamide gel
or slab gel electrophoresis is used, primers for the amplification
reactions can be labeled with a fluorophore, a chromophore or a
radioisotope, or by associated enzymatic reaction. Enzymatic
detection involves binding an enzyme to a primer, e.g., via a
biotin:avidin interaction, following separation of the
amplification products on a gel, then detection by chemical
reaction, such as chemiluminescence generated with luminol. A
fluorescent signal can be monitored dynamically. Detection with a
radioisotope or enzymatic reaction requires an initial separation
by gel electrophoresis, followed by transfer of DNA molecules to a
solid support (blot) prior to analysis. If blots are made, they can
be analyzed more than once by probing, stripping the blot, and then
reprobing. If amplification products are separated using a mass
spectrometer no label is required because nucleic acids are
detected directly.
[0194] A number of the above separation platforms can be coupled to
achieve separations based on two different properties. For example,
some of the PCR.TM. primers can be coupled with a moiety that
allows affinity capture, while some primers remain unmodified.
Modifications can include a sugar (for binding to a lectin column),
a hydrophobic group (for binding to a reverse-phase column), biotin
(for binding to a streptavidin column), or an antigen (for binding
to an antibody column). Samples are run through an affinity
chromatography column. The flow-through fraction is collected, and
the bound fraction eluted (by chemical cleavage, salt elution,
etc.). Each sample is then further fractionated based on a
property, such as mass, to identify individual components.
[0195] 10. Kits
[0196] The materials and reagents required for the disclosed
amplification method may be assembled together in a kit. The kits
of the present disclosure generally will include at least the
enzymes and nucleotides necessary to carry out the claimed method
along with primer sets. In a preferred embodiment, the kit will
also contain directions for amplifying DNA from DNA samples.
[0197] The kits of the present disclosure also will generally
include one or more preselected primer sets and/or probes that may
be either specific or non-specific for genes to be amplified.
Preferably, the kits will include, in a suitable container means,
one or more nucleic acid probes and/or primer sets and means for
detecting nucleic acids. In certain embodiments, such as in kits
for use in amplification reactions, the means for detecting the
nucleic acids may be a label, such as a fluorophore, a radiolabel,
an enzyme tag, etc., that is linked to the nucleic acid primer or
the nucleotides themselves. It is envisioned that kits may contain
pairs of primer sets for each DNA amplification step of the present
disclosure. It is also envisioned that kits may contain
precipitation solutions to process DNA samples stored on solid
mediums according to the precipitation method of the present
disclosure.
[0198] Preferred kits are those suitable for use in amplifying
whole genomic DNA. In a preferred kit, a first primer will
preferably be provided that has a random sequence of nucleotides at
its 3' end and a generic 5' of the random sequence, which
hybridizes randomly to DNA. The kit will also preferably include a
second primer with a generic sequence that is the same as the
generic sequence of the first primer. For example, kits may be used
to amplify all genes and chromosomal regions, unknown and/or known
from an organisms whole genomic or chromosomal DNA. Also included
in the kits may be enzymes suitable for amplifying nucleic acids,
including various polymerases (RT, Taq, etc.), deoxynucleotides and
buffers to provide the necessary single reaction mixture for
amplification.
[0199] The kits of the present disclosure, may also contain primers
with one or more of a variety of other moieties as described
above.
[0200] In each case, the kits will preferably have distinct
containers for each individual reagent and enzyme, as well as for
each probe or primer pair. Each biological agent will generally be
suitably aliquoted in their respective containers. The container
means of the kits will generally include at least one vial or test
tube. Flasks, bottles, and other container means into which the
reagents are placed and aliquoted are also possible. The individual
containers of the kit will preferably be maintained in close
confinement for commercial sale. Suitable larger containers may
include injection or blow-molded plastic containers into which the
desired vials are retained. Instructions are preferably provided
with the kit.
[0201] The following examples are included to demonstrate preferred
embodiments of the present disclosure. It should be appreciated by
those of skill in the art that the techniques disclosed in the
examples which follow represent techniques discovered by the
inventor to function well in the practice of the invention, and
thus can be considered to constitute preferred modes for its
practice. However, those of skill in the art should, in light of
the present disclosure, appreciate that many changes can be made in
the specific embodiments that are disclosed and still obtain a like
or similar result without departing from the spirit and scope of
the invention.
EXAMPLE 1
[0202] The efficiency of PCR.TM. amplification of DNA samples
stored on FTA paper processed using the presently disclosed
precipitation method and the commercially produced FTA Purification
Reagent (manufactured by Whatman) protocol was compared. First,
four bloodstain DNA samples stored on FTA paper were processed
using the disclosed precipitation method according to the following
protocol: A small circle (1-3 mm) in the FTA paper sample was
excised by the commercial Harris Micro-Punch manufactured by
Shunderson Communication, Ottawa, Ontario, Canada, and washed with
distilled water. The circle was transferred to a 96-well plate and
soaked in 200 .mu.l of DD H.sub.2O for 20 minutes. The water was
changed and the circle was soaked in water again for 5 minutes. The
water was next replaced with 200 .mu.l of 0.3M NaOAc/Ethanol (50/50
v/v) solution and the paper was soaked for 5 minutes to fix the
genomic DNA on the paper. The solution was removed and the paper
was washed in 200 .mu.l of 80% ethanol for 5 minutes to remove salt
and to accelerate dehydration. The ethanol was removed and the
paper was dried at room temperature for 15 minutes. The ethanol
wash reduced the dehydration time of the FTA paper sample by at
least 50%. The dehydrated paper was then used directly as the DNA
for PCR amplification.
[0203] Second, the same four bloodstain DNA samples stored on FTA
paper were processed according to the commercial FTA Purification
Reagent manufacturer's protocol. Briefly, for each sample a small
circle (1-3 mm) in the FTA paper sample was excised by the Harris
Micro-Punch. The circle was transferred to a 96-well plate and
soaked in 200 .mu.l of FTA Purification Reagent for 5 minutes. The
FTA reagent was changed and the wash was repeated 2 times. After
the FTA Purification Reagent had been removed for the third time,
200 .mu.l of TE buffer (10 mM Tris-HCl pH 8.0 and 0.1 mM EDTA) was
added to the paper. The FTA paper was soaked in TE for 5 minutes,
and then the TE solution was removed and the paper was air-dried
for 1 hour. The dehydrated paper was then used directly for PCR
amplification.
[0204] Both sets of dehydrated paper samples were amplified using
the following conditions. The reaction mixture for each PCR
contained the DNA-paper sample, 10 mM Tris HCl (pH 8.3), 5 mM
MgCl.sub.2, 50 mM KCl, 0.001% gelatin, 300 .mu.M dNTP (DATP, dGTP,
dCTP, and dTTP), 300 nM of the forward primer having the sequence
5'-CCTTTTCCTCTAGCATCAAGTTA-3' (SEQ ID NO:13), 300 nM of the reverse
primer having the sequence 5'-CAGACTGTGTGCTTCCTACAG-3' (SEQ ID
NO:14), and 1.25 unit Taq DNA polymerase, for a total volume of 50
.mu.M. The thermocycling program for the reaction mixtures was
95.degree. C. for 2 minutes; 15 "touchdown" cycles of 95.degree. C.
for 30 seconds, 66-51.degree. C. for 30 seconds, and 72.degree. C.
for 30 seconds; and 35 cycles of 95.degree. C. for 30 seconds,
50.degree. C. for 30 seconds, and 72.degree. C. for 30 seconds. The
PCR products were subjected to electrophoresis on a 2.0% agarose
gel without purification.
[0205] FIG. 2 shows the results of direct PCR amplification of DNA
samples stored on FTA paper processed using the disclosed
precipitation method as compared to the FTA Purification Reagent
protocol. FIG. 2. clearly demonstrates that the disclosed
precipitation method greatly reduces the variation of PCR
amplification efficiency found when the commercial FTA Purification
Reagent is used to process DNA samples. The presently disclosed
precipitation method not only offers a simpler and faster method
for processing DNA samples stored on FTA paper, it also reduces the
cost of processing the samples and greatly optimizes subsequent PCR
amplification and genetic analysis of the DNA samples.
EXAMPLE 2
[0206] The method of amplifying whole genomic DNA of the present
disclosure was used to amplify genomic DNA from bovine bloodstain
samples stored on FTA paper. This method combines DNA extraction
and amplification in a single operation by allowing genomic DNA in
a bovine bloodstain sample to be amplified in a single reaction
mixture using a single thermocycling reaction. Therefore, this
method greatly reduces the risk of sample contamination and
facilitates high-throughput screening. Additionally, 96-well or
384-well plates can be utilized for amplification of genomic DNA
stored on FTA paper using the presently disclosed methods, which
greatly facilitates a high-throughput operation. The utility and
efficiency of the presently disclosed method of DNA amplification
was tested by comparing PCR amplification of a known bovine SNP
locus using DNA amplified by the disclosed method and DNA bound
directly to FTA paper. In both experiments, the DNA samples stored
on FTA paper were processed using the disclosed precipitation
method as described in Example 1. Therefore, this example is
designed to specifically test the efficacy of the presently
disclosed method of DNA amplification for genetic analysis.
[0207] Bloodstain samples were collected and stored on FTA paper
for 13 individual bovine animals. The FTA paper samples were
processed using the disclosed precipitation method, and genomic DNA
was amplified from one set of samples using the disclosed method of
DNA amplification. Each dehydrated paper sample was amplified using
the following conditions. First, the DNA sample was placed in an
amplification reaction mixture that contained 10 mM Tris HCl (pH
8.3), 5 mM MgCl.sub.2, 50 mM KCl, 0.001% gelatin, 300 .mu.M dNTP
(DATP, dGTP, dCTP, and dTTP), 300 nM of the first primer having the
sequence of SEQ ID NO:1, 30 nM of the second primer having the
sequence of SEQ ID NO:2, and 1.25 unit Taq DNA polymerase, for a
total volume of about 50 .mu.l. The entire reaction mixture was
heated to 95.degree. C. for 5 minutes to denature the sample.
[0208] Next, during the first set of reactions of DNA
amplification, the reaction mixture was heated to a temperature of
95.degree. C. for 1 minute, and cooled to a temperature of
42.degree. C. for 5 minutes. These steps allowed the first primer
to anneal with the denatured sample DNA and the Taq DNA polymerase
to synthesize the complementary strand of DNA from the 3' end of
the first primer. The denaturation, annealing, and extension steps
were repeated again by heating the reaction mixture for 1 minute at
95.degree. C. and then cooling the mixture to 42.degree. C. for 5
minutes.
[0209] The second set of reactions of DNA amplification involved
subsequently heating the reaction mixture to a temperature of
95.degree. C. for 15 seconds, cooling the mixture to a temperature
of 65.degree. C. to allow the second primer to anneal to the
single-stranded DNA products, and raising the mixture to a
temperature of 68.degree. C., thereby allowing the Taq DNA
polymerase to synthesize the complementary strand of DNA from the
3' end of the second primer. These steps of denaturation,
annealing, and extension were repeated 39 times for a total of 40
cycles.
[0210] The set of dehydrated DNA samples processed using the
disclosed precipitation method only, and the set of DNA samples
processed using the disclosed precipitation method, as well as
amplified using the disclosed DNA amplification method, were next
subjected to PCR amplification using the following conditions. The
reaction mixture for each PCR contained either the dehydrated
DNA-paper sample or 20 ng of amplified genomic DNA, 10 mM Tris HCl
(pH 8.3), 5 mM MgCl.sub.2, 50 mM KCl, 0.001% gelatin, 300 .mu.M
dNTP (dATP, dGTP, dCTP, and dTTP), 300 nM of the forward primer
having the sequence 5'-CCAGCAGTTCTGAATGAAAGT-3' (SEQ ID NO:15), 300
nM of the reverse primer having the sequence
5'-ACACACAGAGGCCGTGTA-3' (SEQ ID NO:16), and 1.25 unit Taq DNA
polymerase, for a total volume of 50 .mu.l. The thermocycling
program for the reaction mixtures was 95.degree. C. for 2 minutes;
15 "touchdown" cycles of 95.degree. C. for 30 seconds,
66-51.degree. C. for 30 seconds, and 72.degree. C. for 30 seconds;
and 35 cycles of 95.degree. C. for 30 seconds, 50.degree. C. for 30
seconds, and 72.degree. C. for 30 seconds.
[0211] FIG. 3. shows the products of direct PCR of the known bovine
SNP locus using DNA samples processed according to the disclosed
precipitation method (upper panel), and the identical DNA samples
processed according to the disclosed precipitation and DNA
amplification method (lower panel). The PCR products are
approximately 200 bp in length, which is the same as that
calculated from the known DNA sequence. The visual image of the
agarose gel indicates that the method for amplifying DNA of the
present disclosure generates DNA that can be readily genotyped
using PCR. Additionally, the DNA amplification method generates
significantly greater amounts of genomic DNA than can be directly
isolated from FTA paper. Increasing the amount of available genomic
DNA by DNA amplification for genotyping will allow for more
extensive analysis of an organism's genotype.
EXAMPLE 3
[0212] To compare the efficiency of the presently disclosed method
of DNA amplification, DNA samples stored on FTA paper were first
processed using the presently disclosed precipitation method or the
commercial FTA Purification Reagent protocol, and then amplified
according to the disclosed DNA amplification method. Two sets of
punches from six different bloodstains stored on FTA paper were
first treated using either the disclosed precipitation method or
the FTA Purification Reagent protocol as outlined in Example 1.
Next, the two sets of DNA samples were amplified according to the
disclosed DNA amplification method, as outlined in Example 2.
[0213] FIG. 4. demonstrates the results of genomic DNA
amplification using the disclosed method of DNA amplification. The
figure compares the efficiency of the disclosed DNA amplification
method when the DNA sample is processed using the FTA Purification
Reagent protocol (lanes 2-7) versus the disclosed precipitation
method (lanes 8-13). FIG. 4. clearly demonstrates that the
presently disclosed DNA amplification method generates much greater
quantities of genomic DNA from bloodstains on FTA paper processed
with the disclosed precipitation method than with the commercial
FTA Purification Reagent system.
EXAMPLE 4
[0214] To demonstrate the general applicability of the presently
disclosed method of DNA amplification to amplify DNA, a series of
generic DNA sequences were used to generate first primers and
second primers for amplifying genomic DNA. Each DNA sample on FTA
paper was first processed using the presently disclosed
precipitation method as outlined in Example 1. Next, the processed
DNA samples were amplified according to the disclosed DNA
amplification method, as outlined in Example 2, except that a
different set of primers was used in each reaction. Each set of
primers included a second primer as listed below, and a first
primer with the same generic sequence as the second primer at its
5' end and 6 random nucleotides at its 3' end:
TABLE-US-00005 5'-ACAACGCAGAGTAAGCAGTGGTA-3',; SEQ ID NO: 3
5'-ACAACGGTAGCAGAGTAAGCAGT-3',; SEQ ID NO: 4
5'-GAGTAAGCAGTACAACGGTAGCA-3',; SEQ ID NO: 5
5'-GAGGCATAAGCAGTACAACGGTA-3',; SEQ ID NO: 6
5'-CAACGGTAGAGGCATAAGCAGTA-3',; SEQ ID NO: 7
5'-GGCATAAGCAGTACAACGGTAGA-3',; SEQ ID NO: 8
5'-AACGGTAGAGGCATAAGCAGTAC-3',; SEQ ID NO: 9
5'-AGTACAACGGTAGAGGCATAAGC-3',; SEQ ID NO: 10
5'-AAGCAGTACAACGGTAGAGGCAT-3',; SEQ ID NO: 11
5'-CGGTAGAGGCATAAGCAGTACAA-3',. SEQ ID NO: 12
[0215] For example, in the primer set that included the second
primer having the sequence of SEQ ID NO:3, the first primer in the
same DNA amplification reaction had the sequence
5'-ACAACGCAGAGTAAGCAGTGGTANNNNNN-3' (SEQ ID NO:17).
[0216] As shown in FIG. 5, all of the primer sets were able to
amplify genomic DNA from the samples stored on FTA paper. The
primer sets used to amplify the genomic DNA in each lane of FIG. 5.
used the following second primer: lane 2, SEQ ID NO:3; lane 3, SEQ
ID NO:4; lane 4, SEQ ID NO:5; lane 5, SEQ ID NO:6; lane 6, SEQ ID
NO:7; lane 7, SEQ ID NO:8; lane 8, SEQ ID NO:9; lane 9, SEQ ID
NO:10; lane 10, SEQ ID NO:11; and lane 11, SEQ ID NO:12. FIG. 5.
demonstrates that a person of skill in the art can design an
enormous range of suitable generic sequences for first and second
primers to amplify DNA according to the presently disclosed DNA
amplification method in an efficient and uniform manner.
EXAMPLE 5
[0217] The reliability at the nucleotide sequence level of the
disclosed method of DNA amplification was examined by analyzing PCR
amplified products of a known bovine SNP locus using DNA amplified
by the disclosed method and DNA directly from the FTA paper,
similar to the comparison made in Example 2. In both experiments,
the DNA samples stored on FTA paper were processed using the
disclosed precipitation method as described in Example 1.
Bloodstain samples were collected and stored on FTA paper for 8
individual bovine animals. The FTA paper samples were processed
using the disclosed precipitation method, and genomic DNA was
amplified from one set of samples using the disclosed method of DNA
amplification as described in Example 2. The set of dehydrated DNA
samples and amplified DNA samples were then subjected to PCR
amplification as described in Example 2. The PCR products for each
set were subsequently analyzed in a set of Doublecode OLA
reactions, which were designed to detect SNP variations among the 8
different individual bovine animals.
[0218] Doublecode OLA for SNP detection has been described in U.S.
application Ser. No. 09/755,628, incorporated herein by reference,
and is illustrated in FIG. 6. As illustrated in FIG. 6, Doublecode
OLA requires four different oligonucleotides for SNP detection. A
melting temperature (Tm) of around 55.degree. C. was used for each
of the four oligonucleotides utilized in the Doublecode OLA. The
oligonucleotides used in the Doublecode OLA method, however, may be
of any design that facilitates hybridization and the OLA reaction,
and are not dependent on a particular Tm. The Tm of an
oligonucleotide can be calculated and the length adjusted
accordingly by one of skill in the art using a variety of computer
software programs, such as Oligo Analyzer, which is available at
the website www@idtdna.com. All of the oligonucleotides and their
modifications utilized in Doublecode OLA reactions are commercially
available.
[0219] The first oligonucleotide is an address specific Zipcode
oligonucleotide. The sequence of the Zipcode oligonucleotide is
derived from randomly selected nucleotides, and the 5' end of the
Zipcode is substituted by an amino group with a C.sub.12 spacer. A
color-coded bead is attached to the 5' end of the Zipcode
oligonucleotide via a coupling reaction catalyzed by
1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC).
In one embodiment the color-coded bead is the Luminex color-coded
bead. The Luminex color-coded beads have been specially modified
with carboxyl groups on their surfaces. Carbodiimide catalyzes the
formation of amide bonds between carboxylic acids and amines by
activating carboxyl to form an O-urea derivative. This derivative
reacts readily with nucleophiles, such as amine, to bind the
Zipcode oligonucleotide to the surface of the bead.
[0220] The second oligonucleotide is a Capture oligonucleotide,
which is composed of the complementary sequence on the 5' side of
the target SNP plus one of the two SNP nucleotides at its 3' end.
The Capture oligonucleotide is fitted with an AntiZipcode sequence
at its 5' end which is the reverse complement of the Zipcode
sequence selected above. The AntiZipcode sequence at the 5' end of
the Capture oligonucleotide will hybridize with the Zipcode
oligonucleotide with a color-coded bead, while the 3' end of the
Capture oligonucleotide will hybridize with a specific location in
the target DNA.
[0221] The third oligonucleotide is the Reporter oligonucleotide,
which is composed of the complementary sequence on the 3' side
(downstream) of the target SNP. The Reporter oligonucleotide is
fitted with another randomly selected sequence termed the
Signalcode at its 3' end. The 5' end hydroxyl group of the Reporter
oligonucleotide is substituted with a phosphate group, which
facilitates a ligation reaction catalyzed by Taq ligase with the
Capture oligonucleotide if the latter anneals perfectly at its 3'
end with the SNP in the target DNA. The fourth oligonucleotide is
the AntiSignalcode oligonucleotide, which is the reverse complement
of the random Signalcode sequence selected above. The 3' end of the
AntiSignalcode oligonucleotide is fitted with a biotin that can be
subsequently stained by strepavidin-phycoerythrin conjugate.
[0222] Doublecode OLA to detect SNPs in the two sets of PCR
amplification products of the 8 different individual bovine was
performed in a reaction mixture containing the Zipcode
oligonucleotide, Capture oligonucleotide, Reporter oligonucleotide,
AntiSignalcode oligonucleotide, and Taq ligase. If the specific SNP
designed to be detected by the oligonucleotides was present in the
PCR products, the Capture oligonucleotide was ligated to the
Reporter oligonucleotide by Taq ligase, and in a single
hybridization reaction simultaneously sorted by the color-coded
beads on the Zipcode oligonucleotide as well as stained by a fluor
or biotin-labeled AntiSignalcode oligonucleotide. The fluorescence
of the stained bead was measured on a flow cytometer.
[0223] The three ZipCode oligonucleotides used in the reactions
were 5'-NH.sub.2-CGACTCCCTGTTTGTGATGGACCAC-3' (SEQ ID NO:18);
5'-NH.sub.2-CTTTTCCCGTCCGTCATCGCTCAAG-3' (SEQ ID NO:19); and
5'-NH.sub.2-GGCTGGGTCTACAGATCCCCAACTT-3' (SEQ ID NO:20). The
Zipcode oligonucleotides were coupled to beads according to the
following procedure. The beads were dispersed in 100 .mu.L of 0.1 M
MES (pH 4.5). The amino-substituted oligonucleotides were added to
a final concentration of 2 .mu.M. Next, 5 .mu.l of freshly made EDC
solution (1-ethyl-3-[3-diethylaminopropyl]carbodiimide
hydrochloride, 100 .mu.g/.mu.l) was added to the reaction and
incubated for 20 minutes at room temperature in the dark. Addition
of the EDC solution and the 20 minute incubation was repeated.
Afterwards, the beads were washed with 0.02% Tween 20 and then 0.1%
SDS. The beads were then resuspended in TE buffer.
[0224] Three Capture oligonucleotides used in the reactions were
5'-gtggtccatcacaaacagggagtcgGAAGTCCCAGCTCTGACCTCTCCGG-3' (SEQ ID
NO:21), 5'-cttgagcgatgacggacgggaaaagGAAGTCCCAGCTCTGACCTCTCCGT-3'
(SEQ ID NO:22), and
5'-aagttggggatctgtagacccagccGAAGTCCCAGCTCTGACCTCTCCGM-3' (SEQ ID
NO:23). The "M" in SEQ ID NO:23 is the degenerate nucleotide code
for A or C. In the Capture oligonucleotides, the sequence in small
letters is the AntiZipcode sequence and the sequence in capital
letters is the target sequence 5' upstream of the SNP to be
detected. The oligonucleotides having the sequence of SEQ ID NO:21
and SEQ ID NO:22 are identical except that the first has the
nucleotide G at its 3' end and the second has the nucleotide T at
its 3' end, which reflect the two alternate SNP nucleotides located
at that position in the bovine genome. The sequence of the Reporter
oligonucleotide used was In the Reporter oligonucleotide, the
sequence in small letters is the Signalcode sequence and the
sequence in capital letters is the target sequence 3' downstream of
the target SNP.
[0225] The Doublecode OLA reactions were each carried out in a 20
.mu.l reaction mixture containing: 1.times. Taq ligase buffer, 0.5
.mu.mol of Capture oligonucleotide, 5.0 .mu.mol of Reporter
oligonucleotide with the 5' Signalcode region, and 20 ng of PCR
products. The thermocycling program for the reaction mixtures was
96.degree. C. for 2 minutes, followed by 55 cycles of 94.degree. C.
for 15 seconds and 37.degree. C. for 1 minute.
[0226] After the thermocycling program was completed, the products
were sorted and stained to genotype each of the 8 bovine
individuals. The AntiSignalcode oligonucleotide used to sort the
reaction products was 5'-ctgaacggtagcatcttgac-biotin-3' (SEQ ID
NO:24). The sequence of the AntiSignalcode oligonucleotide is
reverse complementary to the Signalcode sequence at the 5' end of
the SignalCode Reporter oligonucleotide. The reaction products were
simultaneously sorted by the color-coded beads on the Zipcode
oligonucleotides and hybridized with the biotinylated
AntiSignalcode oligonucleotides in a single hybridization. These
reactions were each carried out in a 50 .mu.l hybridization mixture
containing: 1.times.TMAC buffer (2.5 M TMAC (tetramethyl ammonium
chloride), 0.15% SDS, 3 mM EDTA, and 75 mM Tris-HCl (pH 8.0)), 5000
Zipcode oligonucleotides with the color-coded beads for each SNP,
2.5 pmol of biotinylated AntiSignalcode oligonucleotides, and 201
of the Doublecode OLA reaction mixture. The hybridization reaction
mixtures were incubated at 95.degree. C. for 5 minutes and then at
50.degree. C. for 15 minutes.
[0227] The hybridized biotinylated AntiSignalcode oligonucleotides
were stained with fluorescent strepavidin-phycoerythrin conjugate
in a reaction that contained 1.times.TE buffer and the conjugate
(10 .mu.g/ml). The reaction was incubated at room temperature for 5
minutes, and the fluorescent signal of the color-coded beads was
measured in a Luminex 100 flow cytometer. Table 4 summarizes the
genotyping results of DNA samples processed according to the
disclosed precipitation and DNA amplification methods for 8
individual bovine animals. Table 5 summarizes the genotyping
results of DNA samples processed according to the disclosed
precipitation method only for the same 8 bovine animals. As shown
below, both methods give the identical genotype results for each
bovine animal:
TABLE-US-00006 TABLE 4 1 2 3 4 5 6 7 8 G Bead 26 147 99 31 118 106
113 112 T Bead 119 87 106 132 86 188 93 78 A/C Bead 33 40 35 35 26
47 36 23 Genotype T G/T G/T T G/T G/T G/T G/T *relative fluorescent
intensity
TABLE-US-00007 TABLE 5 1 2 3 4 5 6 7 8 G Bead 21 140 140 20 137 139
152 132 T Bead 176 120 113 138 122 114 103 113 A/C Bead 35 39 36 42
40 32 41 38 Genotype T G/T G/T T G/T G/T G/T G/T *relative
fluorescent intensity
[0228] The above results demonstrate that the disclosed method of
DNA amplification is able to reliably amplify genomic DNA with high
fidelity, which indicates that this method can be used to
accurately genotype multiple loci within a single organism, even if
only a very limited amount of DNA is available.
EXAMPLE 6
[0229] To further investigate the fidelity of the presently
disclosed DNA amplification method, genomic DNA was isolated from
the sperm of 8 individual bovine animals. The genomic DNA isolated
from the sperm was subjected to PCR amplification using the
protocol described in Example 2, except that two different primers
were used to amplify the DNA: 5'-CCAGATFCTTTCGGCAGGTA-3' (SEQ ID
NO:25), and 5'-CATGGGAACCAGGCTGAAT (SEQ ID NO:26). The PCR products
were sequenced using the dideoxynucleotide chain termination method
described by Sanger et al. (Proc Natl Acad Sci USA 74:5463-67,
1977). The genotype for each of the 8 bovine individual animals is
listed below in Table 6.
TABLE-US-00008 TABLE 6 1 2 3 4 5 6 7 8 Genotype T T G T T T G
G/T
[0230] Next, genomic DNA isolated from sperm of the same 8
individual bovine animals was subjected to DNA amplification using
the disclosed DNA amplification method as described in Example 2.
Twenty nanograms of starting genomic DNA was amplified. The
amplified DNA samples were then subjected to PCR amplification as
described above, and finally the PCR products were analyzed in a
set of Doublecode OLA reactions, as described in Example 5, which
were designed to detect SNP variations among the 8 different
individual bovine animals. Table 7 summarizes the genotyping
results of the sperm DNA amplified according to the DNA
amplification methods of the present disclosure.
TABLE-US-00009 TABLE 7 1 2 3 4 5 6 7 8 G Bead 24 22 227 18 31 21
277 88 T Bead 133 120 35 178 174 93 28 102 A/C Bead 31 27 41 37 37
31 24 41 Genotype T T G T T T G G/T *relative fluorescent
intensity
[0231] A comparison of the results in Tables 6 and 7 demonstrates
that DNA products are reliably and consistently amplified from
genomic DNA-using the disclosed DNA amplification method. Direct
sequencing of PCR products generated from genomic DNA yield the
exact same genotype results as Doublecode OLA analysis of PCR
products generated from DNA amplified using the DNA amplification
method of the present disclosure. These results demonstrate once
again that the disclosed method of DNA amplification is able to
reliably amplify genomic DNA with high fidelity.
[0232] All of the compositions and methods disclosed and claimed
herein can be made and executed without undue experimentation in
light of the present disclosure. While the compositions and methods
of this invention have been described in terms of preferred
embodiments, it will be apparent to those of skill in the art that
variations may be applied to the compositions and/or methods and in
the steps or in the sequence of steps of the methods described
herein without departing from the concept, spirit and scope of the
invention. More specifically, it will be apparent that certain
agents that are chemically or physiologically related may be
substituted for the agents described herein while the same or
similar results would be achieved. All such similar substitutes and
modifications apparent to those skilled in the art are deemed to be
within the spirit, scope and concept of the invention as defined by
the appended claims.
Sequence CWU 1
1
26128DNAArtificialSynthetic Primer 1tagcagtggt aacaacgcag agannnnn
28223DNAArtificialSynthetic Primer 2tagcagtggt aacaacgcag aga
23323DNAArtificialSynthetic Primer 3acaacgcaga gtaagcagtg gta
23423DNAArtificialSynthetic Primer 4acaacggtag cagagtaagc agt
23523DNAArtificialSynthetic Primer 5gagtaagcag tacaacggta gca
23623DNAArtificialSynthetic Primer 6gaggcataag cagtacaacg gta
23723DNAArtificialSynthetic Primer 7caacggtaga ggcataagca gta
23823DNAArtificialSynthetic Primer 8ggcataagca gtacaacggt aga
23923DNAArtificialSynthetic Primer 9aacggtagag gcataagcag tac
231023DNAArtificialSynthetic Primer 10agtacaacgg tagaggcata agc
231123DNAartificialSynthetic Primer 11aagcagtaca acggtagagg cat
231223DNAArtificialSynthetic Primer 12cggtagaggc ataagcagta caa
231323DNABovine 13ccttttcctc tagcatcaag tta 231421DNABovine
14cagactgtgt gcttcctaca g 211521DNABovine 15ccagcagttc tgaatgaaag t
211618DNABovine 16acacacagag gccgtgta 181729DNAArtificialSynthetic
Primer 17acaacgcaga gtaagcagtg gtannnnnn
291825DNAArtificialSynthetic Primer 18cgactccctg tttgtgatgg accac
251925DNAArtificialSynthetic Primer 19cttttcccgt ccgtcatcgc tcaag
252025DNAArtificialSynthetic Primer 20ggctgggtct acagatcccc aactt
252149DNABovine 21tggtccatca caaacaggga gtcggaagtc ccagctctga
cctctccgg 492250DNABovine 22cttgagcgat gacggacggg aaaaggaagt
cccagctctg acctctccgt 502349DNABovine 23aagttgggga tctgtagacc
cagccgaagt cccagctctg acctctccg 492420DNAArtificialSynthetic Primer
24ctgaacggta gcatcttgac 202520DNABovine 25ccagattctt tcggcaggta
202619DNABovine 26catgggaacc aggctgaat 19
* * * * *
References