Amplification and analysis of whole genome and whole transcriptome libraries generated by a DNA polymerization process
First Claim
1. A method of preparing a plurality of nucleic acid molecules having a known constant region at each end, the method comprising:
- a) obtaining a sample comprising nucleic acid molecules;
b) subjecting said nucleic acid molecules to a population of primers to form a nucleic acid molecule/primer mixture, wherein all the primers of the population have a nucleotide sequence that is substantially non-self-complementary and substantially non-complementary to other primers in the population, wherein all the primers comprise a constant region of at least 6 nucleotides in length, the constant region consisting of all nucleotides of a contiguous known sequence that is constant among all the primers of the population, and a variable region at the distal 3′
end of at least 4 nucleotides in length, wherein the variable region begins with a degenerate nucleotide, the constant region being positioned 5′
to the variable region, wherein the constant region and the variable region each comprise greater than 50% non-complementary nucleotides, wherein the greater than 50% non-complementary nucleotides of both the constant region and the variable region are;
guanines, adenines, or combinations thereof;
cytosines, thymidines/uridines, or combinations thereof;
adenines, cytosines, or combinations thereof;
or guanines, thymidines/uridines, or combinations thereof, rendering the population of primers substantially incapable of at least one of the following;
self-hybridization;
self-priming;
hybridization to another polynucleotide in the plurality;
orinitiation of a polymerization reaction in the plurality; and
c) subjecting said nucleic acid molecule/primer mixture to a thermostable polymerase under conditions to generate the plurality of molecules including the known constant region at each end.
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Abstract
The present invention regards a variety of methods and compositions for whole genome amplification and whole transcriptome amplification. In a particular aspect of the present invention, there is a method of amplifying a genome comprising a library generation step followed by a library amplification step. In specific embodiments, the library generating step utilizes specific primer mixtures and a DNA polymerase, wherein the specific primer mixtures are designed to eliminate ability to self-hybridize and/or hybridize to other primers within a mixture but efficiently and frequently prime nucleic acid templates.
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Citations
33 Claims
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1. A method of preparing a plurality of nucleic acid molecules having a known constant region at each end, the method comprising:
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a) obtaining a sample comprising nucleic acid molecules; b) subjecting said nucleic acid molecules to a population of primers to form a nucleic acid molecule/primer mixture, wherein all the primers of the population have a nucleotide sequence that is substantially non-self-complementary and substantially non-complementary to other primers in the population, wherein all the primers comprise a constant region of at least 6 nucleotides in length, the constant region consisting of all nucleotides of a contiguous known sequence that is constant among all the primers of the population, and a variable region at the distal 3′
end of at least 4 nucleotides in length, wherein the variable region begins with a degenerate nucleotide, the constant region being positioned 5′
to the variable region, wherein the constant region and the variable region each comprise greater than 50% non-complementary nucleotides, wherein the greater than 50% non-complementary nucleotides of both the constant region and the variable region are;
guanines, adenines, or combinations thereof;
cytosines, thymidines/uridines, or combinations thereof;
adenines, cytosines, or combinations thereof;
or guanines, thymidines/uridines, or combinations thereof, rendering the population of primers substantially incapable of at least one of the following;self-hybridization; self-priming; hybridization to another polynucleotide in the plurality;
orinitiation of a polymerization reaction in the plurality; and c) subjecting said nucleic acid molecule/primer mixture to a thermostable polymerase under conditions to generate the plurality of molecules including the known constant region at each end. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15)
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16. A method of preparing a plurality of nucleic acid molecules having a known constant region at each end, the method comprising:
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a) obtaining a sample comprising nucleic acid molecules; b) subjecting said nucleic acid molecules to a population of primers to form a nucleic acid molecule/primer mixture, wherein all the primers of the population have a nucleotide sequence that is substantially non-self-complementary and substantially non-complementary to other primers in the population, wherein all the primers comprise a constant region at the distal 5′
end of at least 6 nucleotides in length, the constant region consisting of all nucleotides of a contiguous known sequence that is constant among all the primers of the population, 1 to 3 random bases at the distal 3′
end, and a variable region of at least 4 nucleotides in length, wherein the variable region begins with a degenerate nucleotide, the variable region being positioned adjacent to the random base(s), wherein the constant region and the variable region each comprise greater than 50% non-complementary nucleotides, wherein the greater than 50% non-complementary nucleotides of both the constant region and the variable region are;
guanines, adenines, or combinations thereof;
cytosines, thymidines/uridines, or combinations thereof;
adenines, cytosines, or combinations thereof;
or guanines, thymidines/uridines, or combinations thereof, rendering the population of primers substantially incapable of at least one of the following;self-hybridization; self-priming; hybridization to another polynucleotide in the plurality;
orinitiation of a polymerization reaction in the plurality; and c) subjecting said nucleic acid molecule/primer mixture to a thermostable polymerase under conditions to generate the plurality of molecules including the known constant region at each end. - View Dependent Claims (17, 18)
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19. A method of preparing a plurality of nucleic acid molecules having a known constant region at each end, the method comprising:
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a) obtaining a sample comprising nucleic acid molecules; b) subjecting said nucleic acid molecules to a population of primers to form a nucleic acid molecule/primer mixture, wherein the primers of the population have a nucleotide sequence that is substantially non-self-complementary and substantially non-complementary to other primers in the population, wherein the primers comprise a constant region at the distal 5′
end of at least 6 nucleotides in length, the constant region consisting of all nucleotides of a contiguous known sequence that is constant among all the primers of the population, and a variable region of at least 4 nucleotides in length, the constant region being positioned 5′
to the variable region, wherein the constant region and the variable region each comprise at least 80% non-complementary nucleotides, wherein the at least 75% non-complementary nucleotides of both the constant region and the variable region are;
guanines, adenines, or combinations thereof;
cytosines, thymidines/uridines, or combinations thereof;
adenines, cytosines, or combinations thereof;
or guanines, thymidines/uridines, or combinations thereof, rendering the population of primers substantially incapable of at least one of the following;self-hybridization; self-priming; hybridization to another polynucleotide in the plurality;
orinitiation of a polymerization reaction in the plurality; and c) subjecting said nucleic acid molecule/primer mixture to a polymerase under conditions to generate the plurality of molecules including the known constant region at each end. - View Dependent Claims (20, 21, 22, 23, 24, 25, 26)
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27. A method of preparing a plurality of nucleic acid molecules having a known constant region at each end, the method comprising:
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a) obtaining a sample comprising nucleic acid molecules; b) subjecting said nucleic acid molecules to a population of primers to form a nucleic acid molecule/primer mixture, wherein the primers of the population have a nucleotide sequence that is substantially non-self-complementary and substantially non-complementary to other primers in the population, wherein the primers comprise a constant region and a variable region, the constant region being positioned 5′
to the variable region, wherein the constant region and the variable region each comprise greater than 50% non-complementary nucleotides, wherein the greater than 50% non-complementary nucleotides of both the constant region and the variable region are;
guanines, adenines, or combinations thereof;
cytosines, thymidines/uridines, or combinations thereof;
adenines, cytosines, or combinations thereof;
or guanines, thymidines/uridines, or combinations thereof, rendering the population of primers substantially incapable of at least one of the following;self-hybridization; self-priming; hybridization to another polynucleotide in the plurality;
orinitiation of a polymerization reaction in the plurality; and c) subjecting said nucleic acid molecule/primer mixture to a polymerase under conditions to generate the plurality of molecules including the known constant region at each end, wherein each primer of the population is comprised of at least 70% of the non-complementary nucleotides. - View Dependent Claims (28, 29)
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30. A method of preparing a plurality of nucleic acid molecules having known constant region at each end, comprising:
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a) obtaining a sample comprising nucleic acid molecules; b) subjecting said nucleic acid molecules to a population of primers to form a nucleic acid molecule/primer mixture, wherein the primers of the population are non-self-complementary and non-complementary to other primers in the population, and comprise in a 5′
to 3′
orientation a constant region and a variable region, wherein the constant region sequence has a known sequence that is constant among the primers of the population and the variable region sequence is degenerate among the primers of the population, and further wherein the sequence of the primers comprises at least 70% of two types of non-complementary nucleotides selected from the group consisting of adenines and guanines;
adenines and cytosines;
guanines and thymidines; and
cytosines and thymidines, such that the primers of the population will not cross-hybridize or self-hybridize under the conditions employed in step c); andc) subjecting said nucleic acid molecule/primer mixture to a polymerase under conditions to generate the plurality of molecules including the known constant region at each end.
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31. A method of preparing a plurality of nucleic acid molecules having known constant region at each end, comprising:
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a) obtaining a sample comprising nucleic acid molecules; b) subjecting said nucleic acid molecules to a population of primers to form a nucleic acid molecule/primer mixture, wherein all the primers of the population are non-self-complementary and non-complementary to other primers in the population, and comprise in a 5′
to 3′
orientation a constant region and a variable region, wherein the constant region sequence consists of all nucleotides of a contiguous known sequence that is constant among all the primers of the population and the variable region sequence is degenerate among all the primers of the population, wherein the variable region begins with a degenerate nucleotide, and further wherein the sequence of the constant region comprises at least 70% of two types of non-complementary nucleotides selected from the group consisting of adenines and guanines;
adenines and cytosines;
guanines and thymidines; and
cytosines and thymidines, and the sequence of the variable region comprises greater than 50% non-complementary nucleotides selected from the group consisting of adenines and guanines;
adenines and cytosines;
guanines and thymidines; and
cytosines and thymidines, such that all the primers of the population will not cross-hybridize or self-hybridize under the conditions employed in step c); andc) subjecting said nucleic acid molecule/primer mixture to a thermostable polymerase under conditions to generate the plurality of molecules including the known constant region at each end. - View Dependent Claims (32, 33)
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Specification