SUBSTANTIALLY NON-SELF COMPLEMENTARY PRIMERS
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.
1 .- 51 . (canceled)
52 . A population of polynucleotide primers, the primers of said population having a sequence that is substantially non-self-complementary and substantially non-complementary to other primers in the population, wherein the primers are composed of a constant region and a variable region, the constant region being positioned 5′ to the variable region, wherein at least 70% of a sequence of a primer in the population is comprised of two non-complementary and non-self-complementary nucleotides.
53 . The population of claim 52 , wherein said nucleic acid sequence is further defined as rendering the polynucleotides substantially incapable of at least one of the following:
self-hybridization;
self-priming;
hybridization to another polynucleotide in the plurality; or
initiation of a polymerization reaction in the plurality.
54 . The population of claim 52 , wherein at least 75% of a sequence of a primer in the population is comprised of two non-complementary and non-self-complementary nucleotides.
55 . The population of claim 54 , wherein at least 80% of a sequence of a primer in the population is comprised of two non-complementary and non-self-complementary nucleotides.
56 . The population of claim 55 , wherein at least 85% of a sequence of a primer in the population is comprised of two non-complementary and non-self-complementary nucleotides.
57 . The population of claim 56 , wherein at least 90% of a sequence of a primer in the population is comprised of two non-complementary and non-self-complementary nucleotides.
58 . The population of claim 57 , wherein at least 95% of a sequence of a primer in the population is comprised of two non-complementary and non-self-complementary nucleotides.
59 . The population of claim 58 , wherein at least 97% of a sequence of a primer in the population is comprised of two non-complementary and non-self-complementary nucleotides.
60 . The population of claim 59 , wherein 100% of a sequence of a primer in the population is comprised of two non-complementary and non-self-complementary nucleotides.
61 . The population claim 52 , wherein the constant and variable regions consist of guanines and adenines; the constant and variable regions consist of cytosines and thymidines; the constant and variable regions consist of adenines and cytosines; or the constant and variable regions consist of guanines and thymidines.
62 . The population of claim 52 , wherein said constant region is 6 to 100 nucleotides.
63 . The population of claim 52 , wherein said variable region is 4 nucleotides to 20 nucleotides.
64 . The population of claim 52 , wherein the primers have 0 to 3 random bases at their 3′ ends.
65 . The plurality of claim 52 , wherein the nucleic acid sequence is comprised of base or backbone analogs.
66 . A population of polynucleotides having primer sequences positioned at their 3′ and 5′ termini, the sequences of the primers being substantially non-self-complementary and substantially non-complementary to other primer sequences in the population, wherein the primers are composed of a constant region and a variable region, the constant region being positioned 5′ to the variable region, wherein at least 70% of a sequence of a primer in the population is comprised of two non-complementary and non-self-complementary nucleotides.
67 . The population of claim 66 , prepared by a method comprising obtaining at least one nucleic acid molecule; subjecting said nucleic acid molecule to a population of primers in accordance with claim 52 to form a nucleic acid molecule/primer mixture; and subjecting said nucleic acid molecule/primer mixture to a polymerase, under conditions wherein said subjecting steps generate a population of polynucleotides including all or part of the constant region at each end.