Substantially non-self complementary primers

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.

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.