Methods of producing nucleic acid libraries

Abstract

Provided are methods of producing nucleic acid libraries. In certain aspects, the methods include combining target nucleic acids (e.g., 5′ phosphorylated nucleic acids) and an oligonucleotide pool. Oligonucleotides of the oligonucleotide pool may include complementarity regions of varying length and nucleotide sequence, and a complementarity region identification sequence. In such aspects, the combining is under conditions in which oligonucleotides of the oligonucleotide pool hybridize to nucleic acids of the target nucleic acids (e.g., 5′ phosphorylated nucleic acids) having overhang regions that are complementary in sequence and have corresponding lengths with respect to the complementarity regions of the oligonucleotides. Compositions and kits that find use, e.g., in practicing the methods of the present disclosure are also provided.

1 .- 123 . (canceled) 
     
     
         124 . A composition, comprising an oligonucleotide pool comprising oligonucleotides, wherein:
 some or all of the oligonucleotides comprise (i) a complementarity region capable of hybridizing to an overhang in a target nucleic acid of a nucleic acid composition, and (ii) a complementarity region identification polynucleotide,   the oligonucleotides in the pool comprising complementarity regions include complementarity regions of different lengths, and   the complementarity region identification polynucleotide is specific to one or more features of the complementarity region, wherein the one or more features comprise length of the complementarity region.   
     
     
         125 . The composition of  claim 124 , wherein the one or more features of the complementarity region further comprise (i) a 5′ overhang, (ii) a 3′ overhang, (iii) a particular sequence, (iv) a combination of (i) and (iii), or (v) a combination of (ii) and (iii). 
     
     
         126 . The composition of  claim 124 , wherein some of the oligonucleotides comprise no complementarity region and comprise an identification polynucleotide specific to no complementary region. 
     
     
         127 . (canceled) 
     
     
         128 . The composition of  claim 124 , wherein the composition is a liquid composition. 
     
     
         129 . The composition of  claim 124 , wherein the composition is a lyophilized composition. 
     
     
         130 . The composition of  claim 124 , wherein oligonucleotides of the oligonucleotide pool are hybridized to target nucleic acids in hybridization products. 
     
     
         131 . The composition of  claim 124 , wherein;
 the oligonucleotide pool comprises oligonucleotides that comprise an overhang;   each of the oligonucleotides comprising an overhang comprises an overhang at one end or an overhang at both ends;   an end, or both ends, of each of the oligonucleotides comprising an overhang independently comprises a 5′ overhang or a 3′ overhang; and   at an end, the overhang comprises the complementarity region.   
     
     
         132 .- 136 . (canceled) 
     
     
         137 . The composition of  claim 131 , wherein the complementarity region identification polynucleotide is specific to whether the overhang comprising the complementarity region is a 5′ overhang or a 3′ overhang. 
     
     
         138 . The composition of  claim 131 , wherein:
 the oligonucleotide pool comprises oligonucleotides each consisting essentially of a first strand and a second strand; and   the first strand comprises a first polynucleotide and the second strand comprises a second polynucleotide complementary to the first polynucleotide.   
     
     
         139 . The composition of  claim 131 , wherein:
 the oligonucleotide pool comprises oligonucleotides each consisting essentially of one strand capable of adopting a hairpin structure; and   the oligonucleotides comprise a first polynucleotide and a second polynucleotide complementary to the first polynucleotide.   
     
     
         140 - 147 . (canceled) 
     
     
         148 . The composition of  claim 131 , wherein the oligonucleotide pool comprises oligonucleotides that comprise different overhang polynucleotides for a particular overhang length. 
     
     
         149 . The composition of  claim 131 , wherein the oligonucleotide pool comprises oligonucleotides that comprise all possible overhang polynucleotide combinations for a particular overhang length. 
     
     
         150 . The composition of  claim 131 , wherein the oligonucleotide pool comprises oligonucleotides that comprise all possible overhang polynucleotide combinations for each overhang length. 
     
     
         151 . The composition of  claim 131 , wherein the overhang polynucleotides in the oligonucleotides of the pool are random. 
     
     
         152 .- 160 . (canceled) 
     
     
         161 . The composition of  claim 131 , wherein the oligonucleotides of the oligonucleotide pool comprise a portion other than the complementarity region and the complementarity region identification polynucleotide, wherein:
 (i) the portion other than the complementarity region and the complementarity region identification polynucleotide comprises a nucleic acid binding domain;   (ii) the portion other than the complementarity region and the complementarity region identification polynucleotide comprises all or a portion of a sequencing adapter; or   (iii) a combination of (i) and (ii).   
     
     
         162 .- 192 . (canceled) 
     
     
         193 . A kit, comprising:
 the composition of  claim 124 ; and   instructions for using the composition to produce a nucleic acid library.   
     
     
         194 . The kit of  claim 193 , further comprising a kinase adapted to 5′ phosphorylate nucleic acids of a nucleic acid sample and/or a DNA ligase. 
     
     
         195 .- 196 . (canceled) 
     
     
         197 . The composition of  claim 124 , wherein each complementarity region identification polynucleotide comprises a nucleic acid sequence that is unique for each oligonucleotide comprising a complementarity region of a particular length. 
     
     
         198 . The composition of  claim 124 , wherein each complementarity region identification polynucleotide comprises a nucleic acid sequence that is unique for each oligonucleotide comprising a complementarity region of a particular length and a particular 5′ or 3′ directionality.