Methods and compositions for analyzing nucleic acid

Abstract

The technology relates in part to methods and compositions for analyzing nucleic acid. In some aspects, the technology relates to methods and compositions for preparing a nucleic acid library. In some aspects, the technology relates to methods and compositions for analyzing ends of nucleic acid fragments.

1 . (canceled) 
     
     
         2 . A composition comprising a plurality of oligonucleotide species, wherein:
 a) each oligonucleotide in the plurality of oligonucleotide species comprises two strands;   b) each oligonucleotide in the plurality of oligonucleotide species comprises an overhang at a first end, or some of the oligonucleotides in the plurality of oligonucleotide species comprise an overhang at a first end and some of the oligonucleotides in the plurality of oligonucleotide species comprise no overhang at a first end, wherein the overhang, when present, is capable of hybridizing to a target nucleic acid overhang, wherein each oligonucleotide species having an overhang has a unique overhang sequence and length;   c) each oligonucleotide in the plurality of oligonucleotide species comprises at a second end (i) two non-complementary strands and (ii) one or more blocked nucleotides; and   d) each oligonucleotide in the plurality of oligonucleotide species comprises an oligonucleotide overhang identification sequence specific to no overhang or specific to one or more features of the oligonucleotide overhang, wherein the one or more features comprise length of the overhang.   
     
     
         3 . The composition of  claim 2 , wherein the plurality of oligonucleotide species comprises oligonucleotides having a 5′ overhang and oligonucleotides having a 3′ overhang. 
     
     
         4 . The composition of  claim 2 , wherein the plurality of oligonucleotide species comprises oligonucleotides having a 5′ overhang, oligonucleotides having a 3′ overhang, and oligonucleotides having no overhang. 
     
     
         5 . The composition of  claim 2 , wherein the oligonucleotides in the plurality of oligonucleotide species having overhangs comprise:
 i) oligonucleotide overhangs having different sequences for a particular overhang length;   ii) all possible overhang sequence combinations for a particular overhang length; or   iii) all possible overhang sequence combinations for each overhang length.   
     
     
         6 . The composition of  claim 5 , wherein the oligonucleotide overhang sequences are random. 
     
     
         7 . The composition of  claim 2 , wherein the oligonucleotide overhang identification sequence is specific to length of the oligonucleotide overhang and is specific to one or more features of the oligonucleotide overhang chosen from (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). 
     
     
         8 . The composition of  claim 2 , wherein an oligonucleotide species comprises no overhang and comprises an oligonucleotide overhang identification sequence specific to having no overhang. 
     
     
         9 . The composition of  claim 2 , wherein each of the two non-complementary strands at the second end of the oligonucleotide species comprises a primer binding domain, wherein one of the non-complementary strands comprises a first primer binding domain, and the other non-complementary strand comprises a second primer binding domain, wherein the first primer binding domain and second primer binding domain are different. 
     
     
         10 . The composition of  claim 2 , wherein each oligonucleotide overhang identification sequence comprises a nucleic acid sequence that is unique for each oligonucleotide comprising an overhang of a particular length or no overhang. 
     
     
         11 . The composition of  claim 2 , wherein each oligonucleotide overhang identification sequence comprises a nucleic acid sequence that is unique for each oligonucleotide comprising an overhang of a particular length or no overhang and a particular 5′ or 3′ overhang directionality, when an overhang is present. 
     
     
         12 . A kit comprising:
 the composition of  claim 2 ; and   instructions for using the composition to produce a nucleic acid library.   
     
     
         13 . The kit of  claim 12 , further comprising an agent comprising a phosphatase activity. 
     
     
         14 . The kit of  claim 12 , further comprising an agent comprising a phosphoryl transfer activity. 
     
     
         15 . The kit of  claim 12 , further comprising an agent comprising a ligase activity. 
     
     
         16 . The kit of  claim 12 , further comprising an agent comprising a nick-sealing ligase activity. 
     
     
         17 . The kit of  claim 12 , further comprising a strand-displacing polymerase.