Methods and compositions for analyzing nucleic acid

A method of producing a nucleic acid library, comprising:

• a) combining i) a first composition comprising nucleic acid molecules and ii) pairs of oligonucleotides, thereby generating a mixture, wherein a first member of each oligonucleotide pair comprises a first portion of an endonuclease recognition site and a second member of each oligonucleotide pair comprises a second portion of an endonuclease recognition site, wherein the first portion of the endonuclease recognition site and the second portion of the endonuclease recognition site are capable of forming an endonuclease recognition site when the first portion is adjacent to the second portion in an oligonucleotide dimer;
• b) covalently linking the first member of an oligonucleotide pair to a first end of a nucleic acid molecule in the mixture, wherein the first portion of the endonuclease recognition site is adjacent to the first end of the nucleic acid molecule;
• and covalently linking the second member of the oligonucleotide pair to a second end of the nucleic acid molecule, wherein the second portion of the endonuclease recognition site is adjacent to the second end of the nucleic acid molecule, thereby generating a second composition comprising covalently linked products;
• and
• c) contacting the second composition with an agent comprising an endonuclease activity, whereby oligonucleotide dimers comprising the endonuclease recognition site, if present, are cleaved by the agent and the covalently linked products are not cleaved by the agent.