Methods for manipulating biomolecules

Abstract

In some embodiments, the present teachings provide compositions, systems, methods and kits for generating a population of nucleic acid fragments. In some embodiments, nucleic acids can be fragmented enzymatically. For example, methods for generating a population of nucleic acid fragments can include a nucleic acid nicking reaction. In one embodiment, the methods can include a nick translation reaction. A nicking reaction can introduce nicks at random positions on either strand of a double-stranded nucleic acid. A nick translation reaction can move the position of nicks to a new position so that the new positions of two of the nicks are aligned to create a double-stranded break. In some embodiments, methods for generating a population of nucleic acid fragments can include joining at least one end of a fragmented nucleic acid to one or more oligonucleotide adaptors.

1 . A method for generating a population of nucleic acid fragments, comprising: introducing one or more nicks into a nucleic acid by subjecting a sample including a plurality of nucleic acids to nicking conditions; and generating at least one double stranded break in at least one of the nucleic acids. 
     
     
         2 . A method for generating a population of nucleic acid fragments comprising: (a) introducing at least one nick into a double stranded nucleic acid; and (b) forming a double stranded break in the nucleic acid by translating at least one nick. 
     
     
         3 . A method for generating a population of nucleic acid fragments comprising: (a) nicking a nucleic acid at least once on each strand; and (b) nick translating the nicks thereby generating a double-stranded break to produce nucleic acid fragments. 
     
     
         4 . The method of  claim 2 , wherein the nicking comprises enzymatic nicking. 
     
     
         5 . The method of  claim 3 , wherein the nick translating comprises a 5′ to 3′ DNA polymerization/degradation reaction or a 5′ to 3′ DNA polymerization/strand displacement reaction. 
     
     
         6 . The method of  claim 2 , wherein the translating includes polymerizing one or more unlabeled nucleotides onto the 3′ end of at least one nick. 
     
     
         7 . The method of  claim 2 , wherein at least one of the nucleic acid fragments is not labeled. 
     
     
         8 . The method of  claim 2 , wherein substantially all of the nucleic acid fragments are not labeled. 
     
     
         9 . The method of  claim 2 , further comprising: ligating at least one oligonucleotide adapter to at least one end of one or more nucleic acid fragments in the population of nucleic acid fragments. 
     
     
         10 . The method of  claim 2 , wherein one strand of at least one end of a fragment of the population can be joined to one strand of a double-stranded oligonucleotide adaptor to generate a fragment-adaptor molecule having a break. 
     
     
         11 . The method of  claim 2 , wherein both strands of at least one end of a fragment of the population can be joined to both strands of a double-stranded oligonucleotide adaptor. 
     
     
         12 . The method of  claim 2 , further comprising modulating the nicking conditions so as to adjust the average size of the nucleic acid fragments. 
     
     
         13 . A population of nucleic acid fragments generated by the method of  claim 2 .