Method for Fragmenting Genomic DNA Using CAS9

Abstract

A method for fragmenting a genome is provided. In certain embodiments, the method comprises: (a) combining a genomic sample containing genomic DNA with a plurality of Cas9-gRNA complexes, wherein the Cas9-gRNA complexes comprise a Cas9 protein and a set of at least 10 Cas9-associated guide RNAs that are complementary to different, pre-defined, sites in a genome, to produce a reaction mixture; and (b) incubating the reaction mixture to produce at least 5 fragments of the genomic DNA. Also provided is a composition comprising at least 100 Cas9-associated guide RNAs that are each complementary to a different, pre-defined, site in a genome. Kits for performing the method are also provided. In addition, other methods, compositions and kits for manipulating nucleic acids are also provided.

What is claimed is: 
     
         1 . A composition comprising: a set of at least 10 Cas9-associated guide RNAs that are each complementary to a different, pre-defined sequence. 
     
     
         2 . The composition of  claim 1 , wherein each sequence is a genomic sequence. 
     
     
         3 . The composition of  claim 1 , wherein each sequence is a human genomic sequence. 
     
     
         4 . The composition of  claim 1 , wherein each sequence is a genomic sequence from a different pathogen. 
     
     
         5 . The composition of  claim 1 , further comprising a Cas9 nuclease. 
     
     
         6 . The composition of  claim 1 , wherein said RNAs are in solution. 
     
     
         7 . The composition of  claim 1 , wherein said RNAs are tethered to a substrate in an array.