Methods of Depleting a Target Nucleic Acid in a Sample and Kits for Practicing the Same

Abstract

Provided are methods of depleting a target nucleic acid in a sample. The methods include contacting a target nucleic acid with two or more polymers that specifically hybridize to the target nucleic acid, and cleaving the hybridized regions of the target nucleic acid to deplete the target nucleic acid in the sample. Kits for practicing the subject methods are also provided.

1 - 38 . (canceled) 
     
     
         39 . A method of depleting a target deoxyribonucleic acid (DNA) in a sample, the method comprising:
 (a) contacting the sample comprising the target DNA with two or more polymers, wherein each of the two or more polymers specifically hybridizes to distinct regions of the target DNA to generate hybridized regions of the target DNA; and   (b) cleaving the hybridized regions to deplete the target DNA in the sample.   
     
     
         40 . The method according to  claim 39 , wherein the target DNA is an undesired target DNA. 
     
     
         41 . The method according to  claim 39 , wherein the method is further for enriching the sample for a desired DNA in the sample. 
     
     
         42 . The method according to  claim 39 , wherein the target DNA is intronic DNA or inter-geneic DNA. 
     
     
         43 . The method according to  claim 39 , wherein the depleting the target DNA in the sample produces a sample enriched for exonic DNA. 
     
     
         44 . The method according to  claim 39 , wherein the sample is isolated from a biological sample. 
     
     
         45 . The method according to  claim 44 , wherein the biological sample is selected from the group consisting of: a tissue sample, a cell sample, and a bacterial sample. 
     
     
         46 . The method according to  claim 44 , wherein the biological sample is a fixed sample. 
     
     
         47 . The method according to  claim 39 , wherein the two or more polymers are independently selected from the group consisting of: a DNA oligonucleotide, an RNA oligonucleotide, a locked nucleic acid (LNA), a peptide nucleic acid (PNA), and a xeno nucleic acid (XNA). 
     
     
         48 . The method according to  claim 39 , wherein the two or more polymers are synthetic oligonucleotides. 
     
     
         49 . The method according to  claim 39 , wherein after cleaving the hybridized regions, the method further comprises removing the two or more polymers. 
     
     
         50 . The method according to  claim 39 , wherein the two or more polymers are removed following the cleaving step by contacting the two or more polymers with an enzyme. 
     
     
         51 . The method according to  claim 50 , wherein the two or more polymers comprise deoxyuridine triphosphate (dUTP). 
     
     
         52 . The method according to  claim 51 , wherein the method comprises contacting the two or more polymers with uracil-N-glycosylase (UDG). 
     
     
         53 . The method according to  claim 39 , wherein the two or more polymers are removed following the cleaving step by a separation protocol. 
     
     
         54 . The method according to  claim 53 , wherein the separation protocol comprising binding the two or more polymers to a solid support. 
     
     
         55 . The method according to  claim 39 , wherein the method further comprises denaturing the target DNA prior to contacting the target DNA with the two or more polymers. 
     
     
         56 . The method according to  claim 55 , wherein the denaturing is denaturing by heating at a temperature and for a duration suitable to denature the target DNA. 
     
     
         57 . The method according to  claim 39 , wherein cleaving the hybridized regions comprises contacting the hybridized regions with an enzyme. 
     
     
         58 . The method according to  claim 57 , wherein the enzyme is a nuclease that specifically cleaves DNA. 
     
     
         59 . The method according to  claim 57 , wherein the enzyme cleaves DNA present in a DNA/RNA duplex. 
     
     
         60 . The method according to  claim 59 , wherein the nuclease is selected from the group consisting of: exonuclease I, DNase I, a ribozyme, and a combination thereof. 
     
     
         61 . The method according to  claim 39 , wherein cleaving the hybridized regions comprises contacting the hybridized regions with a deoxyribonuclease. 
     
     
         62 . A kit for use in depleting a target deoxyribonucleic acid (DNA) in a sample, the kit comprising:
 two or more polymers, wherein each of the two or more polymers specifically hybridizes to distinct regions of the target DNA to generate hybridized regions of the target DNA; and   an enzyme capable of specifically cleaving the hybridized regions of the target DNA.   
     
     
         63 . The kit according to  claim 62 , wherein the two or more polymers comprise deoxyuridine triphosphate (dUTP) and the enzyme comprises uracil-N-glycosylase (UDG). 
     
     
         64 . The kit according to  claim 62 , wherein the enzyme comprises a nuclease that specifically cleaves DNA.