CAPTURE OF NUCLEIC ACIDS USING A NUCLEIC ACID-GUIDED NUCLEASE-BASED SYSTEM

1 . A method of capturing target nucleic acid sequences comprising:

(a) providing a sample comprising a plurality of adapter-ligated nucleic acids, wherein the nucleic acids are ligated to a first adapter at one end and ligated to a second adapter at the other end;

(b) contacting the sample with a plurality of nucleic acid-guided nuclease-gNA complexes, wherein the gNAs are complementary to targeted sites of interest contained in a subset of the nucleic acids, wherein the contacting with the plurality of nucleic acid-guided nuclease-gNA complexes cleaves the targeted sites of interest contained in a subset of the nucleic acids, thereby generating a plurality of nucleic acid fragments ligated to a first or second adapter at one end and no adapter at the other end; and

(c) contacting the plurality of nucleic acid fragments with third adapters, thereby generating a plurality of nucleic acid fragments ligated to either the first or second adapter at one end and the third adapter at the other end.

2 . The method of claim 1 , wherein the nucleic acid-guided nuclease is a CRISPR/Cas system protein.

3 . (canceled)

4 . The method of claim 1 , wherein the nucleic acid-guided nuclease is selected from the group consisting of CAS Class I Type I, CAS Class I Type III, CAS Class I Type IV, CAS Class II Type II, and CAS Class II Type V.

5 . The method of claim 1 , wherein the nucleic acid-guided nuclease is selected from the group consisting of Cas9, Cpf1, Cas3, Cas8a-c, Cas10, Cse1, Csy1, Csn2, Cas4, Csm2, Cmr5, Csf1, C2c2, and NgAgo.

6 . The method of claim 1 , wherein the gNAs are gRNAs.

7 . The method of claim 1 , wherein the gNAs are gDNAs.

8 . (canceled)

9 . The method of claim 1 , wherein the method further comprises amplifying the product of step (c) using first or second and third adapter-specific PCR.

10 . (canceled)

11 . The method of claim 1 , wherein the nucleic acids are double stranded DNA.

12 . The method of claim 1 , wherein nucleic acids are from genomic DNA.

13 . (canceled)

14 . The method of claim 1 , wherein the nucleic acids which are adapter-ligated are from 20 bp to 5000 bp in length.

15 . The method of claim 1 , wherein the targeted sites of interest are single nucleotide polymorphisms (SNPs), short tandem repeats (STRs), cancer genes, inserts, deletions, structural variations, exons, genetic mutations, or regulatory regions.

16 . (canceled)

17 . The method of claim 1 , wherein the adapters are from 20 bp to 100 bp in length.

18 - 20 . (canceled)

21 . The method of claim 1 , wherein the sample is obtained from a biological sample a clinical sample, a forensic sample, or an environmental sample.

22 . The method of claim 1 , wherein the first and second adapters are identical.

23 . The method of claim 1 , wherein the first and second adapters are different.

24 . The method of claim 1 , wherein the sample comprises a sequencing library.

25 - 44 . (canceled)

45 . A method of capturing target nucleic acid sequences of interest comprising:

(a) providing a sample comprising a plurality of adapter-ligated nucleic acids, wherein the nucleic acids are ligated to a first adapter at one end and are ligated to a second adapter at the other end; and

(b) contacting the sample with a plurality of catalytically dead nucleic acid-guided nuclease-gNA complexes, wherein the catalytically dead nucleic acid-guided nuclease is fused to a transposase, wherein the gRNAs are complementary to targeted sites of interest contained in a subset of the nucleic acids, and wherein the complexes are loaded with a plurality of third adapters, to generate a plurality of nucleic acids fragments comprising either a first or second adapter at one end, and a third adapter at the other end.

46 - 49 . (canceled)

50 . The method of claim 45 , wherein the catalytically dead nucleic acid-guided nuclease is selected from the group consisting of dCas9, dCpf1, dCas3, dCas8a-c, dCas10, dCse1, dCsy1, dCsn2, dCas4, dCsm2, dCmr5, dCsf1, dC2C2, and dNgAgo.

51 - 57 . (canceled)

58 . The method of claim 45 , wherein the contacting of step (b) allows for the insertion of the second adapter into the targeted nucleic acid sequences.

59 - 63 . (canceled)

64 . The method of claim 45 , wherein the targeted sites of interest represent less than 50% of the total nucleic acid in the sample.

65 - 175 . (canceled)