Capture of nucleic acids using a nucleic acid-guided nuclease-based system

1. A method comprising:

(a) contacting a sample comprising a plurality of DNA sequences with a plurality of nucleic acid-guided nuclease nickase-gNA complexes, wherein the gNAs are gRNAs that are complementary to targeted sites of interest adjacent to regions of interest in a subset of the DNA sequences, thereby generating a plurality of nicked DNA molecules at sites adjacent to the regions of interest, and wherein the nucleic acid-guided nuclease nickase is a Cas9 nickase;

(b) heating the sample to 65° C., thereby generating double-stranded breaks at the regions of interest with nicks adjacent thereto on both strands;

(c) contacting the double-stranded breaks with a thermostable ligase and a plurality of adapters, thereby allowing ligation of adapters at these sites; and

(d) repeating steps a-c to place a second adapter on the other side of the regions of interest.

2. The method of claim 1 , wherein the DNA is from genomic DNA.

3. The method of claim 2 , wherein the genomic DNA is human genomic DNA.

4. The method of claim 1 , wherein the adapters from step (c) and the adapters from step (d) comprise single-stranded DNA molecules.

5. The method of claim 4 , wherein the double-stranded breaks generated in step (b) comprise 3′ single-stranded overhangs, and wherein the single-stranded DNA molecules are complementary to the 3′ overhangs.

6. The method of claim 1 , wherein the ligase is a thermostable single-stranded DNA/RNA ligase.

7. The method of claim 6 , wherein the thermostable single-stranded DNA/RNA ligase is a 5′ App thermostable DNA/RNA ligase.

8. The method of claim 1 , wherein the Cas9 nickase is derived from Streptococcus pyogenes, Staphylococcus aureus, Neisseria meningitidis, Streptococcus thermophiles, Treponema denticola, Francisella tularensis, Pasteurella multocida, Campylobacter jejuni, Campylobacter lari, Mycoplasma gallisepticum, Nitratifractor salsuginis, Parvibaculum lavamentivorans, Roseburia intestinalis, Neisseria cinerea, Gluconacetobacter diazotrophicus, Azospirillum, Sphaerochaeta globus, Flavobacterium columnare, Fluviicola taffensis, Bacteroides coprophilus, Mycoplasma mobile, Lactobacillus farciminis, Streptococcus pasteurianus, Lactobacillus johnsonii, Staphylococcus pseudintermedius, Filifactor alocis, Legionella pneumophila, Suterella wadsworthensis or Corynebacter diphtheria.

9. The method of claim 1 , wherein the Cas9 nickase is derived from Streptococcus pyogenes, Staphylococcus aureus or Streptococcus thermophiles.

10. The method of claim 1 , comprising (e) amplifying or sequencing the regions of interest.