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

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.