Surface-capture of target nucleic acids

A method of capturing a nucleic acid onto a solid support, the method comprising:

• (i) fragmenting a nucleic acid to produce one or more target fragments, each fragment having at least one defined end sequence;
• (ii) denaturing the target fragment if it is double-stranded, thereby producing a single-stranded target fragment;
• (iii) contacting the single-stranded target fragment with a double-stranded capture probe having two overhang ends specific to two corresponding sites on the target fragment;
• (iv) allowing the capture probe and the target fragment to anneal to each other;
• (v) optionally, cleaving any branched structures;
• (vi) ligating the capture probe and the target fragment to form a closed circular nucleic acid;
• (vii) removing remaining linear nucleic acids;
• (viii) optionally, denaturing the double-stranded circular nucleic acid to create a single-stranded circular nucleic acid;
• (ix) linearizing the single-stranded circular nucleic acid and, optionally, further fragmenting the linearized nucleic acid, or fragmenting the circular single-stranded nucleic acid;
• (x) adding a capture sequence at the 3′ end(s) of the linearized nucleic acid fragment(s), and optionally adding a recognition site at the 5′ end(s) of the linearized nucleic acid fragment(s);
• and
• (xi) capturing the linearized nucleic acids onto the solid support by hybridizing the capture sequence to a complementary sequence covalently attached to the solid support.

A nucleic acid probe comprising:

• (a) a double-stranded nucleic acid having two overhang ends specific to two sites on a target nucleic acid, with one overhang end being complementary to a restriction cut site flanking a target sequence and the other end being complementary to a restriction cut site or an internal sequence;
• (b) a cleavage site within the double-stranded nucleic acid of (a), said cleavage site selected from noncanonical nucleotide(s) and a rare-cutter site;
• and
• (c) a capture sequence.