Patent ID: 7749708

Claim:
A method for identifying the sequence of one or more variant nucleotides in a nucleic acid molecule comprising (a) contacting a double-stranded nucleic acid molecule with a mismatch-specific endonuclease, wherein one strand of said double-stranded nucleic acid molecule has one or more variant nucleotides which create at least one mismatch in the double-stranded nucleic acid molecule so that the double-stranded nucleic acid molecule is cleaved at the 3′-side of the mismatch by the mismatch-specific endonuclease; (b) ligating a double-stranded linker, containing a 3′-overhang, to the 3′-end of the strand with the one or more variant nucleotides, wherein the 3′-overhang of the linker is degenerate and the double-stranded portion of the linker is of a predetermined sequence; and (c) determining the sequence of the one or more variant nucleotides via the predetermined linker sequence thereby identifying the sequence of the one or more variant nucleotides.