Patent ID: 7166432

Claim:
A method for the identification, isolation or separation of identical nucleic acid fragments from a mixture of at least two nucleic acid populations, comprising: a) digesting separately nucleic acids of said at least two populations with at least one restriction enzyme; b) ligating a blunt-ended adaptor sequence to the restriction fragments resulting from the digestion in step (a), said adaptor sequence having a unique 5′ end sequence for each nucleic acid population; c) mixing the ligation products resulting from the ligation in step (b), from said at least two nucleic acid populations each carrying adaptor sequences with unique 5′ end sequences; d) denaturing and re-hybridizing the mixture of nucleic acids resulting from the mixing in step (c) to generate a mixture comprising homoduplexes and heteroduplexes; e) digesting perfectly matched blunt-ended homoduplexes by a blunt ended specific nuclease; f) eliminating mismatched heteroduplexes with mismatch repair enzymes; and g) identifying, isolating or separating fully-matched heteroduplexes, thereby identifying, isolating or separating nucleic acid fragments that are identical between said at least two nucleic acid populations.