Patent ID: 6878530

Claim:
A method for determining the genotype at the site of a polymorphism in a target polynucleotide sequence comprising: a) contacting a first partial duplex comprising a target polynucleotide sequence with a second partial duplex comprising a mutated reference polynucleotide sequence under conditions in which said first and said second partial duplexes form a four-way complex, wherein said mutated reference polynucleotide is designed to be identical to a reference polynucleotide everywhere except at the site of a mutation that is not at the site of the polymorphism, and wherein said reference polynucleotide sequence corresponds to said target polynucleotide sequence and has a known genotype at the site of the polymorphism; b) subjecting said four-way complex to branch migration conditions, wherein branch migration in said four-way complex is impeded at or near the site of the polymorphism if the target polynucleotide sequence has a genotype at the site of the polymorphism that differs from that of the reference polynucleotide sequence, thereby forming a stabilized four-way complex, and wherein branch migration in the four-way complex is capable of continuing until complete strand exchange occurs if the target polynucleotide sequence and the reference polynucleotide sequence share the same genotype at the site of the polymorphism, thereby resulting in the resolution of said four-way complex into two duplex nucleic acids; and c) detecting said stabilized four-way complex as an indication that said target polynucleotide sequence has a genotype that is different from the known genotype of said reference polynucleotide sequence at said site of the polymorphism, or detecting resolution of said four-way complex into two duplex nucleic acids as an indication that said target polynucleotide sequence has a genotype that is the same as the known genotype of said reference polynucleotide sequence at said site of the polymorphism.