Patent ID: 7537892

Claim:
A method of determining the identity of an unknown nucleotide at a position of interest on a target nucleic acid analyte comprising: contacting the target nucleic acid analyte under hybridizing conditions with at least two non-identical oligonucleotide probes having a variable position nucleotide, wherein the variable position nucleotide of at least one of the at least two oligonucleotide probes is a nucleotide that will base pair with at least two nucleotides, the variable position nucleotide of at least one other of the at least two oligonucleotide probes is either a nucleotide that will base pair with at least two nucleotides or a nucleotide incapable of degenerate base pairing, wherein the nucleotides in the variable positions of the at least two oligonucleotide probes collectively base pair with all but one nucleotide; wherein the hybridizing conditions are sufficient to permit the at least two oligonucleotide probes to hybridize to the target nucleic acid analyte when the nucleotide occupying the variable position base pairs with the nucleotide occupying the position of interest, and do not permit the at least two oligonucleotide probes to hybridize to the target nucleic acid analyte when the nucleotide occupying the variable position does not base pair with the nucleotide occupying the position of interest; and wherein the identity of the position of interest is determined by comparing the variable positions of any hybridized oligonucleotide probes for complementarity and the variable positions of any nonhybridized oligonucleotide probes for lack of complementarity.