Patent ID: 9487839
Filing Date: 2016-11-08
CPC Classification: C12Q

Claim Text:
1. A method of detecting at least one single nucleotide polymorphism in a first polynucleotide sequence of a predetermined species, the method comprising: providing a first polynucleotide to be analyzed for the presence of at least one single nucleotide polymorphism (SNP); providing a second polynucleotide consisting of a first sequence, a second sequence adjacent to the first sequence, and a single nucleotide polymorphism interrogating position that is adjacent the second sequence distal to the first sequence, wherein the second sequence is essentially complementary to a first portion of the first polynucleotide and wherein the first sequence is not completely complementary to the first polynucleotide adjacent to the first portion of the first polynucleotide, and wherein the second polynucleotide is at least 50 nucleotides long; providing a third polynucleotide comprising a sequence that is essentially complementary to a second portion of the first polynucleotide immediately adjacent the first portion of the first polynucleotide at a junction; subjecting the first, second and third polynucleotides to conditions under which complementary regions of the first, second and third polynucleotides will anneal; ligating the second and third polynucleotides at a junction between the second and third polynucleotides when no mismatches occur between the first polynucleotide and either of: the single nucleotide polymorphism interrogating position and the position in the second sequence adjacent to the single nucleotide polymorphism interrogating position; and the nucleotide of the third polynucleotide at the junction; optionally denaturing the annealed polynucleotides and repeating the steps of subjecting the polynucleotides to conditions under which complementary regions of the polynucleotides will anneal and treating the annealed polynucleotides with a ligase a predetermined number of times; providing a fourth polynucleotide coupled to a first detectable label, wherein the fourth polynucleotide contains a sequence that is essentially complementary to at least a portion of the first sequence of the second polynucleotide; providing at least one of a fifth and a sixth polynucleotide, wherein the fifth polynucleotide consists of a sequence that is essentially complementary to at least a portion of the third polynucleotide sufficient to cause the fifth polynucleotide to hybridize to the third polynucleotide sequence that is essentially complementary to a second portion of the first polynucleotide but wherein the fifth polynucleotide is devoid of a sequence of about 15 or more nucleotides that are complementary to the second sequence of the second polynucleotide, and wherein the sixth polynucleotide consists of a sequence that is essentially complementary to at least a portion of the second sequence of the second polynucleotide and the single nucleotide polymorphism interrogating position sufficient to cause the sixth polynucleotide to hybridize to the second sequence of the second polynucleotide and the single nucleotide polymorphism interrogating position, but wherein the sixth polynucleotide is devoid of a sequence of about 15 or more nucleotides that are complementary to the third polynucleotide, wherein at least one of the third polynucleotide and the fifth polynucleotide is coupled to a second detectable label, and the sixth polynucleotide is not coupled to the second detectable label; and wherein each of the second, third, fourth, and fifth and sixth polynucleotides is a single-stranded polynucleotide; subjecting the polynucleotides to conditions under which complementary regions of the polynucleotides will anneal; and detecting the presence of the first and second detectable labels.