Patent ID: 7169561

Claim:
A method of determining a target polynucleotide comprising; providing a target polynucleotide, and a probe set, wherein the probe set comprises a first probe, a second probe, and a hairpin linker, wherein the first probe comprises a target specific portion, a single-stranded stem portion, and a protruding tail, wherein the second probe comprises a target specific portion, and a single-stranded stem portion, wherein the hairpin linker comprises a loop portion, a stem portion, and a protruding tail, wherein the single-stranded stem portion of the first probe is complementary to the single-stranded stem portion of the second probe, wherein the protruding tail of the hairpin linker is complementary to the protruding tail of the first probe; hybridizing the first probe one and the second probe to the target polynucleotide; ligating the first probe to the second probe to form a first ligation product; dissociating the first ligation product from the target polynucleotide; hybridizing the single-stranded stem portion of the first probe to the single-stranded stem portion of the second probe to form a self-complementary ligation product; hybridizing the protruding tail of the self-complementary ligation product to the protruding tail of the hairpin linker; ligating the self-complementary ligation product to the hairpin linker to form a loop ligation product; detecting the loop ligation product; and, determining the target polynucleotide.