Detecting single nucleotide polymorphism using hydrolysis probes with 3′ hairpin structure

A kit for detecting a single nucleotide polymorphism (SNP) in a target nucleic acid in a sample, comprising:

• at least one primer comprising a first nucleic acid sequence specific to produce an amplification product comprising a region containing the SNP if the target nucleic acid is present in the sample;
• and
• a SNP specific hydrolysis probe comprising a second nucleic acid sequence complementary to the region containing the SNP of the amplification product, the SNP specific hydrolysis probe comprising a donor fluorescent moiety and an acceptor moiety of the donor fluorescent moiety, a 5′ end and a 3′ end, and a hairpin structure located on the 3′ end, the hairpin structure comprising a region which is located on the 3′ end of the hairpin structure that comprises one or more non-naturally occurring nucleotides to produce the hairpin structure, wherein the acceptor moiety is in an internal position of the SNP specific hydrolysis probe and is located close to the 5′ end of the hairpin structure, the donor fluorescent moiety is at the 5′ terminus, and the acceptor moiety is located within no more than 5 nucleotides from the donor fluorescent moiety on the hydrolysis probe.