Format of probes to detect nucleic acid differences

A method of detecting the presence or absence of a target nucleic acid in a biological sample, the method comprising:

• a) contacting a detectably-labeled probe comprising an anchor nucleic acid domain and a reporter nucleic acid domain with the sample;
• and
• b) detecting the presence or absence of binding of the probe to the target nucleic acid,
• wherein the anchor and reporter domains are linked by a non-nucleoside linker, and neither the anchor nor the reporter domain forms a stem loop in the absence of the target nucleic acid;
• and
• wherein the probe is not extendible by a polymerase;
• and the linker is linked to the anchor domain within 2 nucleotides of the 3′ end of the anchor domain and the linker is linked to the reporter domain within 2 nucleotides of the 5′ end of the reporter domain, wherein the anchor domain is not linked to a detectable label;
• and
• each of the anchor domain and the reporter domain comprises a contiguous sequence of at least 6 nucleotides complementary to the same strand of the target nucleic acid.