Patent ID: 6861222

Claim:
A method of detecting target nucleic acid sequences, the method comprising (a) bringing into contact one or more target samples and one or more structured probes, and incubating under conditions that promote hybridization between target nucleic acid sequences in the target samples and the structured probes, wherein each structured probe is bifunctional, wherein one function is as a probe to a target nucleic acid sequence and the other function is a detection function, wherein the detection function is not possible unless the probe hybridizes to the target nucleic acid sequence, wherein each structured probe has a first end and a second end, wherein each structured probe comprises at least two complementary portions, a target probe portion, and a detection portion, wherein the two or more complementary portions comprise a first complementary portion and a second complementary portion, wherein two or more of the complementary portions form a duplex region, wherein formation of the duplex region forms a loop, wherein at least a portion of the target probe portion is in the loop, wherein hybridization of the target probe portion to the target nucleic acid sequence disrupts the duplex region, (b) detecting the structured probes, wherein, prior to detection, the structured probes are treated to alter unhybridized probes, wherein only probes with intact duplex regions are altered by treatment of the structured probes, wherein altered probes are not detected.