Detectably labeled dual conformation oligonucleotide Probes, Assays and Kits

Claim 1

A labeled unimolecular probe for detecting at least one nucleic acid strand containing a preselected nucleic acid target sequence under preselected assay conditions including a detection temperature, said probe comprising: a single-stranded target complement sequence having from 6 to 9 nucleotides, optionally 7 to 9 nucleotides, having a 5' terminus and a 3' terminus, and being complementary to the target sequence; a stem duplex consisting of a 5' arm sequence adjacent to and covalently linked to said 5' terminus and a 3' arm sequence adjacent to and covalently linked to said 3' terminus, said arms having a length of from 3 to 25 nucleotides, said duplex having a melting temperature above said detection temperature under the preselected assay conditions; and at least one label pair, each pair comprising a first label moiety conjugated to the probe in the vicinity of said 5' arm sequence and a second label moiety proximate to said first label moiety and conjugated to the probe in the vicinity of said 3' arm sequence, said probe having, under said preselected assay conditions in the absence of said target sequence, a characteristic signal whose level is a function of the degree of interaction of said first and second label moieties, said signal having a first level at 10°C below said melting temperature, a second level at 10°C above said melting temperature and a third level at said detection temperature, wherein under the preselected assay conditions at the detection temperature and in the presence of an excess of said target sequence, hybridization of the target complement sequence to the target sequence alters the level of said characteristic signal from said third level toward the second level by an amount of at least ten percent of the difference between the first and second levels, and wherein a duplex of said target complement sequence and its complementary target sequence is larger than said stem duplex.