Abstract: The invention comprises homogeneous nucleotide amplification strategies and assays. The methods involve amplification of a target nucleic acid sequence that includes the use of a probe that forms a duplex with a target nucleic acid sequence having an enzymatically cleavable region. The probe may anneal to other nucleic acid sequences but only forms an enzymatically cleavable region if the nucleic acid sequence is complementary to the probe. In other embodiments, the probe is configured to act as a primer for the amplification reaction if it anneals to a target nucleic acid sequence and is enzymatically cleaved. The target nucleic acid sequences amplified by the methods of this invention may be assayed by labeling the probe, by employing a second probe having features of the invention or by other suitable methods. Preferably, the probes comprise an RNA portion that forms an RNase H cleavable duplex with DNA.

Abstract: A method for performing real time, homogeneous assay of a target nucleic acid comprising annealing a labeled, ribo-oligonucleotide probe to the target DNA sequence and degrading a portion of the probe with RNase H to release labeled fragments. Sequential measurements of the released fragments permits kinetic characterization of the presence of the target sequence. Preferably, the assay is integrated into a polymerase chain reaction so that target amplification can be detected in real time.