Abstract: Assays using enzymatic degradation of RNA/DNA heteroduplexes are provided for the detection of target nucleic acid molecules. Such enzymatic degradation may be obtained by enzymes including RNaseH. Exemplary methods include Probe Trapping (PT), Hybrid Energy Transfer (HET), and Fluorescent Probe Degradation (FPD). The assays make use of an RNA or chimeric RNA/DNA probe which recognizes a target DNA sequence and forms an RNA/DNA heteroduplex that is the substrate for the enzyme RNaseH which degrades the RNA portion of the probe. Degraded probe fragments diffuse away from the DNA target leading to a detectable signal and allowing the DNA target to hybridize to another probe. Probe degradation is cycled over time. The assays disclosed herein are suitable for use in detecting DNA sequences and could be used in a medical diagnostic.

Abstract: An assay system using labeled probe molecules to identify and quantify target molecules in a sample is disclosed. Where labeled probe molecules are present on a substrate such as a microarray, the identification of multiple different target molecules may be examined simultaneously. Alternatively, a known number of like probe molecules may be present on a substrate and a single target molecule may be quantified in a sample. Preferred labeled probe molecules are comprised fluorescent single stranded nucleotide analogs whose fluorescence is quenched by pairing with a homologous nucleotide target sequence.

Abstract: An assay system using labeled probe molecules to identify and quantify target molecules in a sample is disclosed. Where labeled probe molecules are present on a substrate such as a microarray, the identification of multiple different target molecules may be examined simultaneously. Alternatively, a known number of like probe molecules may be present on a substrate and a single target molecule may be quantified in a sample. Preferred labeled probe molecules are comprised fluorescent single stranded nucleotide analogs whose fluorescence is quenched by pairing with a homologous nucleotide target sequence.