Binary probe and clamp composition and methods for target hybridization detection

Abstract

Binary probe and clamp compositions conduct methods for target hybridization detection. Where the probe is a substrate for exonuclease cleavage, the composition provides quantitation and detection of PCR products, by real-time and end-point measurements. Where the probe is an amplification primer, the composition provides an improved method for labelling and detection of PCR products. Probes and clamps may be labelled with fluorescent dyes, quenchers, hybridization-stabilizing moieties, chemiluminescent dyes, and affinity ligands. Clamps may be nucleic acid analogs, such as 2-aminoethylglycine PNA.

1 . A binary composition for hybridizing to a target polynucleotide sequence comprising: 
 a probe comprising a target-specific portion and a clamp-specific portion wherein the target-specific portion is capable of sequence-specific binding to a target polynucleotide sequence; and    a clamp comprising a probe-specific portion and one or more labels wherein the probe-specific portion is capable of sequence-specific binding to the clamp-specific portion of the probe,    wherein the clamp-specific portion of the probe remains bound to the probe-specific portion of the clamp during detection of the labels.    
     
     
         2 . A method for detecting a target polynucleotide sequence comprising: 
 providing a binary probe and clamp composition comprising:    a probe comprising a target-specific portion and a clamp-specific portion wherein the target-specific portion is capable of sequence-specific binding to a target polynucleotide sequence; and    a clamp comprising a probe-specific portion and one or more labels wherein the probe-specific portion is capable of sequence-specific binding to the clamp-specific portion of the probe;    hybridizing the target-specific portion of the probe to the target polynucleotide sequence;    hybridizing the probe-specific portion of the clamp to the clamp-specific portion of the probe; and    detecting the binary probe.