Abstract: The invention relates to compositions and methods for rapidly detecting or isolating a target nucleic acid sequence in a polynucleotide-containing sample. The sample is exposed to a rapid pairing reagent, which contains a rapid capture component, effective to rapidly and non-selectively bind polynucleotides, and a target specific probe, effective to selectively bind the target nucleic acid sequence. Selectively disrupting the binding between the capture component and polynucleotides leaves only target sequence bound to the rapid pairing reagent.