Abstract: In one aspect, the present invention concerns methods and kits for quantifying a target nucleic acid in a sample. In embodiments, a method comprises sequestrating the target nucleic acid by one or more interactors to form a sequestered conjugate that will be further labeled to form a labeled conjugate. The signal produced by the labeled conjugate is measured and correlated to the amount of the target nucleic acid. In another aspect, the present invention concerns a method for quantifying a target nucleic acid in a sample by a reaction of the nucleic acids in the sample with a nucleic acid interactor or set of interactors to form a conjugate. The conjugate is then sequestered from the rest of the sample with a molecule bound to a support, to form a sequestered conjugate. The sequestered conjugate is labeled to form a labeled conjugate. The signal produced by the labeled conjugate is measured and correlated to the amount of the target nucleic acid.