Fluorescent nucleotide analog hairpin formation for detection of nucleic acid hybridization

Abstract

This invention provides methods and compositions for the detection of nucleic acid interactions with other nucleic acids or with proteins. The methods generally utilize a nucleic acid (e.g., an oligonucleotide) that contains one or more fluorescent nucleotide analogues. The fluorescence of the nucleotide analogues is quenched (reduced) when they are incorporated into the oligonucleotide. Alteration of the normal conformation of the oligonucleotide by hybridization (e.g. to form a loop) or by protein binding reduces and/or eliminates the quench thereby causing a detectable increase in fluorescence.