Hybridization-induced dequenching of fluorescein-labeled oligonucleotides: a novel strategy for PCR detection and genotyping

Fluorescence-based detection methods are being increasingly utilized in molecular analyses. Sequence-specific fluorescently-labeled probes are favored because they provide specific product identification. The most established fluorescence-based detection systems employ a resonance energy transfer mechanism effected through the interaction of two or more fluorophores or functional groups conjugated to oligonucleotide probes. The design, synthesis and purification of such multiple fluorophore-labeled probes can be technically challenging and expensive. By comparison, single fluorophore-labeled probes are easier to design and synthesize, and are straightforward to implement in molecular assays. We describe herein a novel fluorescent strategy for specific nucleic acid detection and genotyping. The format utilizes an internally quenched fluorescein-oligonucleotide conjugate that is subsequently dequenched following hybridization to the target with an attendant increase in fluorescence. Reversibility of the process with strand dissociation permits Tm-based assessment of bp complementarity and mismatches. Using this approach, we demonstrated specific detection, and discrimination of base substitutions of a variety of synthetic nucleic acid targets including Factor V Leiden and methylenetetrahydrofolate reductase. We further demonstrated compatibility of the novel chemistry with polymerase chain reaction by amplification and genotyping of the above listed loci and the human hemoglobin beta chain locus. In total, we analyzed 172 clinical samples, comprising wild-type, heterozygous and homozygous mutants of all three loci, with 100% accuracy as confirmed by DNA sequencing, established dual hybridization probe or high performance liquid chromatography-based methods. Our results indicate that the dequenching-based single fluorophore format is a feasible strategy for the specific detection of nucleic acids in solution, and that assays using this strategy can provide accurate genotyping results.