Time-resolved FRET for single-nucleotide polymorphism genotyping

By tens-of-picosecond resolved fluorescence detection (TCSPC, time-correlated single-photon counting) we study F̈orster resonance energy transfer between a donor and a black-hole-quencher acceptor bound at the 5′- and 3′- positions of a synthetic DNA oligonucleotide. This dual labelled oligonucleotide is annealed with either the complementary sequence or with sequences that mimic single-nucleotide polymorphic gene sequences: they differ in one nucleotide at positions near either the ends or the center of the oligonucleotide. We find donor fluorescence decay times whose values are definitely distinct and discuss the feasibility of single nucleotide polymorphism genotyping by this method. © 2009 SPIE.