Feasibility of single nucleotide polymorphism genotyping with a single-probe by time-resolved Forster resonance energy transfer

By tens-of-picosecond resolved fluorescence detection we study Forster 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 differing in one nucleotide at positions near either the ends or the centre 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. (C) 2009 Elsevier Ltd. All rights reserved.