Triad base pairs containing fluorene unit for quencher-free SNP typing

We designed an A-selective fluorescent DNA probe, U^FL, which bears a 2-ethynylfluorene moiety covalently attached to the base dU, and incorporated it into a central position in the hairpin loop. We describe photophysical studies of triad base pairs containing an U^FL DNA probe and their application to single-nucleotide polymorphism (SNP) typing using novel quencher-free molecular beacons (MBs). The drastic changes in the fluorescence properties that arise upon changing the nature of the complementary base and FBs suggest that these triad base pairs are the key elements for quencher-free SNP typing.