Synthesis and properties of novel PRODAN-labeled uridine

We have developed a novel base-discriminating fluorescent (BDF) nucleoside, (PDN)U, which contains a PRODAN chromophore connected at the C-5 position of uracil. The Stokes shift (Deltanu) of (PDN)U was highly dependent on the local dielectric property around the fluorophore. On the excitation at 450 nm, the fluorescence spectrum of the duplex containing a (PDN)U/A base pair showed a strong emission at 520 nm. In contrast, the fluorescence intensities of duplexes containing "mismatched" (PDN)U/N base pairs (N = C, G, or T) were considerably lower. Furthermore, the drastic change of fluorescence intensity by the nature of the complementary base is useful for SNP typing.