3-Fluoro-2-mercuri-6-methylaniline nucleotide as a high-affinity nucleobase-specific hybridization probe.

A 3-fluoro-6-methylaniline nucleoside was synthesized, incorporated into an oligonucleotide and its ability to form mercury-mediated base pairs was studied. UV melting experiments revealed markedly increased duplex stability with thymine, gua-nine and cytosine opposite to the probe and a clear nucleobase-specific binding preference (T > G > C > >A). Moreover, the 3-fluoro group was utilized as a spin label that showed distinct 19F NMR resonance shifts depending on the complementary nucleobase, providing more detailed information on Hg(II)-mediated base pairing.