Fluorescent Oligonucleotide Probes for Screening High-Affinity Nucleobase Surrogates

Double-helical oligonucleotide probes featuring a single-nucleotide gap opposed by one of the canonical nucleobases and flanked by the fluorescent nucleobase analogue pyrrolocytosine have been synthesized and titrated with Pd^II chelates of dipicolinamide and its N² ,N⁶ -dialkylated derivatives. The fluorometric titrations revealed greatly increased affinity of the Pd^II chelates for the nucleobases opposing the gap compared to the respective free nucleotides in solution. Owing to the constrained environment of the single-nucleotide gap, the relative stabilities of the various Pd^II -mediated base pairs were also significantly different from those previously reported at monomer level.