Recognition of T*G mismatched base pairs in DNA by stacked imidazole-containing polyamides: surface plasmon resonance and circular dichroism studies.

An imidazole-containing polyamide trimer, f-ImImIm, where f is a formamido group, was recently found using NMR methods to recognize TG mismatched base pairs. In order to characterize in detail the TG recognition affinity and specificity of imidazole-containing polyamides, f-ImIm, f-ImImIm and f-PyImIm were synthesized. The kinetics and thermodynamics for the polyamides binding to Watson-Crick and mismatched (containing one or two TG, AG or GG mismatched base pairs) hairpin oligonucleotides were determined by surface plasmon resonance and circular dichroism (CD) methods. f-ImImIm binds significantly more strongly to the TG mismatch-containing oligonucleotides than to the sequences with other mismatched or with Watson-Crick base pairs. Compared with the Watson-Crick CCGG sequence, f-ImImIm associates more slowly with DNAs containing TG mismatches in place of one or two CG base pairs and, more importantly, the dissociation rate from the TG oligonucleotides is very slow (small k(d)). These results clearly demonstrate the binding selectivity and enhanced affinity of side-by-side imidazole/imidazole pairings for TG mismatches and show that the affinity and specificity increase arise from much lower k(d) values with the TG mismatched duplexes. CD titration studies of f-ImImIm complexes with TG mismatched sequences produce strong induced bands at approximately 330 nm with clear isodichroic points, in support of a single minor groove complex. CD DNA bands suggest that the complexes remain in the B conformation.