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

摘要

An imidazole-containing polyamide trimer, f-lmlmlm, where f is a formamido group, was recently found using NMR methods to recognize T·G mismatched base pairs. In order to characterize in detail the T·G recognition affinity and specificity of imidazole-containing polyamides, f-lmlm, f-lmlmlm and f-Pylmlm were synthesized. The kinetics and thermo-dynamics for the polyamides binding to Watson-Crick and mismatched (containing one or two T·G, A·G or G·G mismatched base pairs) hairpin oligouncleotides were determined by surface plasmon resonance and circular dichroism (CD) methods. f-lmlmlm binds significantly more strongly to the T·G mismatch-containing oligonucleotides than to the sequences with other mismatched or with Watson-Crick base pairs. Compared with the Watson-Crick CCGG sequence, f-lmlmlm associates more slowly with DNAs containing T·G mismatches in place of one or two C·G base pairs and, more importantly, the dissociation rate from the T·G oligonucleotides is very slow (small k_d). These results clearly demonstrate the binding selectivity and enhanced affinity of side-by-side imidzole/imidazole pairings for T·G mismatches and show that the affinity and specificity increase arise from much lower k_d values with the T·G mismatched duplexes. CD titration studies of f-lmlmlm complexes with T·G mismatched sequences produce strong induced bands at ～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.