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Nucleic Acids Research, 2002, Vol. 30, No. 8 1834-1841
© 2002 Oxford University Press

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

Eilyn R. Lacy, Kari K. Cox1, W. David Wilson and Moses Lee1,*

Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA and 1Department of Chemistry, Furman University, 3300 Poinsett Highway, Greenville, SC 29613, USA

An imidazole-containing polyamide trimer, f-ImImIm, 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-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 T·G, A·G or G·G mismatched base pairs) hairpin oligonucleotides were determined by surface plasmon resonance and circular dichroism (CD) methods. f-ImImIm 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-ImImIm 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 kd). These results clearly demonstrate the binding selectivity and enhanced affinity of side-by-side imidazole/imidazole pairings for T·G mismatches and show that the affinity and specificity increase arise from much lower kd values with the T·G mismatched duplexes. CD titration studies of f-ImImIm 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.

* To whom correspondence should be addressed. Tel: +1 864 294 3368; Fax: +1 864 294 3559; Email: moses.lee{at}furman.edu Correspondence may also be addressed to W. David Wilson. Tel: +1 404 651 3903; Fax: +1 404 651 2751; Email: chewdw{at}panther.gsu.edu


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