Solution structure of an 11-mer duplex containing the 3,N-4-ethenocytosineadduct opposite 2 '-deoxycytidine: Implications for the recognition of exocyclic lesions by DNA glycosylases

Lipid peroxidation products, as well as the metabolic products of vinyl chl oride, react with cellular DNA producing the mutagenic adduct 3,N-4-etheno- 2'-deoxycytidine (epsilon dC), along with several other exocyclic derivativ es. High-resolution NMR spectroscopy and restrained molecular dynamics simu lations were used to establish the solution structure of an Il-mer duplex c ontaining an epsilon dC . dC base-pair at its center. The NMR data suggeste d a regular right-handed helical structure having all residues in the anti orientation around the glycosydic torsion angle and Watson-Crick alignments for all canonical base-pairs of the duplex. Restrained molecular dynamics generated a three-dimensional model in excellent agreement with the spectro scopic data. The (epsilon dC . dC)-duplex structure is a regular right-hand ed helix with a slight bend at the lesion site and no severe distortions of the sugar-phosphate backbone. The epsilon dC adduct and its partner dC wer e displaced towards opposite grooves of the helix, resulting in a lesion-co ntaining base-pair that was highly sheared but stabilized to some degree by the formation of a single hydrogen bond. Such a sheared base-pair alignmen t at the lesion site was previously observed for epsilon dC . dG and epsilo n dC . T duplexes, and was also present in the crystal structures of duplex es containing dG . T and dG . U mismatches. These observations suggest the existence of a substrate structural motif that may be recognized by specifi c DNA glycosylases during the process of base excision repair. (C) 2000 Aca demic Press.