Sequence-dependent conformational perturbation in DNA duplexes containing an epsilonA.T mismatch using molecular dynamics simulation.

Previous experiments from this laboratory showed that 1, N:(6)-ethenoadenine (epsilonA) in 15mer DNA oligonucleotide duplexes with GGepsilonAGG and CCepsilonACC central sequences is repaired 3-5-fold more efficiently than in duplexes containing AAepsilonAAA and TTepsilonATT central sequences. This sequence dependence in repair rates appeared to correlate with the observed thermodynamic stability of these duplexes [Hang et al. (1998) J. Biol. Chem., 273, 33406-33413]. In the present work, unrestrained molecular dynamics was used to evaluate the sequence-dependent structural features of these duplexes. Explicit solvent and the particle mesh Ewald method were applied for the accurate representation of the electrostatic interactions. The differences observed in the axis- and intra-base pair parameters were primarily localized at the epsilonA*T mismatch in all sequences and indicate conformational diversity between the structures. However, all four structures remained in the B-conformational family. In the tip, tilt and propeller twist parameters for the five central base pairs, larger perturbations were found for the two duplexes with epsilonA flanked by A or T bases than for duplexes with epsilonA flanked by G or C bases. As a result of these perturbations, the average global curvature of the AAepsilonAAA and TTvarepsilonATT DNA duplexes was larger by approximately 12 degrees than that of the duplexes with the GGepsilonAGG and CCepsilonACC central sequences. The observed conformational differences between the duplexes containing A or T and G or C neighbors of epsilonA may contribute to the observed differential enzymatic repair of the same sequences.