The relationship between mutation rates for the (C-G) → (T-A) transition and features of T-G mispair structures in different neighbor environments, determined by free energy molecular mechanics

The results of this theoretical study combining sequence analysis and minimization with integral equation liquid structural methods indicate that the local sequence context of a T·G wobble mismatch influences the local conformation of the helix, and that conformational alterations are correlated with mutational activity. Studies on the mismatch in four different 5′ and 3′ neighbor contexts indicate that the nature of the 5′ base to the thymine of the mispair is probably the single most critical factor in determining the structural features that facilitate or discourage mutations. When cytosine is the 5′ neighbor, the helix adopts a mostly B_II conformation, whereas a 5′ guanine preserves the canonical B_I. Structures that vary little from the B_I structure on the incorporation of the mismatch have sequences that correspond to lower rates of transition, whereas those with mostly B_II conformations, have sequences with high mutation rates. Subtle variations in stacking patterns around the mismatch precipitate a structural Domino-effect, with a variety of changes in conformation. The helix opens at the mismatch with increased roll angle and propeller twist, causing the thymine to migrate into the major groove and the guanine into the minor groove, exposing the heteroatomic groups to the solvent in the major and minor grooves, respectively, and allowing for some unusual hydrogen bonds. These alterations show a tentative correlation with mutation rates, implying that stacking and structure around the mismatch are important features in the discrimination by proofreading activities of canonical W-C and wobble mismatch base pairs during replication-repair. Variations in the C1′-C1′ distances, high propeller twists, changes in the electrostatic complementarity leading to unusual hydrogen bonding patterns probably all correlate with detectability.