Figure 5.

Molecular dynamics of the C8-dG-PhIP-modified full and deletion duplexes. Hydrogen atoms and phosphate oxygen atoms are deleted for clarity. The lesion strand backbone is in light gray and the complementary strand is in dark gray. Phosphate atoms are purple. The adduct is red, the modified guanine and its partner base are cyan, and the neighboring bases are blue. (A) Dynamics of phenyl ring of the C8-dG-PhIP-modified full duplex. The structures with the highest and lowest γ′ values (38.4° and −39.9°) are shown on the left to emphasize the dynamics of the phenyl ring. The central trimer is viewed from the minor groove side (left) and along the helix axis (Top view, right). The time dependence of the γ′ torsion angle is shown on the right. (B) Dynamics of phenyl ring of the C8-dG-PhIP-modified deletion duplex. The structures with the highest and the lowest γ′ values (44.1° and −34.8°) are shown on the left to emphasize the dynamics of the phenyl ring. The central trimer is viewed from the minor groove side (left) and along the helix axis (Top view, right). The time dependence of the γ′ torsion angle is shown on the right.