Sequence dependency of canonical base pair opening in the DNA double helix
Fig 4
Sampled base pair configurations.
Representative configurations at different dN1N3 values were chosen from Parmbsc1 L:AT12 (A–D) and M:CG11 trajectories (E–H). The distance values are in the figure, indicated by a dotted line. Carbon atoms are shown in gray, hydrogens in white, oxygens in red and nitrogens in blue. Waters within hydrogen bond distance of donor/acceptor atoms on both bases are also included to show examples of water bridges. Acceptor atoms that are very often in contact with Na+ in similar configurations are marked with a ’+’. Base-paired WC configurations (A), (E) are shown in line representation behind the open configurations, (B–D) and (F–H), to help visualize the extent of opening. Note that no timeline is implied from left to right.