Figure 8.

Illustrative interface geometry of MD trajectories: (A) A ‘5/6-ring’ stacking equilibrium is maintained across the 100-ns trajectory for the 5′–5′ stacking model. (B) The interface of the 3′–3′ model is mostly found in a ‘6-ring’ stacking geometry. (C) Occasionally the 3′–3′ model occupies a ‘Partial 6-ring’ stacking mode. Backbone atoms are shown in light gray and the O1′ atoms of sugar are shown in red. Spherical representation of backbone atoms are the approximate Van der Waals surface of atoms as visualized in PyMOL.