Nearest-neighbor parameters for 7-deaza-adenosine·uridine base pairs in RNA duplexes

The ability of the C7 (blue) on 7DA (red) to impact stacking interactions is likely decided by the positioning (5′ or 3′) of the 7DA relative to the adjacent base (green). Stacks are shown as follows: (A) 5′-U7-3′; (B) 5′-G7-3′; (C) 5′-7U-3′; and (D) 5′-7G-3′. These stacks were generated using InsightII (Accelrys) for standard A-form geometries and PyMOL (The PyMOL Molecular Graphics System, Version 1.7.4, Schrödinger) for visualization.