Fig. 2. Isopotential contours of the GNRA tetraloop. [top] The -1.0 kT/e 3-D isopotential contour of the GNRA tetraloop as seen from a top view. A large hole is clearly visible over the first A of the tetraloop. [bottom left] 2-D isopotential contours (-2.0, -1.5, -1.0 kT/e from innermost to outermost) of the tetraloop as seen from the side view. The hole over the second A (white base) is clearly visible. [bottom right] 2-D isopotential contours (same levels) when charges are placed only on the phosphates and phosphate-oxygens. The hole over the second A disappears at these levels but there is a noticeable collapsing of the field at that region.
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