Figure 6.

Given here is the RMSD for the internal mismatches in RNA-(CAG)₄ and RNA-(GAC)₄ as obtained from 1-μs MD simulations. In each panel, the upper row shows the RMSD for A₅–A₂₀ and the lower row for A₈–A₁₇. Conformations are color-coded to agree with the mismatch conformations in Fig. 2. Initial conformations for each of the three panels in a column are as follows: (top) anti-anti (conformation A1 in Fig. 2); (middle) anti-syn (B1); and (bottom) syn-syn (C1). (Right panels) Shown here is the distribution of the observed conformations. (Gray) Here we show irregular structures observed during the transition. To see this figure in color, go online.