Figure 7.

Given here is the RMSD for the internal mismatches in DNA-(CAG)₄ and DNA-(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. To see this figure in color, go online.