Figure 8.

Rmsd of 1×1 UU base pairs and Na⁺ binding to the pocket seen in 3×CUG_inf/syn–anti MD simulations (see Figure 1C for residue numbering). The initial structures of the terminal UU base pairs, U₃U₂₀ and U₉U₁₄, were anti–anti, while U₆U₁₇ was syn–anti. The color scheme described in Figure 3 was used to display conformational transformations of the UU base pairs. See Figure 7 caption for details of the rmsd analysis. A Na⁺ binding pocket was observed near U₆ when it was in the syn conformation (Figure 9). In the Na⁺ binding analysis different colors represent different Na⁺ ions in the system where the distance between each ion and the center-of-mass (COM) of the three atoms shown in Figure 9 (O₂P and O₂ of U₆, and N₇ of G₇) were calculated. Note that when the binding pocket was not occupied by a Na⁺ ion, U₆ tried to unstack from the helical axis and transformed to the orange state (Figure 3G). However, this state was short-lived, and no syn ↔ anti transformation was observed (Movie S4).