Figure 9.

Na⁺ binding pocket was observed near U₆ when it was in the syn orientation. When occupied by a Na⁺ ion, there are three attractive electrostatic interactions. As shown in Figure 8, these interactions stabilize the syn–anti UU orientation. When no Na⁺ ion was present in the pocket, U₆ unstacked via the minor groove (Movie S4). A full syn → anti transformation, however, was not observed, due to the rapid occupation of the pocket by Na⁺ ions. This can be seen in the rmsd analyses of U₆U₁₇ (Figure 8) where the orange colored state has a short lifetime.