Figure 9.

Mg²⁺ stabilizes the kissing-loop interaction. (A) The free energy differences between the 2SL and 3SL structures for 3′X (□) are not sensitive to Mg²⁺ concentration, indicating that Mg²⁺ is not sufficient to promote the structural switch from 2SL to 3SL in 3′X. The free energy difference between the 5BSL3.2:3′X kissing complex and the unkissed structure (■) decreases significantly as the Mg²⁺ concentration increases, indicating the kissing-loop interaction is favored at high Mg²⁺ concentrations. (B and C) Structures of the 5BSL3.2:3′X kissing complex with the predicted bound Mg²⁺ ions at 0.2 and 2 mM Mg²⁺, respectively. 5BSL3.2 and 3′X are colored red and blue, respectively. Mg²⁺ ions are shown as green spheres.