FIGURE 9.

Models for effects of Mg²⁺, Ba²⁺, and Na⁺ on the folding of P4-P6 RNA. A, Mg²⁺ (red dots) but not Ba²⁺ can bind to the metal ion core (35), and this binding can occur prior to tertiary folding (44). According to this model, Mg²⁺ binding lowers the barrier for folding (ΔG_{F Ba}^‡ > ΔG_{F Mg}^‡) by increasing the probability of formation of the tetraloop/tetraloop receptor interaction (red lines in folded state) via a conformational change or restriction of available conformations in the unfolded state. In addition, unfolding is slowed in Mg²⁺ (ΔG_{U Ba}^‡ < ΔG_{U Mg}^‡) because an additional tertiary interaction is formed (blue lines in folded state) that must be broken prior to the transition state in the unfolding process. The free energy profiles are shown for 17.5 mm metal ion, as this is near the folding midpoint in Ba²⁺. B, near the folding midpoint in Ba²⁺ (orange circles) and Na⁺ (blue circles) (i.e. the fraction folded was 0.39 and 0.45 in 17.5 mm Ba²⁺ and 800 mm Na⁺ respectively), the rate constants for folding and unfolding are nearly identical (ΔG_{F Ba}^‡ = ΔG_{F Na}^‡ and ΔG_{U Ba}^‡ = ΔG_{U Na}^‡), consistent with a simple model of ion effects via electrostatic screening.