Fig. 4.

Folding free energy (kcal/mol, 25 °C) diagram of BWYV pseudoknot at 54 mM KCl in the absence (Left) or presence (Right) of 0.2 mM Mg²⁺. Theoretical values are in red and experimental values are in blue. Experimental data for $\mathrm{\Delta }{G}_{\text{U}-\text{I}}$ (no Mg²⁺) and $\mathrm{\Delta }{G}_{\mathrm{M}\mathrm{g},U}$ are not available. For $\mathrm{\Delta }{G}_{\text{U}-\text{I}}$, data for 40 mM and 74 mM KCl are reported with the hope that they should bracket the 54 mM KCl data. $\mathrm{\Delta }{G}_{\mathrm{M}\mathrm{g},U}$ for experiment is then evaluated based on the other free energies in the cycle. Folding free energies (black arrows) are calculated from thermal denaturation simulations. Mg²⁺–RNA free energies (blue arrows) are taken for each state at 0.2 mM Mg²⁺ from Fig. 3.