Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension

Naoto Hori; Natalia A. Denesyuk; D. Thirumalai

The [C, f ] phase diagrams provide a thermodynamic basis for predicting the structural changes that occur as f and C are varied. However, they capture only the average property of the ensemble within each state without the benefit of providing a molecular picture of the distinct states, which can only be described using simulations done at force values close to those used in LOT experiments. Therefore, we investigated the distribution of interactions to ascertain the factors that stabilize the three states as C and f are varied. Our analysis is based on the HB energy, U HB . The energy function for HB captures the formation of base pairs and loop-stem tertiary interactions, taking into account both distance and angular positions of the donor and the acceptor [37] . Fig. 7 shows that the probability densities of the total HB energy have three peaks at U HB ≈ 0, −30, and −60 kcal/mol. In the high-force regime (f > 12.5 pN), there is only one population at all C around U HB ≈ 0, which obviously corresponds to the fully extended state. The total HB energy can be decomposed into contributions arising from four distinct structural motifs in the PK (Fig. S5) . The peak at U HB ≈ −30 kcal/mol (Fig. 7) arises due to the formation of S1 (compare Figs. 7 and S5A). The broad peak at U HB ≈ −60 kcal/mol (Fig. 7A) is due to the sum of contributions from S2 and the tertiary interactions.