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

Naoto Hori; Natalia A. Denesyuk; D. Thirumalai

Although single-molecule pulling experiments suggest how force affects the stability of RNA [19] , structural information obtained from such experiments is limited only to changes in molecular extensions. In order to provide a theoretical basis for the changes in the stability and structural transitions as f and monovalent salt concentration (C) are altered, we performed simulations using a coarse-grained three-site-interaction model (TIS model) [34] of the PK. After demonstrating that our simulations reproduce the temperature-induced structural transitions observed in ensemble experiments, we calculated the global phase diagrams in the [C, f ] plane. The simulations, performed in the same force range as used in Laser Optical Tweezer (LOT) experiments [19] , quantitatively reproduce the experimental observations. By combining our simulations and a theory based on ion-RNA interactions expressed in terms of preferential interaction coefficients [31, 35] , we produce several key predictions: (1) The phase diagram in the [C, f ] plane shows that the folded state (F) ruptures in stages populating dis-tinct intermediates as f increases. Structurally, the low force intermediate is similar to the one populated during thermal melting. The sequence of f -induced structural transitions can be described as F I E, where E is an extended state; (2) The critical force, f c , to rupture the PK scales as (log C m ) α with α = 1 for the I E transition and α = 0.5 for the I F transition. We expect this result to be valid for H-type PKs composed of stems with vastly different stability, such as the BWYV PK. This result is of general validity and is applicable to other PKs as well.