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

Naoto Hori; Natalia A. Denesyuk; D. Thirumalai

The determination of the parameters for use in simulations of the coarse-grained model of RNA was described in detail in a previous publication [37] . Briefly, we determined the stacking interactions by a learning procedure, which amounts to reproducing the measured melting temperature of dimers. We showed that a single choice of model parameters (stacking interactions, the Debye-Hückel potential for electrostatic interactions, and structure-specific choice for hydrogen bonds) is sufficient to obtain detailed agreements with available experimental data for three different RNA molecules. Thus, the parameters are transferable and we use them verbatim in the present simulations. The determination of hydrogen bond interaction is predicated on the structure. Most of these are taken from the A-form RNA structure and hence can be readily used for any RNA molecule. Only the interaction lengths and angles in hydrogen-bonding interaction of noncanonical base pairs are based on the specific PDB structure, which in our case is the BWYV pseudoknot in this study. We list all the BYWV-PKspecific values used in our simulations in Table S1 .