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

Naoto Hori; Natalia A. Denesyuk; D. Thirumalai

Motivated by the relevance of force-induced transitions in PK to PRF, we have conducted extensive simulations of BWYV PK using a model of RNA, which predicts with near quantitative accuracy the thermodynamics at f = 0. The phase diagram in the [C, f ] plane, which can be measured using single-molecule LOT pulling experiments, shows that the thermodynamics of rupture as f is increased, or the assembly of the PK as f is decreased, involves transitions between the extended, intermediate, and the folded states. The predicted linear relationship between f c and log C m [Eq.4] or f c ∼ √ log C m [Eq.6] shows that ∆Γ can be directly measured in LOT experiments. The theoretical arguments leading to Eqs.(4) and (6) are general. Thus, f can be used as a perturbant to probe ion-RNA interactions through direct measurement of ∆Γ. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/048801 doi: bioRxiv preprint TABLE S1. List of hydrogen bonding interactions in BWYV PK. First 8 pairs correspond canonical base pairs forming stems S1 and S2. Other 15 pairs are all tertially interactions forming either L1 or L2. Since we use the three-interaction-site model, a letter "s", "b" or "p" is put following each nucleotide number to indicate one of sugar, base, or phosphate, respectively.