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

Hori, Naoto; Denesyuk, Natalia A.; Thirumalai, D.

Abstract

Because of the potential link between − 1 programmed ribosomal frameshifting and response of a pseudoknot (PK) RNA to force, a number of single-molecule pulling experiments have been performed on PKs to decipher the mechanism of programmed ribosomal frameshifting. Motivated in part by these experiments, we performed simulations using a coarse-grained model of RNA to describe the response of a PK over a range of mechanical forces (fs) and monovalent salt concentrations (Cs). The coarse-grained simulations quantitatively reproduce the multistep thermal melting observed in experiments, thus validating our model. The free energy changes obtained in simulations are in excellent agreement with experiments. By varying f and C, we calculated the phase diagram that shows a sequence of structural transitions, populating distinct intermediate states. As f and C are changed, the stem–loop tertiary interactions rupture first, followed by unfolding of the 3′-end hairpin (I⇌F). Finally, the 5′-end hairpin unravels, producing an extended state (E⇌I). A theoretical analysis of the phase boundaries shows that the critical force for rupture scales as (logCm)α with α = 1 (0.5) for E⇌I (I⇌F) transition. This relation is used to obtain the preferential ion–RNA interaction coefficient, which can be quantitatively measured in single-molecule experiments, as done previously for DNA hairpins. A by-product of our work is the suggestion that the frameshift efficiency is likely determined by the stability of the 5′-end hairpin that the ribosome first encounters during translation.

Citation

Hori, N., Denesyuk, N. A., & Thirumalai, D. (2016). Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension. Journal of Molecular Biology, 428(14), 2847-2859. https://doi.org/10.1016/j.jmb.2016.06.002

• Journal Article Type: Article
• Acceptance Date: Jun 7, 2016
• Online Publication Date: Jun 15, 2016
• Publication Date: Jul 17, 2016
• Deposit Date: Sep 19, 2020
• Journal: Journal of Molecular Biology
• Print ISSN: 0022-2836
• Publisher: Elsevier
• Peer Reviewed: Peer Reviewed
• Volume: 428
• Issue: 14
• Pages: 2847-2859
• DOI: https://doi.org/10.1016/j.jmb.2016.06.002
• Public URL: https://nottingham-repository.worktribe.com/output/4342431
• Publisher URL: https://www.sciencedirect.com/science/article/pii/S0022283616302108