Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension.
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.
Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA.
Naoto
N
Hori
Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA.
Natalia A
NA
Denesyuk
Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA. Electronic address: dave.thirumalai@gmail.com.
D
D
Thirumalai
D016368:Frameshift Mutation / Q000235:genetics*; D018965:Frameshifting, Ribosomal / Q000235:genetics; D009690:Nucleic Acid Conformation; D012313:RNA / Q000235:genetics*; D059370:RNA Folding / Q000235:genetics; D020871:RNA Stability / Q000235:genetics; D012270:Ribosomes / Q000235:genetics; D013816:Thermodynamics
D012313:RNA
BWYV pseudoknot; RNA folding; mechanical force; phase diagram; preferential ion interaction coefficient