Apr 15, 2016

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

BioRxiv : the Preprint Server for Biology
Naoto HoriDave Thirumalai


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 ( f s) and monovalent salt concentrations ( C s). 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 (log C )α with α = 1 (0.5) for E-I (I-F) transition. This relation is used to obtain the pref...Continue Reading

  • References
  • Citations


  • We're still populating references for this paper, please check back later.
  • References
  • Citations


  • This paper may not have been cited yet.

Mentioned in this Paper

Human neutrophil peptide 3
Concentrate Dosage Form
Blood group antigen S
Hairpin Loop Sequence
Theoretical Study
Protein Biosynthesis

About this Paper

Related Feeds

BioRxiv & MedRxiv Preprints

BioRxiv and MedRxiv are the preprint servers for biology and health sciences respectively, operated by Cold Spring Harbor Laboratory. Here are the latest preprint articles (which are not peer-reviewed) from BioRxiv and MedRxiv.

Related Papers

The Journal of Physical Chemistry. B
Natalia A. DenesyukD Thirumalai
BioRxiv : the Preprint Server for Biology
Dave Thirumalai, Natalia A. Denesyuk
Proceedings of the National Academy of Sciences of the United States of America
Jorjethe RocaAnjum Ansari
© 2020 Meta ULC. All rights reserved