Kinetic barriers in RNA unzipping

Abstract

We consider a simple model for the unfolding of RNA tertiary structure under dynamic loading. The opening of such a structure is regarded as a two step process, each corresponding to the overcoming of a single energy barrier. The resulting two-barrier energy landscape accounts for the dependence of the unfolding kinetics on the pulling rate. Furthermore at intermediate force, the two barriers cannot be distinguished by the analysis of the opening kinetic, which turns out to be dominated by a single macro-barrier, whose properties depend non-trivially on the two single barriers. Our results suggest that in pulling experiments on RNA molecule containing tertiary structures, the details of the single kinetic barriers can only be obtained using a low pulling rate value, or in the high force regime.

to appear on Eur. Phys. J. B

References in corpus (4)

• DNA unzipped under a constant force exhibits multiple metastable intermediates
• Translocation of structured polynucleotides through nanopores
• Probing complex RNA structures by mechanical force
• Effects of intermediate bound states in dynamic force spectroscopy

Cited by in corpus (7)

• Single-molecule experiments in biological physics: methods and applications
• Thermodynamic and kinetic aspects of RNA pulling experiments
• Work probability distribution in single molecule experiments
• Protein mechanical unfolding: a model with binary variables
• Hidden multiple bond effects in dynamic force spectroscopy
• Equilibrium properties and force-driven unfolding pathways of RNA molecules
• Free energy landscape of mechanically unfolded model proteins: extended Jarzinsky versus inherent structure reconstruction