Force-induced denaturation of RNA

Abstract

We describe quantitatively a RNA molecule under the influence of an external force exerted at its two ends as in a typical single-molecule experiment. Our calculation incorporates the interactions between nucleotides by using the experimentally-determined free energy rules for RNA secondary structure and models the polymeric properties of the exterior single-stranded regions explicitly as elastic freely-jointed chains. We find that in spite of complicated secondary structures, force-extension curves are typically smooth in quasi-equilibrium. We identify and characterize two sequence/structure-dependent mechanisms that, in addition to the sequence-independent entropic elasticity of the exterior single-stranded regions, are responsible for the smoothness. These involve compensation between different structural elements on which the external force acts simultaneously, and contribution of suboptimal structures, respectively. We estimate how many features a force-extension curve recorded in non-equilibrium, where the pulling proceeds faster than rearrangements in the secondary structure of the molecule, could show in principle. Our software is available to the public through a `RNA-pulling server'.

final version (with a few minor changes) as will be published in Biophysical Journal

Cited by in corpus (33)

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• Dynamic force spectroscopy of DNA hairpins. I. Force kinetics and free energy landscapes
• Theoretical studies of the kinetics of mechanical unfolding of cross-linked polymer chains and their implications for single molecule pulling experiments
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• Dynamic force spectroscopy of DNA hairpins. II. Irreversibility and dissipation
• Theory for RNA folding, stretching, and melting including loops and salt
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• Extremely rare ultra-fast non-equilibrium processes can be close to equilibrium: RNA unfolding and refolding
• Maximum-entropy calculation of end-to-end distance distribution of force stretching chains
• RNA matrix models with external interactions and their asymptotic behaviour
• Calculation of a fluctuating entropic force by phase space sampling
• Unfolding and unzipping of single-stranded DNA by stretching
• A model for the force stretching double-stranded chain molecules
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• Cold denaturation of RNA secondary structures with loop entropy and quenched disorder
• Field Theory of the RNA Freezing Transition
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