Force dependent fragility in RNA hairpins

Abstract

We apply Kramers theory to investigate the dissociation of multiple bonds under mechanical force and interpret experimental results for the unfolding/refolding force distributions of an RNA hairpin pulled at different loading rates using laser tweezers. We identify two different kinetic regimes depending on the range of forces explored during the unfolding and refolding process. The present approach extends the range of validity of the two-states approximation by providing a theoretical framework to reconstruct free-energy landscapes and identify force-induced structural changes in molecular transition states using single molecule pulling experiments. The method should be applicable to RNA hairpins with multiple kinetic barriers.

arXiv commentLatex file, 4 pages+3 figures

References in corpus (7)

• Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies
• Mechanical properties and formation mechanisms of a wire of single gold atoms
• Mechanical unfolding of RNA hairpins
• Single Molecule Statistics and the Polynucleotide Unzipping Transition
• A two-state kinetic model for the unfolding of single molecules by mechanical force
• Thermodynamic and kinetic aspects of RNA pulling experiments
• Slow nucleic acid unzipping kinetics from sequence-defined barriers

Cited by in corpus (28)

• Single-molecule experiments in biological physics: methods and applications
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• Mechanical unfolding of RNA: From hairpins to structures with internal multiloops
• Non-specific binding of Na${}^{+}$ and Mg${}^{2+}$ to RNA determined by force spectroscopy methods
• Measuring the energy landscape roughness and the transition state location of biomolecules using single molecule mechanical unfolding experiments
• Force Dependent Hopping Rates of RNA Hairpins can be Estimated from Accurate Measurement of the Folding Landscapes
• Force unfolding kinetics of RNA using optical tweezers. II. Modeling experiments
• Physics of base-pairing dynamics in DNA
• Dynamic force spectroscopy of DNA hairpins. I. Force kinetics and free energy landscapes
• Directly measuring single molecule heterogeneity using force spectroscopy
• Compaction and tensile forces determine the accuracy of folding landscape parameters from single molecule pulling experiments
• Dynamic force spectroscopy: analysis of reversible bond-breaking dynamics
• Dynamic force spectroscopy of DNA hairpins. II. Irreversibility and dissipation
• Measurement of work in single-molecule experiments
• Theory for RNA folding, stretching, and melting including loops and salt
• Inferring DNA sequences from mechanical unzipping data: the large-bandwidth case
• Reconstructing a Random Potential from its Random Walks
• Force-Dependent Folding Kinetics of Single Molecules with Multiple Intermediates and Pathways
• Folding and unfolding of a triple-branch DNA molecule with four conformational states
• Force-induced misfolding in RNA
• Nonequilibrium fluctuations in small systems: From physics to biology
• Force-clamp spectroscopy of reversible bond breakage
• Statistics of reversible transitions in two-state trajectories in force-ramp spectroscopy
• Force Dependence of Proteins' Transition State Position and the Bell-Evans Model
• Statistics of reversible bond dynamics observed in force-clamp spectroscopy
• Dynamical modelling of molecular constructions and setups for DNA unzipping
• Extracting folding landscape characteristics of biomolecules using mechanical forces