Efficient methods for determining folding free energies in single-molecule pulling experiments

DOI10.1088/1742-5468/AB4E91MaRDI QIDQ5854096zbMATH OpenOpenAlexFDO

Authors A. Severino, A. M. Monge, P. Rissone, Felix Ritort

Publication date 16 March 2021

Published in Journal of Statistical Mechanics: Theory and Experiment (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1912.06066

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20)

Abstract: The remarkable accuracy and versatility of single-molecule techniques make possible new measurements that are not feasible in bulk assays. Among these, the precise estimation of folding free energies using fluctuation theorems in nonequilibrium pulling experiments has become a benchmark in modern biophysics. In practice, the use of fluctuation relations to determine free energies requires a thorough evaluation of the usually large energetic contributions caused by the elastic deformation of the different elements of the experimental setup (such as the optical trap, the molecular linkers and the stretched-unfolded polymer). We review and describe how to optimally estimate such elastic energy contributions to extract folding free energies, using DNA and RNA hairpins as model systems pulled by laser optical tweezers. The methodology is generally applicable to other force-spectroscopy techniques and molecular systems.

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Cites work

• scientific article; zbMATH DE number 826245 (Why is no real title available?)
• Stochastic thermodynamics: principles and perspectives

Cited in

(9)

• Analysing single-molecule trajectories to reconstruct free-energy landscapes of cyclic motor proteins
• Effect of elastic energy on the folding of an RNA hairpin
• Work fluctuation theorems and single-molecule biophysics
• Role of pulling direction in understanding the anisotropy of the resistance of proteins to force-induced mechanical unfolding
• Energy fluctuations shape free energy of nonspecific biomolecular interactions
• Statistics of work performed by optical tweezers with general time-variation of their stiffness
• Stochastic thermodynamics: experiment and theory
• Equilibrium and nonequilibrium foundations of free energy computational methods
• Bayesian approach to the determination of the kinetic parameters of DNA hairpins under tension

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