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

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.

23 pages, 5 figures

References in corpus (14)

• A nonequilibrium equality for free energy differences
• Stochastic thermodynamics, fluctuation theorems, and molecular machines
• Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies
• Path ensembles averages in systems driven far-from-equilibrium
• The Nonequilibrium Thermodynamics of Small Systems
• Stochastic thermodynamics: Principles and perspectives
• Single-molecule derivation of salt dependent base-pair free energies in DNA
• Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured results
• From mechanical folding trajectories to intrinsic energy landscapes of biopolymers
• Non-specific binding of Na${}^{+}$ and Mg${}^{2+}$ to RNA determined by force spectroscopy methods
• Improving signal-to-noise resolution in single molecule experiments using molecular constructs with short handles
• Improved Approximations for Some Polymer Extension Models
• Experimental measurement of binding energy, selectivity and allostery using fluctuation theorems
• DNA twist stability changes with magnesium(2+) concentration

Cited by in corpus (5)

• Molten globule-like transition state of protein barnase measured with calorimetric force spectroscopy
• Stem-loop formation drives RNA folding in mechanical unzipping experiments
• Cooperativity-Dependent Folding of Single-Stranded DNA
• Statistics of work performed by optical tweezers with general time-variation of their stiffness
• A fit-less approach to the elasticity of the handles in optical tweezers experiments