Dynamic force spectroscopy of DNA hairpins. I. Force kinetics and free energy landscapes
arXiv:0902.3632 · doi:10.1088/1742-5468/2009/02/P02060
Abstract
We investigate the thermodynamics and kinetics of DNA hairpins that fold/unfold under the action of applied mechanical force. We introduce the concept of the molecular free energy landscape and derive simplified expressions for the force dependent Kramers-Bell rates. To test the theory we have designed a specific DNA hairpin sequence that shows two-state cooperative folding under mechanical tension and carried out pulling experiments using optical tweezers. We show how we can determine the parameters that characterize the molecular free energy landscape of such sequence from rupture force kinetic studies. Finally we combine such kinetic studies with experimental investigations of the Crooks fluctuation relation to derive the free energy of formation of the hairpin at zero force.
arXiv comment28 pages, 12 figures
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Cited by in corpus (19)
- Stochastic thermodynamics, fluctuation theorems, and molecular machines
- Inferring entropy production from short experiments
- Jarzynski-like equality for the out-of-time-ordered correlator
- Experimental free energy measurements of kinetic molecular states using fluctuation theorems
- Exact Coarse Graining Preserves Entropy Production out of Equilibrium
- Introducing one-shot work into fluctuation relations
- Beyond heat baths II: Framework for generalized thermodynamic resource theories
- Dynamic force spectroscopy of DNA hairpins. II. Irreversibility and dissipation
- Measurement of work in single-molecule experiments
- Single-molecule stochastic resonance
- Counter-propagating dual-trap optical tweezers based on linear momentum conservation
- Force Feedback Effects on Single Molecule Hopping and Pulling Experiments
- Force-Dependent Folding Kinetics of Single Molecules with Multiple Intermediates and Pathways
- Dissipation reduction and information-to-measurement conversion in DNA pulling experiments with feedback protocols
- Dynamics and energetics of a molecular zipper under external driving
- Unfolding force definition and the unified model for the mean unfolding force dependence on the loading rate
- Information-to-work conversion in single molecule experiments: from discrete to continuous feedback
- Operational work fluctuation theorem for open quantum systems
- Work probability distribution for a ferromagnet with long-ranged and short-ranged correlations