2009
DOI: 10.1088/1742-5468/2009/02/p02060
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Dynamic force spectroscopy of DNA hairpins: I. Force kinetics and free energy landscapes

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 char… Show more

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Cited by 62 publications
(112 citation statements)
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“…Many TRT results concern quasiclassical systems, whose density operators ρ commute with their Hamiltonians H: [ρ, H] = 0 (e.g., [2, 28-31, 63, 72, 73]). Such quasiclassical results might be realized more easily than quantum results: Classical platforms, such as DNA and colloidal particles, have been used to test small-scale statistical mechanics such as fluctuation relations [6][7][8][9][10][11][12][13]. These classical platforms might be recycled to realize TRTs.…”
Section: How Should Trts Model Continuous Spectra?mentioning
confidence: 99%
See 1 more Smart Citation
“…Many TRT results concern quasiclassical systems, whose density operators ρ commute with their Hamiltonians H: [ρ, H] = 0 (e.g., [2, 28-31, 63, 72, 73]). Such quasiclassical results might be realized more easily than quantum results: Classical platforms, such as DNA and colloidal particles, have been used to test small-scale statistical mechanics such as fluctuation relations [6][7][8][9][10][11][12][13]. These classical platforms might be recycled to realize TRTs.…”
Section: How Should Trts Model Continuous Spectra?mentioning
confidence: 99%
“…I could have advocated for bounding, with idealizations, efficiencies achievable in labs. I should have invoked the connections being developed with fluctuation relations [3][4][5], statistical mechanical theorems that have withstood experimental tests [6][7][8][9][10][11][12][13].…”
Section: Introductionmentioning
confidence: 99%
“…In Figure 4 we summarize recent results obtained in the Small Biosystems lab in Barcelona for the mechanical unfolding/refolding of DNA hairpins [21,22] using a dualbeam miniaturized optical tweezers [23]. DNA hairpins are versatile structures formed by a stem of a few tens of base pairs that end in loop.…”
Section: The Crooks Fluctuation Relation and Free Energy Recoverymentioning
confidence: 99%
“…non-equilibrium) experiment and measuring the work done during the process. The identity has been recently experimentally tested (Mossa et al, 2009;Ritort, 2003). In the present Chapter we discuss four illustrative, exactly solvable models in non-equilibrium thermodynamics of small systems.…”
Section: Introductionmentioning
confidence: 99%