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Experimental Free Energy Landscape Reconstruction of DNA Unstacking Using Crooks Fluctuation Theorem

Nonequilibrium work theorems, such as the Jarzynski equality and the Crooks fluctuation theorem, allow one to use nonequilibrium measurements to determine
equilibrium free energies. For example, it has been demonstrated that the Crooks fluctuation theorem can be used to determine RNA folding energies. We used single-molecule manipulation with an atomic force microscope to measure the work done on poly(dA) as it was stretched and relaxed. This single-stranded nucleic acid exhibits
unique base-stacking transitions in its force-extension curve due to the strong interactions among A bases, as well as multiple pathways. Here we showed that free energy curves can be determined by using the Crooks fluctuation theorem. The nonequilibrium work theorem can be used to determine free energy curves even when there are multiple pathways.

Identiferoai:union.ndltd.org:RICE/oai:scholarship.rice.edu:1911/71276
Date05 June 2013
CreatorsFrey, Eric
ContributorsKiang, Ching-Hwa
Source SetsRice University
LanguageEnglish
Detected LanguageEnglish
Typethesis, text
Formatapplication/pdf

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