Kiang, Ching-Hwa2013-06-052013-06-052013-06-052013-06-052012-122013-06-05December 2Frey, Eric. "Experimental Free Energy Landscape Reconstruction of DNA Unstacking Using Crooks Fluctuation Theorem." (2013) Master’s Thesis, Rice University. <a href="https://hdl.handle.net/1911/71276">https://hdl.handle.net/1911/71276</a>.https://hdl.handle.net/1911/71276Nonequilibrium 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.application/pdfengCopyright is held by the author, unless otherwise indicated. Permission to reuse, publish, or reproduce the work beyond the bounds of fair use or other exemptions to copyright law must be obtained from the copyright holder.Crooks fluctuation theoremDNASingle moleculePoly(da)Jarzynski equalityFree energy landscapeThesis2013-06-05123456789/ETD-2012-12-210