title: Reconstructing folding energy landscape profiles from nonequilibrium pulling curves with an inverse Weierstrass integral transform.
abstract: The energy landscapes that drive structure formation in biopolymers are difficult to measure. Here we validate experimentally a novel method to reconstruct landscape profiles from single-molecule pulling curves using an inverse Weierstrass transform (IWT) of the Jarzysnki free-energy integral. The method was applied to unfolding measurements of a DNA hairpin, replicating the results found by the more-established weighted histogram (WHAM) and inverse Boltzmann methods. Applying both WHAM and IWT methods to reconstruct the folding landscape for a RNA pseudoknot having a stiff energy barrier, we found that landscape features with sharper curvature than the force probe stiffness could not be recovered with the IWT method. The IWT method is thus best for analyzing data from stiff force probes such as atomic force microscopes.
authors.affiliation: Department of Physics, University of Alberta, Edmonton, Alberta, T6G 2E1 Canada.
authors.forename: Megan C
authors.initials: MC
authors.lastname: Engel
authors.affiliation: Department of Physics, University of Alberta, Edmonton, Alberta, T6G 2E1 Canada.
authors.forename: Dustin B
authors.initials: DB
authors.lastname: Ritchie
authors.affiliation: Department of Physics, University of Alberta, Edmonton, Alberta, T6G 2E1 Canada.
authors.forename: Daniel A N
authors.initials: DA
authors.lastname: Foster
authors.affiliation: Department of Physics, University of Alberta, Edmonton, Alberta, T6G 2E1 Canada and Department of Physics and Astronomy, University of Mississippi, University, Mississippi 38677 USA.
authors.forename: Kevin S D
authors.initials: KS
authors.lastname: Beach
authors.affiliation: Department of Physics, University of Alberta, Edmonton, Alberta, T6G 2E1 Canada and National Institute for Nanotechnology, National Research Council, Edmonton, Alberta, T6G 2M9 Canada.
authors.forename: Michael T
authors.initials: MT
authors.lastname: Woodside
mesh_terms: D004247:DNA / Q000737:chemistry*; D018625:Microscopy, Atomic Force; D008956:Models, Chemical; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D012313:RNA; D004247:DNA