title: Mechanically probing the folding pathway of single RNA molecules.
abstract: We study theoretically the denaturation of single RNA molecules by mechanical stretching, focusing on signatures of the (un)folding pathway in molecular fluctuations. Our model describes the interactions between nucleotides by incorporating the experimentally determined free energy rules for RNA secondary structure, whereas exterior single-stranded regions are modeled as freely jointed chains. For exemplary RNA sequences (hairpins and the Tetrahymena thermophila group I intron), we compute the quasiequilibrium fluctuations in the end-to-end distance as the molecule is unfolded by pulling on opposite ends. Unlike the average quasiequilibrium force-extension curves, these fluctuations reveal clear signatures from the unfolding of individual structural elements. We find that the resolution of these signatures depends on the spring constant of the force-measuring device, with an optimal value intermediate between very rigid and very soft. We compare and relate our results to recent experiments by Liphardt et al. (2001).
authors.affiliation: Department of Physics, University of California at San Diego, La Jolla 92093-0319, USA. gerland@physics.ucsd.edu
authors.forename: Ulrich
authors.initials: U
authors.lastname: Gerland
authors.forename: Ralf
authors.initials: R
authors.lastname: Bundschuh
authors.forename: Terence
authors.initials: T
authors.lastname: Hwa
mesh_terms: D000818:Animals; D003198:Computer Simulation; D004548:Elasticity; D008958:Models, Molecular; D009038:Motion; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D010812:Physical Stimulation / Q000379:methods*; D012313:RNA / Q000737:chemistry*; D020871:RNA Stability; D013314:Stress, Mechanical; D016808:Tetrahymena thermophila / Q000737:chemistry / Q000378:metabolism
chemical_list: D012313:RNA