title: Localization of denaturation bubbles in random DNA sequences.
abstract: We study the thermodynamic and dynamic behaviors of twist-induced denaturation bubbles in a long, stretched random sequence of DNA. The small bubbles associated with weak twist are delocalized. Above a threshold torque, the bubbles of several tens of bases or larger become preferentially localized to AT-rich segments. In the localized regime, the bubbles exhibit "aging" and move around subdiffusively with continuously varying dynamic exponents. These properties are derived by using results of large-deviation theory together with scaling arguments and are verified by Monte Carlo simulations.
authors.affiliation: Department of Physics and Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093-0319, USA. hwa@ucsd.edu
authors.forename: Terence
authors.initials: T
authors.lastname: Hwa
authors.forename: Enzo
authors.initials: E
authors.lastname: Marinari
authors.forename: Kim
authors.initials: K
authors.lastname: Sneppen
authors.forename: Lei-han
authors.initials: LH
authors.lastname: Tang
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D055592:Biophysical Phenomena; D001703:Biophysics; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D019277:Entropy; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D013816:Thermodynamics
chemical_list: D004247:DNA