Localization of denaturation bubbles in random DNA sequences.
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.
Hwa
Terence
T
Department of Physics and Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093-0319, USA. hwa@ucsd.edu
Marinari
Enzo
E
Sneppen
Kim
K
Tang
Lei-han
LH
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
D004247:DNA