Localization of Denaturation Bubbles in Random DNA Sequences

Details Localization of Denaturation Bubbles in Random DNA Sequences Localization of Denaturation Bubbles in Random DNA Sequences

2003-02-28

arxiv.org/abs/cond-mat/0302603v1

Physics

Condensed Matter

Statistical Mechanics

TeX file with postscript figures

Scientific paper

10.1073/pnas.0736291100

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 sub-diffusively with continuously varying dynamic exponents. These properties are derived using results of large-deviation theory together with scaling arguments, and are verified by Monte-Carlo simulations.

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