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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 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.

preprint2003arXivOpen access
Terence HwaEnzo MarinariKim SneppenLei-Han Tang
cond-mat.stat-mechBiological Physicscond-mat.softQuantitative Methodscond-mat.dis-nn
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Terence HwaEnzo MarinariKim SneppenLei-Han Tang

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