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Localization of Denaturation Bubbles in Random DNA Sequences

Terence Hwa·Enzo Marinari·Kim Sneppen·Lei-han Tang
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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 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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Terence Hwa, Enzo Marinari, Kim Sneppen, Lei-han Tang. 2003-02-28. Localization of Denaturation Bubbles in Random DNA Sequences. https://doi.org/10.1073/pnas.0736291100

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