Localization of Denaturation Bubbles in Random DNA Sequences

TL;DR

This paper investigates how twist-induced denaturation bubbles in long, random DNA sequences behave thermodynamically and dynamically, revealing localization phenomena, aging, and sub-diffusive motion above certain torque thresholds.

Contribution

It introduces a theoretical framework combining large-deviation theory and scaling arguments to analyze bubble localization and dynamics in DNA under twist.

Findings

Weak twist bubbles are delocalized in DNA.

Above a critical torque, bubbles localize to AT-rich regions.

Localized bubbles exhibit aging and sub-diffusive motion.

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.