Localization of denaturation bubbles in random DNA sequences

Terence Hwa*, Enzo Marinari, Kim Sneppen, Lei Han TANG

*Corresponding author for this work

Research output: Contribution to journalJournal articlepeer-review

77 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)4411-4416
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number8
Publication statusPublished - 15 Apr 2003

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