Bubble coalescence in breathing DNA: Two vicious walkers in opposite potentials

Tomas Novotný, Jonas Nyvold Pedersen, Tobias Ambjörnsson, Mikael Sonne Hansen, Ralf Metzler

    Research output: Contribution to journalJournal articleResearchpeer-review

    Abstract

    We investigate the coalescence of two DNA bubbles initially located at weak segments and separated by a more stable barrier region in a designed construct of double-stranded DNA. The characteristic time for bubble coalescence and the corresponding distribution are derived, as well as the distribution of coalescence positions along the barrier. Below the melting temperature, we find a Kramers-type barrier crossing behaviour, while at high temperatures, the bubble corners perform drift-diffusion towards coalescence. The results are obtained by mapping the bubble dynamics on the problem of two vicious walkers in opposite potentials.
    Original languageEnglish
    JournalEPL
    Volume77
    Pages (from-to)48001
    ISSN0295-5075
    DOIs
    Publication statusPublished - 2007

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