Nucleation at the DNA supercoiling transition

Bryan C. Daniels, James P. Sethna

Research output: Contribution to journalArticle

16 Scopus citations

Abstract

Twisting DNA under a constant applied force reveals a thermally activated transition into a state with a supercoiled structure known as a plectoneme. Using transition-state theory, we predict the rate of this plectoneme nucleation to be of order 104 Hz. We reconcile this with experiments that have measured hopping rates of order 10 Hz by noting that the viscous drag on the bead used to manipulate the DNA limits the measured rate. We find that the intrinsic bending caused by disorder in the base-pair sequence is important for understanding the free-energy barrier that governs the transition. Both analytic and numerical methods are used in the calculations. We provide extensive details on the numerical methods for simulating the elastic rod model with and without disorder.

Original languageEnglish (US)
Article number041924
JournalPhysical Review E - Statistical, Nonlinear, and Soft Matter Physics
Volume83
Issue number4
DOIs
StatePublished - Apr 26 2011
Externally publishedYes

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ASJC Scopus subject areas

  • Statistical and Nonlinear Physics
  • Statistics and Probability
  • Condensed Matter Physics

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