Modeling self-contact forces in the elastic theory of DNA supercoiling

Timothy P. Westcott, Irwin Tobias, Wilma K. Olson

Research output: Contribution to journalArticlepeer-review

43 Scopus citations

Abstract

A DNA polymer with thousands of base pairs is modeled as an elastic rod with the capability of treating each base pair independently. Elastic theory is used to develop a model of the double helix which incorporates intrinsic curvature as well as inhomogeneities in the bending, twisting, and stretching along the length of the polymer. Inhomogeneities in the elastic constants can also be dealt with; thus, sequence-dependent structure and deformability can be taken into account. Additionally, external forces have been included in the formalism, and since these forces can contain a repulsive force, DNA self-contact can be explicitly treated. Here the repulsive term takes the form of a modified Debye-Hückel force where screening can be varied to account for the effect of added salt. The supercoiling of a naturally straight, isotropic rod in 0.1M NaCl is investigated and compared with earlier treatments of supercoiled DNA modeled by a line of point charges subject to electrostatic interactions and an elastic potential.

Original languageEnglish (US)
Pages (from-to)3967-3980
Number of pages14
JournalJournal of Chemical Physics
Volume107
Issue number10
DOIs
StatePublished - Sep 8 1997

All Science Journal Classification (ASJC) codes

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

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