Configurational transitions in Fourier series-represented DNA supercoils

Guohua Liu, Tamar Schlick, Andrew J. Olson, Wilma K. Olson

Research output: Contribution to journalArticlepeer-review

Abstract

A new Fourier series representation of supercoiled DNA is employed in Langevin dynamics simulations to study large-scale configurational motions of intermediate-length chains. The polymer is modeled as an ideal elastic rod subject to long-range van der Waals' interactions. The van der Waals' term prevents the self-contact of distant chain segments and also mimics attractive forces thought to stabilize the association of closely spaced charged rods. The finite Fourier series-derived polymer formulation is an alternative to the piecewise B-spline curves used in past work to describe the motion of smoothly deformed supercoiled DNA in terms of a limited number of independent variables. This study focuses on two large-scale configurational events: the interconversion between circular and figure-8 forms at a relatively low level of supercoiling, and the transformation between branched and interwound structures at a higher superhelical density.

Original languageEnglish (US)
Pages (from-to)1742-1762
Number of pages21
JournalBiophysical journal
Volume73
Issue number4
DOIs
StatePublished - Oct 1997

ASJC Scopus subject areas

  • Biophysics

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