Composite model for DNA torsion dynamics

Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Feb;75(2 Pt 1):021919. doi: 10.1103/PhysRevE.75.021919. Epub 2007 Feb 28.

Abstract

DNA torsion dynamics is essential in the transcription process; a simple model for it, in reasonable agreement with experimental observations, has been proposed by Yakushevich (Y) and developed by several authors; in this, the nucleotides (the DNA subunits made of a sugar-phosphate group and the attached nitrogen base) are described by a single degree of freedom. In this paper we propose and investigate, both analytically and numerically, a "composite" version of the Y model, in which the sugar-phosphate group and the base are described by separate degrees of freedom. The model proposed here contains as a particular case the Y model and shares with it many features and results, but represents an improvement from both the conceptual and the phenomenological point of view. It provides a more realistic description of DNA and possibly a justification for the use of models which consider the DNA chain as uniform. It shows that the existence of solitons is a generic feature of the underlying nonlinear dynamics and is to a large extent independent of the detailed modeling of DNA. The model we consider supports solitonic solutions, qualitatively and quantitatively very similar to the Y solitons, in a fully realistic range of all the physical parameters characterizing the DNA.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computer Simulation
  • DNA / chemistry*
  • DNA / ultrastructure*
  • Kinetics
  • Models, Chemical*
  • Models, Molecular*
  • Motion
  • Nucleic Acid Conformation

Substances

  • DNA