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A composite model for DNA torsion dynamics

M. Cadoni·R. De Leo·G. Gaeta
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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 DNA subunits made of a nucleoside and the attached nitrogen bases 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 nucleoside 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 modelling 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.

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M. Cadoni, R. De Leo, G. Gaeta. 2006-04-20. A composite model for DNA torsion dynamics. https://doi.org/10.1103/physreve.75.021919

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