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.

A composite model for DNA torsion dynamics

CADONI, MARIANO;
2007

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.
Solitons; Mathematical models of DNA
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/11584/34690
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