title: Composite model for DNA torsion dynamics.
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.
authors.affiliation: Dipartimento di Fisica, Università di Cagliari and INFN, Sezione di Cagliari, Cittadella Universitaria, 09042 Monserrato, Italy. mariano.cadoni@ca.infn.it
authors.forename: Mariano
authors.initials: M
authors.lastname: Cadoni
authors.forename: Roberto
authors.initials: R
authors.lastname: De Leo
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Gaeta
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure*; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D009038:Motion; D009690:Nucleic Acid Conformation
chemical_list: D004247:DNA