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A twist opening model for DNA

Barbi M.
•
Cocco S.
•
Peyrard M.
•
Ruffo S.
1999
  • journal article

Periodico
JOURNAL OF BIOLOGICAL PHYSICS
Abstract
The real mechanisms of several biological processes involving DNA are not yet understood. We discuss here some aspects of the initiation of transcription, in particular the formation of the open complex and the activation mechanism associated to enhancer binding proteins. Transcription activation seems to be governed by underlying dynamical mechanisms related to several distortions of the double chain structure: a dynamical approach on a mesoscopic description level could then allow a deeper understanding of this complex process. Starting from the Peyrard Bishop (PB) model, that considers only the hydrogen bond stretching of each base pair, we describe here an extended DNA model, proposed in [1], that allows a rather good representation of the double helix geometry and of its structural features by the introduction of angular variables related to the twist angle. Using a generalized multiple scale expansion for the case of vectorial lattices derived elsewhere [2], we derive analytically small amplitude approximate solutions of the model which are movable and spatially localized: we present here the results of this calculation and show how the special shape of the solutions is in good agreement with what can be expected for coupled angular radial distortions in the real molecule.
DOI
10.1023/a:1005139326775
WOS
WOS:000081055400004
Archivio
http://hdl.handle.net/20.500.11767/116525
info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-0002080392
https://link.springer.com/article/10.1023/A:1005139326775
Diritti
metadata only access
Soggetti
  • DNA modeling

  • Helix

  • Hydrogen bond stretch...

  • Nonlinear dynamics

  • Solitons

  • Transcription initiat...

  • Twist

  • Morse potential

  • Settore FIS/03 - Fisi...

  • Settore FIS/02 - Fisi...

Web of Science© citazioni
68
Data di acquisizione
Feb 27, 2024
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