Transverse interaction in DNA molecule

Interaction between nucleotides at a same site belonging to different strands is studied. This interaction is modelled by a Morse potential which depends on two parameters. We study a relationship between the parameters characterizing AT and CG pairs. We show that certain circumstances, i.e. certain values of these parameters, bring about a negligible influence of inhomogeneity on the solitonic dynamics.

[1]  Carlos Bustamante,et al.  Single molecule transcription elongation. , 2009, Methods.

[2]  C. B. Tabi,et al.  Discrete instability in the DNA double helix. , 2009, Chaos.

[3]  C. B. Tabi,et al.  Wave propagation of nonlinear modes and formation of bubble in a two-component helicoidal lattice , 2008 .

[4]  M. Sataric,et al.  DNA dynamics - Experiment proposals , 2009 .

[5]  R. Karpel,et al.  Single molecule force spectroscopy studies of DNA denaturation by T4 gene 32 protein , 2004 .

[6]  Gil U. Lee,et al.  Direct measurement of the forces between complementary strands of DNA. , 1994, Science.

[7]  Kyle Forinash,et al.  Local modes and localization in a multicomponent nonlinear lattice , 1997 .

[8]  T. Kofané,et al.  Modulated Wave Packets in DNA and Impact of Viscosity , 2009 .

[9]  V. Vasumathi,et al.  Perturbed soliton-like molecular excitations in a deformed DNA chain , 2008 .

[10]  Thierry Dauxois,et al.  Dynamics of breather modes in a nonlinear “helicoidal” model of DNA , 1991 .

[11]  S. Smith,et al.  Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. , 1992, Science.

[12]  Solitons in Yakushevich-like models of DNA dynamics with improved intrapair potential , 2006, q-bio/0604004.

[13]  S. Cocco,et al.  Helicoidal model for DNA opening , 1999, chao-dyn/9904032.

[14]  L. Manevitch,et al.  Nonlinear dynamics of topological solitons in DNA. , 2002, Physical review. E, Statistical, nonlinear, and soft matter physics.

[15]  M. Sataric,et al.  Parameter selection in a Peyrard―Bishop―Dauxois model for DNA dynamics , 2009 .

[16]  M. Rief,et al.  Mechanical stability of single DNA molecules. , 2000, Biophysical journal.

[17]  V. Vasumathi,et al.  Perturbed soliton excitations in the DNA double helix , 2006, nlin/0602037.

[18]  David Bensimon,et al.  Measurement of the torque on a single stretched and twisted DNA using magnetic tweezers. , 2009, Physical review letters.

[19]  B D Ratner,et al.  Direct measurement of hydrogen bonding in DNA nucleotide bases by atomic force microscopy. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[20]  U. Bockelmann,et al.  DNA strand separation studied by single molecule force measurements , 1998 .

[21]  R. Lavery,et al.  Wringing out DNA. , 2006, Physical review letters.

[22]  S. Lindsay,et al.  The speed of sound in DNA , 1984, Biopolymers.

[23]  R Lavery,et al.  Stretched and overwound DNA forms a Pauling-like structure with exposed bases. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[24]  Bishop,et al.  Statistical mechanics of a nonlinear model for DNA denaturation. , 1989, Physical review letters.

[25]  Michel Peyrard.  Nonlinear dynamics and statistical physics of DNA , 2004 .

[26]  H. Güntherodt,et al.  Dynamic force spectroscopy of single DNA molecules. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[27]  V. Vasumathi,et al.  Nonlinear molecular excitations in a completely inhomogeneous DNA chain , 2008, 0807.2506.

[28]  Gilles Charvin,et al.  Stretching of macromolecules and proteins , 2003 .

[29]  Solitons in the Yakushevich model of DNA beyond the contact approximation. , 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

[30]  Ulrich Bockelmann,et al.  MOLECULAR STICK-SLIP MOTION REVEALED BY OPENING DNA WITH PICONEWTON FORCES , 1997 .

[31]  L. V. I︠A︡kushevich.  Nonlinear Physics of DNA , 1998 .

[32]  Francisco Tirado,et al.  Numerical Simulations and Parallel Implementation of Some Nonlinear Schrödinger Systems , 1994 .

[33]  L. V. Yakushevich,et al.  Nonlinear DNA dynamics: A new model , 1989 .

[34]  Bishop,et al.  Entropy-driven DNA denaturation. , 1993, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[35]  John W. Miles,et al.  An Envelope Soliton Problem , 1981 .

[36]  E. Siggia,et al.  Entropic elasticity of lambda-phage DNA. , 1994, Science.

[37]  T. Dauxois,et al.  Simple models of non-linearDNA dynamics , 1994 .

[38]  Carlos Bustamante,et al.  Recent advances in optical tweezers. , 2008, Annual review of biochemistry.

[39]  A. Heeger,et al.  Nature of the open state in long polynucleotide double helices: possibility of soliton excitations. , 1980, Proceedings of the National Academy of Sciences of the United States of America.

[40]  M. Sataric,et al.  Solitonic speed in DNA. , 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.

[41]  M. Sataric,et al.  Single-molecule unzippering experiments on DNA and Peyrard-Bishop-Dauxois model. , 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

[42]  C. Bustamante,et al.  Overstretching B-DNA: The Elastic Response of Individual Double-Stranded and Single-Stranded DNA Molecules , 1996, Science.