Abstract.
DNA is not the static entity suggested by the famous double helix structure. It shows large fluctuational openings, in which the bases, which contain the genetic code, are temporarily open. Therefore it is an interesting system to study the effect of nonlinearity on the physical properties of a system. A simple model for DNA, at a mesoscopic scale, can be investigated by computer simulation, in the same spirit as the original work of Fermi, Pasta and Ulam. These calculations raise fundamental questions in statistical physics because they show a temporary breaking of equipartition of energy, regions with large amplitude fluctuations being able to coexist with regions where the fluctuations are very small, even when the model is studied in the canonical ensemble. This phenomenon can be related to nonlinear excitations in the model. The ability of the model to describe the actual properties of DNA is discussed by comparing theoretical and experimental results for the probability that base pairs open an a given temperature in specific DNA sequences. These studies give us indications on the proper description of the effect of the sequence in the mesoscopic model.
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References
J.D. Watson, F.H.C. Crick, Nature 171, 737 (1953)
W. Saenger, Principles of Nucleic Acid Structure (Springer-Verlag, Berlin, 1984)
C.R. Calladine, H.R. Drew, Understanding DNA (Academic Press, London, 1992)
M. Gueron, M. Kochoyan, J.L. Leroy, Nature 328, 89 (1987)
M. Frank-Kamennetskii, Nature 328, 17 (1987)
R.B. Inman, R.L. Baldwin, J. Mol. Biol. 8, 452 (1964)
R.M. Wartell, A.S. Benight, Phys. Rep. 126, 67 (1985)
G. Altan-Bonnet, A. Libchaber, O. Krichevsky, Phys. Rev. Lett. 90, 138101 (2003)
A. Spassky, D. Angelov, J. Mol. Biol. 323, 9 (2002)
T. Douki, D. Angelov, J. Cadet, J. Am. Chem. Soc. 123, 11360 (2001)
D. Angelov, B. Beylot, A. Spassky, Biophys. J. 88, 2766 (2005)
S. Cuesta-López, D. Angelov, M. Peyrard (unpublished)
T.S. van Erp, S. Cuesta-Lopez, J.-G. Hagmann, M. Peyrard, Phys. Rev. Lett. 95, 218104 (2005)
D. Poland, H.A. Scheraga, J. Chem. Phys. 45, 1464 (1966)
E. Yeramian, Gene 255, 139 (2000)
I. Daumont, T. Dauxois, M. Peyrard, Nonlinearity 10, 617 (1997)
R.S. MacKay, S. Aubry, Nonlinearity 7, 1623 (1994)
S. Nose, J. Chem. Phys. 81, 511 (1984)
G.J. Martyna, M.L. Klein, M, Tuckerman, J. Chem. Phys. 97, 2635 (1992)
I. Daumont, M. Peyrard, Chaos 13, 624 (2003)
M. Peyrard, Nonlinearity 17, R1 (2004)
T. Dauxois, N. Theodorakopoulos, M. Peyrard, J. Stat. Phys. 107, 869 (2002)
J.A. Cuesta, A. Sanchez, J. Stat. Phys. 115, 869 (2004)
Nonlinearity with disorder, Tashkent, October 1-7, 1990; edited by A. Fatkulla, A.R. Bishop, P. Stephanos (Springer, Berlin, 1984); Nonlinearity and Disorder: Theory and Applications, Tashkent, October 2-6, 2001, edited by F. Abdullaev, O. Bang, M.P. Sørensen, NATO Sci. Ser. (Kluwer Academic Publishers, 2001)
A. Campa, A. Giansanti, Phys. Rev. E 58, 3585 (1998)
C.H. Choi, G. Kalosakas, K.O. Rasmussen, M. Hiromura, A.R. Bishop, A. Usheva, Nucl. Acid Res. 32, 1584 (2004)
O. Gotoh, Y. Tagashira, Biopolymers 20, 1033 (1981)
A. Montrichok, G. Gruner, G. Zocchi, Europhys. Lett. 62, 452 (2003)
T.S. van Erp, S. Cuesta-Lopez, M. Peyrard, Eur. Phys. J. E 20, 421 (2006)
N. Theodorakopoulos, M. Peyrard, R.S. MacKay, Phys. Rev. Lett. 93, 258101-1-4 (2004)
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Peyrard, M., López, S. & Angelov, D. Fluctuations in the DNA double helix. Eur. Phys. J. Spec. Top. 147, 173–189 (2007). https://doi.org/10.1140/epjst/e2007-00208-6
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DOI: https://doi.org/10.1140/epjst/e2007-00208-6