Entropy-driven DNA denaturation

Thierry Dauxois; Michel Peyrard; A. R. Bishop

doi:10.1103/PhysRevE.47.R44

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Entropy-driven DNA denaturation

Thierry Dauxois and Michel Peyrard

A. R. Bishop

Physique Non Linéaire: Ondes et Structures Cohérentes, Faculté des Sciences, 6 Boulevard Gabriel, 21000 Dijon, France
Center for Nonlinear Studies and Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545

Center for Nonlinear Studies and Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545

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Phys. Rev. E 47, R44(R) – Published 1 January, 1993

DOI: https://doi.org/10.1103/PhysRevE.47.R44

Abstract

We present a nonlinear dynamical model for DNA denaturation which includes cooperativity effects through anharmonic nearest-neighbor stacking interactions. Transfer-integral calculations show that this one-dimensional model, without including long-range interactions, exhibits a sharp denaturation reminiscent of a first-order transition at a temperature lower than a similar model with harmonic coupling. Self-consistent phonon calculations point out the essential role of nonlinear effects in the mechanism.

References (22)

A. E. Garcia, Phys. Rev. Lett. 68, 2696 (1992), and references therein.
For a review, see R. M. Wartell and A. S. Benight, Phys. Rep. 126, 67 (1985).
J. L. Leroy et al., Mol. Biol. 200, 223 (1988).
S. M. Englander et al., Proc. Natl. Acad. Sci. (USA) 77, 7222 (1980).
M. Peyrard and A. Bishop, Phys. Rev. Lett. 62, 2755 (1989).
M. Techera, L. L. Daemen and E.W. Prohofsky, Phys. Rev. A 41, 4543 (1990); ibid. 42, 5033 (1990).
M. Peyrard, T. Dauxois and H. Hoyet, Nanobiol. 1, 313 (1992).
W. Saenger, in Principles of Nucleic Acid Structure (Springer, Berlin, 1984).
L. Van Hove, Physica 16, 137 (1950).
D. Poland and H. Scheraga, J. Chem. Phys. 45, 1456 (1966).
M. Ya. Azbel, J. Chem. Phys. 62, 3635 (1975).
The important role of entropy change in biophysical transitions has been pointed out for membranes phase transitions by J. Day and C. Willis, J. Theor. Biol. 88, 693 (1981).
C. Reiss (private communication).
The free energy of a single classical harmonic oscillator is scrF =- $k_{B}$ T ln [2 π $k_{B}$ T / ω ].
J. A. Krumhansl and R. J. Gooding, Phys. Rev. B 39, 3047 (1989); W. C. Kerr et al., ibid. 45, 7036 (1992).
T. Schneider and E. Stoll, Phys. Rev. B 22, 5317 (1980).
J. A. Krumhansl and J. R. Schrieffer, Phys. Rev. B 11, 3535 (1975).
Since the substrate potential is bounded from below, the eigenspectrum of the TI operator is also bounded from below.
S. Nosé, Mol. Phys. 52, 255 (1984).
R. P. Feynman, in Statistical Mechanics (Benjamin, New York, 1972).
J. R. Morris and R. J. Gooding, Phys. Rev. B 46, 8733 (1992).
J. R. Morris and R. J. Gooding, J. Stat. Phys. 67, 471 (1992).

[c1] A. E. Garcia, Phys. Rev. Lett. 68, 2696 (1992), and references therein.

[c2] For a review, see R. M. Wartell and A. S. Benight, Phys. Rep. 126, 67 (1985).

[c3] J. L. Leroy et al., Mol. Biol. 200, 223 (1988).

[c4] S. M. Englander et al., Proc. Natl. Acad. Sci. (USA) 77, 7222 (1980).

[c5] M. Peyrard and A. Bishop, Phys. Rev. Lett. 62, 2755 (1989).

[c6] M. Techera, L. L. Daemen and E.W. Prohofsky, Phys. Rev. A 41, 4543 (1990); ibid. 42, 5033 (1990).

[c7] M. Peyrard, T. Dauxois and H. Hoyet, Nanobiol. 1, 313 (1992).

[c8] W. Saenger, in Principles of Nucleic Acid Structure (Springer, Berlin, 1984).

[c9] L. Van Hove, Physica 16, 137 (1950).

[c10] D. Poland and H. Scheraga, J. Chem. Phys. 45, 1456 (1966).

[c11] M. Ya. Azbel, J. Chem. Phys. 62, 3635 (1975).

[c12] The important role of entropy change in biophysical transitions has been pointed out for membranes phase transitions by J. Day and C. Willis, J. Theor. Biol. 88, 693 (1981).

[c13] C. Reiss (private communication).

[c14] The free energy of a single classical harmonic oscillator is scrF =- $k_{B}$ T ln [2 π $k_{B}$ T / ω ].

[c15] J. A. Krumhansl and R. J. Gooding, Phys. Rev. B 39, 3047 (1989); W. C. Kerr et al., ibid. 45, 7036 (1992).

[c16] T. Schneider and E. Stoll, Phys. Rev. B 22, 5317 (1980).

[c17] J. A. Krumhansl and J. R. Schrieffer, Phys. Rev. B 11, 3535 (1975).

[c18] Since the substrate potential is bounded from below, the eigenspectrum of the TI operator is also bounded from below.

[c19] S. Nosé, Mol. Phys. 52, 255 (1984).

[c20] R. P. Feynman, in Statistical Mechanics (Benjamin, New York, 1972).

[c21] J. R. Morris and R. J. Gooding, Phys. Rev. B 46, 8733 (1992).

[c22] J. R. Morris and R. J. Gooding, J. Stat. Phys. 67, 471 (1992).

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Entropy-driven DNA denaturation

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