Anharmonic stacking in supercoiled DNA

Details Anharmonic stacking in supercoiled DNA Anharmonic stacking in supercoiled DNA

2012-03-19

arxiv.org/abs/1203.4195v1

Journal of Physics: Condensed Matter Vol.24, 195103 (2012)

Physics

Condensed Matter

Soft Condensed Matter

In press

Scientific paper

10.1088/0953-8984/24/19/195103

Multistep denaturation in a short circular DNA molecule is analyzed by a mesoscopic Hamiltonian model which accounts for the helicoidal geometry. Computation of melting profiles by the path integral method suggests that stacking anharmonicity stabilizes the double helix against thermal disruption of the hydrogen bonds. Twisting is essential in the model to capture the importance of nonlinear effects on the thermodynamical properties. In a ladder model with zero twist, anharmonic stacking scarcely affects the thermodynamics. Moderately untwisted helices, with respect to the equilibrium conformation, show an energetic advantage against the overtwisted ones. Accordingly moderately untwisted helices better sustain local fluctuational openings and make more unlikely the thermally driven complete strand separation.

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