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Please use this identifier to cite or link to this item: http://apo.ansto.gov.au/dspace/handle/10238/1134

Title: Atomistic model of DNA: phonons and base-pair opening.
Authors: Merzel, F
Fontaine-Vive, F
Johnson, MR
Kearley, GJ
Keywords: Dispersion Relations
DNA
Biophysics
Intermolecular Forces
Equilibrium
Molecular Dynamics Method
Issue Date: Sep-2007
Publisher: American Physical Society
Citation: Merzel, F., Fontaine-Vive, F., Johnson, M. R., & Kearley, G. J. (2007). Atomistic model of DNA: phonons and base-pair opening. Physical Review E, 76(3), 031917.
Abstract: A fully atomistic model of B-DNA using the CHARMM (chemistry at Harvard molecular mechanics) force field is presented. Molecular dynamics simulations were used to prepare an equilibrium structure. The Hessian of interatomic forces obtained from CHARMM for the equilibrium structure was used as input to a large scale phonon calculation. The calculated dispersion relations at low frequency are compared with recently published experimental data, which shows the model to have good accuracy for the low frequency, vibrational modes of DNA. These are discussed in the context of base-pair opening. In addition to the widely reported modes at, or below, ~12.5 meV, a continuous band of modes with strong base-pair opening character is found up to 40 meV, which coincides with the typical denaturation temperature of DNA. © 2007, American Physical Society
URI: http://dx.doi.org/10.1103/PhysRevE.76.031917
http://apo.ansto.gov.au/dspace/handle/10238/1134
ISSN: 1539-3755
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