Anharmonic dynamics of intramolecular hydrogen bonds driven by DNA breathing

B. S. Alexandrov, V. G. Stanev, A. R. Bishop, and K. Ø. Rasmussen

Phys. Rev. E 86, 061913 – Published 26 December 2012

Abstract

We study the effects of the anharmonic strand-separation dynamics of double-stranded DNA on the infrared spectra of the intramolecular base-pairing hydrogen bonds. Using the extended Peyrard-Bishop-Dauxois model for the DNA breathing dynamics coupled with the Lippincott-Schroeder potential for $N - H$ $\dots$ N and $N - H$ $\dots$ O hydrogen bonding, we identify a high-frequency ( $\sim$ 96 THz) feature in the infrared spectra. We show that this sharp peak arises as a result of the anharmonic base-pair breathing dynamics of DNA. In addition, we study the effects of friction on the infrared spectra. For higher temperatures ( $\sim$ 300 K), where the anharmonicity of DNA dynamics is pronounced, the high-frequency peak is always present irrespective of the friction strength.

Received 24 October 2012

DOI:https://doi.org/10.1103/PhysRevE.86.061913

Published by the American Physical Society

Authors & Affiliations

B. S. Alexandrov¹, V. G. Stanev², A. R. Bishop¹, and K. Ø. Rasmussen¹

¹Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
²Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439, USA

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Vol. 86, Iss. 6 — December 2012

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