Alexandrov BS, Stanev VG, Bishop AR, Rasmussen KØ. Anharmonic dynamics of intramolecular hydrogen bonds driven by DNA breathing.
PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012;
86:061913. [PMID:
23367981 DOI:
10.1103/physreve.86.061913]
[Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Indexed: 06/01/2023]
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· · ·N and N-H· · ·O hydrogen bonding, we identify a high-frequency (~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 (~300 K), where the anharmonicity of DNA dynamics is pronounced, the high-frequency peak is always present irrespective of the friction strength.
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