Anharmonic dynamics of intramolecular hydrogen bonds driven by DNA breathing.
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.
Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA.
B S
BS
Alexandrov
V G
VG
Stanev
A R
AR
Bishop
K Ø
KØ
Rasmussen
D001703:Biophysics / Q000379:methods*; D004247:DNA / Q000737:chemistry*; D017276:Friction; D006860:Hydrogen Bonding; D008956:Models, Chemical; D015233:Models, Statistical; D009038:Motion; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D013055:Spectrophotometry, Infrared / Q000379:methods; D013696:Temperature
D004247:DNA