On a simple model of low-frequency vibrations in DNA macromolecules.
A simple quasi-continuity model of low-frequency dynamics of DNA macromolecules is presented. The model is based on the phenomenological theory by Volkov and Kosevich (J. Biomol. Struct. Dyn. 8, 1069 (1991)). We propose improvements to their theory by correcting the model energy and corresponding equations of motion, recalculating the model DNA parameters, and estimating the effects of hydration and counterion binding on the masses of DNA subunits. Comparing the calculated low-frequency vibration spectrum and the results of classical Raman scattering experiments from the literature, the values for the model force constants are determined. These values differ significantly from the estimations made by Volkov and Kosevich. A good quantitative agreement with experiment can be obtained both for the case when the "25 cm-1 mode" is an external one, and when it is considered as an intrahelical mode. Problems connected with the qualitative assignments of the calculated and experimentally observed modes are discussed.
Biophysics Division, P.J. Safarik University, Kosice, Slovakia. lisy@kosice.upjs.sk
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Lisy
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Miskovsky
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Schreiber
D004247:DNA / Q000737:chemistry*; D008432:Mathematical Computing; D008958:Models, Molecular; D014732:Vibration
D004247:DNA