Counterion vibrations in the DNA low-frequency spectra
Department of Physics, Taras Shevchenko National University, 64 Volodymyrska St., 01033, Kiev, Ukraine
2 Bogolyubov Institute for Theoretical Physics, NAS of Ukraine, 14-b Metrologichna St., 03680, Kiev, Ukraine
Accepted: 26 October 2007
Published online: 5 December 2007
The vibrations of univalent metal cations with respect to phosphate groups of the DNA backbone are described using the four-mass model approach (S.N. Volkov, S.N. Kosevich, J. Biomol. Struct. Dyn. 8, 1069 (1991)) extended in this paper. The force constant of the counterion-phosphate interaction is determined by considering the DNA with counterions as a lattice of ion crystal. For such ion-phosphate lattice the Madelung constant and the dielectric constant are estimated. The obtained value of the Madelung constant is lower than for the NaCl crystal, and its value is about 1.3. The dielectric constant is within 2.3-2.7 depending on the counterion type and form of the double helix. The calculations of the low-frequency spectra show that for the DNA with metal cations Na+ , K+ , Rb+ and Cs+ the frequency of ion-phosphate vibrations decreases from 174 to 96cm^-1 as the counterion mass increases. The obtained frequencies agree well with the vibrational spectra of polynucleotides in a dry state which prove our suggestion about the existence of the ion-phosphate lattice around the DNA double helix. The amplitudes of conformational vibrations for DNA in B -form are calculated as well. The results demonstrate that light counterions ( Na+ do not disturb the internal dynamics of the DNA. However, heavy counterions ( Cs+ have effect on the internal vibrations of the DNA structural elements.
PACS: 87.14.Gg DNA, RNA – / 87.15.-v Biomolecules: structure and physical properties – / 87.15.He Dynamics and conformational changes –
© EDP Sciences, Società Italiana di Fisica and Springer-Verlag, 2007