Perepelytsya S. Role of alkali metal counterions in the conformational dynamics of double helical polynucleotides

In the thesis the molecule of the double helical polynucleotide with counterions of alkali metals is considered as as lattice of ion crystal. The dynamics of such a lattice is studied in frame of the four mass model approach by Volkov and Kosevich and using the theory of ion crystals. To determine the electrostatic interactions between charges of the double helix and counterions, the spasial approach for estimation of the dielectric constant of ion-hydrate shell of polynucleotide and the Madelung constant of ion-phosphate lattice is developed. The obtained values of the dielectric constant changes from 2,3 to 2,6, depending on counteriontype. The values of the Madelung constant appear close to the value of one-dimensional ion crystal (1,386). In the result it was shown that in the low-frequency spectra of the double helical polynucleotides the mode of counterion vibrations with respect of the phosphate groups of the double helix. The calculated frequencies of ion-phosphate vibrations for polynucleotides in dry state and for polynucleotides in В- and А-forms of the double helix with Li+, Na+, K+, Rb+ and Cs+ counterions. It was shown that the frequency of ion-phosphate vibrations decreases from 250 до 95 см-1 as the counterion mass increases. The calculations of the amplitudes of conformational vibrations show that light counterions (Li+, Na+ and K+) moving with respect to the phosphate groups do not disturb the internal dynamics of the double helix, but heavy counterions (Rb+ and Cs+) make move all structure elements of polynucleotide. To observe the mode of ion-phosphate vibrations the Raman spectra of DNA water solutions with Na+ and Cs+ are studied. It was shown that in the both spectra the band 100 cm-1 is observed. The intensity of this band in the spectra of Cs-DNA is about twice higher than in the spectra of Na-DNA. In thesis it is shown that the intensification of this band in the spectra of Cs-DNA is caused because the mode of ion-phosphate vibrations is inside this band. Observation the mode of ion-phosphate vibrations proves the existence of the dynamical ion-phosphate lattice in the solutions of double helical polynucleotides with alkali metal counterions.