Perepelytsya S. Structure and dynamics of counterion ordering around the DNA double helix

The concept of the dynamical DNA ion-phosphate lattice has been formulated in the thesis, according to which the counterions around the double helix form a regular structure similar to an ionic lattice. To determine the manifestations of counterion ordering in vibrational spectra, models of the dynamics of the ion-phosphate lattice of DNA were developed and an approach was built to describe the intensities of modes in low-frequency Raman spectra. As the result, the modes of ion-phosphate vibrations in the range from 100 to 180 cm–1 have been determined for Na+, K+, Rb+ and Cs+ counterions. Manifestations of the arrangement of DNA counterions in experiments on the electrical conductivity of aqueous solutions of DNA and in experiments on the study of the textures of dried DNA films with alkali metal salts are explained. Within the framework of the molecular dynamics method, it is shown that the distribution of counterions with respect to the DNA essentially depends on the character of hydration, and the movement of counterions under the action of an external electric field is modulated by the sequence of base pairs. For the first time, the structure of characteristic complexes in the solvate shell of phosphate groups of the backbone of the DNA double helix was determined in the presence of hydrogen peroxide molecules and Na+ counterions. The study of ordering of molecular counterions (molecules of polyamines putrescine2+, spermidine3+, spermine4+) showed that they are mainly localized in the minor groove of the double helix with the smallest width, which determines their preferential binding to the A-tract nucleotide motif. In the regions where DNA-DNA contacts occur, polyamines are arranged, forming interhelical crosslinks.