Work

The research within the framework of this project will be carried out in 3 stages: 1. Molecular-dynamic simulations of two systems will be carried out. The first system will consist of a DNA fragment (Drew-Dickerson dodecamer) neutralized by K+ counterions in a water cube, under the action of an external periodic electric field directed perpendicular to the axis of the double helix. Simulations will be performed for different values of the frequency and the field amplitude. The second system will consist of a DNA oligomer 20 base pairs long, with periodic boundary conditions, placed in a water-ion cube. 2. The obtained in the previous step trajectories will be analysed. For the first system, the change in the structural parameters of the DNA macromolecule during the base pairs opening under the action of an electric field (field-induced melting) will be calculated. In particular, the nucleic base parameters ("opening", "propeller", "buckle", "shear", "stretch", "stagger"), as well as the parameters of nucleic base pairs ("twist", "roll" , "tilt", "rise", "slide", "shift")) will be calculated. From the simulation results of the second system, the vibrational density of states will be calculated, which describes the correlated vibrational motions of DNA and water atoms, and, accordingly, the vibrational spectra of water molecules of the DNA hydration shell. The obtained results will be compared with the experimental spectra obtained by the methods of Raman scattering and infrared absorption. 3. Based on the results of the performed work publications will be prepared.