Molecular Dynamics of DNA Damage and Conformational Behavior on a Zirconium-Dioxide Surface

Abstract

This work is aimed at a comprehensive study of the processes of immobilization and conformational behavior of DNA on a zirconium-dioxide (ZrO₂) surface. The computer-aided molecular dynamics (MD) method is used to study model systems of nanoparticles and nanoscale DNA + ZrO₂ films, as well as elucidate the experimental spectral and integrated measurements, including the neutron-nuclear physical aspects of the study. Using hybrid MD potentials of classical mechanics and quantum chemistry for DNA solvated in an aquatic environment, the DNA/ZrO₂ surface interactions are studied, and different DNA damage scenarios with various charge modifications are simulated. The charge modifications are introduced into the central part of the DNA molecule by means of two phosphorus atoms, P_a and P_b, for which a number of MD models of DNA + surface are constructed, thereby estimating the dynamic changes of the distance D[DNA(P_a, P_b)-ZrO₂(O)] between the phosphorus atoms (P_a, P_b) and a selected oxygen atom on the surface of the ZrO₂ film. In conclusion, this work is aimed at the development of the functional heterojunctions, such as biological molecules with wide-gap dielectrics. These heterojunctions are intended for use in the field of molecular electronics, in particular, to create biochips and memory arrays in computer architectures of the future.