Computer Simulation of Biomolecular Interactions Involved in Genetic Processes

Computational results are described of interactions between nucleic acid bases and of searching for local minima of the interaction energy. As the bases are the elementary units of genetic material, their interactions are important for understanding the molecular mechanisms of genetic processes. The results allow us to reveal three different types of energy minima, which are responsible for various functions of nucleic acids. The minima of one type, corresponding to in-plane base arrangement and inter-base hydrogen bond formation, are responsible for the specificity of base-base interactions, i.e. for the fidelity of genetic processes. The minima of second type correspond to nearly parallel base arrangement; they, together with the first minima, stabilize the double helical DNA structure. The last type of minima corresponds to nearly perpendicular mutual base positions with single hydrogen bond. These minima are important for monomer interactions with the DNA duplex and for the duplex unwinding during nucleic acid biosynthesis. Key-Words: Molecular Mechanics, Computer Simulations, Intermolecular Interactions, Nucleic Acids