Peculiarities of long-range interaction between the nucleotides after DNA damage

Abstract

In this work, the long-range interaction between the pairs of nucleotides situated on the opposite ends of a double broken DNA helix have been studied theoretically. The long-range energy was considered as a sum of electrodynamics Van der Waals and electrostatic Coulomb interactions. The most important region for the problem under consideration is about 5–15 Å between the nucleotides. The calculations of the energy of long-range interaction have shown that during the interaction between the pairs CG–CG, there is a potential repulsive barrier with the amplitude of about 4 kT at the distance of 7–9 Å, and during the interaction between the pairs TA–TA, there is a potential repulsive barrier with the amplitude of about 1.5 kT at the same distance, which can prevent DNA from enzyme selfrepairing after a double DNA break. This barrier vanishes as the pH of intracellular medium increases. The remainder pairs of nucleotides do not have such barrier, and there is always an attraction like interaction.