ABSTRACT

The factors providing the stability of the nucleic acid secondary structure in water are already displayed in the interactions between separate nucleotide bases in different associates. By means of the thermodynamic and spectroscopic study of interactions of the bases, their derivatives, nucleosides and nucleotides, it is shown that stacked dimers are exclusively formed in aqueous solutions. Despite numerous experiments, the energetic advantage of the base association reaction in water have been studied insufficiently. As starting configurations for stacked uracil (Ura) and thymine (Thy) dimers, the most preferable for vacuum antiparallel configuration and the antiparallel configuration with the further rotation of a base by 180° around the glycosidic bond were chosen. The chapter presents the results of the study of association reaction obtained from the Monte Carlo-Metropolis hydration simulation of Ura, Thy, and their hydrogen-bonded and stacked dimers. A less preferable dimer is stabilized by the water-base interaction to a greater extent.