Hydration of Uracil and Thymine Methylderivatives: a Monte Carlo Simulation

Abstract

The simulation performed shows that under methylation of uracil and thymine NH-groups the interaction energy between a base and water (Uwb) is increased. It is also detected that the increase in this energy was observed in the 1st and the 3rd sectors. These conclusions do not confirm the assumption made in the literature on the character of an interaction between methylated bases and water. According to this assumption, when the NH-groups are methylated, the energy of Uwb in these sectors decreases as a result of the van der Waals interactions between a methyl group and water, whose energy compensates the increase in the Uwb energy due to the breaking of an H-bond. Regularity of water molecules near a hydrophobic group under the hydration of polar molecules is detected for the first time.

Structure, Thermodynamics and Energetics of Drug-DNA Interactions: Computer Modeling and Experiment

“…The application of Monte Carlo method for the study of hydration of nucleic acids, their components [77][78][79][80], and hydration of the DNA-ligand complexes (for example, dCpG with proflavine [81] and DNA with azinomycin B [82] intercalated complexes) was described in literature in detail. Monte Carlo simulations enable to evaluate the low energy conformations of various complexes of DNA fragments, including their complexes with ligands, and to determine the hydration properties of the complexes being formed [54,55,83,84].…”

The possibilities of the soft-ionization mass-spectrometry in the molecular-biological studies

“…В заключение отметим, что ценность приведенных данных, полученных с помощью нового экспериментального подхода, значительно возрастает при их дополнении современными теоретическими расчетами, подобными проводимым в [27,28], с учетом особенностей МС-эксперимента.…”