

These simulations can reveal mechanisms underlying many biologically important, yet completely unintuitive phenomena, often not accessible experimentally. Compared to the steric repulsion between the ion and the methyl group, the desolvation penalty interaction has a longer range and may be important to consider in the context of methylation effects on DNA condensation.Īll-atom explicit solvent molecular dynamics (MD) simulations allow one to quantify thermodynamic properties and structural details of ion-nucleic acid interactions at atomic resolution. The simulations suggest that the ion desolvation penalty due to proximity to the low dielectric volume of the methyl group can contribute significantly to CoHex-thymine interactions. dT) DNA duplex with modified (de-methylated) and native thymine bases are used to explore the physics behind CoHex-thymine interactions.MC simulations of CoHex ions interacting with the homopolymeric poly(dA These features include preferential CoHex binding inside the major groove of the RNA duplex, in contrast to CoHex biding at the “external” surface of the sugar-phosphate backbone of the DNA duplex these differences in the counterion binding patters were earlier shown to be responsible for the observed drastic differences in condensation propensities between short DNA and RNA duplexes. The proposed explicit ions/implicit water GB model is able to resolve subtle features and differences of CoHex distributions around DNA and RNA duplexes. Expressed in the units of energy, the maximum deviations of local ion concentrations from the reference are within k B T. The monovalent (Na +) and trivalent (CoHex 3+) counterion distributions predicted by the model are in close quantitative agreement with all-atom explicit water molecular dynamics simulations used as reference. The effectiveness of the approach is demonstrated by calculating the potential of mean force for Na +–Cl − ion pair and by carrying out a set of Monte Carlo (MC) simulations of mono- and trivalent ions interacting with DNA and RNA duplexes. A fully analytical description of all energy components for charge-charge interactions is provided. Specifically, the model includes modifications to the GB interaction terms for the case of multiple interacting solutes-disconnected dielectric boundary around the solute-ion or ion-ion pairs. The proposed explicit ions/implicit water model is based on a significantly modified generalized Born (GB) model and utilizes a non-standard approach to define the solute/solvent dielectric boundary. Here we utilized the implicit solvent framework to develop a model for the explicit treatment of ions interacting with nucleic acid molecules. The ion atmosphere around highly charged nucleic acid molecules plays a significant role in their dynamics, structure, and interactions.
