However, on microsecond time scales that may be needed for adequate sampling of large nucleic acid systems in the presence of complex multivalent ions with strong binding affinities, these simulations can be very demanding. 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.
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