Ion atmosphere around nucleic acids plays a significant role for their dynamics, structure and interactions. Within the implicit solvent framework and the generalized Born (GB) approximation, we have developed a model for explicit treatment of ions interacting with highly charged nucleic acid molecules. The new GB model includes the modification of the interactions in the case of discontinuous dielectric boundary (DB) around the solute-ion or ion-ion pairs. This reduces the overestimation of the repulsive desolvation contributions of the standard GB approach. The model utilizes a special geometry of the DB related to the position of the solvent accessible surface. Fully analytical description of all energy components for charge-charge interactions is provided. The effectiveness of the approach is demonstrated by calculating the potential of mean force for Na-Cl ion pair and carrying out Monte Carlo simulations of mono- and trivalent (CoHex) ion distributions around DNA and RNA duplexes. The derived distributions are in close quantitative agreement with the results of fully explicit solvent simulations. The new implicit solvent/explicit ions GB model is able to resolve the main features of CoHex interactions with DNA and RNA duplexes, i.e. the preferential CoHex binding inside the major groove of RNA duplex opposite to the biding of CoHex mostly to the externally exposed surface of the DNA phosphate backbone.

Implicit solvent/explicit ions GB model for nucleic acid simulations

254th National Meeting (2017)

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