Predicting Site-Binding Modes of Ions and Water to Nucleic Acids Using Molecular Solvation Theory.

ABSTRACT: Site binding of ions and water shapes nucleic acids folding, dynamics, and biological function, complementing the more diffuse, nonspecific "territorial" ion binding. Unlike territorial binding, prediction of site-specific binding to nucleic acids remains an unsolved challenge in computational biophysics. This work presents a new toolset based on the 3D-RISM molecular solvation theory and topological analysis that predicts cation and water site binding to nucleic acids. 3D-RISM is shown to accurately capture alkali cations and water binding to the central channel, transversal loops, and grooves of the Oxytricha nova's telomeres' G-quadruplex ( Oxy-GQ), in agreement with high-resolution crystallographic data. To improve the computed cation occupancy along the Oxy-GQ central channel, it was

SUBMITTER: Giambasu GM 

PROVIDER: S-EPMC6574206 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature