Ions and water play a fundamental role in structure and stability of DNA. Computational methods, such as molecular dynamics (MD), Poisson-Boltzmann (PB) and generalized-Born (GB), can make predictions about solvent distributions and forces but obtaining molecular levels of detail at modest computational expense remains a challenge. The 3D-referenence interaction site model (3D-RISM) of solvation combines explicit solvent molecular models with rigorous statistical mechanics to provide microscopic details and predict thermodynamic observables that closely agree with both MD and experiment.  Using 3D-RISM we have calculated the microscopic distribution of ions and water around DNA for bulk ionic concentrations ranging from 0.005 to 2 M.  We then use solvation forces to compute the structure of DNA and RNA, comparing PB, GB and 3D-RISM models.

DNA structure and solvation calculated with the 3D-RISM molecular theory of solvation

246th National Meeting (2013)

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