One of the fundamental problems in nucleic acids biophysics is to predict the di?erent forces that stabilize nucleic acid tertiary folds.  Using the generalized Born model and the improved atomistic tightly binding ions (TBI) model, we evaluated the ion correlation and solvent polarization e?ects in interhelix interactions. The results indicate that hydration, Coulomb correlation and ion entropy act together to cause the repulsion and attraction between nucleic acid helices in Mg2+ and Mn2+ solutions, respectively.  Detailed analysis suggests that solvent polarization and ion correlation both are crucial for the interhelix interactions.  Furthermore, by combining the virtual bond RNA folding model (Vfold) for conformational sampling and the TBI model,  we also investigated the Mg2+-facilitated tetraloop-receptor docking in RNA folding.  the theoretical analysis shows that the Mg2+-induced stabilizing force for the docked state is predominantly entropic.

Exploring Coulombic and solvent polarization-mediated forces in nucleic acids folding

248th National Meeting (2014)

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