Predicting RNA-Metal Ion Binding with Ion Dehydration Effects (Biophysical Journal)

Metal ions play essential roles in nucleic acids folding and stability. The interaction between metal ions and nucleic acids can be highly complicated due to the interplay between the various effects such as ion correlation, fluctuation, and dehydration. These effects may be particularly important for multivalent ions such as Mg2+ ions. Previous efforts to model ion correlation and fluctuation effects led to the development of the Monte Carlo Tightly Bound Ion (MCTBI) model. Here, by incorporating ion hydration/dehydration effects into the MCTBI model, we develop a new approach to predict ion binding.