Effect of initial ion positions on the interactions of monovalent and divalent ions with a DNA duplex as revealed with atomistic molecular dynamics simulations

Abstract

Monovalent (Na⁺) and divalent (Mg²⁺) ion distributions around the Dickerson-Drew dodecamer were studied by atomistic molecular dynamics (MD) simulations with AMBER molecular modeling software. Different initial placements of ions were tried and the resulting effects on the ion distributions around DNA were investigated. For monovalent ions, results were found to be nearly independent of initial cation coordinates. However, Mg²⁺ ions demonstrated a strong initial coordinate dependent behavior. While some divalent ions initially placed near the DNA formed essentially permanent direct coordination complexes with electronegative DNA atoms, Mg²⁺ ions initially placed further away from the duplex formed a full, nonexchanging, octahedral first solvation shell. These fully solvated cations were still capable of binding with DNA with events lasting up to 20 ns, and in comparison were bound much longer than Na⁺ ions. Force field parameters were also investigated with modest and little differences arising from ion (ions94 and ions08) and nucleic acid description (ff99, ff99bsc0, and ff10), respectively. Based on known Mg²⁺ ion solvation structure, we conclude that in most cases Mg²⁺ ions retain their first solvation shell, making only solvent-mediated contacts with DNA duplex. The proper way to simulate Mg²⁺ ions around DNA duplex, therefore, should begin with ions placed in the bulk water.

Keywords:

• molecular dynamics simulations
• nucleic acids
• monovalent cations
• divalent cations

Acknowledgments

We acknowledge partial financial support provided by Oak Ridge Associated University in partnership with Oak Ridge National Laboratory through ORAU/ORNL high performance computing grant (project BIP011) and by National Science Foundation through TN-SCORE project. The high-performance facility at the University of Memphis is also acknowledged. The authors also wish to thank the fruitful discussions with Dr. Don Bashford and Dr. Mohamed Laradji.