Influence of divalent magnesium ion on DNA: molecular dynamics simulation studies

Abstract

A large amount of experimental evidence is available on the effect of magnesium ions on the structure and stability of DNA double helix. Less is known, however, on how these ions affect the stability and dynamics of the molecule. The static time average pictures from X-ray structures or the quantum chemical energy minimized structures lack understanding of the dynamic DNA–ion interaction. The present work addresses these questions by molecular dynamics simulation studies on two DNA duplexes and their interaction with magnesium ions. Results show typical B-DNA character with occasional excursions to deviated states. We detected expected stability of the duplexes in terms of backbone conformations and base pair parameter by the CHARMM-27 force field. Ion environment analysis shows that Mg²⁺ retains the coordination sphere throughout the simulation with a preference for major groove over minor. An extensive analysis of the influence of the Mg²⁺ ion shows no evidence of the popular predictions of groove width narrowing by dipositive metal ion. The major groove atoms show higher occupancy and residence time compared to minor groove for magnesium, where no such distinction is found for the charge neutralizing Na⁺ ions. The determining factor of Mg²⁺ ion’s choice in DNA binding site evolves as the steric hindrance faced by the bulky hexahydrated cation where wider major groove gets the preference. We have shown that in case of binding of Mg²⁺ to DNA non electrostatic contributions play a major role.

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Keywords:

• DNA–ion interaction
• molecular dynamics simulation
• hexahydrated magnesium
• divalent metal ion
• residence time

Acknowledgement

This work was partially supported by Department of Atomic Energy and Department of Biotechnology, Government of India. We sincerely acknowledge computational facilities at Bioinformatics Resources and Application Facility at Center for Development of Advanced Computing, Pune, India. We are thankful to Aditi Borker for technical support.

Notes

Present address: Computational Science Division, Saha Institute of Nuclear Physics, Kolkata.