Dissociation of the Watson-Crick base pairs in vacuum and in aqueous solution: a first-principles molecular dynamics study

Abstract

The damage of the DNA structure can affect the correct functioning of the cellular processes. This work investigates the required forces to dissociate the Watson-Crick (WC) base pairs AT into A and T, and GC into G and C. The WC base pairs are immersed in water under realistic conditions of temperature, volume, and density that reproduce the main characteristics of a biological system. The simulations are based on first-principles molecular dynamics combined with steering atomic forces. In addition to the force intensities, the charge transfers between the nucleic acid bases, energy variations, and temperature fluctuations in the cleavage moments are reported. With the purpose of evaluating the effects of the aqueous medium, simulations of the WC base pairs in vacuum are included. The results considering the solvated medium are consistent with the experimental measurements, and show the importance of the aqueous solution to regulate the structural modifications of the nucleic acid bases. The investigation contributes with a novel molecular model in molecular simulations, and to better understand the biological processes where the DNA compounds play an active role in life forms.

Communicated by Ramaswamy H. Sarma

Keywords:

• DNA nucleic acid bases
• hydrogen bridges
• solvation effects
• density functional theory
• steering molecular forces

Acknowledgments

The authors acknowledge DGTIC for access to the Miztli computer, and express gratitude to Carlos E. Lopez Nataren of IF-UNAM for valuable support.

Disclosure statement

No potential conflict of interest was reported by the authors.