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

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.

The damage of the Watson-Crick base pairs by nickel nanoparticles: A first-principles molecular dynamics study.

The nickel nanoparticles are harmful atmospheric pollutants, and the damage caused by them in humans has become a topic of great relevance. In this study we investigate the interaction of the Ni2 and Ni3 clusters with the AT and GC Watson-Crick base pairs in an aqueous medium. Molecular dynamics in combination with density functional theory are employed. A novel method is implemented to create realistic thermodynamic conditions (NVT) in the simulations. The energies, the charges of the interacting compounds, the temperature changes, and the geometric rearrangements are reported. The results show the formation of stable organometallic compounds of the nickel nanoparticles with the DNA nucleic acid bases. In this respect, the biological processes where the DNA is implicated may be altered by the formation of such super-structures.