Regioselectivity of the OH Radical Addition to Uracil in Nucleic Acids. A Theoretical Approach Based on QM/MM Simulations

• Published in: Journal of chemical theory and computation Vol. 13; no. 10; pp. 5089 - 5096
• Main Authors: Aranda, Juan, Francés-Monerris, Antonio, Tuñón, Iñaki, Roca-Sanjuán, Daniel
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 10.10.2017
• Subjects: Biological effects; Degeneration; Deoxyribonucleic acid; DNA; Hydroxyl Radical - chemistry; Molecular chains; Molecular dynamics; Molecular structure; Nucleic acids; Oxidation; Pollutants; Quantum chemistry; Quantum Theory; Regioselectivity; Ribonucleic acid; RNA; RNA - chemistry; Solutions; Stereoisomerism; Uracil; Uracil - chemistry; Water - chemistry
• ISSN: 1549-9618; 1549-9626; 1549-9626
• DOI: 10.1021/acs.jctc.7b00610

Oxidation of nucleic acids is ubiquitous in living beings under metabolic impairments and/or exposed to external agents such as radiation, pollutants, or drugs, playing a central role in the development of many diseases mediated by DNA/RNA degeneration. Great efforts have been devoted to unveil the molecular mechanisms behind the OH radical additions to the double bonds of nucleobases; however, the specific role of the biological environment remains relatively unexplored. The present contribution tackles the study of the OH radical addition to uracil from the gas phase to a full RNA macromolecule by means of quantum-chemistry methods combined with molecular dynamics simulations. It is shown that, in addition to the intrinsic reactivity of each position driven by the electronic effects, the presence of bridge water molecules intercalated into the RNA structure favors the addition to the C5 position of uracil in biological conditions. The results also suggest that diffusion of the OH radical does not play a relevant role in the regioselectivity of the reaction, which is mainly controlled at the chemical stage of the addition process.