| Texto completo | |
| Autor(es): |
Santos, Vinicius Lemes de Souza
;
Ribeiro, Felipe Augusto
;
Kim, Chang Dong
;
Lopez-Castillo, Alejandro
Número total de Autores: 4
|
| Tipo de documento: | Artigo Científico |
| Fonte: | Journal of Molecular Modeling; v. 30, n. 11, p. 9-pg., 2024-11-01. |
| Resumo | |
Context Phosphodiester bonds, which form the backbone of DNA, are highly stable in the absence of catalysts. This stability is crucial for maintaining the integrity of genetic information. However, when exposed to catalytic agents, these bonds become susceptible to cleavage. In this study, we investigated the role of different metal dications (Ca2+, Mg2+, Zn2+, Mn2+, and Cu2+) in promoting the hydrolysis of phosphodiester bonds. A minimal DNA model was constructed using two pyrimidine nucleobases (cytosine and thymine), two deoxyribose units, one phosphate group, and one metallic dication coordinated by six water molecules. The results highlight that Cu2+ is the most efficient in lowering the energy barrier for bond cleavage, with an energy barrier of 183 kJ/mol, compared to higher barriers for metals like Zn2+ (202 kJ/mol), Mn2+ (202 kJ/mol), Mg2+ (210 kJ/mol), and Ca2+ (223 kJ/mol). Understanding the interaction between these metal ions and phosphodiester bonds offers insight into DNA stability and organic data storage systems. Methods DFT calculations were employed using Gaussian 16 software, applying the B3LYP hybrid functional with def2-SVP basis sets and GD3BJ dispersion corrections. Full geometry optimizations were performed for the initial and transition states, followed by identifying energy barriers associated with phosphodiester bond cleavage. The optimization criteria included maximum force, root-mean-square force, displacement, and energy convergence thresholds. (AU) | |
| Processo FAPESP: | 19/12501-0 - Estudo teórico de sistemas bidimensionais |
| Beneficiário: | Alejandro López Castillo |
| Modalidade de apoio: | Auxílio à Pesquisa - Regular |
| Processo FAPESP: | 23/11272-3 - Estudo sobre a des/estabilização da ligação fosfodiéster de nucleotídeos de DNA (e RNA) visando o armazenamento de dados |
| Beneficiário: | Felipe Augusto Ribeiro |
| Modalidade de apoio: | Bolsas no Brasil - Iniciação Científica |