Evaluación del campo de fuerza Charmm27 implementado en NAMD para la simulación de ADN G-Cuádruple Tetramoleculares y Paralelos.

Abstract

The current research was carried out at Computational and Theoretical Chemistry Laboratory of San Francisco de Quito University, located in Quito city in order to study the G-Quadruplex deoxyribonucleic acid (DNA) which is very important due to its participation in the cellular processes. The G-Quadruplex molecular conformation has been obtained experimentally through a Nuclear Magnetic Resonance (NMR) also called X-ray Crystallography. However, the details of the formation process in these structures is unknown from the double-stranded DNA segments. The evaluation of CHARMM27 force field for these structures by means of simulations using Nanoscale Molecular Dynamics (NAMD) is disclosed. Two same-sequence G-Quadruplex DNA structures were evaluated, to prepare the model, it was necessary to use Visual Molecular Dynamics program (VMD), the structural conformations in a trajectory of 200 nanoseconds were also analyzed with the use of GROMACS Tools and Machine Learning. The results obtained for the two system settings were compared with the experimental data information and it was shown that the molecular dynamics simulations are able to reproduce the experimental values with an error range less than 10%. All together, these results provide substantial evidence for G-Quadruplex structure formation in physiological conditions. It means: 25° grades centigrade with sodium Chloride NaCl, 1 atmosphere. According to this study, to obtain better results it is necessary that the researchers take into account the analyses such as: Radial Distribution Function, DNA backbone angles, Principal Component Analysis, among others.