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ACI Avances en Ciencias e Ingenierías

SECTION A: EXACT SCIENCES

Vol. 3 No. 2 (2011): Número especial por el Año Internacional de la Química

G-quadruplex DNA: initial characterization of the mechanisms of formation of oligomers by molecular mechanics

DOI
https://doi.org/10.18272/aci.v3i2.67
Submitted
July 29, 2015

Abstract

The fabrication of nanostructures based on DNA as a material to build systems capable of complex functions is a frontier in continuous exploration. In this article it is reported the detailed characterization at atomic level of G-quadruplex units in order to obtain a better comprehension on how these units can self assemble into interlocked G-quadruplexes. The method used is modeling with molecular mechanics. Previously we reported the construction of interlocked G-quadruplexes by a thermal cyclic procedure (similar in implementation as the ones used in the cycling steps in a PCR protocol) parting from the sequence 5"™-TGGG-3"™. Based on our experimental data reported previously, models were built for the structures, and minimization and analyses via molecular mechanics was carried out in order to understand the factors that determine the more stable structures. It was found that the identity of the 5"™and 3"™ ends of the oligonucleotides is of the uppermost importance in the stability of the DNA assemblies in this study. Furthermore, the presence of cations in the regions of the molecule where the degree of steric hindrance allows more room for the cations could play a significant role in the dynamics of conformation of the supramolecule at those sites and possibly limiting or capping the self assembly of the structure. In summary, the results allow a better comprehension of the system at a molecular scale with the finality of developing more efficient procedures for the controlled fabrication of nanostructures based on G-quadruplex DNA.

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