G-quadruplexes, such as TBA-15, are four-stranded nucleic acids secondary structures formed by guanine-rich sequences of DNA and RNA. These “non-canonical” structures are located in key genome functional regions, and thus are considered as potential pharmacological targets for the development of anticancer drugs. G-quadruplexes are structurally characterized by stacked guanine-quartets held together by Hoogsteen hydrogen bonds and stabilized by monovalent cations, such as K<sup>+</sup> and Na<sup>+</sup>, sited within two guanine planes. We report here a series of microsecond time scale explicit solvent molecular dynamics simulations to gain insight into the structural behavior of the TBA-15 quadruplex. Of particular interest was to investigate the ion exchange, the stability of the quadruplex in different monovalent cation environments, and the dependence on the stability using different force fields.

Molecular dynamics study of the structural behavior of TBA-15 in the presents of monovalent ions

ACS Spring 2022

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