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Zaccaria F, Paragi G, Fonseca Guerra C. The role of alkali metal cations in the stabilization of guanine quadruplexes: why K(+) is the best. Phys Chem Chem Phys. 2016;18(31):20895-904doi: 10.1039/c6cp01030j.
Zaccaria, F., Paragi, G., & Fonseca Guerra, C. (2016). The role of alkali metal cations in the stabilization of guanine quadruplexes: why K(+) is the best. Physical chemistry chemical physics : PCCP, 18(31), 20895-904. https://doi.org/10.1039/c6cp01030j
Zaccaria, F, et al. "The role of alkali metal cations in the stabilization of guanine quadruplexes: why K(+) is the best." Physical chemistry chemical physics : PCCP vol. 18,31 (2016): 20895-904. doi: https://doi.org/10.1039/c6cp01030j
Zaccaria F, Paragi G, Fonseca Guerra C. The role of alkali metal cations in the stabilization of guanine quadruplexes: why K(+) is the best. Phys Chem Chem Phys. 2016 Aug 21;18(31):20895-904. doi: 10.1039/c6cp01030j. Epub 2016 May 17. PMID: 27185388.
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Phys Chem Chem Phys. 2016 Aug 21;18(31):20895-904. doi: 10.1039/c6cp01030j. Epub 2016 May 17.

The role of alkali metal cations in the stabilization of guanine quadruplexes: why K(+) is the best.

Physical chemistry chemical physics : PCCP

F Zaccaria, G Paragi, C Fonseca Guerra

Affiliations

  1. Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands. [email protected].

PMID: 27185388 DOI: 10.1039/c6cp01030j

Abstract

The alkali metal ion affinity of guanine quadruplexes has been studied using dispersion-corrected density functional theory (DFT-D). We have done computational investigations in aqueous solution that mimics artificial supramolecular conditions where guanine bases assemble into stacked quartets as well as biological environments in which telomeric quadruplexes are formed. In both cases, an alkali metal cation is needed to assist self-assembly. Our quantum chemical computations on these supramolecular systems are able to reproduce the experimental order of affinity of the guanine quadruplexes for the cations Li(+), Na(+), K(+), Rb(+), and Cs(+). The strongest binding is computed between the potassium cation and the quadruplex as it occurs in nature. The desolvation and the size of alkali metal cations are thought to be responsible for the order of affinity. Until now, the relative importance of these two factors has remained unclear and debated. By assessing the quantum chemical 'size' of the cation, determining the amount of deformation of the quadruplex needed to accommodate the cation and through the energy decomposition analysis (EDA) of the interaction energy between the cation and the guanines, we reveal that the desolvation and size of the alkali metal cation are both almost equally responsible for the order of affinity.

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