Understanding alkali metal cation affinities of multi-layer guanine quadruplex DNA
| Autor: | C. Fonseca Guerra, Celine Nieuwland, Francesco Zaccaria |
|---|---|
| Přispěvatelé: | AIMMS, Theoretical Chemistry |
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
Guanine
Metal ions in aqueous solution Supramolecular chemistry General Physics and Astronomy 010402 general chemistry G-quadruplex 01 natural sciences Nucleobase chemistry.chemical_compound SDG 7 - Affordable and Clean Energy Physical and Theoretical Chemistry Density Functional Theory Aqueous solution Metals Alkali 010405 organic chemistry Chemistry Solvation DNA Interaction energy 0104 chemical sciences G-Quadruplexes Crystallography Models Chemical Thermodynamics |
| Zdroj: | Physical chemistry chemical physics : PCCP, 22(37), 21108-21118. The Royal Society of Chemistry Nieuwland, C, Zaccaria, F & Fonseca Guerra, C 2020, ' Understanding alkali metal cation affinities of multi-layer guanine quadruplex DNA ', Physical chemistry chemical physics : PCCP, vol. 22, no. 37, pp. 21108-21118 . https://doi.org/10.1039/d0cp03433a Physical Chemistry Chemical Physics |
| ISSN: | 1463-9076 |
| Popis: | To gain better understanding of the stabilizing interactions between metal ions and DNA quadruplexes, dispersion-corrected density functional theory (DFT-D) based calculations were performed on double-, triple- and four-layer guanine tetrads interacting with alkali metal cations. All computations were performed 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. To facilitate the computations on these significant larger systems, optimization of the DFT description was performed first by evaluating the performance of partial reduced basis sets. Analysis of the stabilizing interactions between alkali cations and the DNA bases in double and triple-layer guanine quadruplex DNA reproduced the experimental affinity trend of the order Li+< Rb+ < Na+ < K+. The desolvation and the size of alkali metal cations are thought to be responsible for the order of affinity. Nevertheless, for the alkali metal cation species individually, the magnitude of the bond energy stays equal for binding as first, second or third cation in double, triple and four-layer guanine quadruplexes, respectively. This is the result of an interplay between a decreasingly stabilizing interaction energy and increasingly stabilizing solvation effects, along the consecutive binding events. This diminished interaction energy is the result of destabilizing electrostatic repulsion between the hosted alkali metal cations. This work emphasizes the stabilizing effect of aqueous solvent on large highly charged biomolecules. Stabilizing solvent effects and electrostatic repulsion are responsible for the constant alkali metal cation affinity in multi-layer guanine quadruplexes. |
| Databáze: | OpenAIRE |
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