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Issue 2, 2021
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Interactions of a DNA G-quadruplex with TMAO and urea: a molecular dynamics study on co-solute compensation mechanisms

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Abstract

We study the individual and combined influence of TMAO and urea on a basket-type DNA G-quadruplex by means of atomistic molecular dynamics (MD) simulations. In combination with the Kirkwood–Buff theory of solutions, we propose a simple mechanism to elucidate the impact of TMAO and urea on the G-quadruplex. Our results reveal the importance of the molecular accumulation around the DNA in terms of stabilizing or destabilizing effects. The results for mixtures show only a weak interaction between both co-solutes, which highlights the additivity of contributions. Despite the fact, that TMAO can to some extent compensate the adverse impact of urea on the G-quadruplex structure, the destabilizing influence is not completely eliminated. This observation opens the door for further research on selective stabilization of DNA G-quadruplexes by modulating the concentrations of TMAO and urea in solution.

Graphical abstract: Interactions of a DNA G-quadruplex with TMAO and urea: a molecular dynamics study on co-solute compensation mechanisms

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Article information


Submitted
12 Oct 2020
Accepted
01 Dec 2020
First published
08 Dec 2020

Phys. Chem. Chem. Phys., 2021,23, 1254-1264
Article type
Paper

Interactions of a DNA G-quadruplex with TMAO and urea: a molecular dynamics study on co-solute compensation mechanisms

E. A. Oprzeska-Zingrebe and J. Smiatek, Phys. Chem. Chem. Phys., 2021, 23, 1254
DOI: 10.1039/D0CP05356B

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