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Article

Dynamic Structure and Stability of DNA Duplexes Bearing a Dinuclear Hg(II)-Mediated Base Pair

1
Institute for Solid State Theory and Center for Multiscale Theory and Computation, Westfälische-Wilhelms Universität Münster, Wilhelm-Klemm-Straße 10, 48149 Münster, Germany
2
Institut für Anorganische und Analytische Chemie, Westfälische-Wilhelms Universität Münster, Corrensstraße 30, 48149 Münster, Germany
*
Authors to whom correspondence should be addressed.
Academic Editor: Martin Brehm
Molecules 2020, 25(21), 4942; https://doi.org/10.3390/molecules25214942
Received: 28 September 2020 / Revised: 21 October 2020 / Accepted: 22 October 2020 / Published: 26 October 2020
(This article belongs to the Special Issue Describing Bulk Phase Effects with Ab Initio Methods)
Quantum mechanical (QM) and hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations of a recently reported dinuclear mercury(II)-mediated base pair were performed aiming to analyse its intramolecular bonding pattern, its stability, and to obtain clues on the mechanism of the incorporation of mercury(II) into the DNA. The dynamic distance constraint was employed to find initial structures, control the dissociation process in an unbiased fashion and to determine the free energy required. A strong influence of the exocyclic carbonyl or amino groups of neighbouring base pairs on both the bonding pattern and the mechanism of incorporation was observed. During the dissociation simulation, an amino group of an adenine moiety of the adjacent base pair acts as a turnstile to rotate the mercury(II) ion out of the DNA core region. The calculations provide an important insight into the mechanism of formation of this dinuclear metal-mediated base pair and indicate that the exact location of a transition metal ion in a metal-mediated base pair may be more ambiguous than derived from simple model building. View Full-Text
Keywords: Ab initio calculations; DNA structures; molecular dynamics; free energy; mercury; Hg(II); metal-mediated base pairs; metal-modified DNA Ab initio calculations; DNA structures; molecular dynamics; free energy; mercury; Hg(II); metal-mediated base pairs; metal-modified DNA
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MDPI and ACS Style

Bachmann, J.; Schönrath, I.; Müller, J.; Doltsinis, N.L. Dynamic Structure and Stability of DNA Duplexes Bearing a Dinuclear Hg(II)-Mediated Base Pair. Molecules 2020, 25, 4942. https://doi.org/10.3390/molecules25214942

AMA Style

Bachmann J, Schönrath I, Müller J, Doltsinis NL. Dynamic Structure and Stability of DNA Duplexes Bearing a Dinuclear Hg(II)-Mediated Base Pair. Molecules. 2020; 25(21):4942. https://doi.org/10.3390/molecules25214942

Chicago/Turabian Style

Bachmann, Jim, Isabell Schönrath, Jens Müller, and Nikos L. Doltsinis 2020. "Dynamic Structure and Stability of DNA Duplexes Bearing a Dinuclear Hg(II)-Mediated Base Pair" Molecules 25, no. 21: 4942. https://doi.org/10.3390/molecules25214942

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