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Molecular Modeling and Simulations of DNA and RNA: DNAzyme as a Model System

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DNAzymes

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2439))

Abstract

Nowadays, the structural dynamics of DNA and RNA is accessible on an atomistic level on a micro- to millisecond time scale via molecular dynamics simulations. However, as DNA or RNA are highly charged molecules, performing such simulations is challenging as to the representation of intramolecular electrostatic interactions and those to solvent molecules and ions. This is particularly true for DNAzymes, where DNA and RNA backbones can come as close as 2.4 Å with their charged phosphate groups during the catalytic cycle. Here, we present tools to simulate the structural dynamics of a DNAzyme, with a focus on detailed instructions for the Amber suite of programs. Furthermore, we will show how to analyze metal ion binding within the DNAzyme.

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Notes

  1. 1.

    During typesetting of this article, an NMR structure of a 10-23 DNAzyme in complex with RNA has been solved: PDB ID 7PDU; [23].

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Acknowledgments

H.G. is grateful for computational support and infrastructure provided by the “Zentrum für Informations- und Medientechnologie” (ZIM) at the Heinrich Heine University Düsseldorf and the John von Neumann Institute for Computing (NIC) (user ID: HKF7), VSK33. The Center for Structural Studies is funded by the DFG (Grant number 417919780).

Author information

Authors and Affiliations

  1. Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany

    Christoph G. W. Gertzen & Holger Gohlke

  2. Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Düsseldorf, Germany

    Christoph G. W. Gertzen

  3. John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and Institute of Bio- and Geoscences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich, Germany

    Holger Gohlke

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  1. Christoph G. W. Gertzen
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  2. Holger Gohlke
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Correspondence to Holger Gohlke .

Editor information

Editors and Affiliations

  1. Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany

    Gerhard Steger

  2. Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany

    Hannah Rosenbach

  3. Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany

    Ingrid Span

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Gertzen, C.G.W., Gohlke, H. (2022). Molecular Modeling and Simulations of DNA and RNA: DNAzyme as a Model System. In: Steger, G., Rosenbach, H., Span, I. (eds) DNAzymes. Methods in Molecular Biology, vol 2439. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2047-2_11

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  • DOI: https://doi.org/10.1007/978-1-0716-2047-2_11

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2046-5

  • Online ISBN: 978-1-0716-2047-2

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