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Licensed Unlicensed Requires Authentication Published by De Gruyter September 30, 2020

Influence of monovalent metal ions on metal binding and catalytic activity of the 10–23 DNAzyme

  • Hannah Rosenbach , Jan Borggräfe , Julian Victor , Christine Wuebben , Olav Schiemann , Wolfgang Hoyer , Gerhard Steger , Manuel Etzkorn EMAIL logo and Ingrid Span ORCID logo EMAIL logo
From the journal Biological Chemistry


Deoxyribozymes (DNAzymes) are single-stranded DNA molecules that catalyze a broad range of chemical reactions. The 10–23 DNAzyme catalyzes the cleavage of RNA strands and can be designed to cleave essentially any target RNA, which makes it particularly interesting for therapeutic and biosensing applications. The activity of this DNAzyme in vitro is considerably higher than in cells, which was suggested to be a result of the low intracellular concentration of bioavailable divalent cations. While the interaction of the 10–23 DNAzyme with divalent metal ions was studied extensively, the influence of monovalent metal ions on its activity remains poorly understood. Here, we characterize the influence of monovalent and divalent cations on the 10–23 DNAzyme utilizing functional and biophysical techniques. Our results show that Na+ and K+ affect the binding of divalent metal ions to the DNAzyme:RNA complex and considerably modulate the reaction rates of RNA cleavage. We observe an opposite effect of high levels of Na+ and K+ concentrations on Mg2+- and Mn2+-induced reactions, revealing a different interplay of these metals in catalysis. Based on these findings, we propose a model for the interaction of metal ions with the DNAzyme:RNA complex.

Corresponding authors: Manuel Etzkorn, Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, D-40225Düsseldorf, Germany; Institute for Biological Information Processing: Structural Biochemistry (IBI-7), Research Center Jülich, Wilhelm-Johnen-Str., D-52428Jülich, Germany; and Ingrid Span, Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, D-40225Düsseldorf, Germany, E-mail: (M. Etzkorn), (I. Span)

Funding source: Chemical Industry Fund

Award Identifier / Grant number: 196/05

Award Identifier / Grant number: 700080

Funding source: German Academic Scholarship Foundation

Funding source: German Research Foundation

Award Identifier / Grant number: 103/2

Award Identifier / Grant number: 103/4


We gratefully thank D. Riesner for fruitful discussions and Matthias R. Steger for help with python programming.

  1. Author contribution: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Research funding: This work was supported by the Chemical Industry Fund (Li 196/05 to I.S. and Hoe 700080 to H.R.); the German Academic Scholarship Foundation (to H.R.); and the German Research Foundation (ET 103/2, ET 103/4 to M.E.).

  3. Conflict of interest statement: The authors declare that they have no conflict of interest regarding the contents of this article.


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Supplementary Material

Supplementary Figures S1–S13 and Tables S1–4 are available online.

The online version of this article offers supplementary material (

Received: 2020-06-03
Accepted: 2020-09-13
Published Online: 2020-09-30
Published in Print: 2020-11-18

© 2020 Walter de Gruyter GmbH, Berlin/Boston

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