Time-resolved structural analysis of an RNA-cleaving DNA catalyst

Jan Borggräfe, Julian Victor, Hannah Rosenbach, Aldino Viegas, Christoph G. W. Gertzen, Christine Wuebben, Helena Kovacs, Mohanraj Gopalswamy, Detlev Riesner, Gerhard Steger, Olav Schiemann, Holger Gohlke, Ingrid Span and Manuel Etzkorn ()
Additional contact information
Jan Borggräfe: Heinrich Heine University Düsseldorf
Julian Victor: Heinrich Heine University Düsseldorf
Hannah Rosenbach: Heinrich Heine University Düsseldorf
Aldino Viegas: Heinrich Heine University Düsseldorf
Christoph G. W. Gertzen: Heinrich Heine University Düsseldorf
Christine Wuebben: University of Bonn
Helena Kovacs: Bruker Switzerland AG
Mohanraj Gopalswamy: Heinrich Heine University Düsseldorf
Detlev Riesner: Heinrich Heine University Düsseldorf
Gerhard Steger: Heinrich Heine University Düsseldorf
Olav Schiemann: University of Bonn
Holger Gohlke: Forschungszentrum Jülich
Ingrid Span: Heinrich Heine University Düsseldorf
Manuel Etzkorn: Heinrich Heine University Düsseldorf

Nature, 2022, vol. 601, issue 7891, 144-149

Abstract: Abstract The 10–23 DNAzyme is one of the most prominent catalytically active DNA sequences1,2. Its ability to cleave a wide range of RNA targets with high selectivity entails a substantial therapeutic and biotechnological potential2. However, the high expectations have not yet been met, a fact that coincides with the lack of high-resolution and time-resolved information about its mode of action3. Here we provide high-resolution NMR characterization of all apparent states of the prototypic 10–23 DNAzyme and present a comprehensive survey of the kinetics and dynamics of its catalytic function. The determined structure and identified metal-ion-binding sites of the precatalytic DNAzyme–RNA complex reveal that the basis of the DNA-mediated catalysis is an interplay among three factors: an unexpected, yet exciting molecular architecture; distinct conformational plasticity; and dynamic modulation by metal ions. We further identify previously hidden rate-limiting transient intermediate states in the DNA-mediated catalytic process via real-time NMR measurements. Using a rationally selected single-atom replacement, we could considerably enhance the performance of the DNAzyme, demonstrating that the acquired knowledge of the molecular structure, its plasticity and the occurrence of long-lived intermediate states constitutes a valuable starting point for the rational design of next-generation DNAzymes.

Date: 2022
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DOI: 10.1038/s41586-021-04225-4

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