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

Borggraefe J, Victor J, Rosenbach H, Viegas A, Gertzen CGW, Wuebben C, Kovacs H, Gopalswamy M, Riesner D, Steger G, Schiemann O, Gohlke H, Span I, Etzkorn M (2021)

Publication Type: Journal article

Publication year: 2021

Journal

Nature Nature Research

DOI: 10.1038/s41586-021-04225-4

Abstract

The 10-23 DNAzyme is one ofthe most prominent catalytically active DNA sequences(1,2). Its ability to cleave a wide range of RNA targets with high selectivity entails a substantial therapeutic and biotechnological potential(2). 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 action(3). Here we provide high-resolution NMR characterization of all apparent states ofthe prototypic 10-23 DNAzyme and present a comprehensive survey ofthe kinetics and dynamics of its catalytic function. The determined structure and identified metal-ion-binding sites ofthe precatalytic DNAzyme-RNA complex reveal that the basis ofthe 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 processvia real-time NMR measurements. Using a rationally selected single-atom replacement, we could considerably enhance the performance ofthe DNAzyme, demonstrating that the acquired knowledge ofthe 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.

Authors with CRIS profile

Ingrid Span

Involved external institutions

Heinrich-Heine-Universität Düsseldorf DE Germany (DE) Rheinische Friedrich-Wilhelms-Universität Bonn DE Germany (DE) Bruker (Switzerland) CH Switzerland (CH) Forschungszentrum Jülich / Research Centre Jülich (FZJ) DE Germany (DE)

How to cite

APA:

Borggraefe, J., Victor, J., Rosenbach, H., Viegas, A., Gertzen, C.G.W., Wuebben, C.,... Etzkorn, M. (2021). Time-resolved structural analysis of an RNA-cleaving DNA catalyst. Nature. https://doi.org/10.1038/s41586-021-04225-4

MLA:

Borggraefe, Jan, et al. "Time-resolved structural analysis of an RNA-cleaving DNA catalyst." Nature (2021).

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