7PDU

Pre-catalytic complex of 10-23 DNAzyme with RNA target

Summary for 7PDU

• Entry DOI: 10.2210/pdb7pdu/pdb
• NMR Information: BMRB: 34654
• Descriptor: 10-23 DNAzyme (33-MER), RNA target (19-MER) (2 entities in total)
• Functional Keywords: 10-23 dnazyme, rna-cleaving dnazyme, pre-catalytic complex, dna-rna hybrid
• Biological source: synthetic construct; More
• Total number of polymer chains: 2
• Total formula weight: 16247.23

Authors

Etzkorn, M.,Borggrafe, J.,Viegas, A. (deposition date: 2021-08-07, release date: 2021-12-15, Last modification date: 2024-06-19)

Primary citation

Borggrafe, J.,Victor, J.,Rosenbach, H.,Viegas, A.,Gertzen, C.G.W.,Wuebben, C.,Kovacs, H.,Gopalswamy, M.,Riesner, D.,Steger, G.,Schiemann, O.,Gohlke, H.,Span, I.,Etzkorn, M.
Time-resolved structural analysis of an RNA-cleaving DNA catalyst.
Nature, 601:144-149, 2022

PubMed Abstract: The 10-23 DNAzyme is one of the most prominent catalytically active DNA sequences. Its ability to cleave a wide range of RNA targets with high selectivity entails a substantial therapeutic and biotechnological potential. 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. 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.

PubMed: 34949858
DOI: 10.1038/s41586-021-04225-4

Experimental method

SOLUTION NMR