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

被引：94

作者：

Borggraefe, Jan ^{[1
,2
]}

Victor, Julian ^{[1
]}

Rosenbach, Hannah ^{[1
]}

Viegas, Aldino ^{[1
,11
]}

Gertzen, Christoph G. W. ^{[3
,4
]}

Wuebben, Christine ^{[5
]}

Kovacs, Helena ^{[6
]}

Gopalswamy, Mohanraj ^{[3
]}

Riesner, Detlev ^{[1
]}

Steger, Gerhard ^{[1
]}

Schiemann, Olav ^{[5
]}

Gohlke, Holger ^{[2
,3
,7
,8
]}

Span, Ingrid ^{[1
,9
]}

Etzkorn, Manuel ^{[1
,2
,10
]}

机构：

[1] Heinrich Heine Univ Dusseldorf, Inst Phys Biol, Dusseldorf, Germany

[2] Forschungszentrum Julich, Inst Biol Informat Proc IBI 7 Struct Biochem, Julich, Germany

[3] Heinrich Heine Univ Dusseldorf, Inst Pharmaceut & Med Chem, Dusseldorf, Germany

[4] Heinrich Heine Univ Dusseldorf, Ctr Struct Studies CSS, Dusseldorf, Germany

[5] Univ Bonn, Inst Phys & Theoret Chem, Bonn, Germany

[6] Bruker Switzerland AG, Fallanden, Switzerland

[7] Forschungszentrum Julich, John von Neumann Inst Comp NIC, Julich Supercomp Ctr JSC, Julich, Germany

[8] Forschungszentrum Julich, Inst Bio & Geosci IBG 4 Bioinformat, Julich, Germany

[9] Friedrich Alexander Univ Erlangen Nurnberg, Dept Chem & Pharm, Bioinorgan Chem, Erlangen, Germany

[10] Forschungszentrum Julich, Julich Ctr Struct Biol JuStruct, Julich, Germany

[11] Univ Nova Lisboa, NOVA Sch Sci & Technol, Dept Chem, UCIBIO, Caparica, Portugal

来源：

NATURE | 2022年 / 601卷 / 7891期

关键词：

PARTICLE MESH EWALD; HAMMERHEAD RIBOZYME; MOLECULAR-DYNAMICS; CRYSTAL-STRUCTURE; PARAMETERS; STABILITY; DNAZYME; BINDING; MODULATION; RELAXATION;

D O I：

10.1038/s41586-021-04225-4

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页码：144 / 149

页数：26

共 52 条

[1] Protein folding monitored at individual residues during a two-dimensional NMR experiment [J].