Crystal structure of an RNA-cleaving DNAzyme

Hehua Liu, Xiang Yu, Yiqing Chen, Jing Zhang, Baixing Wu, Lina Zheng, Phensinee Haruehanroengra, Rui Wang, Suhua Li, Jinzhong Lin, Jixi Li, Jia Sheng, Zhen Huang (), Jinbiao Ma () and Jianhua Gan ()
Additional contact information
Hehua Liu: School of Life Sciences, Fudan University
Xiang Yu: School of Life Sciences, Fudan University
Yiqing Chen: School of Life Sciences, Fudan University
Jing Zhang: School of Life Sciences, Fudan University
Baixing Wu: Institute of Plant Biology, School of Life Sciences, Fudan University
Lina Zheng: Institute of Plant Biology, School of Life Sciences, Fudan University
Phensinee Haruehanroengra: University at Albany, State University of New York
Rui Wang: University at Albany, State University of New York
Suhua Li: School of Life Sciences, Fudan University
Jinzhong Lin: Institute of Plant Biology, School of Life Sciences, Fudan University
Jixi Li: School of Life Sciences, Fudan University
Jia Sheng: University at Albany, State University of New York
Zhen Huang: Georgia State University
Jinbiao Ma: Institute of Plant Biology, School of Life Sciences, Fudan University
Jianhua Gan: School of Life Sciences, Fudan University

Nature Communications, 2017, vol. 8, issue 1, 1-10

Abstract: Abstract In addition to storage of genetic information, DNA can also catalyze various reactions. RNA-cleaving DNAzymes are the catalytic DNAs discovered the earliest, and they can cleave RNAs in a sequence-specific manner. Owing to their great potential in medical therapeutics, virus control, and gene silencing for disease treatments, RNA-cleaving DNAzymes have been extensively studied; however, the mechanistic understandings of their substrate recognition and catalysis remain elusive. Here, we report three catalytic form 8–17 DNAzyme crystal structures. 8–17 DNAzyme adopts a V-shape fold, and the Pb2+ cofactor is bound at the pre-organized pocket. The structures with Pb2+ and the modification at the cleavage site captured the pre-catalytic state of the RNA cleavage reaction, illustrating the unexpected Pb2+-accelerated catalysis, intrinsic tertiary interactions, and molecular kink at the active site. Our studies reveal that DNA is capable of forming a compacted structure and that the functionality-limited bio-polymer can have a novel solution for a functional need in catalysis.

Date: 2017
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DOI: 10.1038/s41467-017-02203-x

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