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Proc Natl Acad Sci U S A. 2017 Jul 18;114(29):7659-7664. doi: 10.1073/pnas.1704006114. Epub 2017 Jul 3.

Insight into the mechanism of nonenzymatic RNA primer extension from the structure of an RNA-GpppG complex.

Zhang W1,2,3,4, Tam CP1,2,3,5, Walton T1,2,3,4, Fahrenbach AC1,2,3,4,6, Birrane G7, Szostak JW8,2,3,4,5,6.

Author information

1
Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114.
2
Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114.
3
Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114.
4
Department of Genetics, Harvard Medical School, Boston, MA 02115.
5
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138.
6
Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan.
7
Division of Experimental Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215.
8
Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114; szostak@molbio.mgh.harvard.edu.

Abstract

The nonenzymatic copying of RNA templates with imidazole-activated nucleotides is a well-studied model for the emergence of RNA self-replication during the origin of life. We have recently discovered that this reaction can proceed through the formation of an imidazolium-bridged dinucleotide intermediate that reacts rapidly with the primer. To gain insight into the relationship between the structure of this intermediate and its reactivity, we cocrystallized an RNA primer-template complex with a close analog of the intermediate, the triphosphate-bridged guanosine dinucleotide GpppG, and solved a high-resolution X-ray structure of the complex. The structure shows that GpppG binds the RNA template through two Watson-Crick base pairs, with the primer 3'-hydroxyl oriented to attack the 5'-phosphate of the adjacent G residue. Thus, the GpppG structure suggests that the bound imidazolium-bridged dinucleotide intermediate would be preorganized to react with the primer by in-line SN2 substitution. The structures of bound GppG and GppppG suggest that the length and flexibility of the 5'-5' linkage are important for optimal preorganization of the complex, whereas the position of the 5'-phosphate of bound pGpG explains the slow rate of oligonucleotide ligation reactions. Our studies provide a structural interpretation for the observed reactivity of the imidazolium-bridged dinucleotide intermediate in nonenzymatic RNA primer extension.

KEYWORDS:

RNA self-replication; crystal structure; diguanosine dinucleotide; origin of life

PMID:
28673998
PMCID:
PMC5530681
DOI:
10.1073/pnas.1704006114
[Indexed for MEDLINE]
Free PMC Article

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