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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.

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Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114.
Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114.
Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114.
Department of Genetics, Harvard Medical School, Boston, MA 02115.
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138.
Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan.
Division of Experimental Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215.
Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114;


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.


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

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