Insight into the mechanism of nonenzymatic RNA primer extension from the structure of an RNA-GpppG complex.
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.
['Zhang|Wen|W|', 'Tam|Chun Pong|CP|0000-0001-6381-9011', 'Walton|Travis|T|', 'Fahrenbach|Albert C|AC|', 'Birrane|Gabriel|G|', 'Szostak|Jack W|JW|']
D018360:Crystallography, X-Ray D015226:Dinucleoside Phosphates D006151:Guanosine D007093:Imidazoles D009690:Nucleic Acid Conformation D009711:Nucleotides D009841:Oligonucleotides D000069497:Origin of Life D012313:RNA D013698:Templates, Genetic
RNA self-replication origin of life crystal structure diguanosine dinucleotide