ArticleBiochemistry2017
A Kinetic Model of Nonenzymatic RNA Polymerization by Cytidine-5'-phosphoro-2-aminoimidazolide.
Article in Biochemistry, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- Various inorganic phosphorus species in prebiotic Earth and extraterrestrial settings.Discover chemistry · 2026Review
- Article
- Nonenzymatic Primer Extension Experiments in the Presence of Coacervates.Current protocols · 2025Article
- Simulations predict preferred MgBiophysical journal · 2024Article
- Diaminopurine in Nonenzymatic RNA Template Copying.Journal of the American Chemical Society · 2024Article
- Constraints on the emergence of RNA through non-templated primer extension with mixtures of potentially prebiotic nucleotides.Nucleic acids research · 2024Article
- Insight into the structures of unusual base pairs in RNA complexes containing a primer/template/adenosine ligand.RSC chemical biology · 2023Article
- Small-Molecule Organocatalysis Facilitates In Situ Nucleotide Activation and RNA Copying.Journal of the American Chemical Society · 2023Article
- Enhanced nonenzymatic RNA copying with in-situ activation of short oligonucleotides.Nucleic acids research · 2023Article
- Growth of Prebiotically Plausible Fatty Acid Vesicles Proceeds in the Presence of Prebiotic Amino Acids, Dipeptides, Sugars, and Nucleic Acid Components.Langmuir : the ACS journal of surfaces and colloids · 2022Article
- Growth, replication and division enable evolution of coacervate protocells.Chemical communications (Cambridge, England) · 2022Review
- Freeze-thaw cycles enable a prebiotically plausible and continuous pathway from nucleotide activation to nonenzymatic RNA copying.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Thermodynamic and Kinetic Sequence Selection in Enzyme-Free Polymer Self-Assembly inside a Non-equilibrium RNA Reactor.Life (Basel, Switzerland) · 2022Article
- Kinetic explanations for the sequence biases observed in the nonenzymatic copying of RNA templates.Nucleic acids research · 2022Article
- Structure-Activity Relationships in Nonenzymatic Template-Directed RNA Synthesis.Angewandte Chemie (International ed. in English) · 2021Article
- Competition between bridged dinucleotides and activated mononucleotides determines the error frequency of nonenzymatic RNA primer extension.Nucleic acids research · 2021Article
- A Potential Role for Aminoacylation in Primordial RNA Copying Chemistry.Biochemistry · 2021Article
- Structural interpretation of the effects of threo-nucleotides on nonenzymatic template-directed polymerization.Nucleic acids research · 2021Article
- The virtual circular genome model for primordial RNA replication.RNA (New York, N.Y.) · 2021Article
- Potentially Prebiotic Activation Chemistry Compatible with Nonenzymatic RNA Copying.Journal of the American Chemical Society · 2020Article
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2 authors.
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Abstract
The nonenzymatic polymerization of RNA may have enabled copying of functional sequences during the origin of life. Recent progress utilizing 5'-phosphoro-2-aminoimidazole activation has reinvigorated the possibility of using nonenzymatic RNA polymerization for copying arbitrary sequences. However, the reasons why 2-aminoimidazole (AI) is a superior activation group remain unclear. Here we report that the predominant mechanism of polymerization using cytidine-5'-phosphoro-2-aminoimidazolide (Cp*) involves a 2-aminoimidazolium-bridged dinucleotide (Cp*pC) intermediate. To explore the role of this intermediate, we first identify and quantify four reactions involving the synthesis and breakdown of Cp*pC that occur in the absence of the primer-template duplex. We then analyze the dependence of the rate of polymerization on the concentration of the Cp*pC intermediate in the presence and absence of the competitive inhibitor Cp. We also show that the contribution of the monomer Cp* to the polymerization rate is negligible under our primer extension conditions. Finally, we use the experimentally determined rate constants of these reactions to develop a kinetic model that helps explain the changing rate of nonenzymatic RNA polymerization over time. Our model accounts for the concentration of Cp*pC formed by Cp* under primer extension conditions. The model does not completely account for the decline in polymerization rate observed over long times, which indicates that additional important inhibitory processes have not yet been identified. Our results suggest that the superiority of 2-aminoimidazole over the traditional 2-methylimidazole activation is mostly due to the higher level of accumulation of the imidazolium-bridged intermediate under primer extension conditions.
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