A Kinetic Model of Nonenzymatic RNA Polymerization by Cytidine-5′-phosphoro-2-aminoimidazolide
Open accessAbstract
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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The slow ligation is explained by primer extension with monomers proceeding through the highly reactive imidazolium-bridged dinucleotide intermediate.
“This is now explained by the fact that primer extension with monomers proceeds through the highly reactive imidazolium-bridged dinucleotide intermediate discussed above”
From Protocells and RNA Self-Replication (2018) · cites this paper as Walton and Szostak 2017
The Conclusions (page not available) state that primer extension with activated cytidine monomers predominantly involves reaction with the imidazolium-bridged dinucleotide Cp*pC, whose reactivity is enhanced relative to the monomer. The cited passages do not explain slow ligation or establish that this mechanism is the reason ligation is slow. (LLM, conf=0.86)
Experimental — accuracy not yet measuredAll detectable primer extension with 2-aminoimidazole (2AI)-activated monomers occurs via the 2-aminoimidazolium intermediate and not through direct reaction of a primer with an activated monomer.
“all detectable primer extension occurs via the 2-aminoimidazolium intermediate and not through the reaction of a primer with an activated monomer”
From Protocells and RNA Self-Replication (2018) · cites this paper as Walton and Szostak 2017
The catalytic effect reflects, at least in part, the greater stability of the 2-aminoimidazolium-bridged dinucleotide intermediate compared with the relatively unstable 2-methylimidazolium intermediate.
“This effect is now understood to reflect, at least in part, the greater stability of the 2-aminoimidazolium-bridged dinucleotide intermediate compared with the relatively unstable 2-methylimidazolium intermediate.”
From Protocells and RNA Self-Replication (2018) · cites this paper as Walton and Szostak 2017
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Protocells and RNA Self-Replication
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- Authors
- Walton, T., & Szostak, J. W.
- Affiliations
- Howard Hughes Medical Institute (US)
- Corresponding author
- Szostak, Jack W.
- Venue
- Biochemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2017-10-12
- Volume
- 56
- Issue
- 43
- Pages
- 5739-5747
- ISSN
- 0006-2960 (ISSN-L)
- 1520-4995
- PMC
- PMC6340129
- OpenAlex
- W2762359702
- Cited by
- 55
- References
- 1
- Citations by year
- 2026: 2 · 2025: 8 · 2024: 6 · 2023: 5 · 2022: 5 · 2021: 7 · 2020: 8 · 2019: 5 · 2018: 8 · 2017: 1
- FWCI
- 3.29
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Biochemistry (publishedVersion, other-oa)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Howard Hughes Medical Institute (NA)
- Division of Chemistry (CHE-1607034)
- Simons Foundation (290363)
- Topics
- Physical Sciences › Physics and Astronomy › Astronomy and Astrophysics › Origins and Evolution of Life
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Keywords
- primer extension, polymerization kinetics, kinetic model, origin of life, competitive inhibition
- MeSH terms
- Cytidine Monophosphate, Kinetics, Models, Chemical, RNA, DNA-Directed RNA Polymerases
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