The DOI matches its Crossref record; 70 of the 70 references it cites were found in a registry or an index.
Ribozyme speed limits
Open accessAbstract
The speed at which RNA molecules decompose is a critical determinant of many biological processes, including those directly involved in the storage and expression of genetic information. One mechanism for RNA cleavage involves internal phosphoester transfer, wherein the 2′-oxygen atom carries out an S N 2-like nucleophilic attack on the adjacent phosphorus center (transesterification). In this article, we discuss fundamental principles of RNA transesterification and define a conceptual framework that can be used to assess the catalytic power of enzymes that cleave RNA. We deduce that certain ribozymes and deoxyribozymes, like their protein enzyme counterparts, can bring about enormous rate enhancements.
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“All of these tasks might be performed by RNA (Narlikar and Herschlag 1997;Emilsson et al. 2003), acting either alone (Strobel and Ortoleva-Donnelly 1999) or with the help of a suitably positioned metal cation or other cofactor (Shan et al. 1999(Shan et al. , 2001)).”
From Protocells and RNA Self-Replication (2018) · cites this paper as Emilsson et al. 2003
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Cites
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“Both the stability of phosphate esters and their chemical pliability have been suggested as foremost reasons why a phosphate ester has emerged as the backbone of choice for the molecules responsible for genetic information storage and transfer (Westheimer 1987).”
BackgroundA general purpose RNA-cleaving DNA enzyme
Santoro, S. W., & Joyce, G. F. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.9.4262 · Cited by 1,546
In Vitro Selection of Functional Nucleic Acids
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A general two-metal-ion mechanism for catalytic RNA
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Pseudo-rotation in the hydrolysis of phosphate esters
Westheimer, F. H. (1968) · Accounts of Chemical Research · doi:10.1021/ar50003a002 · Cited by 772
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Self-citationRelationship between internucleotide linkage geometry and the stability of RNA
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Self-citation
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Cited by
Sorted by citations
Control of gene expression by a natural metabolite-responsive ribozyme
Winkler, W. C., Nahvi, A., Roth, A., Collins, J. A., & Breaker, R. R. (2004) · Nature · doi:10.1038/nature02362 · Cited by 976
Self-citationChemistry, structure and function of approved oligonucleotide therapeutics
Egli, M., & Manoharan, M. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad067 · Cited by 909
RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
Šponer, J., Bussi, G., Krepl, M., Banáš, P., Bottaro, S., Cunha, R. A., Gil-Ley, A., Pinamonti, G., Poblete, S., Jurečka, P., et al. (2018) · Chemical Reviews · doi:10.1021/acs.chemrev.7b00427 · Cited by 606
Robertson, M. P., & Joyce, G. F. (2012) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a003608 · Cited by 556
McConnell, E. M., Cozma, I., Mou, Q., Brennan, J. D., Lu, Y., & Li, Y. (2021) · Chemical Society Reviews · doi:10.1039/d1cs00240f · Cited by 492
Metadata
- Authors
- EMILSSON, G. M., NAKAMURA, S., ROTH, A., & BREAKER, R. R.
- Affiliations
- Yale University (US)
- Corresponding author
- BREAKER, RONALD R.
- Venue
- RNA
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2003-07-17
- Volume
- 9
- Issue
- 8
- Pages
- 907-918
- ISSN
- 1355-8382 (ISSN-L)
- 1469-9001
- PMC
- PMC1370456
- OpenAlex
- W2160498409
- Cited by
- 216
- References
- 70
- Citations by year
- 2026: 4 · 2025: 5 · 2024: 11 · 2023: 6 · 2022: 11 · 2021: 18 · 2020: 7 · 2019: 16 · 2018: 9 · 2017: 16 · 2016: 8 · 2015: 6 · 2014: 5 · 2013: 10 · 2012: 5
- FWCI
- 0.68
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- RNA (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- David and Lucile Packard Foundation
- National Institutes of Health (5r01gm057500-03)
- National Institute of General Medical Sciences (GM559343, GM57500)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Physical Sciences › Chemistry › Organic Chemistry › Physical Organic Chemistry and Reaction Kinetics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Keywords
- ribozymes, deoxyribozymes, RNA cleavage, catalytic rate enhancement
- MeSH terms
- Esterification, Hydrolysis, Oxygen, RNA, RNA, Catalytic, Hydroxyl Radical
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