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, acting either alone or with the help of a suitably positioned metal cation or other cofactor.
“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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- 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 › Chemical Reaction Mechanisms
- 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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