The DOI matches its Crossref record; 73 of the 74 references it cites were found in a registry or an index.
Small Self-cleaving Ribozymes
Open accessAbstract
The hammerhead, hairpin, hepatitis delta virus (HDV), Varkud Satellite (VS), and glmS ribozymes catalyze sequence-specific intramolecular cleavage of RNA. They range between 50 and 150 nucleotides in length, and are known as the "small self-cleaving ribozymes." Except for the glmS ribozyme that functions as a riboswitch in Gram-positive bacteria, they were originally discovered as domains of satellite RNAs. However, recent studies show that several of them are broadly distributed in genomes of organisms from many phyla. Each of these ribozymes has a unique overall architecture and active site organization. Crystal structures have revealed how RNA active sites can bind preferentially to the transition state of a reaction, whereas mechanistic studies have shown that nucleobases can efficiently perform general acid-base and electrostatic catalysis. This versatility explains the abundance of ribozymes in contemporary organisms and also supports a role for catalytic RNAs early in evolution.
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“The fidelity of the primer extension products resulting from the sequential addition of activated monomers, when catalyzed by activated oligomers, is sufficient to sustain a genome long enough to encode active ribozymes.”
From Nonenzymatic copying of RNA templates containing all four letters is catalyzed by activated oligonucleotides (2016) · cites this paper as Ferré-D'Amaré and Scott, 2010
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“Assuming an error threshold of one mutation per genome (Eigen, 1971), this value of fidelity allows for effective genome sizes of 50 nucleotides, long enough to produce functional ribozymes (Ferré-D'Amaré and Scott, 2010).”
From Nonenzymatic copying of RNA templates containing all four letters is catalyzed by activated oligonucleotides (2016) · cites this paper as Ferré-D'Amaré and Scott, 2010
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Cites
In Vitro Selection of Functional Nucleic Acids
Wilson, D. S., & Szostak, J. W. (1999) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.68.1.611 · Cited by 1,217
A general two-metal-ion mechanism for catalytic RNA
Steitz, T. A., & Steitz, J. A. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.14.6498 · Cited by 1,171
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
Three-dimensional structure of a hammerhead ribozyme
Pley, H. W., Flaherty, K. M., & McKay, D. (1994) · Nature · doi:10.1038/372068a0 · Cited by 946
A small catalytic oligoribonucleotide
Uhlenbeck, O. C. (1987) · Nature · doi:10.1038/328596a0 · Cited by 932
Crystal structure of a hepatitis delta virus ribozyme
Ferré-D’Amaré, A. R., Zhou, K., & Doudna, J. A. (1998) · Nature · doi:10.1038/26912 · Cited by 790
Riboswitches and the RNA WorldPreprint
Breaker, R. R. (2010) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a003566 · Cited by 712
Scott, W. G., Finch, J. T., & Klug, A. (1995) · Cell · doi:10.1016/s0092-8674(05)80004-2 · Cited by 684
Self-citationAutolytic Processing of Dimeric Plant Virus Satellite RNA
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Robertson, M. P., & Joyce, G. F. (2012) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a003608 · Cited by 556
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1 of the 74 references couldn’t be matched to a known paper.
Research works printed but not linked: 2
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The eightfold path to non-enzymatic RNA replication
Szostak, J. W. (2012) · Journal of Systems Chemistry · doi:10.1186/1759-2208-3-2 · Cited by 359
Gee, P., Lung, M. S. Y., Okuzaki, Y., Sasakawa, N., Iguchi, T., Makita, Y., Hozumi, H., Miura, Y., Yang, L. F., Iwasaki, M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-14957-y · Cited by 372
A widespread self-cleaving ribozyme class is revealed by bioinformatics
Roth, A., Weinberg, Z., Chen, A. G. Y., Kim, P. B., Ames, T. D., & Breaker, R. R. (2013) · Nature Chemical Biology · doi:10.1038/nchembio.1386 · Cited by 287
Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes
Micura, R., & Höbartner, C. (2020) · Chemical Society Reviews · doi:10.1039/d0cs00617c · Cited by 265
Cech, T. R. (2012) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a006742 · Cited by 244
Metadata
- Authors
- Ferre-D'Amare, A. R., & Scott, W. G.
- Affiliations
- University of California, Santa Cruz (US)
- Corresponding author
- Scott, W. G.
- Venue
- Cold Spring Harbor Perspectives in Biology
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2010-09-15
- Volume
- 2
- Issue
- 10
- Pages
- a003574-a003574
- ISSN
- 1943-0264 (ISSN-L)
- PMC
- PMC2944367
- OpenAlex
- W2105638515
- Cited by
- 205
- References
- 74
- Citations by year
- 2026: 4 · 2025: 5 · 2024: 8 · 2023: 11 · 2022: 12 · 2021: 10 · 2020: 12 · 2019: 24 · 2018: 7 · 2017: 14 · 2016: 16 · 2015: 25 · 2014: 17 · 2013: 7 · 2012: 15
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Cold Spring Harbor Perspectives in Biology (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- W. M. Keck Foundation
- National Institutes of Health (Z99 HL999999)
- National Heart, Lung, and Blood Institute (ZIAHL006102)
- National Institute of General Medical Sciences (GM63576, R01GM063576, R01GM087721)
- National Institute of Allergy and Infectious Diseases (AI043393, R01AI043393, R21AI043393)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Keywords
- self-cleaving ribozymes, hammerhead ribozyme, hairpin ribozyme, hepatitis delta virus ribozyme, glmS ribozyme, riboswitches, RNA catalysis, crystal structure, ribozyme evolution, satellite RNA
- MeSH terms
- Hepatitis Delta Virus, Models, Molecular, Ribonuclease, Pancreatic, RNA, Catalytic, Catalytic Domain
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