ArticleRNA (New York, N.Y.)2011
Do the hairpin and VS ribozymes share a common catalytic mechanism based on general acid-base catalysis? A critical assessment of available experimental data.
Article in RNA (New York, N.Y.), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 58 citations in OpenAlex.
- An integrative NMR-SAXS approach for structural determination of large RNAs defines the substrate-free state of a trans-cleaving Neurospora Varkud Satellite ribozyme.Nucleic acids research · 2021Article
- Beyond the Plateau: pL Dependence of Proton Inventories as a Tool for Studying Ribozyme and Ribonuclease Catalysis.Biochemistry · 2021Article
- Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme.Nature chemistry · 2020Article
- The L-platform/L-scaffold framework: a blueprint for RNA-cleaving nucleic acid enzyme design.RNA (New York, N.Y.) · 2020Article
- Comparison of the Structures and Mechanisms of the Pistol and Hammerhead Ribozymes.Journal of the American Chemical Society · 2019Article
- Insights into RNA structure and dynamics from recent NMR and X-ray studies of the Neurospora Varkud satellite ribozyme.Wiley interdisciplinary reviews. RNA · 2017Review
- Overcoming evolved resistance to population-suppressing homing-based gene drives.Scientific reports · 2017Article
- The structure of a nucleolytic ribozyme that employs a catalytic metal ion.Nature chemical biology · 2017Article
- RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme.RNA (New York, N.Y.) · 2017Article
- Molecular Dynamics Study of Twister Ribozyme: Role of Mg(2+) Ions and the Hydrogen-Bonding Network in the Active Site.Biochemistry · 2016Article
- Prohead RNA: a noncoding viral RNA of novel structure and function.Wiley interdisciplinary reviews. RNA · 2016Review
- Crystal structure of the Varkud satellite ribozyme.Nature chemical biology · 2015Article
- The NMR structure of the II-III-VI three-way junction from the Neurospora VS ribozyme reveals a critical tertiary interaction and provides new insights into the global ribozyme structure.RNA (New York, N.Y.) · 2015Article
- Nucleic acid reactivity: challenges for next-generation semiempirical quantum models.Journal of computational chemistry · 2015Article
- Small-angle X-ray scattering: a bridge between RNA secondary structures and three-dimensional topological structures.Current opinion in structural biology · 2015Review
- Crystal structure and mechanistic investigation of the twister ribozyme.Nature chemical biology · 2014Article
- Linear free energy relationships in RNA transesterification: theoretical models to aid experimental interpretations.Physical chemistry chemical physics : PCCP · 2014Article
- Nucleic acid catalysis: metals, nucleobases, and other cofactors.Chemical reviews · 2014Review
- NMR localization of divalent cations at the active site of the Neurospora VS ribozyme provides insights into RNA-metal-ion interactions.Biochemistry · 2014Article
- Structural insights into substrate recognition by the Neurospora Varkud satellite ribozyme: importance of U-turns at the kissing-loop junction.Biochemistry · 2014Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
The active centers of the hairpin and VS ribozymes are both generated by the interaction of two internal loops, and both ribozymes use guanine and adenine nucleobases to accelerate cleavage and ligation reactions. The centers are topologically equivalent and the relative positioning of key elements the same. There is good evidence that the cleavage reaction of the VS ribozyme is catalyzed by the guanine (G638) acting as general base and the adenine (A756) as general acid. We now critically evaluate the experimental mechanistic evidence for the hairpin ribozyme. We conclude that all the available data are fully consistent with a major contribution to catalysis by general acid-base catalysis involving the adenine (A38) and guanine (G8). It appears that the two ribozymes are mechanistically equivalent.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.