ArticleRNA (New York, N.Y.)2008
The ionic environment determines ribozyme cleavage rate by modulation of nucleobase pK a.
Article in RNA (New York, N.Y.), 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 31 citations in OpenAlex.
- Scaling Catalytic Contributions of Small Self-Cleaving Ribozymes.Angewandte Chemie (Weinheim an der Bergstrasse, Germany) · 2022Article
- Scaling Catalytic Contributions of Small Self-Cleaving Ribozymes.Angewandte Chemie (International ed. in English) · 2022Article
- Insights into RNA structure and dynamics from recent NMR and X-ray studies of the Neurospora Varkud satellite ribozyme.Wiley interdisciplinary reviews. RNA · 2017Review
- Structural and Biochemical Properties of Novel Self-Cleaving Ribozymes.Molecules (Basel, Switzerland) · 2017Review
- Rational engineering of the Neurospora VS ribozyme to allow substrate recognition via different kissing-loop interactions.Nucleic acids research · 2016Article
- 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 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
- Lewis acid catalysis of phosphoryl transfer from a copper(II)-NTP complex in a kinase ribozyme.Nucleic acids research · 2013Article
- Additional roles of a peripheral loop-loop interaction in the Neurospora VS ribozyme.Nucleic acids research · 2011Article
- NMR structure of the A730 loop of the Neurospora VS ribozyme: insights into the formation of the active site.Nucleic acids research · 2011Article
- Metal ions: supporting actors in the playbook of small ribozymes.Metal ions in life sciences · 2011Review
- Analysis of metal ion dependence in glmS ribozyme self-cleavage and coenzyme binding.Chembiochem : a European journal of chemical biology · 2010Article
- Effect of high hydrostatic pressure on hydration and activity of ribozymes.Molecular biology reports · 2010Article
- Deciphering the role of glucosamine-6-phosphate in the riboswitch action of glmS ribozyme.RNA (New York, N.Y.) · 2010Article
- Hammerhead ribozymes: true metal or nucleobase catalysis? Where is the catalytic power from?Molecules (Basel, Switzerland) · 2010Article
- Nucleobase-mediated general acid-base catalysis in the Varkud satellite ribozyme.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Threshold occupancy and specific cation binding modes in the hammerhead ribozyme active site are required for active conformation.Journal of molecular biology · 2009Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Several small ribozymes employ general acid-base catalysis as a mechanism to enhance site-specific RNA cleavage, even though the functional groups on the ribonucleoside building blocks of RNA have pK (a) values far removed from physiological pH. The rate of the cleavage reaction is strongly affected by the identity of the metal cation present in the reaction solution; however, the mechanism(s) by which different cations contribute to rate enhancement has not been determined. Using the Neurospora VS ribozyme, we provide evidence that different cations confer particular shifts in the apparent pK (a) values of the catalytic nucleobases, which in turn determines the fraction of RNA in the protonation state competent for general acid-base catalysis at a given pH, which determines the observed rate of the cleavage reaction. Despite large differences in observed rates of cleavage in different cations, mathematical models of general acid-base catalysis indicate that k (1), the intrinsic rate of the bond-breaking step, is essentially constant irrespective of the identity of the cation(s) in the reaction solution. Thus, in contrast to models that invoke unique roles for metal ions in ribozyme chemical mechanisms, we find that most, and possibly all, of the ion-specific rate enhancement in the VS ribozyme can be explained solely by the effect of the ions on nucleobase pK (a). The inference that k (1) is essentially constant suggests a resolution of the problem of kinetic ambiguity in favor of a model in which the lower pK (a) is that of the general acid and the higher pK (a) is that of the general base.
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