ArticleRNA (New York, N.Y.)2006
Nucleobase catalysis in the hairpin ribozyme.
Article in RNA (New York, N.Y.), 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Article
- Identification of over 200-fold more hairpin ribozymes than previously known in diverse circular RNAs.Nucleic acids research · 2021Article
- Elucidation of Catalytic Strategies of Small Nucleolytic Ribozymes From Comparative Analysis of Active Sites.ACS catalysis · 2018Article
- Structural and Biochemical Properties of Novel Self-Cleaving Ribozymes.Molecules (Basel, Switzerland) · 2017Review
- Chemistry and Biology of Self-Cleaving Ribozymes.Trends in biochemical sciences · 2015Review
- Evidence for the role of active site residues in the hairpin ribozyme from molecular simulations along the reaction path.Journal of the American Chemical Society · 2014Article
- Direct observation of multiple tautomers of oxythiamine and their recognition by the thiamine pyrophosphate riboswitch.ACS chemical biology · 2014Article
- pH-dependent dynamics of complex RNA macromolecules.Journal of chemical theory and computation · 2013Article
- General acid-base catalysis mediated by nucleobases in the hairpin ribozyme.Journal of the American Chemical Society · 2012Article
- Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent.Journal of chemical theory and computation · 2012Article
- Mechanisms of RNA catalysis.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2011Article
- Do the hairpin and VS ribozymes share a common catalytic mechanism based on general acid-base catalysis? A critical assessment of available experimental data.RNA (New York, N.Y.) · 2011Article
- DNA as a versatile chemical component for catalysis, encoding, and stereocontrol.Angewandte Chemie (International ed. in English) · 2010Review
- 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
- Scope and mechanism of interstrand cross-link formation by the C4'-oxidized abasic site.Journal of the American Chemical Society · 2009Article
- Identification of an imino group indispensable for cleavage by a small ribozyme.Journal of the American Chemical Society · 2009Article
- Molecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme.RNA (New York, N.Y.) · 2009Article
- The Small Ribozymes: Common and Diverse Features Observed through the FRET Lens.Springer series in biophysics · 2009Article
- The ionic environment determines ribozyme cleavage rate by modulation of nucleobase pK a.RNA (New York, N.Y.) · 2008Article
- Electrostatic interactions in the hairpin ribozyme account for the majority of the rate acceleration without chemical participation by nucleobases.RNA (New York, N.Y.) · 2008Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
RNA catalysis is important in the processing and translation of RNA molecules, yet the mechanisms of catalysis are still unclear in most cases. We have studied the role of nucleobase catalysis in the hairpin ribozyme, where the scissile phosphate is juxtaposed between guanine and adenine bases. We show that a modified ribozyme in which guanine 8 has been substituted by an imidazole base is active in both cleavage and ligation, with ligation rates 10-fold faster than cleavage. The rates of both reactions exhibit bell-shaped dependence on pH, with pK(a) values of 5.7 +/- 0.1 and 7.7 +/- 0.1 for cleavage and 6.1 +/- 0.3 and 6.9 +/- 0.3 for ligation. The data provide good evidence for general acid-base catalysis by the nucleobases.
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