ArticleJournal of the American Chemical Society2012
General acid-base catalysis mediated by nucleobases in the hairpin ribozyme.
Article in Journal of the American Chemical Society, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed, 84 citations in OpenAlex.
- Article
- Functional Analysis of Histidine-Dependent Self-Cleaving RNAs Obtained by In Vitro Selection.Chembiochem : a European journal of chemical biology · 2025Article
- The Role of General Acid Catalysis in the Mechanism of an Alkyl Transferase Ribozyme.ACS catalysis · 2024Article
- Catalytic mechanism and pH dependence of a methyltransferase ribozyme (MTR1) from computational enzymology.Nucleic acids research · 2023Article
- In vitro evolution of ribonucleases from expanded genetic alphabets.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Scaling Catalytic Contributions of Small Self-Cleaving Ribozymes.Angewandte Chemie (International ed. in English) · 2022Article
- Scaling Catalytic Contributions of Small Self-Cleaving Ribozymes.Angewandte Chemie (Weinheim an der Bergstrasse, Germany) · 2022Article
- Article
- 1-Deazaguanosine-Modified RNA: The Missing Piece for Functional RNA Atomic Mutagenesis.Journal of the American Chemical Society · 2022Article
- Structure and mechanism of a methyltransferase ribozyme.Nature chemical biology · 2022Article
- Self-cleaving ribozymes: substrate specificity and synthetic biology applications.RSC chemical biology · 2021Review
- Identification of over 200-fold more hairpin ribozymes than previously known in diverse circular RNAs.Nucleic acids research · 2021Article
- Prebiotically Plausible RNA Activation Compatible with Ribozyme-Catalyzed Ligation.Angewandte Chemie (International ed. in English) · 2021Article
- The Positively Charged Active Site of the Bacterial Toxin RelE Causes a Large Shift in the General Base pBiochemistry · 2020Article
- Crucial Roles of Two Hydrated MgAngewandte Chemie (International ed. in English) · 2020Article
- Nucleic Acid Catalysis under Potential Prebiotic Conditions.Chemistry, an Asian journal · 2020Review
- Novel ribozymes: discovery, catalytic mechanisms, and the quest to understand biological function.Nucleic acids research · 2019Article
- Comparison of the Structures and Mechanisms of the Pistol and Hammerhead Ribozymes.Journal of the American Chemical Society · 2019Article
- Classification of the nucleolytic ribozymes based upon catalytic mechanism.F1000Research · 2019Review
- Adenine protonation enables cyclic-di-GMP binding to cyclic-GAMP sensing riboswitches.RNA (New York, N.Y.) · 2018Article
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6 authors at 1 institution in 1 country.
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Abstract
The catalytic mechanism by which the hairpin ribozyme accelerates cleavage or ligation of the phosphodiester backbone of RNA has been incompletely understood. There is experimental evidence for an important role for an adenine (A38) and a guanine (G8), and it has been proposed that these act in general acid-base catalysis. In this work we show that a large reduction in cleavage rate on substitution of A38 by purine (A38P) can be reversed by replacement of the 5'-oxygen atom at the scissile phosphate by sulfur (5'-PS), which is a much better leaving group. This is consistent with A38 acting as the general acid in the unmodified ribozyme. The rate of cleavage of the 5'-PS substrate by the A38P ribozyme increases with pH log-linearly, indicative of a requirement for a deprotonated base with a relatively high pK(a). On substitution of G8 by diaminopurine, the 5'-PS substrate cleavage rate at first increases with pH and then remains at a plateau, exhibiting an apparent pK(a) consistent with this nucleotide acting in general base catalysis. Alternative explanations for the pH dependence of hairpin ribozyme reactivity are discussed, from which we conclude that general acid-base catalysis by A38 and G8 is the simplest and most probable explanation consistent with all the experimental data.
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