ArticleThe EMBO journal2001
Functional involvement of G8 in the hairpin ribozyme cleavage mechanism.
Article in The EMBO journal, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed, 122 citations in OpenAlex.
- Identification and characterization of shifted G•U wobble pairs resulting from alternative protonation of RNA.Nucleic acids research · 2025Article
- Engineering of Small Ribozymes Acting on RNA: What is Needed to Make a New Function Work with an Existing Catalyst?Chembiochem : a European journal of chemical biology · 2025Review
- Article
- Investigation of the pThe journal of physical chemistry. B · 2021Article
- Identification of over 200-fold more hairpin ribozymes than previously known in diverse circular RNAs.Nucleic acids research · 2021Article
- Structural Insights Into Tautomeric Dynamics in Nucleic Acids and in Antiviral Nucleoside Analogs.Frontiers in molecular biosciences · 2021Review
- 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
- Evidence of a General Acid-Base Catalysis Mechanism in the 8-17 DNAzyme.Biochemistry · 2018Article
- Elucidation of Catalytic Strategies of Small Nucleolytic Ribozymes From Comparative Analysis of Active Sites.ACS catalysis · 2018Article
- The structure of a nucleolytic ribozyme that employs a catalytic metal ion.Nature chemical biology · 2017Article
- 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
- Crystal structure of the Varkud satellite ribozyme.Nature chemical biology · 2015Article
- Role of tautomerism in RNA biochemistry.RNA (New York, N.Y.) · 2015Review
- Arginine as a general acid catalyst in serine recombinase-mediated DNA cleavage.The Journal of biological chemistry · 2013Article
- A transition-state interaction shifts nucleobase ionization toward neutrality to facilitate small ribozyme catalysis.Journal of the American Chemical Society · 2012Article
- General acid-base catalysis mediated by nucleobases in the hairpin ribozyme.Journal of the American Chemical Society · 2012Article
- QM/MM studies of hairpin ribozyme self-cleavage suggest the feasibility of multiple competing reaction mechanisms.The journal of physical chemistry. B · 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
Corrections and comments
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Authors and funding
7 authors at 1 institution in 2 countries.
Funding
Abstract
The catalytic determinants for the cleavage and ligation reactions mediated by the hairpin ribozyme are integral to the polyribonucleotide chain. We describe experiments that place G8, a critical guanosine, at the active site, and point to an essential role in catalysis. Cross-linking and modeling show that formation of a catalytic complex is accompanied by a conformational change in which N1 and O6 of G8 become closely apposed to the scissile phosphodiester. UV cross-linking, hydroxyl-radical footprinting and native gel electrophoresis indicate that G8 variants inhibit the reaction at a step following domain association, and that the tertiary structure of the inactive complex is not measurably altered. Rate-pH profiles and fluorescence spectroscopy show that protonation at the N1 position of G8 is required for catalysis, and that modification of O6 can inhibit the reaction. Kinetic solvent isotope analysis suggests that two protons are transferred during the rate-limiting step, consistent with rate-limiting cleavage chemistry involving concerted deprotonation of the attacking 2'-OH and protonation of the 5'-O leaving group. We propose mechanistic models that are consistent with these data, including some that invoke a novel keto-enol tautomerization.
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Registered trials
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.