ArticleACS chemical biology2019
An Ontology for Facilitating Discussion of Catalytic Strategies of RNA-Cleaving Enzymes.
Article in ACS chemical biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- Substrate energetics in non-templated DNA synthesis by terminal deoxynucleotidyl transferase.Nucleic acids research · 2026Article
- Origins of Reactivity in SAM-Utilizing Ribozyme SAMURI-Catalyzed RNA Alkylation.Journal of the American Chemical Society · 2026Article
- 1-Deazainosine-impact on RNA structure and role in exploring ribozyme catalysis.Chemical science · 2026Article
- Nucleobase Coordination With MgChemistry (Weinheim an der Bergstrasse, Germany) · 2026Article
- MgJournal of the American Chemical Society · 2026Article
- Article
- Transferability of MACE Graph Neural Network for Range Corrected Δ-Machine Learning Potential QM/MM Applications.The journal of physical chemistry. B · 2025Article
- Enhanced hammerhead ribozyme turnover rates: Reevaluating therapeutic space for small catalytic RNAs.Molecular therapy. Nucleic acids · 2025Article
- The 8-17 DNAzyme can operate in a single active structure regardless of metal ion cofactor.Nature communications · 2024Article
- RNA targeting and cleavage by the type III-Dv CRISPR effector complex.Nature communications · 2024Article
- Catalytic Metal Ion-Substrate Coordination during Nonenzymatic RNA Primer Extension.Journal of the American Chemical Society · 2024Article
- Rapid Kinetics of Pistol Ribozyme: Insights into Limits to RNA Catalysis.Biochemistry · 2023Article
- Catalytic mechanism and pH dependence of a methyltransferase ribozyme (MTR1) from computational enzymology.Nucleic acids research · 2023Article
- Modern semiempirical electronic structure methods and machine learning potentials for drug discovery: Conformers, tautomers, and protonation states.The Journal of chemical physics · 2023Article
- QDπ: A Quantum Deep Potential Interaction Model for Drug Discovery.Journal of chemical theory and computation · 2023Article
- Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis.Journal of the American Chemical Society · 2023Article
- Multireference Generalization of the Weighted Thermodynamic Perturbation Method.The journal of physical chemistry. A · 2022Article
- A modular XNAzyme cleaves long, structured RNAs under physiological conditions and enables allele-specific gene silencing.Nature chemistry · 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
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Authors and funding
8 authors.
Funding
Abstract
A predictive understanding of the mechanisms of RNA cleavage is important for the design of emerging technology built from biological and synthetic molecules that have promise for new biochemical and medicinal applications. Over the past 15 years, RNA cleavage reactions involving 2'-O-transphosphorylation have been discussed using a simplified framework introduced by Breaker that consists of four fundamental catalytic strategies (designated α, β, γ, and δ) that contribute to rate enhancement. As more detailed mechanistic data emerge, there is need for the framework to evolve and keep pace. We develop an ontology for discussion of strategies of enzymes that catalyze RNA cleavage via 2'-O-transphosphorylation that stratifies Breaker's framework into primary (1°), secondary (2°), and tertiary (3°) contributions to enable more precise interpretation of mechanism in the context of structure and bonding. Further, we point out instances where atomic-level changes give rise to changes in more than one catalytic contribution, a phenomenon we refer to as "functional blurring". We hope that this ontology will help clarify our conversations and pave the path forward toward a consensus view of these fundamental and fascinating mechanisms. The insight gained will deepen our understanding of RNA cleavage reactions catalyzed by natural protein and RNA enzymes, as well as aid in the design of new engineered DNA and synthetic enzymes.
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