ArticlePLoS biology2008
Capturing hammerhead ribozyme structures in action by modulating general base catalysis.
Article in PLoS biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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Who cites it
61 citing papers in PubMed.
- Tunable gene expression in zebrafish using RiboSCALE.bioRxiv : the preprint server for biology · 2026Article
- Cat_Wiz: a stereochemistry-guided toolkit for locating, diagnosing, and annotating Mg2+ ions in RNA structures.Nucleic acids research · 2026Article
- Plasmid-Based Reverse Genetics System Enabling One-Step Generation of Genotype 3 Hepatitis E Virus.Viruses · 2025Article
- Enhanced hammerhead ribozyme turnover rates: Reevaluating therapeutic space for small catalytic RNAs.Molecular therapy. Nucleic acids · 2025Article
- Structural investigation of an RNA device that regulates PD-1 expression in mammalian cells.Nucleic acids research · 2025Article
- The structure and catalytic mechanism of a pseudoknot-containing hammerhead ribozyme.Nature communications · 2024Article
- CircularSTAR3D: a stack-based RNA 3D structural alignment tool for circular matching.Nucleic acids research · 2023Article
- Article
- Structural variants and modifications of hammerhead ribozymes targeting influenza A virus conserved structural motifs.Molecular therapy. Nucleic acids · 2022Article
- Toehold-mediated strand displacement to measure released product from self-cleaving ribozymes.RNA (New York, N.Y.) · 2022Article
- Integral equation models for solvent in macromolecular crystals.The Journal of chemical physics · 2022Article
- Self-cleaving ribozymes: substrate specificity and synthetic biology applications.RSC chemical biology · 2021Review
- Article
- A Singular and Widespread Group of Mobile Genetic Elements: RNA Circles with Autocatalytic Ribozymes.Cells · 2020Review
- Molecular Features and Metal Ions That Influence 10-23 DNAzyme Activity.Molecules (Basel, Switzerland) · 2020Review
- An Evolutionary Trace method defines functionally important bases and sites common to RNA families.PLoS computational biology · 2020Article
- RNA Switches for Synthetic Biology.Cold Spring Harbor perspectives in biology · 2019Review
- Increased Flexibility between Stems of Intramolecular Three-Way Junctions by the Insertion of Bulges.Biophysical journal · 2018Article
- Thermodynamics and kinetics of RNA tertiary structure formation in the junctionless hairpin ribozyme.Biophysical chemistry · 2017Article
- Investigation of the Melting Behavior of DNA Three-Way Junctions in the Closed and Open States.Biophysical journal · 2017Article
1 more citing papers are in PubMed but not listed here.
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6 authors.
Funding
Abstract
We have obtained precatalytic (enzyme-substrate complex) and postcatalytic (enzyme-product complex) crystal structures of an active full-length hammerhead RNA that cleaves in the crystal. Using the natural satellite tobacco ringspot virus hammerhead RNA sequence, the self-cleavage reaction was modulated by substituting the general base of the ribozyme, G12, with A12, a purine variant with a much lower pKa that does not significantly perturb the ribozyme's atomic structure. The active, but slowly cleaving, ribozyme thus permitted isolation of enzyme-substrate and enzyme-product complexes without modifying the nucleophile or leaving group of the cleavage reaction, nor any other aspect of the substrate. The predissociation enzyme-product complex structure reveals RNA and metal ion interactions potentially relevant to transition-state stabilization that are absent in precatalytic structures.
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