ArticlePLoS computational biology2011
Identification of hammerhead ribozymes in all domains of life reveals novel structural variations.
Article in PLoS computational biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers.
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Who cites it
91 citing papers in PubMed, 154 citations in OpenAlex.
- Structure and mechanism of HDV ribozymes revealing Lewis acid catalysis by a metal ion.Nature communications · 2026Article
- RNA aptamers as tools for the purification and analysis of in vivo assembled ribonucleoproteins.RNA (New York, N.Y.) · 2025Review
- Hammerhead Ribozymes: Structural Insights, Catalytic Mechanisms, and Cutting-Edge Applications in Synthetic Biology.International journal of molecular sciences · 2025Review
- Traces of a Primitive RNA Ring in Current Genomes.Biology · 2025Article
- Enhanced hammerhead ribozyme turnover rates: Reevaluating therapeutic space for small catalytic RNAs.Molecular therapy. Nucleic acids · 2025Article
- Hammerhead ribozymes directed against mRNA of an essential gene inhibitFrontiers in microbiology · 2025Article
- Article
- Emergent ribozyme behaviors in oxychlorine brines indicate a unique niche for molecular evolution on Mars.Nature communications · 2024Article
- Genome-Wide Computational Prediction and Analysis of Noncoding RNAs inMicroorganisms · 2024Article
- Identification of Hammerhead-variant ribozyme sequences in SARS-CoV-2.Nucleic acids research · 2024Article
- Inhibition ofeLife · 2024Article
- A comparative survey of the influence of small self-cleaving ribozymes on gene expression in human cell culture.RNA biology · 2024Article
- Computational design and experimental verification of pseudoknotted ribozymes.RNA (New York, N.Y.) · 2023Article
- Discovery of natural non-circular permutations in non-coding RNAs.Nucleic acids research · 2023Article
- Article
- Toehold-mediated strand displacement to measure released product from self-cleaving ribozymes.RNA (New York, N.Y.) · 2022Article
- cyPhyRNA-seq: a genome-scale RNA-seq method to detect active self-cleaving ribozymes by capturing RNAs with 2',3'RNA biology · 2021Article
- Satellite-Like W-Elements: Repetitive, Transcribed, and Putative Mobile Genetic Factors with Potential Roles for Biology and Evolution of Schistosoma mansoni.Genome biology and evolution · 2021Article
- Digital Microfluidics Chips for the Execution and Real-Time Monitoring of Multiple Ribozymatic Cleavage Reactions.ACS omega · 2021Article
- The hammerhead self-cleaving motif as a precursor to complex endonucleolytic ribozymes.RNA (New York, N.Y.) · 2021Article
31 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
Abstract
Hammerhead ribozymes are small self-cleaving RNAs that promote strand scission by internal phosphoester transfer. Comparative sequence analysis was used to identify numerous additional representatives of this ribozyme class than were previously known, including the first representatives in fungi and archaea. Moreover, we have uncovered the first natural examples of "type II" hammerheads, and our findings reveal that this permuted form occurs in bacteria as frequently as type I and III architectures. We also identified a commonly occurring pseudoknot that forms a tertiary interaction critical for high-speed ribozyme activity. Genomic contexts of many hammerhead ribozymes indicate that they perform biological functions different from their known role in generating unit-length RNA transcripts of multimeric viroid and satellite virus genomes. In rare instances, nucleotide variation occurs at positions within the catalytic core that are otherwise strictly conserved, suggesting that core mutations are occasionally tolerated or preferred.
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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.