ArticleRNA (New York, N.Y.)2004
Artificial tertiary motifs stabilize trans-cleaving hammerhead ribozymes under conditions of submillimolar divalent ions and high temperatures.
Article in RNA (New York, N.Y.), 2004. 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.
- Coevolution of RNase P and the ribosome.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Enhanced hammerhead ribozyme turnover rates: Reevaluating therapeutic space for small catalytic RNAs.Molecular therapy. Nucleic acids · 2025Article
- A limitation lifted: A conditional knockdown system reveals essential roles for Polo-like kinase and Aurora kinase 1 inProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Pushing the Limits of Nucleic Acid Function.Chemistry (Weinheim an der Bergstrasse, Germany) · 2022Review
- Nucleic Acid Catalysis under Potential Prebiotic Conditions.Chemistry, an Asian journal · 2020Review
- Article
- Intracellular selection of trans-cleaving hammerhead ribozymes.Nucleic acids research · 2019Article
- RNA Structure Design Improves Activity and Specificity of trans-Splicing-Triggered Cell Death in a Suicide Gene Therapy Approach.Molecular therapy. Nucleic acids · 2018Article
- Evolution of ribozymes in the presence of a mineral surface.RNA (New York, N.Y.) · 2016Article
- Article
- Inhibition of miR-21 in glioma cells using catalytic nucleic acids.Scientific reports · 2016Article
- Automated design of hammerhead ribozymes and validation by targeting the PABPN1 gene transcript.Nucleic acids research · 2016Article
- Two Active Site Divalent Ions in the Crystal Structure of the Hammerhead Ribozyme Bound to a Transition State Analogue.Biochemistry · 2016Article
- Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction.Biochemistry · 2015Article
- In vitro evolution of distinct self-cleaving ribozymes in diverse environments.Nucleic acids research · 2015Article
- A general design strategy for protein-responsive riboswitches in mammalian cells.Nature methods · 2014Article
- Improved design of hammerhead ribozyme for selective digestion of target RNA through recognition of site-specific adenosine-to-inosine RNA editing.RNA (New York, N.Y.) · 2014Article
- A versatile cis-blocking and trans-activation strategy for ribozyme characterization.Nucleic acids research · 2013Article
- The hammerhead ribozyme: structure, catalysis, and gene regulation.Progress in molecular biology and translational science · 2013Review
- Robust suppression of HIV replication by intracellularly expressed reverse transcriptase aptamers is independent of ribozyme processing.Molecular therapy : the journal of the American Society of Gene Therapy · 2012Article
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5 authors.
Funding
Abstract
Tertiary stabilizing motifs (TSMs) between terminal loops or internal bulges facilitate folding of natural hammerhead ribozymes (hRz) under physiological conditions. However, both substrate and enzyme strands contribute nucleotides to the TSMs of trans-cleaving hRz, complicating the design of hRz that exploit TSMs to target specific mRNA. To overcome this limitation, we used SELEX to identify new, artificial TSMs that are less sensitive to sequence context. Nucleotides in loop II or in a bulge within the ribozyme strand of stem I were randomized, while the interaction partner was held constant. All nucleotides of the substrate pair with the ribozyme, minimizing their possible recruitment into the TSM, as such recruitment could constrain choice of candidate target sequences. Six cycles of selection identified cis-acting ribozymes that were active in 100 microM MgCl2. The selected motifs partially recapitulate TSMs found in natural hRz, suggesting that the natural motifs are close to optimal for their respective contexts. Ribozyme "RzB" showed enhanced thermal stability by retaining trans-cleavage activity at 80 degrees C in 10 mM MgCl2 and at 70 degrees C in 2 mM MgCl2. A variant of ribozyme "RzB" with a continuously paired stem 1 rapidly lost activity as temperature was increased. The selected motifs are modular, in that they permit trans-cleavage of several substrates in submillimolar MgCl2, including two substrates derived from the U5 genomic region of HIV-1. The new, artificial tertiary stabilized hRz are thus nearly independent of sequence context and enable for the first time the use of highly active hRz targeting almost any mRNA at physiologically relevant magnesium concentrations.
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