ArticleNucleic acids research2009
Structure-function analysis of the ribozymes of chrysanthemum chlorotic mottle viroid: a loop-loop interaction motif conserved in most natural hammerheads.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Molecular Dynamics Simulations of RNA Stem-Loop Folding Using an Atomistic Force Field and a Generalized Born Implicit Solvent.ACS omega · 2025Article
- Enhanced hammerhead ribozyme turnover rates: Reevaluating therapeutic space for small catalytic RNAs.Molecular therapy. Nucleic acids · 2025Article
- Accurately Modeling RNA Stem-Loops in an Implicit Solvent Environment.Journal of chemical information and modeling · 2024Article
- RNA folding pathways from all-atom simulations with a variationally improved history-dependent bias.Biophysical journal · 2023Article
- On the early identification and characterization of pear blister canker viroid, apple dimple fruit viroid, peach latent mosaic viroid and chrysanthemum chlorotic mottle viroid.Virus research · 2023Article
- A Singular and Widespread Group of Mobile Genetic Elements: RNA Circles with Autocatalytic Ribozymes.Cells · 2020Review
- Systematic Screening, Rational Development, and Initial Optimization of Efficacious RNA Silencing Agents for Human Rod Opsin Therapeutics.Translational vision science & technology · 2019Article
- Article
- Direct visualization of the native structure of viroid RNAs at single-molecule resolution by atomic force microscopy.RNA biology · 2019Article
- Increased Flexibility between Stems of Intramolecular Three-Way Junctions by the Insertion of Bulges.Biophysical journal · 2018Article
- ICTV Virus Taxonomy Profile: Avsunviroidae.The Journal of general virology · 2018Article
- Highly motif- and organism-dependent effects of naturally occurring hammerhead ribozyme sequences on gene expression.RNA biology · 2018Article
- Investigation of the Melting Behavior of DNA Three-Way Junctions in the Closed and Open States.Biophysical journal · 2017Article
- The Hammerhead Ribozyme: A Long History for a Short RNA.Molecules (Basel, Switzerland) · 2017Review
- A remarkably stable kissing-loop interaction defines substrate recognition by the Neurospora Varkud Satellite ribozyme.RNA (New York, N.Y.) · 2014Article
- G17-modified hammerhead ribozymes are active in vitro and in vivo.RNA (New York, N.Y.) · 2013Article
- Review
- A high-throughput, quantitative cell-based screen for efficient tailoring of RNA device activity.Nucleic acids research · 2012Article
- The ubiquitous hammerhead ribozyme.RNA (New York, N.Y.) · 2012Review
- Viroids: from genotype to phenotype just relying on RNA sequence and structural motifs.Frontiers in microbiology · 2012Article
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Authors and funding
5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Loop-loop tertiary interactions play a key role in the folding and catalytic activity of natural hammerhead ribozymes. Using a combination of NMR spectroscopy, site-directed mutagenesis and kinetic and infectivity analyses, we have examined the structure and function of loops 1 and 2 of the (+) and (-) hammerheads of chrysanthemum chlorotic mottle viroid RNA. In both hammerheads, loop 1 is a heptanucleotide hairpin loop containing an exposed U at its 5' side and an extrahelical U at its 3'-side critical for the catalytic activity of the ribozyme in vitro and for viroid infectivity in vivo, whereas loop 2 has a key opened A at its 3'-side. These structural features promote a specific loop-loop interaction motif across the major groove. The essential features of this tertiary structure element, base pairing between the 5' U of loop 1 and the 3' A of loop 2, and interaction of the extrahelical pyrimidine of loop 1 with loop 2, are likely shared by a significant fraction of natural hammerheads.
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