ArticleBMC bioinformatics2007
A structural analysis of in vitro catalytic activities of hammerhead ribozymes.
Article in BMC bioinformatics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 13 citations in OpenAlex.
- A cellular high-throughput screening approach for therapeutic trans-cleaving ribozymes and RNAi against arbitrary mRNA disease targets.Experimental eye research · 2016Article
- Automated design of hammerhead ribozymes and validation by targeting the PABPN1 gene transcript.Nucleic acids research · 2016Article
- RNA Thermodynamic Structural Entropy.PloS one · 2015Article
- Design and analysis of hammerhead ribozyme activity against an artificial gene target.Methods in molecular biology (Clifton, N.J.) · 2014Article
- siRNAs target sites selection of ezrin and the influence of RNA interference on ezrin expression and biological characters of osteosarcoma cells.Molecular and cellular biochemistry · 2012Article
- Computational prediction of efficient splice sites for trans-splicing ribozymes.RNA (New York, N.Y.) · 2012Article
- Ezrin mRNA target site selection for DNAzymes using secondary structure and hybridization thermodynamics.Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine · 2011Article
- Effective suppression of Dengue fever virus in mosquito cell cultures using retroviral transduction of hammerhead ribozymes targeting the viral genome.Virology journal · 2009Article
- A structural interpretation of the effect of GC-content on efficiency of RNA interference.BMC bioinformatics · 2009Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundRibozymes are small catalytic RNAs that possess the dual functions of sequence-specific RNA recognition and site-specific cleavage. Trans-cleaving ribozymes can inhibit translation of genes at the messenger RNA (mRNA) level in both eukaryotic and prokaryotic systems and are thus useful tools for studies of gene function. However, identification of target sites for efficient cleavage poses a challenge. Here, we have considered a number of structural and thermodynamic parameters that can affect the efficiency of target cleavage, in an attempt to identify rules for the selection of functional ribozymes.
resultsWe employed the Sfold program for RNA secondary structure prediction, to account for the likely population of target structures that co-exist in dynamic equilibrium for a specific mRNA molecule. We designed and prepared 15 hammerhead ribozymes to target GUC cleavage sites in the mRNA of the breast cancer resistance protein (BCRP). These ribozymes were tested, and their catalytic activities were measured in vitro. We found that target disruption energy owing to the alteration of the local target structure necessary for ribozyme binding, and the total energy change of the ribozyme-target hybridization, are two significant parameters for prediction of ribozyme activity. Importantly, target disruption energy is the major contributor to the predictability of ribozyme activity by the total energy change. Furthermore, for a target-site specific ribozyme, incorrect folding of the catalytic core, or interactions involving the two binding arms and the end sequences of the catalytic core, can have detrimental effects on ribozyme activity.
conclusionThe findings from this study suggest rules for structure-based rational design of trans-cleaving hammerhead ribozymes in gene knockdown studies. Tools implementing these rules are available from the Sribo module and the Srna module of the Sfold program available through Web server at http://sfold.wadsworth.org.
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