ArticleNucleic acids research2000
Secondary structure prediction and in vitro accessibility of mRNA as tools in the selection of target sites for ribozymes.
Article in Nucleic acids research, 2000. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 67 citations in OpenAlex.
- Enhanced hammerhead ribozyme turnover rates: Reevaluating therapeutic space for small catalytic RNAs.Molecular therapy. Nucleic acids · 2025Article
- A cellular high-throughput screening approach for therapeutic trans-cleaving ribozymes and RNAi against arbitrary mRNA disease targets.Experimental eye research · 2016Article
- Silencing efficacy prediction: a retrospective study on target mRNA features.Bioscience reports · 2015Article
- Deoxyribozymes and bioinformatics: complementary tools to investigate axon regeneration.Cell and tissue research · 2012Review
- Selection of the most potent specific on/off adaptor-hepatitis delta virus ribozymes for use in gene targeting.Nucleic acid therapeutics · 2011Article
- Variables and strategies in development of therapeutic post-transcriptional gene silencing agents.Journal of ophthalmology · 2011Article
- Article
- Development of lead hammerhead ribozyme candidates against human rod opsin mRNA for retinal degeneration therapy.Experimental eye research · 2009Article
- Bottlenecks in development of retinal therapeutic post-transcriptional gene silencing agents.Vision research · 2008Review
- Gene silencing of HIV chemokine receptors using ribozymes and single-stranded antisense RNA.The Biochemical journal · 2006Article
- Secondary structure in the target as a confounding factor in synthetic oligomer microarray design.BMC genomics · 2005Article
- A systematic analysis of the silencing effects of an active siRNA at all single-nucleotide mismatched target sites.Nucleic acids research · 2005Article
- Profiled support vector machines for antisense oligonucleotide efficacy prediction.BMC bioinformatics · 2004Article
- Ribozyme-based gene-inactivation systems require a fine comprehension of their substrate specificities; the case of delta ribozyme.Current medicinal chemistry · 2003Article
- Promoter choice affects the potency of HIV-1 specific RNA interference.Nucleic acids research · 2003Article
- The activity of siRNA in mammalian cells is related to structural target accessibility: a comparison with antisense oligonucleotides.Nucleic acids research · 2003Article
- Similar behaviour of single-strand and double-strand siRNAs suggests they act through a common RNAi pathway.Nucleic acids research · 2003Article
- Tolerance for mutations and chemical modifications in a siRNA.Nucleic acids research · 2003Article
- Design of a ribozyme targeting human telomerase reverse transcriptase and cloning of it's gene.World journal of gastroenterology · 2003Article
- Development and comparison of procedures for the selection of delta ribozyme cleavage sites within the hepatitis B virus.Nucleic acids research · 2002Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have investigated the relative merits of two commonly used methods for target site selection for ribozymes: secondary structure prediction (MFold program) and in vitro accessibility assays. A total of eight methylated ribozymes with DNA arms were synthesized and analyzed in a transient co-transfection assay in HeLa cells. Residual expression levels ranging from 23 to 72% were obtained with anti-PSKH1 ribozymes compared to cells transfected with an irrelevant control ribozyme. Ribozyme efficacy depended on both ribozyme concentration and the steady state expression levels of the target mRNA. Allylated ribozymes against a subset of the target sites generally displayed poorer efficacy than their methylated counterparts. This effect appeared to be influenced by in vivo accessibility of the target site. Ribozymes designed on the basis of either selection method displayed a wide range of efficacies with no significant differences in the average activities of the two groups of ribozymes. While in vitro accessibility assays had limited predictive power, there was a significant correlation between certain features of the predicted secondary structure of the target sequence and the efficacy of the corresponding ribozyme. Specifically, ribozyme efficacy appeared to be positively correlated with the presence of short stem regions and helices of low stability within their target sequences. There were no correlations with predicted free energy or loop length.
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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.