ArticleNucleic acids research2000
RNA accessibility prediction: a theoretical approach is consistent with experimental studies in cell extracts.
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 25 papers.
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Who cites it
25 citing papers in PubMed, 90 citations in OpenAlex.
- Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites.PLoS computational biology · 2021Article
- Effects of Pathogenic Variations in the Human Rhodopsin Gene (hRHO) on the Predicted Accessibility for a Lead Candidate Ribozyme.Investigative ophthalmology & visual science · 2017Article
- Rational design of inducible CRISPR guide RNAs for de novo assembly of transcriptional programs.Nature communications · 2017Article
- A cellular high-throughput screening approach for therapeutic trans-cleaving ribozymes and RNAi against arbitrary mRNA disease targets.Experimental eye research · 2016Article
- Variables and strategies in development of therapeutic post-transcriptional gene silencing agents.Journal of ophthalmology · 2011Article
- Antisense gapmers selectively suppress individual oncogenic p73 splice isoforms and inhibit tumor growth in vivo.Molecular cancer · 2009Article
- Development of lead hammerhead ribozyme candidates against human rod opsin mRNA for retinal degeneration therapy.Experimental eye research · 2009Article
- Ribozyme cleavage of Plasmodium falciparum gyrase A gene transcript affects the parasite growth.Parasitology research · 2008Article
- Bottlenecks in development of retinal therapeutic post-transcriptional gene silencing agents.Vision research · 2008Review
- Hitting bacteria at the heart of the central dogma: sequence-specific inhibition.Microbial cell factories · 2007Article
- Identification of sequence motifs significantly associated with antisense activity.BMC bioinformatics · 2007Article
- Integrated siRNA design based on surveying of features associated with high RNAi effectiveness.BMC bioinformatics · 2006Article
- Selection of antisense oligonucleotides based on multiple predicted target mRNA structures.BMC bioinformatics · 2006Article
- Secondary structure in the target as a confounding factor in synthetic oligomer microarray design.BMC genomics · 2005Article
- Selection of optimal antisense accessible sites of survivin and its application in treatment of gastric cancer.World journal of gastroenterology · 2005Article
- Profiled support vector machines for antisense oligonucleotide efficacy prediction.BMC bioinformatics · 2004Article
- Downregulation of osteopontin and bone sialoprotein II is related to reduced colony formation and metastasis formation of MDA-MB-231 human breast cancer cells.Cancer gene therapy · 2004Article
- Thermodynamic criteria for high hit rate antisense oligonucleotide design.Nucleic acids research · 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
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
The use of antisense oligodeoxyribonucleotides (ODN) or ribozymes to specifically suppress gene expression is simple in concept and relies on efficient binding of the antisense strand to the target RNA. Although the identification of target sites accessible to base pairing is gradually being overcome by different techniques, it remains a major problem in the antisense and ribozyme approaches. In this study we have investigated the potential of a recent experimental and theoretical approach to predict the local accessibility of murine DNA-methyltransferase (MTase) mRNA in a comparative way. The accessibility of the native target RNA was probed with antisense ODN in cellular extracts. The results strongly correlated with the theoretically predicted target accessibility. This work suggests an effective two-step procedure for predicting RNA accessibility: first, computer-aided selection of ODN binding sites defined by an accessibility score followed by a more detailed experimental procedure to derive information about target accessibility at the single nucleotide level.
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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.