ArticleNucleic acids research2007
A systematic analysis of the effect of target RNA structure on RNA interference.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed.
- Rational dsRNA design, scalable production and nanodelivery to enhance spray-induced gene silencing.Communications biology · 2026Review
- Article
- Evaluation of the effect of RNA secondary structure on Cas13d-mediated target RNA cleavage.Molecular therapy. Nucleic acids · 2024Article
- mRNA Nuclear Clustering Leads to a Difference in Mutant Huntingtin mRNA and Protein Silencing by siRNAsNucleic acid therapeutics · 2024Article
- mRNA nuclear clustering leads to a difference in mutant huntingtin mRNA and protein silencing by siRNAsbioRxiv : the preprint server for biology · 2024Article
- In Silico Prediction and Selection of Target Sequences in the SARS-CoV-2 RNA Genome for an Antiviral Attack.Viruses · 2022Article
- Targeting genomic SARS-CoV-2 RNA with siRNAs allows efficient inhibition of viral replication and spread.Nucleic acids research · 2022Article
- Self-crosslinkable chitosan-hyaluronic acid dialdehyde nanoparticles for CD44-targeted siRNA delivery to treat bladder cancer.Bioactive materials · 2021Article
- RNA Secondary Structure as a First Step for Rational Design of the Oligonucleotides towards Inhibition of Influenza A Virus Replication.Pathogens (Basel, Switzerland) · 2020Review
- RNA Secondary Structure Motifs of the Influenza A Virus as Targets for siRNA-Mediated RNA Interference.Molecular therapy. Nucleic acids · 2020Article
- Highly efficacious antiviral protection of plants by small interfering RNAs identified in vitro.Nucleic acids research · 2019Article
- Structure of HIV-1 RT/dsRNA initiation complex prior to nucleotide incorporation.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Review
- Strategies for Improving siRNA-Induced Gene Silencing Efficiency.Advanced pharmaceutical bulletin · 2017Article
- Silencing of HIV-1 by AgoshRNA molecules.Gene therapy · 2017Article
- Improving miRNA Delivery by Optimizing miRNA Expression Cassettes in Diverse Virus Vectors.Human gene therapy methods · 2017Review
- Article
- Precise and efficient siRNA design: a key point in competent gene silencing.Cancer gene therapy · 2016Review
- A Method to Predict the Structure and Stability of RNA/RNA Complexes.Methods in molecular biology (Clifton, N.J.) · 2016Article
- The impact of HIV-1 genetic diversity on the efficacy of a combinatorial RNAi-based gene therapy.Gene therapy · 2015Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNAi efficiency is influenced by local RNA structure of the target sequence. We studied this structure-based resistance in detail by targeting a perfect RNA hairpin and subsequently destabilized its tight structure by mutation, thereby gradually exposing the target sequence. Although the tightest RNA hairpins were completely resistant to RNAi, we observed an inverse correlation between the overall target hairpin stability and RNAi efficiency within a specific thermodynamic stability (DeltaG) range. Increased RNAi efficiency was shown to be caused by improved binding of the siRNA to the destabilized target RNA hairpins. The mutational effects vary for different target regions. We find an accessible target 3' end to be most important for RNAi-mediated inhibition. However, these 3' end effects cannot be reproduced in siRNA-target RNA-binding studies in vitro, indicating the important role of RISC components in the in vivo RNAi reaction. The results provide a more detailed insight into the impact of target RNA structure on RNAi and we discuss several possible implications. With respect to lentiviral-mediated delivery of shRNA expression cassettes, we present a DeltaG window to destabilize the shRNA insert for vector improvement, while avoiding RNAi-mediated self-targeting during lentiviral vector production.
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