ArticleNucleic acids research2009
Selection of hyperfunctional siRNAs with improved potency and specificity.
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 36 papers, 2 of them syntheses that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
36 citing papers in PubMed, 2 syntheses or guidelines pooled it, 68 citations in OpenAlex.
- RNA Drugs and RNA Targets for Small Molecules: Principles, Progress, and Challenges.Pharmacological reviews · 2020Pooled it
- An overview and metanalysis of machine and deep learning-based CRISPR gRNA design tools.RNA biology · 2020Pooled it
- Two-Stage Probability-Enhanced Regression on Property Matrices and LLM Embeddings Enables State-of-the-Art Prediction of Gene Knockdown by Modified siRNAs.International journal of molecular sciences · 2025Article
- siRNA Cocktail Targeting Multiple Enterovirus 71 Genes Prevents Escape Mutants and Inhibits Viral Replication.International journal of molecular sciences · 2025Article
- Small Interfering RNAs Targeting VP4, VP3, 2B, or 3A Coding Regions of Enterovirus A71 Inhibit Viral Replication In Vitro.Biomedicines · 2025Article
- RNAi-directed knockdown in the cnidarian fish blood parasite Sphaerospora molnari.Scientific reports · 2024Article
- Advancements in genome editing tools for genetic studies and crop improvement.Frontiers in plant science · 2024Review
- Small interfering RNA (siRNA)-based therapeutic applications against viruses: principles, potential, and challenges.Journal of biomedical science · 2023Review
- Gene targeting as a therapeutic avenue in diseases mediated by the complement alternative pathway.Immunological reviews · 2023Review
- Computational Approaches for Designing Highly Specific and Efficient sgRNAs.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Review
- The double edge of anti-CD40 siRNA therapy: It increases renal microcapillar density but favours the generation of an inflammatory milieu in the kidneys of ApoEJournal of inflammation (London, England) · 2019Article
- Editorial focus: understanding off-target effects as the key to successful RNAi therapy.Cellular & molecular biology letters · 2019Review
- A review on current status of antiviral siRNA.Reviews in medical virology · 2018Review
- A delayed proinflammatory response of human preadipocytes to PCB126 is dependent on the aryl hydrocarbon receptor.Environmental science and pollution research international · 2018Article
- Pseudohypoxia induced by miR-126 deactivation promotes migration and therapeutic resistance in renal cell carcinoma.Cancer letters · 2017Article
- Calreticulin is required for calcium homeostasis and proper pollen tube tip growth in Petunia.Planta · 2017Article
- Cellular localization of long non-coding RNAs affects silencing by RNAi more than by antisense oligonucleotides.Nucleic acids research · 2016Article
- WU-CRISPR: characteristics of functional guide RNAs for the CRISPR/Cas9 system.Genome biology · 2015Article
- siRNA Versus miRNA as Therapeutics for Gene Silencing.Molecular therapy. Nucleic acids · 2015Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
One critical step in RNA interference (RNAi) experiments is to design small interfering RNAs (siRNAs) that can greatly reduce the expression of the target transcripts, but not of other unintended targets. Although various statistical and computational approaches have been attempted, this remains a challenge facing RNAi researchers. Here, we present a new experimentally validated method for siRNA design. By analyzing public siRNA data and focusing on hyperfunctional siRNAs, we identified a set of sequence features as potency selection criteria to build an siRNA design algorithm with support vector machines. Additional bioinformatics filters were also included in the algorithm to increase RNAi specificity by reducing potential sequence cross-hybridization or microRNA-like effects. Independent validation experiments were performed, which indicated that the newly designed siRNAs have significantly improved performance, and worked effectively even at low concentrations. Furthermore, our cell-based studies demonstrated that the siRNA off-target effects were significantly reduced when the siRNAs were delivered into cells at the 3 nM concentration compared to 30 nM. Thus, the capability of our new design program to select highly potent siRNAs also renders increased RNAi specificity because these siRNAs can be used at a much lower concentration. The siRNA design web server is available at http://www5.appliedbiosystems.com/tools/siDesign/.
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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.