ArticleNucleic acids research2008
Efficient siRNA selection using hybridization thermodynamics.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
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Who cites it
83 citing papers in PubMed.
- Accurately modeling RNase H-mediated antisense oligonucleotide efficacy.Molecular therapy. Nucleic acids · 2026Article
- Nearest Neighbor Parameters for Estimating the Folding Stability of RNA Including Pseudouridine.bioRxiv : the preprint server for biology · 2026Article
- Design of therapeutic siRNAs for potential application to infection with chikungunya virus.Heliyon · 2025Article
- Haemaphysalis longicornis subolesin controls the infection and transmission of severe fever with thrombocytopenia syndrome virus.NPJ vaccines · 2025Article
- siRNAEfficacyDB: An experimentally supported small interfering RNA efficacy database.IET systems biology · 2024Article
- Using the RNAstructure Software Package to Predict Conserved RNA Structures.Current protocols · 2024Article
- OligoFormer: an accurate and robust prediction method for siRNA design.Bioinformatics (Oxford, England) · 2024Article
- CheRRI-Accurate classification of the biological relevance of putative RNA-RNA interaction sites.GigaScience · 2024Article
- Estimating RNA Secondary Structure Folding Free Energy Changes with efn2.Methods in molecular biology (Clifton, N.J.) · 2024Article
- RNAi-Mediated Silencing in the Insect Cell-Baculovirus Expression System.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Asymmetric trichotomous partitioning overcomes dataset limitations in building machine learning models for predicting siRNA efficacy.Molecular therapy. Nucleic acids · 2023Article
- RNA Secondary Structure Analysis Using RNAstructure.Current protocols · 2023Article
- Nearest-neighbor parameters for the prediction of RNA duplex stability in diverse in vitro and cellular-like crowding conditions.Nucleic acids research · 2023Article
- LazySampling and LinearSampling: fast stochastic sampling of RNA secondary structure with applications to SARS-CoV-2.Nucleic acids research · 2023Article
- DeepRaccess: high-speed RNA accessibility prediction using deep learning.Frontiers in bioinformatics · 2023Article
- Therapeutic siRNA: State-of-the-Art and Future Perspectives.BioDrugs : clinical immunotherapeutics, biopharmaceuticals and gene therapy · 2022Review
- Nearest neighbor rules for RNA helix folding thermodynamics: improved end effects.Nucleic acids research · 2022Article
- A Comprehensive Computational Investigation into the Conserved Virulent Proteins ofMolecules (Basel, Switzerland) · 2022Article
- Secondary structure prediction for RNA sequences including NNature communications · 2022Article
- CaSilico: A versatile CRISPR package forFrontiers in bioengineering and biotechnology · 2022Article
23 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
Abstract
Small interfering RNA (siRNA) are widely used to infer gene function. Here, insights in the equilibrium of siRNA-target hybridization are used for selection of efficient siRNA. The accessibilities of siRNA and target mRNA for hybridization, as measured by folding free energy change, are shown to be significantly correlated with efficacy. For this study, a partition function calculation that considers all possible secondary structures is used to predict target site accessibility; a significant improvement over calculations that consider only the predicted lowest free energy structure or a set of low free energy structures. The predicted thermodynamic features, in addition to siRNA sequence features, are used as input for a support vector machine that selects functional siRNA. The method works well for predicting efficient siRNA (efficacy >70%) in a large siRNA data set from Novartis. The positive predictive value (percentage of sites predicted to be efficient for silencing that are) is as high as 87.6%. The sensitivity and specificity are 22.7 and 96.5%, respectively. When tested on data from different sources, the positive predictive value increased 8.1% by adding equilibrium terms to 25 local sequence features. Prediction of hybridization affinity using partition functions is now available in the RNAstructure software package.
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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.