ArticleNucleic acids research2008
Fundamental differences in the equilibrium considerations for siRNA and antisense oligodeoxynucleotide design.
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 16 papers.
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Who cites it
16 citing papers in PubMed.
- Internal cap-initiated translation for efficient protein production from circular mRNA.Nature biotechnology · 2026Article
- 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
- RNA Secondary Structure Analysis Using RNAstructure.Current protocols · 2023Article
- Nearest neighbor rules for RNA helix folding thermodynamics: improved end effects.Nucleic acids research · 2022Article
- LinearTurboFold: Linear-time global prediction of conserved structures for RNA homologs with applications to SARS-CoV-2.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- LinearTurboFold: Linear-Time Global Prediction of Conserved Structures for RNA Homologs with Applications to SARS-CoV-2.bioRxiv : the preprint server for biology · 2021Article
- Ribosome as a Translocase and Helicase.Biochemistry. Biokhimiia · 2021Review
- Making ends meet: New functions of mRNA secondary structure.Wiley interdisciplinary reviews. RNA · 2021Review
- Article
- RNAstructure: Web servers for RNA secondary structure prediction and analysis.Nucleic acids research · 2013Article
- Quantifying the sequence-function relation in gene silencing by bacterial small RNAs.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- RNAstructure: software for RNA secondary structure prediction and analysis.BMC bioinformatics · 2010Article
- Secondary RNA structure and its role in RNA interference to silence the respiratory syncytial virus fusion protein gene.Molecular biotechnology · 2009Article
- RNA secondary structure analysis using RNAstructure.Current protocols in bioinformatics · 2006Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Both siRNA and antisense oligodeoxynucleotides (ODNs) inhibit the expression of a complementary gene. In this study, fundamental differences in the considerations for RNA interference and antisense ODNs are reported. In siRNA and antisense ODN databases, positive correlations are observed between the cost to open the mRNA target self-structure and the stability of the duplex to be formed, meaning the sites along the mRNA target with highest potential to form strong duplexes with antisense strands also have the greatest tendency to be involved in pre-existing structure. Efficient siRNA have less stable siRNA-target duplex stability than inefficient siRNA, but the opposite is true for antisense ODNs. It is, therefore, more difficult to avoid target self-structure in antisense ODN design. Self-structure stabilities of oligonucleotide and target correlate to the silencing efficacy of siRNA. Oligonucleotide self-structure correlations to efficacy of antisense ODNs, conversely, are insignificant. Furthermore, self-structure in the target appears to correlate with antisense ODN efficacy, but such that more effective antisense ODNs appear to target mRNA regions with greater self-structure. Therefore, different criteria are suggested for the design of efficient siRNA and antisense ODNs and the design of antisense ODNs is more challenging.
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Registered trials
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