ArticleBMC bioinformatics2009
A structural interpretation of the effect of GC-content on efficiency of RNA interference.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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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
52 citing papers in PubMed.
- GC content mismatch of transgene destabilizes RNA virus genomes.Journal of virology · 2026Article
- Rational dsRNA design, scalable production and nanodelivery to enhance spray-induced gene silencing.Communications biology · 2026Review
- Unfolding of RNA secondary structure impairs RNA stability to fine-tune phosphate starvation responses in rice roots.Plant communications · 2026Article
- Single-round evolution of RNA aptamers with GRAPE-LM.Nature biotechnology · 2026Article
- Coarse-Grained Modeling and Simulation of Multistranded RNA Nanostars.Chem & bio engineering · 2026Article
- In vivo RNA structure influences the translation and stability of plant long non-coding RNAs.Plant communications · 2026Article
- siRNA Cocktail Targeting Multiple Enterovirus 71 Genes Prevents Escape Mutants and Inhibits Viral Replication.International journal of molecular sciences · 2025Article
- Designing siRNAs against non-structural genes of all serotypes of Dengue virus using RNAi technology - A computational investigation.Journal, genetic engineering & biotechnology · 2025Article
- Review
- Small Interfering RNAs Targeting VP4, VP3, 2B, or 3A Coding Regions of Enterovirus A71 Inhibit Viral Replication In Vitro.Biomedicines · 2025Article
- The quantitative impact of 3'UTRs on gene expression.Nucleic acids research · 2025Article
- Unraveling unbreakable hairpins: characterizing RNA secondary structures that are persistent after dinucleotide shuffling.RNA (New York, N.Y.) · 2025Article
- Comparative Analysis of Codon Optimization Tools: Advancing toward a Multi-Criteria Framework for Synthetic Gene Design.Journal of microbiology and biotechnology · 2025Article
- Article
- Tips to Design Effective Splice-Switching Antisense Oligonucleotides for Exon Skipping and Exon Inclusion.Methods in molecular biology (Clifton, N.J.) · 2025Article
- A Reverse Vaccinology and Immunoinformatic Approach for the Designing of a Novel mRNA Vaccine Against Stomach Cancer Targeting the Potent Pathogenic Proteins ofBioinformatics and biology insights · 2025Article
- Personalized mRNA vaccines in glioblastoma therapy: from rational design to clinical trials.Journal of nanobiotechnology · 2024Review
- Exploring the challenges of RNAi-based strategies for crop protection.Advanced biotechnology · 2024Review
- Evaluating storage conditions and enhancement strategies on viral biomarker recovery for WBE applications.Water science and technology : a journal of the International Association on Water Pollution Research · 2024Article
- Sensing nucleotide composition in virus RNA.Bioscience reports · 2023Review
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
backgroundRNA interference (RNAi) mediated by small interfering RNAs (siRNAs) or short hairpin RNAs (shRNAs) has become a powerful technique for eukaryotic gene knockdown. siRNA GC-content negatively correlates with RNAi efficiency, and it is of interest to have a convincing mechanistic interpretation of this observation. We here examine this issue by considering the secondary structures for both the target messenger RNA (mRNA) and the siRNA guide strand.
resultsBy analyzing a unique homogeneous data set of 101 shRNAs targeted to 100 endogenous human genes, we find that: 1) target site accessibility is more important than GC-content for efficient RNAi; 2) there is an appreciable negative correlation between GC-content and RNAi activity; 3) for the predicted structure of the siRNA guide strand, there is a lack of correlation between RNAi activity and either the stability or the number of free dangling nucleotides at an end of the structure; 4) there is a high correlation between target site accessibility and GC-content. For a set of representative structural RNAs, the GC content of 62.6% for paired bases is significantly higher than the GC content of 38.7% for unpaired bases. Thus, for a structured RNA, a region with higher GC content is likely to have more stable secondary structure. Furthermore, by partial correlation analysis, the correlation for GC-content is almost completely diminished, when the effect of target accessibility is controlled.
conclusionThese findings provide a target-structure-based interpretation and mechanistic insight for the effect of GC-content on RNAi efficiency.
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Registered trials
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