ArticleNucleic acids research2006
Rational design and rapid screening of antisense oligonucleotides for prokaryotic gene modulation.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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
27 citing papers in PubMed, 50 citations in OpenAlex.
- Silencing with precision: In silico strategies for antisense oligonucleotide engineering.Molecular biology reports · 2026Review
- Accurately modeling RNase H-mediated antisense oligonucleotide efficacy.Molecular therapy. Nucleic acids · 2026Article
- Functional characterization of dynamic nascent RNA folding ensembles in real time.Science advances · 2026Article
- Surface Plasmon Resonance Analysis for Evaluating ASO Targeting Structured RNA.Methods and protocols · 2026Article
- New approaches to uncover COPD pathobiology and develop therapies.JCI insight · 2026Review
- ASOptimizer: optimizing chemical diversity of antisense oligonucleotides through deep learning.Nucleic acids research · 2025Article
- RNA toehold switch-based reporter assay to assess bacterial uptake of antisense oligomers.mBio · 2025Article
- Review
- ASOptimizer: Optimizing antisense oligonucleotides through deep learning for IDO1 gene regulation.Molecular therapy. Nucleic acids · 2024Article
- Post-transcriptional modification of mCell death & disease · 2023Article
- Article
- Morpholino Oligomer-Induced Dystrophin Isoforms to Map the Functional Domains in the Dystrophin Protein.Molecular therapy. Nucleic acids · 2020Article
- Exploring of the feature space of de novo developed post-transcriptional riboregulators.PLoS computational biology · 2018Article
- Optimization of a novel biophysical model using large scale in vivo antisense hybridization data displays improved prediction capabilities of structurally accessible RNA regions.Nucleic acids research · 2017Article
- A molecular nanodevice for targeted degradation of mRNA during protein synthesis.Scientific reports · 2016Article
- Bolaamphiphile-based nanocomplex delivery of phosphorothioate gapmer antisense oligonucleotides as a treatment for Clostridium difficile.International journal of nanomedicine · 2016Article
- The 5'-tail of antisense RNAII of pMV158 plays a critical role in binding to the target mRNA and in translation inhibition of repB.Frontiers in genetics · 2015Article
- Fine-Tuning of the Fatty Acid Pathway by Synthetic Antisense RNA for Enhanced (2S)-Naringenin Production from l-Tyrosine in Escherichia coli.Applied and environmental microbiology · 2014Article
- Global or local? Predicting secondary structure and accessibility in mRNAs.Nucleic acids research · 2012Article
- Computational prediction of efficient splice sites for trans-splicing ribozymes.RNA (New York, N.Y.) · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Antisense oligodeoxynucleotides (oligos) are widely used for functional studies of both prokaryotic and eukaryotic genes. However, the identification of effective target sites is a major issue in antisense applications. Here, we study a number of thermodynamic and structural parameters that may affect the potency of antisense inhibition. We develop a cell-free assay for rapid oligo screening. This assay is used for measuring the expression of Escherichia coli lacZ, the antisense target for experimental testing and validation. Based on a training set of 18 oligos, we found that structural accessibility predicted by local folding of the target mRNA is the most important predictor for antisense activity. This finding was further confirmed by a direct validation study. In this study, a set of 10 oligos was designed to target accessible sites, and another set of 10 oligos was selected to target inaccessible sites. Seven of the 10 oligos for accessible sites were found to be effective (>50% inhibition), but none of the oligos for inaccessible sites was effective. The difference in the antisense activity between the two sets of oligos was statistically significant. We also found that the predictability of antisense activity by target accessibility was greatly improved for oligos targeted to the regions upstream of the end of the active domain for beta-galactosidase, the protein encoded by lacZ. The combination of the structure-based antisense design and extension of the lacZ assay to include gene fusions will be applicable to high-throughput gene functional screening, and to the identification of new drug targets in pathogenic microbes. Design tools are available through the Sfold Web server at http://sfold.wadsworth.org.
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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.