ArticleNucleic acids research2003
Thermodynamic criteria for high hit rate antisense oligonucleotide design.
Article in Nucleic acids research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 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
32 citing papers in PubMed, 75 citations in OpenAlex.
- Survivin-Targeting Antisense Oligonucleotides in Cancer Therapy.Molecules (Basel, Switzerland) · 2026Review
- RNA G‑Quadruplex Reprogramming with Guanine-Rich Antisense Oligonucleotides Inhibits Monoamine Oxidase B's Translation.ACS bio & med chem Au · 2025Article
- RNA Secondary Structure Analysis Using RNAstructure.Current protocols · 2023Article
- Small Drugs, Huge Impact: The Extraordinary Impact of Antisense Oligonucleotides in Research and Drug Development.Molecules (Basel, Switzerland) · 2022Review
- Sequence characteristics define trade-offs between on-target and genome-wide off-target hybridization of oligoprobes.PloS one · 2018Article
- Managing the sequence-specificity of antisense oligonucleotides in drug discovery.Nucleic acids research · 2017Review
- Silencing efficacy prediction: a retrospective study on target mRNA features.Bioscience reports · 2015Article
- Reversion of antibiotic resistance by inhibiting mecA in clinical methicillin-resistant Staphylococci by antisense phosphorothioate oligonucleotide.The Journal of antibiotics · 2015Article
- 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
- RNAstructure: Web servers for RNA secondary structure prediction and analysis.Nucleic acids research · 2013Article
- Optimized models for design of efficient miR30-based shRNAs.Frontiers in genetics · 2012Article
- Co-blockade of mecR1/blaR1 signal pathway to restore antibiotic susceptibility in clinical isolates of methicillin-resistant Staphylococcus aureus.Archives of medical science : AMS · 2011Article
- Variables and strategies in development of therapeutic post-transcriptional gene silencing agents.Journal of ophthalmology · 2011Article
- Article
- Antisense DNA parameters derived from next-nearest-neighbor analysis of experimental data.BMC bioinformatics · 2010Article
- RNAstructure: software for RNA secondary structure prediction and analysis.BMC bioinformatics · 2010Article
- Fundamental differences in the equilibrium considerations for siRNA and antisense oligodeoxynucleotide design.Nucleic acids research · 2008Article
- Identification of sequence motifs significantly associated with antisense activity.BMC bioinformatics · 2007Article
- RNA secondary structure prediction.Current protocols in nucleic acid chemistry · 2007Article
- The orphan receptor GPR17 identified as a new dual uracil nucleotides/cysteinyl-leukotrienes receptor.The EMBO journal · 2006Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
Antisense oligonucleotides are used for therapeutic applications and in functional genomic studies. In practice, however, many of the oligonucleotides complementary to an mRNA have little or no antisense activity. Theoretical strategies to improve the 'hit rate' in antisense screens will reduce the cost of discovery and may lead to identification of antisense oligonucleotides with increased potency. Statistical analysis performed on data collected from more than 1000 experiments with phosphorothioate-modified oligonucleotides revealed that the oligo-probes, which form stable duplexes with RNA (DeltaG(o)37 < or = -30 kcal/mol) and have small self-interaction potential, are more frequently efficient than molecules that form less stable oligonucleotide-RNA hybrids or more stable self-structures. To achieve optimal statistical preference, the values for self-interaction should be (DeltaG(o)37) > or = -8 kcal/mol for inter-oligonucleotide pairing and (DeltaG(o)37) > or = -1.1 kcal/mol for intra-molecular pairing. Selection of oligonucleotides with these thermodynamic values in the analyzed experiments would have increased the 'hit rate' by as much as 6-fold.
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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.