ArticleNucleic acids research2003
OligoDesign: Optimal design of LNA (locked nucleic acid) oligonucleotide capture probes for gene expression profiling.
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 48 papers.
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48 citing papers in PubMed, 127 citations in OpenAlex.
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- Tips to Design Effective Splice-Switching Antisense Oligonucleotides for Exon Skipping and Exon Inclusion.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Improving DNA nanostructure stability: A review of the biomedical applications and approaches.International journal of biological macromolecules · 2024Review
- Multiplex Real-Time PCR for the Detection of Tetracycline, Ciprofloxacin, and Erythromycin Resistance Determinants from Human and FoodborneMicroorganisms · 2023Article
- Simultaneous detection of miRNA and mRNA at the single-cell level in plant tissues.Plant biotechnology journal · 2023Article
- Exciton Delocalization and Scaffold Stability in Bridged Nucleotide-Substituted, DNA Duplex-Templated Cyanine Aggregates.The journal of physical chemistry. B · 2021Article
- Article
- MicroRNAs as regulators of brain function and targets for treatment of epilepsy.Nature reviews. Neurology · 2020Review
- Likelihood of Nonspecific Activity of Gapmer Antisense Oligonucleotides Is Associated with Relative Hybridization Free Energy.Nucleic acid therapeutics · 2020Article
- Multiplex Real-Time PCR-shortJournal of clinical microbiology · 2019Article
- Anti-Niemann Pick C1 Single-Stranded Oligonucleotides with Locked Nucleic Acids Potently Reduce Ebola Virus Infection In Vitro.Molecular therapy. Nucleic acids · 2019Article
- Nucleoporin 107, 62 and 153 mediate Kcnq1ot1 imprinted domain regulation in extraembryonic endoderm stem cells.Nature communications · 2018Article
- A real-time PCR approach to identify anthelmintic-resistant nematodes in sheep farms.Parasitology research · 2017Article
- Zebrafish as an In Vivo Model to Assess Epigenetic Effects of Ionizing Radiation.International journal of molecular sciences · 2016Review
- Current Technologies and Recent Developments for Screening of HPV-Associated Cervical and Oropharyngeal Cancers.Cancers · 2016Review
- Mapping the nicking efficiencies of nickase R.BbvCI for side-specific LNA-substituted substrates using rolling circle amplification.Scientific reports · 2016Article
- Amplification-free in situ KRAS point mutation detection at 60 copies per mL in urine in a background of 1000-fold wild type.The Analyst · 2016Article
- Preimplantation genetic screening of blastocysts by multiplex qPCR followed by fresh embryo transfer: validation and verification.Molecular cytogenetics · 2015Article
- LNA-modified isothermal oligonucleotide microarray for differentiating bacilli of similar origin.Journal of biosciences · 2014Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We report the development of new software, OligoDesign, which provides optimal design of LNA (locked nucleic acid) substituted oligonucleotides for functional genomics applications. LNAs constitute a novel class of bicyclic RNA analogs having an exceptionally high affinity and specificity toward their complementary DNA and RNA target molecules. The OligoDesign software features recognition and filtering of the target sequence by genome-wide BLAST analysis in order to minimize cross-hybridization with non-target sequences. Furthermore it includes routines for prediction of melting temperature, self-annealing and secondary structure for LNA substituted oligonucleotides, as well as secondary structure prediction of the target nucleotide sequence. Individual scores for all these properties are calculated for each possible LNA oligonucleotide in the query gene and the OligoDesign program ranks the LNA capture probes according to a combined fuzzy logic score and finally returns the top scoring probes to the user in the output. We have successfully used the OligoDesign tool to design a Caenorhabditis elegans LNA oligonucleotide microarray, which allows monitoring of the expression of a set of 120 potential marker genes for a variety of stress and toxicological processes and toxicologically relevant pathways. The OligoDesign program is freely accessible at http://lnatools.com/.
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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.