ArticleNucleic acids research2003
Prioritized selection of oligodeoxyribonucleotide probes for efficient hybridization to RNA transcripts.
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.
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Who cites it
32 citing papers in PubMed.
- Developing, Characterizing, and Modeling CRISPR-Based Point-of-Use Pathogen Diagnostics.ACS synthetic biology · 2025Article
- Developing, characterizing and modeling CRISPR-based point-of-use pathogen diagnostics.bioRxiv : the preprint server for biology · 2024Article
- Single molecule fluorescence approaches shed light on intracellular RNAs.Chemical reviews · 2014Review
- Subtyping clinical specimens of influenza A virus by use of a simple method to amplify RNA targets.Journal of clinical microbiology · 2013Article
- Engineering insights for multiplexed real-time nucleic acid sequence-based amplification (NASBA): implications for design of point-of-care diagnostics.Molecular diagnosis & therapy · 2013Article
- Detection of HIV-1 minority variants containing the K103N drug-resistance mutation using a simple method to amplify RNA targets (SMART).The Journal of molecular diagnostics : JMD · 2013Article
- Physico-chemical foundations underpinning microarray and next-generation sequencing experiments.Nucleic acids research · 2013Review
- A simple method for amplifying RNA targets (SMART).The Journal of molecular diagnostics : JMD · 2012Article
- A species independent universal bio-detection microarray for pathogen forensics and phylogenetic classification of unknown microorganisms.BMC microbiology · 2011Article
- Strand-specific transcriptome profiling with directly labeled RNA on genomic tiling microarrays.BMC molecular biology · 2011Article
- Dynamic probe selection for studying microbial transcriptome with high-density genomic tiling microarrays.BMC bioinformatics · 2010Article
- Hybridization thermodynamics of NimbleGen microarrays.BMC bioinformatics · 2010Article
- Absolute quantification of microRNAs by using a universal reference.RNA (New York, N.Y.) · 2009Article
- Rapid determination of RNA accessible sites by surface plasmon resonance detection of hybridization to DNA arrays.Analytical chemistry · 2009Article
- Imaging intracellular RNA distribution and dynamics in living cells.Nature methods · 2009Review
- Model-based probe set optimization for high-performance microarrays.Nucleic acids research · 2009Article
- Impact of point-mutations on the hybridization affinity of surface-bound DNA/DNA and RNA/DNA oligonucleotide-duplexes: comparison of single base mismatches and base bulges.BMC biotechnology · 2008Article
- In situ-synthesized virulence and marker gene biochip for detection of bacterial pathogens in water.Applied and environmental microbiology · 2008Article
- Use of a multi-thermal washer for DNA microarrays simplifies probe design and gives robust genotyping assays.Nucleic acids research · 2008Article
- Monitoring of transcriptional regulation in Pichia pastoris under protein production conditions.BMC genomics · 2007Article
Corrections and comments
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3 authors.
Funding
Abstract
Only a small fraction of short oligonucleotide probes bind efficiently to complementary segments in long RNA transcripts. Technologies such as array-based transcript profiling and antisense control of gene expression would benefit greatly from a method for predicting probes that bind well to a given target RNA. To develop an algorithm for prioritizing selection of probes, we have analyzed predicted thermodynamic parameters for the binding of several large sets of probes to complementary RNA transcripts. The binding of five of these sets of probes to their RNA targets has been reported by others. In addition, we have used a method for light-directed synthesis of oligonucleotide arrays that we developed to generate two new arrays of surface-bound probes and measured the binding of these probes to their RNA targets. We considered predicted free energies for intramolecular base pairing of the oligonucleotide and its RNA target as well as the predicted free energy of intermolecular hybridization of probe and target. We find that a reliable predictor of probes that will hybridize significantly with their targeted transcripts is the predicted free energy of hybridization minus the predicted free energy for intramolecular folding of the probe.
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