ArticleApplied and environmental microbiology2003
Optimization strategies for DNA microarray-based detection of bacteria with 16S rRNA-targeting oligonucleotide probes.
Article in Applied and environmental microbiology, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed, 197 citations in OpenAlex.
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- Molecular Techniques for the Detection of Organisms in Aquatic Environments, with Emphasis on Harmful Algal Bloom Species.Sensors (Basel, Switzerland) · 2017Review
- Development of oligonucleotide microarrays for simultaneous multi-species identification of Phellinus tree-pathogenic fungi.Microbial biotechnology · 2016Article
- Application of reverse dot blot hybridization to simultaneous detection and identification of harmful algae.Environmental science and pollution research international · 2015Article
- Influence of the length of target DNA overhang proximal to the array surface on discrimination of single-base mismatches on a 25-mer oligonucleotide array.BMC research notes · 2014Article
- Single-stranded DNA catalyzes hybridization of PCR-products to microarray capture probes.PloS one · 2014Article
- Effect of Target Length on Specificity and Sensitivity of Oligonucleotide Microarrays: A Comparison between Dendrimer and Modified PCR based Labelling Methods.The open biochemistry journal · 2014Article
- Microarray testing for the presence of toxic algae monitoring programme in Galicia (NW Spain).Environmental science and pollution research international · 2013Article
- The human gut chip "HuGChip", an explorative phylogenetic microarray for determining gut microbiome diversity at family level.PloS one · 2013Article
- Evaluation of a fosmid-clone-based microarray for comparative analysis of swine fecal metagenomes.Journal of microbiology (Seoul, Korea) · 2012Article
- Identification of non-specific hybridization using an empirical equation fitted to non-equilibrium dissociation curves.Journal of microbiological methods · 2012Article
- Application of phylogenetic microarrays to interrogation of human microbiota.FEMS microbiology ecology · 2012Review
- Modeling formamide denaturation of probe-target hybrids for improved microarray probe design in microbial diagnostics.PloS one · 2012Article
- Simultaneous detection of multiple fish pathogens using a naked-eye readable DNA microarray.Sensors (Basel, Switzerland) · 2012Article
- Analysis of methanotroph community composition using a pmoA-based microbial diagnostic microarray.Nature protocols · 2011Article
- Detection of representative enteropathogenic bacteria, Vibrio spp., pathogenic Escherichia coli, Salmonella spp., Shigella spp., and Yersinia enterocolitica, using a virulence factor gene-based oligonucleotide microarray.Journal of microbiology (Seoul, Korea) · 2010Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The usability of the DNA microarray format for the specific detection of bacteria based on their 16S rRNA genes was systematically evaluated with a model system composed of six environmental strains and 20 oligonucleotide probes. Parameters such as secondary structures of the target molecules and steric hindrance were investigated to better understand the mechanisms underlying a microarray hybridization reaction, with focus on their influence on the specificity of hybridization. With adequate hybridization conditions, false-positive signals could be almost completely prevented, resulting in clear data interpretation. Among 199 potential nonspecific hybridization events, only 1 false-positive signal was observed, whereas false-negative results were more common (17 of 41). Subsequent parameter analysis revealed that this was mainly an effect of reduced accessibility of probe binding sites caused by the secondary structures of the target molecules. False-negative results could be prevented and the overall signal intensities could be adjusted by introducing a new optimization strategy called directed application of capture oligonucleotides. The small number of false-positive signals in our data set is discussed, and a general optimization approach is suggested. Our results show that, compared to standard hybridization formats such as fluorescence in situ hybridization, a large number of oligonucleotide probes with different characteristics can be applied in parallel in a highly specific way without extensive experimental effort.
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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.