ArticleApplied and environmental microbiology2003
Sequence versus structure for the direct detection of 16S rRNA on planar oligonucleotide microarrays.
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 25 papers.
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Who cites it
25 citing papers in PubMed, 85 citations in OpenAlex.
- Specificity of LSU rRNA-targeted oligonucleotide probes for Pseudo-nitzschia species tested through dot-blot hybridisation.Environmental science and pollution research international · 2014Article
- Specific discrimination of three pathogenic Salmonella enterica subsp. enterica serotypes by carB-based oligonucleotide microarray.Applied and environmental microbiology · 2014Article
- Detection of bacterial 16S rRNA using a molecular beacon-based X sensor.Biosensors & bioelectronics · 2013Article
- Profiling in situ microbial community structure with an amplification microarray.Applied and environmental microbiology · 2013Article
- Operating Cooperatively (OC) sensor for highly specific recognition of nucleic acids.PloS one · 2013Article
- Evaluation of a fosmid-clone-based microarray for comparative analysis of swine fecal metagenomes.Journal of microbiology (Seoul, Korea) · 2012Article
- Simultaneous detection of multiple fish pathogens using a naked-eye readable DNA microarray.Sensors (Basel, Switzerland) · 2012Article
- In-depth characterization via complementing culture-independent approaches of the microbial community in an acidic hot spring of the Colombian Andes.Microbial ecology · 2012Article
- Molecular-beacon-based tricomponent probe for SNP analysis in folded nucleic acids.Chemistry (Weinheim an der Bergstrasse, Germany) · 2011Article
- Detection of tmRNA molecules on microarrays at low temperatures using helper oligonucleotides.BMC biotechnology · 2010Article
- In situ-synthesized virulence and marker gene biochip for detection of bacterial pathogens in water.Applied and environmental microbiology · 2008Article
- Diagnostic microarray for influenza B viruses.Analytical chemistry · 2007Article
- Influence of dangling ends and surface-proximal tails of targets on probe-target duplex formation in 16S rRNA gene-based diagnostic arrays.Applied and environmental microbiology · 2007Article
- Effects of target length on the hybridization efficiency and specificity of rRNA-based oligonucleotide microarrays.Applied and environmental microbiology · 2007Article
- Microarray-based analysis of microbial community RNAs by whole-community RNA amplification.Applied and environmental microbiology · 2007Article
- Robust sequence selection method used to develop the FluChip diagnostic microarray for influenza virus.Journal of clinical microbiology · 2006Article
- Microarray applications in microbial ecology research.Microbial ecology · 2006Review
- A DNA microarray platform based on direct detection of rRNA for characterization of freshwater sediment-related prokaryotic communities.Applied and environmental microbiology · 2006Article
- Suspension array analysis of 16S rRNA from Fe- and SO(4)2- reducing bacteria in uranium-contaminated sediments undergoing bioremediation.Applied and environmental microbiology · 2006Article
- Bacterial genotyping by 16S rRNA mass cataloging.BMC bioinformatics · 2006Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A two-probe proximal chaperone detection system consisting of a species-specific capture probe for the microarray and a labeled, proximal chaperone probe for detection was recently described for direct detection of intact rRNAs from environmental samples on oligonucleotide arrays. In this study, we investigated the physical spacing and nucleotide mismatch tolerance between capture and proximal chaperone detector probes that are required to achieve species-specific 16S rRNA detection for the dissimilatory metal and sulfate reducer 16S rRNAs. Microarray specificity was deduced by analyzing signal intensities across replicate microarrays with a statistical analysis-of-variance model that accommodates well-to-well and slide-to-slide variations in microarray signal intensity. Chaperone detector probes located in immediate proximity to the capture probe resulted in detectable, nonspecific binding of nontarget rRNA, presumably due to base-stacking effects. Species-specific rRNA detection was achieved by using a 22-nt capture probe and a 15-nt detector probe separated by 10 to 14 nt along the primary sequence. Chaperone detector probes with up to three mismatched nucleotides still resulted in species-specific capture of 16S rRNAs. There was no obvious relationship between position or number of mismatches and within- or between-genus hybridization specificity. From these results, we conclude that relieving secondary structure is of principal concern for the successful capture and detection of 16S rRNAs on planar surfaces but that the sequence of the capture probe is more important than relieving secondary structure for achieving specific hybridization.
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