ArticleApplied and environmental microbiology2003
Is the in situ accessibility of the 16S rRNA of Escherichia coli for Cy3-labeled oligonucleotide probes predicted by a three-dimensional structure model of the 30S ribosomal subunit?
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 24 papers.
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Who cites it
24 citing papers in PubMed, 77 citations in OpenAlex.
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- Selected fluorescent techniques for identification of the physiological state of individual water and soil bacterial cells - review.Folia microbiologica · 2010Review
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- Evaluation of single-nucleotide primer extension for detection and typing of phylogenetic markers used for investigation of microbial communities.Applied and environmental microbiology · 2009Article
- Fluorescent probes for live-cell RNA detection.Annual review of biomedical engineering · 2009Review
- Design and performance of a 16S rRNA-targeted oligonucleotide probe for detection of members of the genus Bdellovibrio by fluorescence in situ hybridization.Applied and environmental microbiology · 2007Article
- Prokaryotic community analysis with CARD-FISH in comparison with FISH in ultra-oligotrophic ground- and drinking water.Journal of applied microbiology · 2007Article
- Enigmatic dual symbiosis in the excretory organ of Nautilus macromphalus (Cephalopoda: Nautiloidea).Proceedings. Biological sciences · 2007Article
- Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies.Applied and environmental microbiology · 2007Article
- Targeting species-specific low-affinity 16S rRNA binding sites by using peptide nucleic acids for detection of Legionellae in biofilms.Applied and environmental microbiology · 2006Article
- Improved in situ hybridization efficiency with locked-nucleic-acid-incorporated DNA probes.Applied and environmental microbiology · 2006Article
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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
Systematic studies on the hybridization of fluorescently labeled, rRNA-targeted oligonucleotides have shown strong variations in in situ accessibility. Reliable predictions of target site accessibility would contribute to more-rational design of probes for the identification of individual microbial cells in their natural environments. During the past 3 years, numerous studies of the higher-order structure of the ribosome have advanced our understanding of its spatial conformation. These studies range from the identification of rRNA-rRNA interactions based on covariation analyses to physical imaging of the ribosome for the identification of protein-rRNA interactions. Here we reevaluate our Escherichia coli 16S rRNA in situ accessibility data with regard to a tertiary-structure model of the small subunit of the ribosome. We localized target sequences of 176 oligonucleotides on a 3.0-A-resolution three-dimensional (3D) model of the 30S ribosomal subunit. Little correlation was found between probe hybridization efficiency and the proximity of the probe target region to the surface of the 30S ribosomal subunit model. We attribute this to the fact that fluorescence in situ hybridization is performed on fixed cells containing denatured ribosomes, whereas 3D models of the ribosome are based on its native conformation. The effects of different fixation and hybridization protocols on the fluorescence signals conferred by a set of 10 representative probes were tested. The presence or absence of the strongly denaturing detergent sodium dodecyl sulfate had a much more pronounced effect than a change of fixative from paraformaldehyde to ethanol.
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