ArticleApplied and environmental microbiology2006
Making all parts of the 16S rRNA of Escherichia coli accessible in situ to single DNA oligonucleotides.
Article in Applied and environmental microbiology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
31 citing papers in PubMed.
- Supergroup F Wolbachia with extremely reduced genome: transition to obligate insect symbionts.Microbiome · 2023Article
- Imaging biofilms using fluorescenceFrontiers in cellular and infection microbiology · 2023Review
- Development of a Novel Peptide Nucleic Acid Probe for the Detection ofMicroorganisms · 2022Article
- Spectral imaging and nucleic acid mimics fluorescenceFrontiers in microbiology · 2022Article
- Application of Nucleic Acid Mimics in Fluorescence In Situ Hybridization.Methods in molecular biology (Clifton, N.J.) · 2021Article
- GAL08, an Uncultivated Group ofFrontiers in microbiology · 2021Article
- A Multicolor FluorescenceFrontiers in microbiology · 2019Article
- Article
- The Phylogeny, Biodiversity, and Ecology of theFrontiers in microbiology · 2019Review
- Optimizing locked nucleic acid/2'-O-methyl-RNA fluorescence in situ hybridization (LNA/2'OMe-FISH) procedure for bacterial detection.PloS one · 2019Article
- CaMicrobes and environments · 2017Article
- DNA nanotechnology for nucleic acid analysis: multifunctional molecular DNA machine for RNA detection.Chemical communications (Cambridge, England) · 2016Article
- PCR-Independent Detection of Bacterial Species-Specific 16S rRNA at 10 fM by a Pore-Blockage Sensor.Biosensors · 2016Article
- "Candidatus Fokinia solitaria", a Novel "Stand-Alone" Symbiotic Lineage of Midichloriaceae (Rickettsiales).PloS one · 2016Article
- Article
- Detection of bacterial 16S rRNA using a molecular beacon-based X sensor.Biosensors & bioelectronics · 2013Article
- CLASI-FISH: principles of combinatorial labeling and spectral imaging.Systematic and applied microbiology · 2012Article
- A straightforward DOPE (double labeling of oligonucleotide probes)-FISH (fluorescence in situ hybridization) method for simultaneous multicolor detection of six microbial populations.Applied and environmental microbiology · 2012Article
- Interaction of Vibrio cholerae non-O1/non-O139 with copepods, cladocerans and competing bacteria in the large alkaline lake Neusiedler See, Austria.Microbial ecology · 2011Article
- mathFISH, a web tool that uses thermodynamics-based mathematical models for in silico evaluation of oligonucleotide probes for fluorescence in situ hybridization.Applied and environmental microbiology · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
rRNA accessibility is a major sensitivity issue limiting the design of working probes for fluorescence in situ hybridization (FISH). Previous studies empirically highlighted the accessibility of target sites on rRNA maps by grouping probes into six classes according to their brightness levels. In this study, a recently proposed mechanistic model of FISH, based on the thermodynamics of secondary nucleic acid interactions, was used to evaluate the accessibility of the 16S rRNA of Escherichia coli to fluorescein-labeled oligonucleotides when thermodynamic and kinetic barriers were eliminated. To cover the entire 16S rRNA, 109 probes were designed with an average thermodynamic affinity (DeltaGo (overall)) of -13.5 kcal/mol. Fluorescence intensity was measured by flow cytometry, and a brightness threshold between classes 3 and 4 was used as the requirement for proof of accessibility. While 46% of the probes were above this threshold with conventional 3-h hybridizations, extending the incubation period to 96 h dramatically increased the fraction of bright probes to 86%. Insufficient thermodynamic affinity and/or fluorophore quenching was demonstrated to cause the low fluorescence intensity of the remaining 14% of the probes. In the end, it was proven that every nucleotide in the 16S rRNA of E. coli could be targeted with a bright probe and, therefore, that there were no truly inaccessible target regions in the 16S rRNA. Based on our findings and mechanistic modeling, a rational design strategy involving DeltaGo(overall), hybridization kinetics, and fluorophore quenching is recommended for the development of bright probes.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.