ArticleNucleic acids research2003
Fingerprinting of prokaryotic 16S rRNA genes using oligodeoxyribonucleotide microarrays and virtual hybridization.
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 15 papers.
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Who cites it
15 citing papers in PubMed.
- Considerations When Designing a Microbiome Study: Implications for Nursing Science.Biological research for nursing · 2019Article
- In Silico Genomic Fingerprints of the Bacillus anthracis Group Obtained by Virtual Hybridization.Microarrays (Basel, Switzerland) · 2015Article
- Highly specific and efficient primers for in-house multiplex PCR detection of Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma hominis and Ureaplasma urealyticum.BMC research notes · 2014Article
- A low density microarray method for the identification of human papillomavirus type 18 variants.Sensors (Basel, Switzerland) · 2013Article
- Bioinformatics prediction of siRNAs as potential antiviral agents against dengue viruses.Bioinformation · 2012Article
- Universal fingerprinting chip server.Bioinformation · 2012Article
- LifePrint: a novel k-tuple distance method for construction of phylogenetic trees.Advances and applications in bioinformatics and chemistry : AABC · 2011Article
- Article
- Specific mutation screening of TP53 gene by low-density DNA microarray.Nanotechnology, science and applications · 2009Article
- In situ-synthesized virulence and marker gene biochip for detection of bacterial pathogens in water.Applied and environmental microbiology · 2008Article
- 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
- The theoretical basis of universal identification systems for bacteria and viruses.Journal of biological physics and chemistry : JBPC · 2005Article
- Dissociation analysis in polymerase chain reaction and 1X SSC buffer as a prerequisite for selection of 13mer microarray probe sets with uniform hybridization behavior.Molecular biotechnology · 2005Article
- Viral and microbial genotyping by a combination of multiplex competitive hybridization and specific extension followed by hybridization to generic tag arrays.Nucleic acids research · 2003Article
- Detection of mutations in RET proto-oncogene codon 634 through double tandem hybridization.Molecular biotechnology · 2003Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
An oligonucleotide microarray hybridization system to differentiate microbial species was designed and tested. Seven microbial species were studied, including one Bacillus and six Pseudomonas strains. DNA sequences near the 5' end of 16S rRNA genes were aligned and two contiguous regions of high variability, flanked by highly conserved sequences, were found. The conserved sequences were used to design PCR primers which efficiently amplified these polymorphic regions from all seven species. The amplicon sequences were used to design 88 9mer hybridization probes which were arrayed onto glass slides. Single-stranded, fluorescence-tagged PCR products were hybridized to the microarrays at 15 degrees C. The experimental results were compared with the DeltaG(0) values for all matched and mismatched duplexes possible between the synthetic probes and the 16S target sequences of the seven test species, calculated using a 'virtual hybridization' software program. Although the observed hybridization patterns differed significantly from patterns predicted solely on the basis of perfect sequence matches, a unique hybridization fingerprint was obtained for each of the species, including closely related Pseudomonas species, and there was a reasonable correlation between the intensity of observed hybridization signals and the calculated DeltaG(0) values. The results suggest that both perfect and mismatched pairings can contribute to microbial identification by hybridization fingerprinting.
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