probeBase 2016
Published on probeBase 2016 (https://probebase.csb.univie.ac.at)

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Probe/primer details

DSBAC357 Tested for in situ hybridization.
Accession no. pB-1320
Taxonomy Desulfobacterales [1]; Deltaproteobacteria [1]; delta/epsilon subdivisions [1]; Proteobacteria [1]; Bacteria [1]
Specificity Most Desulfobacteraceae and Syntrophobacteraceae
Category sulfate-reducing microbes [1]
Competitor 5'-CCA TTG CGC AAA ATT CCC CAC -3'
5'-CCA TTG CGC AAA ATC CCT CAC -3'
Target rRNA 16S rRNA
Position 357-377
Sequence 5'- CCA TTG CGC AAA ATT CCT CAC -3'
G+C content [%] 48
Length [nt] 21
Check specificity/coverage [2]
Formamide [%] 35
Hybridization efficiency [2]
References

Improved 16S rRNA-targeted probe set for analysis of sulfate-reducing bacteria by fluorescence in situ hybridization. Lücker S, Steger D, Kjeldsen KU, MacGregor BJ, Wagner M, Loy A. Journal of microbiological methods. 2007. Pubmed [2]

Remarks Competitors are also known as c1DSBAC357 and c2DSAC357

Print [1]

Glossary
Name (Alm et al., 1996). Probe designation according to Alm, E. W., Oerther, D. B., Larsen, N., Stahl, D. A., Raskin, L. (1996). The oligonucleotide probe database. Appl Environ Microbiol 62: 3557-9. Abstract (PUBMED) [2].
Position. Probe position according to the E. coli gene numbering.
Sequence. Sequence in IUPAC code: R=G/A, Y=T/C, M=A/C, K=G/T, S=G/C, W=A/T, H=A/C/T, B=G/T/C, V=G/C/A, D=G/A/T, N=G/A/T/C
Tm. Dissoziation temperature according to: Tm=64.9 + 41 x ((G + C - 16.4)/length).
Hybridization efficiency. Use this tool to assess in silico sensitivity (i.e. the hybridization efficiency of the oligonucleotide with its fully complementary target sequence, calculated with ProbeMelt [2].
Formamide. Percent formamide in the hybridization buffer for optimal hybridization conditions in FISH experiments.
Coverage. Coverage of the three domains calculated using the SILVA reference database 106 if no or a single mismatch is allowed. The detailed method is described in Klindworth et al., 2012. Nucleic Acids Res. 10.1093/nar/gks808 Full Text [2]
Check specificity/coverage. Use these options to reveal the in silico specificity (i.e. number of matching rRNA sequences outside the target taxon) and coverage (i.e. percentage of matching rRNA sequences within the target taxon) of an oligonucleotide against the most recent SSU and LSU rRNA sequence databases.

probeBase by Daniel Greuter, Alexander Loy, Matthias Horn, and Thomas Rattei, Department of Microbiology and Ecosystem Science, University of Vienna
Questions, comments, bug reports, and suggestions are welcome at probebase@microbial-ecology.net
Greuter et al. 2016. Nucleic Acids Res. 10.1093/nar/gkv1232

Imprint

Source URL:https://probebase.csb.univie.ac.at/pb_report/probe/1320

Links
[1] https://probebase.csb.univie.ac.at/https [2] https://probebase.csb.univie.ac.at/http