||Tested for in situ hybridization.|
|Specificity||Sulfurihydrogenibium spp. (except S. Yellowstonense) including Nakabusa microbial mat sequences|
|Target molecule||16S rRNA|
|Position*||646 - 663|
5'- CTC CCT GCC TCA AGT CCA -3'
|G+C content [%]||61.1|
|Reference||Kubo K, Knittel K, Amann R, Fukui M, Matsuura K. (2011). Sulfur-metabolizing bacterial populations in microbial mats of the Nakabusa hot spring, Japan. Systematic and Applied Microbiology 34 (2011) 293-302
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.|
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).
delta Gs. deltaG's: ΔG1 and ΔG2 are standard free energy changes for probe/rRNA duplex formation and probe folding, respectively. ΔG12 is a combined free energy parameter obtained from equilibrium chemistry using ΔG1 and ΔG2 (i.e., it is the thermodynamic affinity of the probe to a hypothetical perfectly accessible target site). All values calculated according to Yilmaz and Noguera (2006). Making all Parts of the 16S rRNA of Escherichia coli accessible in situ to single DNA oligonucleotides. Appl Environ Microbiol 72: 733-744.
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
If you use probeBase as a tool in your published research, we ask that this paper be cited:|
Loy A, Maixner F, Wagner M, Horn M. 2007. probeBase - an online resource for rRNA-targeted oligonucleotide probes: new features 2007. Nucleic Acids Res. 35: D800-D804. Full text
Suggested wording: (i) "Oligonucleotide probe sequences have been deposited at probeBase.", or (ii) "Details on oligonucleotide probes are available at probeBase."