TABLE 1.
Oligonucleotide probes used in this study and optimized experimental conditions
| Probe | OPD namea | Specificity | Sequence (5′-3′)b | Formamide concn (%)c | Reference |
|---|---|---|---|---|---|
| ARC915 | S-D-Arch-0915-a-A-20 | Archaea | GTGCTCCCCCGCCAATTCCT | 30 | 46 |
| EUB338 | S-D-Bact-0338-a-A-18 | Eubacteria | GCTGCCTCCCGTAGGAGT | 30 | 5 |
| EUK502 | S-D-Euk-0502-a-A-16 | Eukarya | ACCAGACTTGCCCTCC | 15 | 4 |
| EURY498 | S-K-Eury-0498-a-A-14 | Euryarchaeota | CTTGCCCRGCCCTT | 10 | 13 |
| CREN499 | S-K-Cren-0499-a-A-18 | Crenarchaeota | CCAGRCTTGCCCCCCGCT | 20 | 13 |
| MC688 | S-G-Mcocc-0688-a-A-20 | Methanococcales | GGATCAACRCATTTCACCGC | 30 | This study |
| MC1109 | S-G-Mcocc-1109-a-A-20 | Methanococcales | GCAACATRGGGCACGGGTCT | 30 | 41 |
| TC589 | S-G-Tcocc-0589-a-A-18 | Thermococcales | CGCCAGGGACTTACGGGC | 25 | This study |
a
Oligonucleotide Probe Database (OPD) nomenclature (2).
b
R = G or A.
c
Optimal deionized formamide concentration in hybridization solutions.