TABLE 1.
Oligonucleotidea | Sequence (5′ to 3′) | Target site (positions)b | Td/Ta (°C)c | Assay(s)d |
---|---|---|---|---|
GM5Fe | CCT ACG GGA GGC AGC AG | 341–357 | —/55 | 1 |
907R | CCG TCA ATT CCT TTR AGT TTf | 907–926 | —/55 | 1 |
TMS128F | GAA TCT RCC CTT TAG TTGf | 128–145 | —/44 | 1,2 |
TMS849R | CTT TTT AAT AAG RCC AAC AGf | 830–849 | 52/44 | 1,2,3 |
TMS849A | CTT TTT AAT AAG ACC AAC A | 831–849 | 41/— | 4 |
TMS849G | CTT TTT AAT AAG GCC AAC A | 831–849 | 41/— | 4 |
S-*-Univ-1392-a-A-15g | ACG GGC GGT GTG TRCf | 1392–1406 | 44/— | 4 |
S-D-Bact-0338-a-A-18g | GCT GCC TCC CGT AGG AGT | 338–355 | 54/— | 4 |
The suffixes F and R (forward and reverse, respectively) indicate the primer orientation in relation to the rRNA gene.
E. coli numbering of 16S rRNA nucleotides (10).
Td, dissociation temperature in the hybridization assays; Ta, annealing temperature in the PCR; —, not applicable.
1, PCR; 2, sequencing; 3, DNA hybridization; 4, rRNA slot blot hybridization.
This primer has a GC-clamp attached to its 5′ end (23).
R, adenine-guanine degeneracy.
Designation according to the Oligonucleotide Probe Database (http://www.cme.msu.edu./OPD/) (1).