TABLE 2.
Oligonucleotides
| Primer | Sequencea | Use (locationb) | Source or reference |
|---|---|---|---|
| oMC44 | 5′-CTAGCTGCTCCTATGTCTCACATC-3′ | rpoC qPCR (CD0067) | 45 |
| oMC45 | 5′-CCAGTCTCTCCTGGATCAACTA-3′ | rpoC qPCR (CD0067) | 45 |
| oMC112 | 5′-GGCAAATGTAAGATTTCGTACTCA-3′ | tcdB qPCR (CD0660) | 19 |
| oMC113 | 5′-TCGACTACAGTATTCTCTGAC-3′ | tcdB qPCR (CD0660) | 19 |
| oMC152 | 5′-GTTATGGAAGTCAAGGACATGCAC-3′ | ilvC qPCR (CD1565) | 37 |
| oMC153 | 5′-GCTTCTGCTACACTCTTAACTTCA-3′ | ilvC qPCR (CD1565) | 37 |
| oMC331 | 5′-CTCAAAGCGCAATAAATCTAGGAGC-3′ | spo0A qPCR (CD1214) | 19 |
| oMC332 | 5′-TTGAGTCTCTTGAACTGGTCTAGG-3′ | spo0A qPCR (CD1214) | 19 |
| oMC339 | 5′-GGGCAAATATACTTCCTCCTCCAT-3′ | sigE qPCR (CD2643) | 19 |
| oMC340 | 5′-TGACTTTACACTTTCATCTGTTTCTAGC-3′ | sigE qPCR (CD2643) | 19 |
| oMC349 | 5′-CCTTTGTGCTAGCCTTATTGTTAGG-3′ | oppB qPCR (CD0853) | 19 |
| oMC350 | 5′-AAGTATGAGTACTAAGGCAACCCA-3′ | oppB qPCR (CD0853) | 19 |
| oMC365 | 5′-GGAAGTAACTGTTGCCAGAGAAGA-3′ | sigF qPCR (CD0772) | 19 |
| oMC366 | 5′-CGCTCCTAACTAGACCTAAATTGC-3′ | sigF qPCR (CD0772) | 19 |
| oMC425 | 5′-CTGTGACTTTGTAGCTTGG-3′ | codY PCR (CD1275) | This study |
| oMC426 | 5′-CTGCTAAAGGCATTTTCTCACTC-3′ | codY PCR (CD1275) | This study |
| oMC427 | 5′-GTGGTGTTAATACATCAGAACTTCC-3′ | sigG qPCR (CD2642) | 19 |
| oMC428 | 5′-CAAACTGTTGTCTGGCTTCTTC-3′ | sigG qPCR (CD2642) | 19 |
| oMC429 | 5′-GCCTGTGCTTCCAATGATAAAG-3′ | appA qPCR (CD2672) | 19 |
| oMC430 | 5′-ATATCTGGGTCACTTGCCATAG-3′ | appA qPCR (CD2672) | 19 |
| oMC527 | 5′-AGGCAGGTTTACATCCAACATA-3′ | sinR qPCR (CD2214) | 19 |
| oMC528 | 5′-AGTGGTATGTCTAAAGCAGTAGC-3′ | sinR qPCR (CD2214) | 19 |
| oMC529 | 5′-GCCTTGGTATATAACTCAAATCGAAAGT-3′ | sinI qPCR (CD2215) | 19 |
| oMC530 | 5′-ATCTGTGATATCAGATTTAGTTCTCTTGAAT-3′ | sinI qPCR (CD2215) | 19 |
| oMC547 | 5′-TGGATAGGTGGAGAAGTCAGT-3′ | tcdA qPCR (CD0663) | 19 |
| oMC548 | 5′-GCTGTAATGCTTCAGTGGTAGA-3′ | tcdA qPCR (CD0663) | 19 |
| oMC1008 | 5′-GCGGGATCCTTATTATCCCTCCACTTTAGATTATATTC-3′ | PsinR cloning (CD2214) | This study |
| oMC1009 | 5′-GCGGAATTCATTAAATTATTTTATAAGATTATTACTCTACTATA-3′ | PsinR cloning (CD2214) | This study |
| oMC1012 | 5′-GCGGGATCCACCCCAACCCCCCTTTG-3′ | PoppB cloning (CD0853) | This study |
| oMC1015 | 5′-GCGGAATTCACTGTGTACATAGTTTTAGAATAAAG-3′ | PoppB cloning (CD0853) | This study |
| oMC1025 | 5′-GCGGGATCCATTCTTATAAAACCTCCATAAAATAATAT-3′ | PappA cloning (CD2672) | This study |
| oMC1026 | 5′-GCGGAATTCCTTCTTCCTTTGATAAATCTTGATG-3′ | PappA cloning (CD2672) | This study |
| oMC1074 | 5′-GCGGAATTCAATTTTATAGAAAATAATGAAGAATAGAATATA-3′ | PoppB cloning (CD0853) | This study |
| oMC1076 | 5′-GCGGAATTCAATTTTTAAAAAGTTTGTTTACACAG-3′ | PoppB cloning (CD0853) | This study |
| oMC1077 | 5′-GCGGAATTCACACAGTTAATAAATGATGCTAAA-3′ | PoppB cloning (CD0853) | This study |
| oMC1178 | 5′-GAAAATTTTTTTAATTTTAAAAATATATTCTACATATC-3′ | PsinR cloning (CD2214) | This study |
| oMC1179 | 5′-GATATGTAGAATATATTTTTAAAATTAAAAAAATTTTC-3′ | PsinR cloning (CD2214) | This study |
| oMC1180 | 5′-GTATAAATAAAATAATTTGATAAAATTTTAACAATTTTT-3′ | PoppB cloning (CD0853) | This study |
| oMC1181 | 5′-AAAAATTGTTAAAATTTTATCAAATTATTTTATTTATAC-3′ | PoppB cloning (CD0853) | This study |
| 3′ catP | 5′-AAACGCGTTTAACTATTTATCAATTCCTGCAAT-3′ | catP cloning | J. Sorg |
| 5′ catP2 | 5′-AAACGCGTAATTAGATGCTAAAAATTTGTAATT-3′ | catP cloning | J. Sorg |
| oLB275 | 5′-AAGGATCCAGAGTGAAAATTGAAAAAAATC-3′ | codY cloning (CD1274) | This study |
| oLB276 | 5′-CCCAAGCTTCTAATCTAAACCTATAAAATATAG-3′ | codY cloning (CD1275) | This study |
| oLB344 | 5′-AAGCGCTCATGAGCCCGAAG-3′ | codY cloning (CD1275) | This study |
| tcdRqF | 5′-AGCAAGAAATAACTCAGTAGATGATT-3′ | tcdR qPCR (CD0659) | 53 |
| tcdRqR | 5′-TTATTAAATCTGTTTCTCCCTCTTCA-3′ | tcdR qPCR (CD0659) | 53 |
| ITR | 5′-CCCACATGCATGCTAACAGGTTGGCTGATAAGTCCCCGGTCT-3′ | catP cloning | This study |
a
Underlined regions denote restriction enzyme cut sites.
b
Locus number in reference to the 630 genome (NC_009089.1). qPCR, quantitative PCR.