Table 1. Primers used in this study.
| Targets; application | Forward (F) and reverse (R) primer sequences (5’-3’), and probe (P) if applicable | Amplicon length (bp) | Sub-panel # in Fig 2B |
|---|---|---|---|
| pUC57 vector primers; sequencing, assessing plasmid carry-over | (F) TAAAACGACGGCCAGTGAAT (R) GACCATGATTACGCCAAGC |
2,967 | 1 |
| tp0574; qualitative PCR | (F) TGTGGCTCGTCTCATCATGA (R) CTGGGCCACTACCTTCGCAC |
313 | 2 |
| kanR (F primer), right DC flanking region (R primer); qualitative PCR and sequencing (F) | (F) GAGCCATATTCAACGGGAGA (R) CTTCTCCTTCGCCCTCGAC |
1,799 | 3 |
| Left DC flanking region (F primer), Right DC flanking region (R primer); qualitative PCR |
(F) CACAGAAGGGCAGCAGTACA (R) CTTCTCCTTCGCCCTCGAC |
2,982 (SS14-DCKO) or 5,980 (WT) | 4 |
| kanR; qualitative PCR; RT-qPCR | (F) GAGCCATATTCAACGGGAGA (R) ATTCCGACTCGTCCAACATC |
663 | 5 |
| Left DC flanking region (F primer), kanR (R primer); qualitative PCR and sequencing |
(F) CACAGAAGGGCAGCAGTACA (R) ATTCCGACTCGTCCAACATC |
1,846 | |
| tp0131 (tprD); RT-qPCR | (F) CACTAGTCTTGGGGACACGC (R) TCCTGGTTGCAATTCACGTA |
273 | |
| tp0897 (tprK); RT-qPCR | (F) GAAAATCGCCTGTGCCCTAC (R) GGTTCCCCACGTTTAGTTAG |
80 | |
| tp0574; qPCR, RT-qPCR | (F) CAAGTACGAGGGGAACATCG (R) TGATCGCTGACAAGCTTAGG (P) 6FAM-CGGAGACTCTGATGGATGCTGCAGTT-NFQMGB1 |
132 | |
| tp0127; ddPCR | (F) GCGTGTATGGAGAAGCATTG (R) CGCCTGATAGCCTATATCCAC (P) HEX-AGATATGGT/ZEN/ACTACGCGCCGC-3IABkFQ2 |
139 | |
| kanR; ddPCR | (F) CACTCAGGCGCAATCAC (R) CCAGACTTGTTCAACAGGC (P) FAM-ACGGTTTGGTTGATGCGAGTGATTT-BkFQ3 |
91 | |
| tp0001 (dnaA); ddPCR, | (F) CTCATGGAAATACTGCTCC (R) CGGATACAAAGTTCTCGAAG (P) FAM-AGCTTTCACCCCGACCTGAAC-BkFQ3 |
135 | |
| tp0574 promoter; sequencing | (F) AGCGGATCCTCCCAAAAAGA (R) GATTACACCTCCGTATAGAG |
N/A | |
| pUC57 vector primers; sequencing, assessing plasmid carry-over | (F) TAAAACGACGGCCAGTGAAT (R) GACCATGATTACGCCAAGC |
2,967 |
1Minor groove binder nonfluorescent quencher
23′ Iowa Black fluorescence quencher
3Black hole fluorescence quencher