TABLE 1.
Oligonucleotides used in this study
| Oligonucleotide pair | Sequences (5′–3′)a | Relevant property | Restriction sites |
|---|---|---|---|
| 46f/68r | ACTGCTCGAGTGCTCCCTCAAGTCGTGCAGTCA/ACTGACTAGTCCATCGCTTAACTGCTCATCAATC | Primer pair to amplify left fragment of L1, L5, L6, and L3 deletions | XhoI/SpeI |
| 133F/137R | ACTGCTCGAGGGTGTTTTTCGTTTGAAGAC/ACTGACTAGTTACTTTTCGGCCTCTTCCTG | Primer pair to amplify right fragment of L1 and F2 deletions | XhoI/SpeI |
| 68seqF/134seqR | TACTTACGAAATATAACCCG/TGTTCCAATTCACTTAGCTC | Primer pair to verify L1 deletion | |
| 190F/191R | ACTGACTAGTCAGCTTATGGTATAGCAACG/ACTGCTCGAGGTCTTGGATAACCACTATCATA | Primer pair to amplify left fragment of L2 deletion | SpeI/XhoI |
| 19F/19R | ACTGACTAGTTCAGGATCAAAGAAACCAGC/ACTGCTCGAGGCAGAGTTCTGAAACAAAGGTATT | Primer pair to amplify right fragment of L2 deletion | SpeI/XhoI |
| 190seqF/19seqR | GGGGAAAGACAGCGATAAGT/GTTAATGGAAAGAGATGGCT | Primer pair to verify L2 deletion | |
| 190F1/191R1 | ACTGCTCGAGCAGCTTATGGTATAGCAACG/ACTGACTAGTGTCTTGGATAACCACTATCATA | Primer pair to amplify right fragment of L3 deletion | XhoI/SpeI |
| 68seqF/190seqR | TACTTACGAAATATAACCCG/TGGCCCCTCATAAGTATATG | Primer pair to verify L3 deletion | |
| 26F/29R | ACTGCTCGAGCATTTTAATTGTTCCAGGGG/ACTGACTAGTATTGCCCGTCACTCCTTTCT | Primer pair to amplify left fragment of F1 and F2 deletions | XhoI/SpeI |
| 66F/67R | ACTGCTCGAGGTTCGGACAGCCTAACAATTTA/ACTGACTAGTGTGCTTTAGCAAACGAATATAC | Primer pair to amplify right fragment of F1 deletion | XhoI/SpeI |
| 26seqF/67seqR | TCCTTAATTCCGGATCAATCAC/CATTCTAAACAAAAGACCGACA | Primer pair to verify F1 deletion | |
| 27seqF/133seqR | CTATCTTTTTAATTGCAGCT/ATTGTTTTCCTACAGTTTGT | Primer pair to verify F2 deletion | |
| 172F/172R | ACGTCTCGAGAAGCATCTTTCCCATAAATGTC/ACGTACTAGTCCAAAAAAATCACACTGTCAAG | Primer pair to amplify right fragment of L5 deletion | XhoI/SpeI |
| 69seqF/172seqR | AATATTACGGAATTCAGTCCCGCTATATATGC/GGAAGAGCATTTAAAGGAAATCATGAAACAC | Primer pair to verify L5 deletion | |
| 182F/184R | ACGTCTCGAGGCCCATGCCCATAATTTTTTCGAAATGACT/ACTGTCTAGAAACGATATCCGCCATCTGCTTTCCA | Primer pair to amplify right fragment of L6 deletion | XhoI/XbaI |
| 69seqF1/183seqR | CTTACGAAATATAACCCGTAATAACAACCGT/TCCTCCTACCGCATTTGGATTGAAA | Primer pair to verify L6 deletion | |
| 67F/69R | ACGTCGATCGGTTCGGACAGCCTAACAATTTATTG/ACGTACCGGCGTCATCAATCTCTTCAGCATAAACG | Primer pair to amplify tubZR gene cluster | PvuI/BsrFI |
| IntF/IntR | ACGTCATATGAATATTATAAATTACGAACA/ACGTGATATCGCATCAAATCGAGAATCTTC | Primer pair to amplify IntXO recombinase gene | NdeI/EcoRV |
| 183F/181R | ACGTCCCGGGGAGTACTCCTTATACTGAAGATAC/ACGTCCCGGGAAAATAGGAAGAAACCGATG | Primer pair to amplify IntXO recombinase gene along with PSL sequence | SmaI/SmaI |
| ESATF/ESATR | ACGTACTAGTCGGACAGGATGAAAATGTATTTAGTAAGCTT/ACGTCTCGAGAGAAGAACCTGGATCAATGGAGAAA | Primer pair to amplify DNA region downstream of esat6 gene | SpeI/XhoI |
| seqFESAT/seqRESAT | ACATTCAACTTCTACTCTCAAACAACTC/GGATAACTCCTTAATGATTCCGATTGT | Primer pair to verify esat6 gene deletion | |
| PSCP1F/PSCPR | CGGGAGGAAATAATTCTATG/GCTTGGTTTAGTTGTCAAGAGAGAATAACT | Primer pair to verify Ω Kmr cassette deletion |
a
Restriction enzyme recognition sites are underlined.