Volume 10, Number 9—September 2004
Research
Silent Nucleotide Polymorphisms and a Phylogeny for Mycobacterium tuberculosis
Lucy Baker*, Tim Brown*, Martin Maiden†, and Francis Drobniewski*
Table 2
Sequencing primersa
| Locus/PCR product | Forward primers | Reverse primers |
|---|---|---|
| gyrA | gyrA-1F 5′-CAGCTACATCGACTATG-3′ | gyrA-1R 5′-GGGCTTCGGTGTACCTCAT-3′ |
| inhA promoter | mabA-1F 5′-AGAAAGGGATCCGTCATGGT-3′ | mabA-1R 5′-GTCACATTCGACGCCAAAC-3′ |
| katG 3F-3R | katG-1F 5′-ACGCGGGGTCTGACAAAT-3′ | katG-1R 5′-GACAAGGCGAACCTGCTTAC-3′ |
| katg-2F 5′-GTAAGCAGGTTCGCCTTGT-3′ | katG-2R 5′-TCGGGATTGACTGTCTCACA-3′ | |
| katG-3F 5′-ATCTCTTCCAGGGTGCGAAT-3′ | katG-3R 5′-GAGTGGGAGCTGACGAAGAG-3′ | |
| katG 5F-5R | katG-4F 5′-AGAGGTCAGTGGCCAGCAT-3′ | katG-4R 5′-AGATGGGGCTGATCTACGTG-3′ |
| katG-5F 5′-GCTGTTTCGACGTCGTTCAT-3′ | katG-5R 5′-ACTACGGGCCGCTGTTTATC-3′ | |
| katG-6R 5′-ACACTTCGCGATCACATCC-3′ | katG-6R 5′-ACACTTCGCGATCACATCC-3′ | |
| oxyR-ahpC | oxyR–1 5′-CTGGCCAGGTAAGACGACC-3′ | oxyR-2 5′-CAGACGCTCGATGCTGCC-3′ |
| oxyR-7 5′-TCATATCGAGAATGCTTGCGG-3′ | oxyR-4 5′-TGCTTGGCGTCCACCTTGG-3′ | |
| oxyR-6 5′-TGATGTCTTTGGCGTACTCGG–3′ | oxyR-6 5′-CAATGACGAGTTCGAGGACC-3′ | |
| pncA | pncA-P1 5′-GCTGGTCATGTTCGCGATCG-3′ | pncA-R 5′-CGATGAAGGTGTCGTAGAAGC-3′ |
| pncA –F 5′-AACCAAGGACTTCCACATCG–3′ | pncA-2F 5′-ATACCGACCACATCGACCTC-3′ | |
| rpoB–46-1868 | rpoB –41F 5′-GTGGGCACCGCTCCTCTAAGG-3′ | rpoB 509R 5′-TGACCACCACACGCTCGGTCC-3′ |
| rpoB 331F 5′-CGTTTCGACGATGTCAAGGCA-3′ | rpoB 975R 5′-GTCGACGACGTGATGGGCTCG-3′ | |
| rpoB 783F 5′-CTGGAGAAGGACAACACCGTCG-3′ | rpoB 2 5′-GCACGTCGCGGACCTCCAGCC-3′ | |
| rpoB 1 5′-GGTCGGCATGTCGCGGATGGA-3′ | rpoB 1845R 5′-CGCTACGGACCAGCGGCACC-3′ | |
| rpoB 1711-3602 | rpoB 1725F 5′-GGTGGACTACATGGACGTCTC-3′ | rpoB 2313R 5′-GTCGGAGATGTTCGGGATGTCG-3′ |
| rpoB 2134F 5′-GAGATGGCGCTGGGCAAGAAC-3′ | rpoB 2770R 5′-TCTGGCCGATGTTCATCCGTCG-3′ | |
| rpoB 2600F 5′-AGCTGGTGCGTGTGTATGTGG-3′ | rpoB 3213R 5′-GGCCTGCATGCCCCAGCACTCC-3′ | |
| rpoB 3013F 5′-CCGTTCCCGTACCCGGTCACG-3′ | rpoB 3581R 5′-GAAGAAGTTGACGTCGAGCAC-3′ | |
| rpsL | rpsL F 5′-ACGTGAAAGCGCCCAAGATAGA -3′ | rpsL R 5′-ACCAACTGCGATCCGTAGACC-3′ |
aAll sequencing reactions were performed in 96-well plates (Abgene, UK) in a DNA Thermal Cycler 9600 (Applied Biosystems, Warrington, UK) by using the following thermocycling conditions: 30 cycles of denaturation at 96°C for 10 s, annealing at 50°C for 5 s, and extension at 60°C for 2 min.
