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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*Comments to Author 
Author affiliations: *Heal Protection Agency, London, UK; †University of Oxford, Oxford, UK

Main Article

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.

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