|
Primer
|
Length of product
|
Sequence 5' – 3'
|
Reference
|
|---|
|
IS1081_F2
|
135 bp
|
CTGCTCTCGACGTTCATCGCCG
|
Insertion sequence IS1081
|
|
IS1081_R2
| |
GGCACGGGTGTCGAAATCACG
|
[2]
|
|
IS1081_R3
|
113 bp
|
TGGCGGTAGCCGTTGCGC
| |
|
OxyR_F3
|
110 bp
|
CACTGCCTACGCGACCAGACG
|
oxidative stress regulator OxyR pseudogene
|
|
OxyR _R1
| |
TCTGCGGAATCAGTGTCACC
|
[2]
|
|
OxyR _F4
|
94 bp
|
AGACGCTCGATGCTGCCCAA
| |
|
pncA_F2
|
117 bp
|
GGCGGACTACCATCACGTCG
|
Pyrazinamidase gene
|
|
pncA _R2
| |
GGAGTACCGCTGACGCAATGCGGT
|
[2]
|
|
pncA _R3
|
96 bp
|
GGCCACGACGAGGAATAGTC
| |
|
D1flanking_F
|
112 bp
|
ATCGAAAGGCTAACGGGTGC
|
flanking sections of TbD1 region
|
|
D1flanking _R2
| |
CTGCTCGCCGAGTTGGTCGATA
|
[2]
|
|
D1flanking _R3
|
96 bp
|
TCGATACCGTCGATCGTGTCAAAG
| |
|
D1internal _F3
|
115 bp
|
CGAGCTACGACGCTCGCTATTA
|
TbD1 region
|
|
D1internal _R3
| |
GCATATCGTGATCCGTCTCGAT
|
[2]
|
|
D1internal _R4
|
105 bp
|
CTCGATCATCAGTAGTTCGGGATTC
| |
|
TbA
|
TbA/TbB:
|
CTCGTCCAGCGCCGCTTCGG
|
insertion sequence IS6110
|
|
TbB
|
120 bp
|
CCTGCGAGCGTAGGCGTCGG
|
[1]
|
|
TbC
|
TbC/TbD:
|
GCTTCGGACCACCAGCACCT
| |
|
TbD
|
95 bp
|
GCGTCGGTGACAAAGGCCAC
| |
- For the primers of [2], F (forward) and R (reverse) denote orientation of the primer and for each gene amplification was performed with the first two primers followed by reamplification with the third primer in combination with one of the original primers.
- Target Sequences: IS108 = Insertion sequence IS1081; OxyR = oxidative stress regulator OxyR pseudogene; pncA = Pyrazinamidase gene; D1 = TbD1 region described in [25] that is deleted in modern strains of M. tuberculosis; TbA-TbD: insertion sequence IS6110.
