Table 1 Oligonucleotide primers used for polymerase chain reaction (PCR), PCR conditions, and product size of vacA alleles and cagA
Genes | Primers | Product size (bp) | Initial denaturation temperature °C (min) | Denaturation temperature °C (min) | Annealing temperature °C (min) | Extension temperature °C (min) | Cycles | Final extension temperature °C (min) |
|---|---|---|---|---|---|---|---|---|
s1a | F:5′-GTCAGCATCACACCGCAAC-3′ | 190 |  | 94 (1) | 52 (1) | 72 (1) | 35 | 72 (5) |
R:5′-CTGCTTGAATGCGCCAAAC-3′ | ||||||||
s1b | F:5′-AGCGCCATACCGCAAGAG-3′ | 187 |  | 94 (1) | 52 (1) | 72 (1) | 35 | 72 (5) |
R:5′-CTGCTTGAATGCGCCAAAC-3′ | ||||||||
s2 | F: 5′-GCTAACACGCCAAATGATCC-3′ | 199 |  | 94 (1) | 52 (1) | 72 (1) | 35 | 72 (5) |
R: 5′-CTGCTTGAATGCGCCAAAC-3′ | ||||||||
m1a | F: 5′-GGTCAAAATGCGGTCATGG-3′ | 290 | 95 (2) | 94 (0.5) | 52 (0.5) | 72 (0.5) | 40 | 72 (5) |
R: 5′-CCATTGGTACCTGTAGAAAC-3′ | ||||||||
m1b | F: 5′-GGCCCCAATGCAGTCATGGAT-3′ | 240–270 | 95 (2) | 94 (0.5) | 52 (0.5) | 72 (0.5) | 40 | 72 (5) |
R: 5′-GCTGTTAGTGCCTAAAGAAGCAT-3′ | ||||||||
m2 | F: 5′-GGAGCCCCAGGAAACATTG-3′ | 352 | 95 (2) | 94 (0.5) | 52 (0.5) | 72 (0.5) | 40 | 72 (5) |
R: 5′-CATAACTAGCGCCTTGCAC-3′ | ||||||||
cagA | F:5′-TTGACCAACAACCACAAACCGAAG-3′ | 183 | 94 (2) | 95 (0.5) | 50 (0.75) | 72 (0.75) | 40 | 72 (5) |
R:5′-CTTCCCTTAATTGCGAGATTCC-3′ |