TABLE 1.
PCR primers for amplification of vacA and cagA sequences
| Gene and primer (polarity) | Sequence (5′-3′)a | Position |
|---|---|---|
| vacA s region | ||
| VA1F (+)b | ATGGAAATACAACAAACACAC | 1–21c,d |
| VA1R (−)b | CTGCTTGAATGCGCCAAAC | 241–259c and 268–286d |
| VA1XR (−) | CCTGARACCGTTCCTACAGC | 157–176c and 184–203d |
| vacA m region | ||
| HPMGF (+) | CACAGCCACTTTCAATAACGA | 1443–1463c and 1419–1439d |
| HPMGR (−) | CGTCAAAATAATTCCAAGGG | 1824–1843c and 1875–1894d |
| MF1 (+) | GTGGATGCYCATACRGCTWA | 1495–1514c and 1471–1490d |
| MR1 (−) | RTGAGCTTGTTGATATTGAC | 1582–1601c and 1633–1652d |
| cagA | ||
| cagAF (+) | TTGACCAACAACCACAAACCGAAG | 17–40e |
| cagAR (−) | CTTCCCTTAATTGCGAGATTCC | 178–199e |
a
R is A or G, W is A or T, and Y is = C or T.
b
VA1F and VA1R have been published earlier by Atherton et al. (3).
c
Nucleotide position numbers are according to the start codon of the vacA open reading frame in strain 60190 (GenBank accession no. U05676) for s1 and m1.
d
Nucleotide position numbers are according to the start codon of the vacA open reading frame in strain Tx30a (GenBank accession no. U29401) for s2 and m2.
e
For detection of cagA the positions are according to the start codon of the cagA open reading frame in the sequence of the strain with GenBank accession no. L11714.