TABLE 1.
Primers used in this study
| Type and primer no. | Primer name | Sequence | Locationa |
|---|---|---|---|
| Specific for flanking jhp0924 sequenceb | |||
| 1 | jhp0924R | 5"-TGCGCTAGTGCAAAAGTTAC | Left of ISHp608 in PeCan2A |
| 20 | jhp0924F | 5"-TTATTAAAGTCATTAGGCAAATT | Right of ISHp608 in PeCan2A |
| Leftward-facingc ISHp608-specific | |||
| 2 | 608-3a | 5"-GATATGGTATTTGCAAGAATAGAC | 233 bp from left end of ISHp608 |
| 3 | 608-1 | 5"-ACTAATACCTTACGCCTGTA | 268 bp from left end of ISHp608 |
| 4 | 608-F1 | 5"-CCATAACGCCTTAATAGTGTGTC | 683 bp from left end of ISHp608 |
| 5 | 608-F | 5"-ATCCTCTCAGTCAAATCTTGCATG | 851 bp from left end of ISHp608 |
| 6 | 608a112-Rd | 5"-TTTTGTCAATCTTACTCTTA | 958 bp from left end of ISHp608 |
| 7 | 608a113-Re | 5"-TAGAGAGCGGTTGCAAGCACG | 1,444 bp from left end of ISHp608 |
| 8 | 608neutral-Fnew | 5"-CAAGCAAACTCAGCCTACTAG | 1,772 bp from left end of ISHp608 |
| 9 | 608neutral-F | 5"-CTAAAGCTAGGGGATTCTAGC | 1,815 bp from left end of ISHp608 |
| Rightward-facingc ISHp608-specific | |||
| 10 | 608a112-Fd | 5"-TATATAAAAACAACCACAACA | 1,647 bp from right end of ISHp608 |
| 11 | 608-3out | 5"-GTCTATTCTTGCAAATACCATATCG | 1,624 bp from right end of ISHp608 |
| 12 | 608-R | 5"-CAAGCTTTGGAGTGATGAAGTTC | 1,446 bp from right end of ISHp608 |
| 13 | 608-4out | 5"-GTAGCCAACTACAAGTCTTTCAC | 921 bp from right end of ISHp608 |
| 14 | 608a113-Fe | 5"-CGAGTTCAATGGCAAACCCAAG | 620 bp from right end of ISHp608 |
| 15 | 608-6out | 5"-TAGCGAGTTTGTGAAGATCCT | 343 bp from right end of ISHp608 |
| 16 | 608-7out | 5"-AAGAAAGAGAATACCACTGCA | 200 bp from right end of ISHp608 |
| 17 | 608-8out | 5"-CTATCAACATTCATAGGGTTG | 140 bp from right end of ISHp608 |
| 18 | 608neutral-Rnew | 5"-TGCTTGATCCCAATTTTCCTC | 67 bp from right end of ISHp608 |
| 19 | 608neutral-R | 5"-TTAGCTATGGGGAGTATGTCA | 22 bp from right end of ISHp608 |
| Universal primers for adapter PCR | |||
| C1 | 5"-GTACATATTGTCGTTAGAACGCG | Adapter-specific primer (TaKaRa) | |
| C2 | 5"-TAATACGACTCACTATAGGGAGA | Adapter-specific primer (TaKaRa) |
a
Where specified in base pairs, location refers to position of 5" end of primer in sequence of ISHp608 from H. pylori strain PeCan2A (GenBank accession no. AF357223).
b
jhp094 refers to an ORF of unknown function in the genome of H. pylori strain J99 (4). The ISHp608 element found in strain PeCan2A is inserted in this ORF.
c
Left and right ends of ISHp608 are diagrammed in Fig. 1.
d
ISHp608 type 2 specific.
e
ISHp608 type 3 specific