TABLE 1.
Oligonucleotide primers used in this studya
| ORF name (homologue or reference) | Primer sequencesb | PCR product size (bp) | Annealing temp (°C) |
|---|---|---|---|
| HP0520 | f: GTGGTGCGATAAAAATCTT | 637 | 55 |
| r: GGTCATGCAGTGAGTGATAA | |||
| HP0521 | f: CTAAAGATTGAGGCAAAAC | 414 | 55 |
| r: AAGTAATGCAGCTGTAAAAA | |||
| HP0522 | f: ACAGCTGCATTACTTACCTT | 624 | 58 |
| r: CTTCTTTTTGGCACTCTTA | |||
| HP0523 | f: AAGGACAAGCTCAAATACGAC | 725 | 63 |
| r: GCCTGTGGGTTCAAGTGA | |||
| HP0524 (virD4) | f: CGCAAAGGCTGAAGTGTA | 1,485 | 58 |
| r: TATCAACCACCACAAACAGT | |||
| HP0525 (virB11) | f: CGCTATTAACCCTATGAAACT | 1,132 | 58 |
| r: AAGAGCTAAATTGATAACCCA | |||
| HP0526 | f: ACTCAATCTGTCTTCAGTCAT | 690 | 50 |
| r: ACAGGCTCTTCTAGAGGATA | |||
| HP0527 (virB10) | f: TAGAAGAGCCTGTTGTTGGT | 979 | 55 |
| r: AAAGATGTCGCAGAAACTG | |||
| HP0528 (virB9) | f: CAAAATGAATTGATACAAGG | 962 | 55 |
| r: AGTTGGTGGATCTATGTTTA | |||
| HP0529 | f: AAGACAGAAACAGCCAACA | 808 | 55 |
| r: GTCTCTTTTATCGCCTATGC | |||
| HP0530 | f: AACAATGGGCAAATCAATAG | 899 | 55 |
| r: TTTTACAACCAACAAACCAAT | |||
| HP0531 | f: GATAAGACAATCACAACTCAG | 797 | 58 |
| r: GATTAAAACACTTGCTCTCA | |||
| HP0532 | f: GTGCAGAATGAAACTAATGA | 980 | 58 |
| r: CTAATTGATCGCCTTACTTAT | |||
| HP0533 + 0534 | f: GGGCGTTAGCTTTACTTGAT | 866 | 58 |
| r: TGAATTATGACCGCTCTGAA | |||
| HP0535 | f: CTCTGCGTGAAAGATGAAAA | 522 | 58 |
| r: GCGATTGGTGGCTACTTAT | |||
| HP0536 | f: ATGCTAATGTTTGGAAATAA | 492 | 55 |
| r: TAGATTAGGGTGGTTTTGTA | |||
| HP0537 | f: AAAATTGTGGTAAAATGTGTT | 1,250 | 55 |
| r: AAGAATAAAGAGCGACAGAA | |||
| HP0538 | f: TTGAATAGGAAAGGAGACACT | 1,027 | 58 |
| r: TGATTTTTCTGAGACGATAGG | |||
| HP0539 | f: GAGAAACAAATCCCAAAGGTT | 809 | 58 |
| r: AGAAACGACAGCAAGAAACA | |||
| HP0540 | f: TGCCATCAAAACAGACAAG | 1,274 | 55 |
| r: TTAAGGGGCAAAAAGATAGC | |||
| HP0541 | f: TGTGCCATTCAGAGACAAAC | 1,251 | 55 |
| r: GCACCAACATACTCAGATTCA | |||
| HP0542 | f: GAAATTTCCGATAAGAATCCT | 551 | 60 |
| r: TTAATGCGCTAGAATAGTGCT | |||
| HP0543 | f: AGCACTATTCTAGCGCATTA | 886 | 58 |
| r: AGATAAATATCAGGCCTTGAG | |||
| HP0544 (virB4) | f: CCAAAATCGTCAAGACATCA | 994 | 58 |
| r: AAACAAATGCAACAATGGAG | |||
| HP0545 | f: GCGCTTTTGAACCTCTTG | 772 | 60 |
| r: GGCAGGCGGTATTATCTATT | |||
| HP0546 | f: TTTTTGGCTTCTTTATCGTC | 620 | 58 |
| r: GGTTGGGACAAGTAGGTTTA | |||
| HP0547 | f: GTGTAGCGGTTTTTAGCAGT | 836 | 60 |
| r: CCTTGTATGTCGGTGGTAG | |||
| CagAZ (6) | 1: TTGGAAACCACCTTTTGTATTAGC | 400 | 58 |
| 2: GTGCCTGCTAGTTTGTCAGCG | |||
| cagAsbra | f: ATGATGGCGTGATGTTTGT | 823 | 62 |
| r: TTTTCAAGGTCGCTTTTTGC | |||
| 16S rRNA (17) | f: TGGCAATCAGCGTCAGGTAATG | 520 | 58 |
| r: GCTAAGAGATCAGCCTATGTCC | |||
| cag PAI empty site (6) | f: ACTTTCACGCCCTTTCCCTCC | 593 | 50 |
| r: TTGCATGCGTTATTATTTCAC |
a
For construction of microarrays, DNA fragments were amplified from strain 26695. A 55-μl reaction mixture contained 100 ng of genomic DNA, 25 to 35 pmol of primer, 100 μM deoxynucleoside triphosphates, PCR buffer, and 0.4 U of DyNAzyme Taq polymerase (Finnzymes). The PCRs were carried out for 35 cycles (95°C, 1 min; 50 to 63°C, 1 min; 72°C, 1 min).
b
5′—3′. f, forward; r, reverse.