Table 2.
Primers used for this study
| Primer use and name | Sequence (5′→3′)a | Site created/modified |
|---|---|---|
| Cloning of padR into pET28a+ | ||
| BSR1 | GACTCATGAGAGTATTAAAATACGCC | BspHI |
| BSR2 | GCTCTCGAGATCCTTATCTATCATAG | XhoI |
| Cloning of padR into pHT315 | ||
| BSR3 | TACGTCTAGAGACAGGATTATGTACTGACT | XbaI |
| BSR4 | AAGCTGCAGGATCGACATTGAA | PstI |
| Random mutagenesis of padR by error-prone PCR | ||
| BSR5 | ATGCTGCAGATTATCGCTAACGGTGCC | PstI |
| BSR101 | ATGAGAGTATTAAAATACGCC | BseRI (native) |
| Production of padC::lacZ fusions | ||
| BSDF1 | CCAGAATTCACGGCAAGTCAGCAAGCCGT | EcoRI |
| BSDFR | TCAGGATCCGATAAAGTTTTCCATCTTACAC | BamHI |
| Sequencing of padR mutants | ||
| BSR6 | TCGGATACCTTCTGACAA | |
| Probes for DNA binding | ||
| BSD1 | CAAAGCTAGCTTCAGACAAGG | |
| BSD2 | CACTTTAACACCATTGCAG | |
| BSD4 | ATGTAACTATTTACATGTTCAC | |
| BSD5 | GCAATGGTGTTAAAGTGAACATGT | |
| BSD5IR1 (forward) | GCAATGGTGTTAAAGTGAACΔAAATAGTTACATGATTTTTTC | ΔIR1 (ATGT) |
| BSD5IR2 (forward) | GCAATGGTGTTAAAGTGAACATGTAAATAGTTΔGATTTTTTCTGAAGGTGAGGTG | ΔIR2 (ACAT) |
| BSD5IR12 (forward) | GCAATGGTGTTAAAGTGAACΔAAATAGTTΔGATTTTTTC | ΔIR1, ΔIR2 |
| BSD6 | ACATGTTCACTTTAACACCATTGC | |
| BSD8 (reverse) | GAATCATCTCAGTCCCAGGCTTG |
a
Underlined nucleotides correspond to restriction sites for the enzymes given in the right column.