TABLE 1.
Oligonucleotide primers and the RNA probe used in this studya
| Primer | Description | Sequence |
|---|---|---|
| P1 | Upstream of csrABb (F) | 5′-CGTTGCAAAAATCAATGAATC-3′ |
| P2 | Upstream of csrABb (R) | 5′-TCTAGATGATTGGTGCCTTTAGGTTAG-3′ |
| P3 | Downstream of csrABb (F) | 5′-TCTAGATAACCTCTGCATTTTGTC-3′ |
| P4 | Downstream of csrABb (R) | 5′-CATATGTTCTTTGGAAGAATTTGAGC-3′ |
| P5 | Kan (F) | 5′-TCTAGATAATACCCGAGCTTCAAG-3′ |
| P6 | Kan (R) | 5′-TCTAGATCAAGTCAGCGTAATGCTCTG-3′ |
| P7 | Complementation, PflgK (F) | 5′-GGATCCGCACTACTTAAAAAAGGTGTTGC-3′ |
| P8 | Complementation, PflgK (R) | 5′-CATATGTTTTATGAAATTAATTATAAGC-3′ |
| P9 | Complementation, csrABb (F) | 5′-CATATGCTAGTATTGTCAAGAAAAGC-3′ |
| P10 | Complementation, csrABb (R) | 5′-GGATCCTTATTTGTCATCGTCGTCC-3′ |
| P11 | qRT-PCR, rpoS (F) | 5′-ACCTATCTCCTGCTCAGTATATAA-3′ |
| P12 | qRT-PCR, rpoS (R) | 5′-CAAGGGTAATTTCAGGGTTAAAAG-3′ |
| P13 | qRT-PCR, ospC (F) | 5′-TGTTACTGATGCTGATGCAA-3′ |
| P14 | qRT-PCR, ospC (R) | 5′-AAGCTCTTTAACTGAATTAGC-3′ |
| P15 | qRT-PCR, dbpA (F) | 5′-GGACTAACAGGAGCAACA-3′ |
| P16 | qRT-PCR, dbpA (R) | 5′-CACCACTACTTCCAGTTTC-3′ |
| P17 | qRT-PCR, ospA (F) | 5′-GCAGCCTTGACGAGAAAAACA-3′ |
| P18 | qRT-PCR, ospA (R) | 5′-CGCCTTCAAGTACTCCAGATCC-3′ |
| P19 | qRT-PCR, dsrA (F) | 5′-AATGAAGTTAGTGGGCGTTACTC-3′ |
| P20 | qRT-PCR, dsrA (R) | 5′-TTTTTTTGAATAGGGTCACCAG-3′ |
| P21 | qRT-PCR, eno (F) | 5′-AACAGGAATTAACGAGGCTG-3′ |
| P22 | qRT-PCR, eno (R) | 5′-AAATTGCATTAGCACCAAGC-3′ |
| P23 | qRT-PCR, bb0589 (F) | 5′-GAGTTTTAAAGGCAGCTATTGT-3′ |
| P24 | qRT-PCR, bb0589 (R) | 5′-CTTTGCTTCGTAACTCCCTA-3′ |
| P25 | Co-RT, bb0588 (F) | 5′-CTGCTTTCAATTCAGCCAAAG-3′ |
| P26 | Co-RT, bb0589 (R) | 5′-GCCTATCAAAATAATCGAATCTGC-3′ |
| P27 | rCsrABb (F) | 5′-CACCATGCTAGTATTGTCAAGAAAAG-3′ |
| P28 | rCsrABb (R) | 5′-ATTTTCATTCTTGAAATAATG-3′ |
| P29 | EMSA probe | 5′-UUUAUUAUAAGGAGUGUGAUUUU-3′ |
| P30 | EMSA probe (mutated) | 5′-UUUAUUAUAAAAAGUGUGAUUUU-3′ |
a
The underlined sequences are the engineered restriction cut sites for DNA cloning; the bold “GGA” in P29 is the essential binding site for CsrA (36), and it was mutated to “AAA” in P30. F, foward; R, reverse.