Table 1.
EMSA probes and oligonucleotide primers used in this studya
| Oligonucleotide name | Modification | Sequence (5′→3′) | Target/purpose |
|---|---|---|---|
| BioRNAbpuRp-F (RNA) | 5′ biotin | CUUAAAUGUAGUCAAGUACAAAAACUUGUGUGGAGGAAAUUGAUGGGAGAGAGAGGGGAAGUAUACUCU | bpuR TSS to nt +30/EMSA |
| BioRNAbpuRORF (RNA) | 5′ biotin | AAACUAUUUACAGAGUCUGAGAGAACUUAUUUUUUUAAUGUCAAGGAAAAUAGAAAAGGAGAUUAUUUU | bpuR nt +31 to +100/EMSA |
| BioRNA61-F (RNA) | 5′ biotin | AAUGGAGAGAUUUUGGGGGAGUUGUUUAAAAUUACAUUUGCGUUUUGUUAAAAUG | erp operator/EMSA |
| bpuRp-12 | None | GCTAGCTAAAAATAACATTAC | bpuR NCD/EMSA-dsDNA |
| BiobpuRp-13 | 5′ biotin | GTAATGTTATTTTTAGCTCGA | bpuR NCD/EMSA-dsDNA |
| bpuRp-14 | None | CCACACAAGTTTTTGTACTTGAC | bpuR NCD/EMSA-dsDNA |
| Bioerp 129-F | 5′ biotin | GAGACGGGGAGTTGTTAAATT | erp operator/EMSA-dsDNA |
| A69-R | None | GTAACAGCTGAATGTAAC | erp operator/EMSA-dsDNA |
| GFP-5 | None | GTGACAAGTGTTGGCCATGGAAC | gfp mRNA |
| GFP-6 | None | CACTGGAGTTGTCCCAATTCTTGTTG | gfp mRNA |
| BpuR-1 | None | GGAGAGAGAGGGGAACTATAC | bpuR RIP-PCR |
| BpuR-2 | None | GCCTTGCAAAGGAGCCAACG | bpuR RIP-PCR |
| Fla-3 | None | GGGTCTCAAGCGTCTTGG | flaB RIP-PCR |
| Fla-4 | None | GAACCGGTGCAGCCTGAG | flaB RIP-PCR |
a
All nucleic acids were DNA, except as noted. NCD, noncoding DNA region; ORF, open reading frame; TSS, transcription start site.