TABLE 1.
Oligonucleotides used in this study
Oligonucleotide | Oligonucleotide sequence, 5′-3a | Locationb | Use(s) |
---|---|---|---|
Linker and PCR oligonucleotides | |||
Sau3AI Linker-1 | GATCGAGTGACTCTTGACCTCGACTAGTGC | Linker construction; amplification of SmcR-target DNA | |
Sau3AI Linker-2
|
GCACTAGTCGAGGTCAAGAGTCACTC
|
Linker construction; amplification of SmcR target DNA
|
|
PCR oligonucleotides | |||
T7 | GAATTGTAATACGACTCACTATAGG | pGEM-T easy vector | DNase I footprinting or EMSA |
SP6 | CATACGATTTAGGTGACACTATAG | pGEM-T easy vector | DNase I footprinting or EMSA |
VVPE021 | AGAATGGCGATTTTCATAG | -300 to -282 | EMSA |
VVPE022 | GAATCCATCTCACTGCGA | -118 to -101 | EMSA |
VVPE501 | GTACTGCAGGTTTGGCTAATGAGTTTTAAG | -510 to -490 | Amplification of vvpE upstream |
VVPE502
|
TATGGATCCGACGTTGATTGAGTTTCATTATCG
|
+69 to +92
|
Amplification of vvpE upstream
|
Mutagenic oligonucleotides An and Bnc | |||
AWC | CAAATTTATCAATAAGAAAAATGGG | -217 to -193 | Construction of WCd |
BWC | TATTGATAAATTTGTGAATAAAATAAAAAGC | -206 to -176 | WC |
AIR-L | ATGAGGTACCTGGAAAAATGGGACAGTCATC | -226 to -196 | WCIR-L |
BIR-L | TCCAGGTACCTCATTTGTGAATAAAATAAAA | -209 to -179 | WCIR-L |
AIR-R | TTGAGGTACCTGATTTATCAATAAGAAAAATG | -215 to -184 | WCIR-R |
BIR-R | ATCAGGTACCTCAATAAAAAGCACAATTTTA | -197 to -167 | WCIR-R |
APAL | AAATTGTGCTTTTTATTTTATTGATAAATTT | -199 to -169 | WCPAL |
BPAL | AAATTTATCAATAAAATAAAAAGCACAATTT | -199 to -169 | WCPAL |
A-11 | CACAAATTTATCAATAGGAAAAATGGG | -217 to -191 | WC-11 |
A-10 | CACAAATTTATCAATGAGAAAAATGGG | -217 to -191 | WC-10 |
A-9 | CACAAATTTATCAAGAAGAAAAATGGG | -217 to -191 | WC-9 |
A-8 | CACAAATTTATCAGTAAGAAAAATGGG | -217 to -191 | WC-8 |
A-7 | GCTTTTTATTTTATTCACAAATTTATCGAT | -191 to -162 | WC-7 |
A-6 | CAAATTTATGAATAAGAAAAATGGGAC | -219 to -193 | WC-6 |
A-5 | CACAAATTTAGCAATAAGAAAAATGGG | -217 to -191 | WC-5 |
A-4 | AAATTTGTCAATAAGAAAAATGGGACA | -220 to -194 | WC-4 |
B-11 ∼ -7;-5 | TAAATTTGTGAATAAAATAAAAAGCACA | -200 to -173 | WC-11 ∼ -7; -5 |
B-6 | GTCCCATTTTTCTTATTCATAAATTTG | -219 to -193 | WC-6 |
B-4 | CTGTCCCATTTTTCTTATTGACAAATT | -221 to -195 | WC-4 |
Regions of oligonucleotide(s) not complementary to corresponding templates are underlined.
Shown are the oligonucleotide positions, where +1 is the transcription start site of vvpE.
Numbers in An and Bn primers represent the positions of point mutation from the center of the working consensus sequence. Base substitutions to mutate the working consensus sequence are underlined.
Sequences of the constructs are listed in Fig. 3B.