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. 2008 Aug 29;283(35):23610–23618. doi: 10.1074/jbc.M801480200

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
a

Regions of oligonucleotide(s) not complementary to corresponding templates are underlined.

b

Shown are the oligonucleotide positions, where +1 is the transcription start site of vvpE.

c

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.

d

Sequences of the constructs are listed in Fig. 3B.

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