TABLE 2.
Primer function and gene or primer name | Primer directiona | Primer sequence (5′→3′)b | Efficiencyc | Restriction site added |
---|---|---|---|---|
Expression studies | ||||
rpoA | F | AAACCGCGCCTGGTAGATA | 1.78 | |
R | CCTTTCAGGTTGAGCAGGAT | |||
rhlA | F | GCATATTTCCGATCCTGCAC | 1.93 | |
R | CCCAGGAAATCGACAGGATA | |||
virK | F | CGTCCAAGTCGCTGAAAAGC | 1.93 | |
R | CCTGATAACGCATGAACTGC | |||
nipE | F | CAACATTCCCCCTCTGGATT | 1.94 | |
R | GTGCAACGTGTTGGATTTGT | |||
avrL | F | GCTTGTCGCAGGCAGTTTAC | 1.94 | |
R | CGGGAACTTGATCTGGTTGA | |||
avrM | F | GATTATCGGCGGCTTATTCA | 1.96 | |
R | CGGCCTCGACATCTTTTATG | |||
ahpC | F | AGAAAAGCATCGAAGGCAAA | 1.92 | |
R | CATGCCAGGCTTTGTGAGTA | |||
fabI | F | CATCTTCCGCAACATCACAC | 1.94 | |
R | ACGGTAAGCGCATTCTGGTA | |||
indA | F | TACGGCCAGAAAGATTGAGG | 1.95 | |
R | GCCAGAATCACCGGAATATC | |||
fadR | F | GGATTCGCGGAAGAGTACAT | 1.80 | |
R | GGTTTACCGTGCTGAATCGT | |||
rsmA | F | GAGTTGGCGAAACCCTCAT | 1.96 | |
R | GCTGAGACTTCTCTGCCTGAA | |||
hns | F | GCGAAGCACTTAAGATTCTAAACA | 1.86 | |
R | CTTTACCGGCAACTTTGCTT | |||
rpmE2 | F | CGGGTATCCATCCCAACTAC | 1.94 | |
R | CGCTACCTTCTTTGGCGTAT | |||
ffh | F | TGGTGCGTGATTTCATCAAT | ||
R | CTTACCAACGCTGGTGGTTT | 1.92 | ||
Gene cloning | ||||
rhlAdeb | GCTCTAGACTGTCTGAAGACACAGTCAGATTC | XbaI | ||
rhlAstop | CCGTGATAGCGCTGGTTATTC | |||
virKdeb | GCTCTAGACTGCTGAGTCCCGACAGCGG | XbaI | ||
virKstop | CGATGGCTGCCGGAACCGGC | |||
nipEdeb | CAGATGTTCGAGTTGGCG | |||
nipEstop | CGCCAGTTACAGCCAGAC | |||
ahpCdeb | GCTCTAGATGGGCCGCATCTGTGCCG | XbaI | ||
ahpCstop | CGTCCAGCGTCGCCACTAAC | |||
avr1B1 | CAACGATATCATCCGAATCATG | |||
avr1B2 | CTTAAGTCCGTTTTCCGAGCATG | |||
avr2B1 | CTTAAGTGCTGGATGGAACGGTATTCAC | |||
avr2B2 | TGATCAGGCGAAATTCGGCACGCAGTTC | |||
Regulatory region cloning | ||||
RRrhlA5′ | GCTCTAGACTGTCTGAAGACACAGTCAGATTC | XbaI | ||
RRrhlA3′ | GGAATTCAATAATGGTTTCATGTGCAGG | EcoRI | ||
RRvirK5′ | GCTCTAGACTGCTGAGTCCCGACAGCGG | XbaI | ||
RRvirK3′ | GGAATTCGACTTGGACGCCACGGCC | EcoRI | ||
RRnipE5′ | GCTCTAGAGAATATTATCCCTCATGGGTG | XbaI | ||
RRnipE3′ | GGAATTCCAGTTTGTCAAAATCATCG | EcoRI | ||
RRavrL5′ | GCTCTAGACAACGATATCATCCGAATCATG | XbaI | ||
RRavrL3′ | GGAATTCGCATAAGCGGCTCTCGCCGCC | EcoRI | ||
RRaphC5′ | GCTCTAGATGGTGCCGCATCTGTTGCCG | XbaI | ||
RRahpC3′ | GGAATCGTAAAGTCAGCCGGATAGAAG | EcoRI | ||
mfhR5′ | CCGTTTTGGTGAATTGCGCAAAG | |||
mfhR3′ | GCAGATCTTTTAGCCTTGCGCCCGCGCG | BglII | ||
Primer extension | ||||
rhlA-pExt1 | GACAATGCATTTTTCTATGG | |||
virK-pExt1 | GCAGCACAGGGGTAATACG | |||
nipE-pExt1 | GCCAGTACAGCTGTCTTCTT | |||
avrL-pExt1 | GCGCCCCAGAGAAATATGC | |||
ahpC-pExt2 | GTAAAGTCAGCCGGATAGAAG |
F, forward; R, reverse.
Restriction sites are underlined.
Primer PCR efficiency was estimated via a calibration dilution curve and slope calculation. Efficiency = 10−1/slope.