Table 2

Oligonucleotides used in this study

Primer (gene)Purpose5′ to 3′ sequencea
P1 (dnaE, 5′)qRT-PCRAACGTTACCTTCAGCAAGCGGTTC
P2 (dnaE, 3′)qRT-PCRGGCGTTTGGGATCGTCGAGTGTAT
P3 (uspA-alaS, 5′)RT-PCRCCGTTAATTGATGAATAATAGCCAC
P4 (uspA-alaS, 3′)RT-PCRTTCATTTACACTTTACTCTGGATG
P5 (alaS-csrA, 5′)RT-PCRAGATACTGCACTTGCCTTTGC
P6 (alaS-csrA, 3′)RT-PCRCGTGTTAGTACAAGCATTATACCACCTT
P7 (csrA-galU, 5′)RT-PCRAGCATTAGCAGATAATATACCGGA
P8 (csrA-galU, 3′)RT-PCRTCCTAAGCCTGCAACAGGAA
P9 (csrA, 5′)qRT-PCRGGCGATGATATTGAAATTACCGTGC
P10 (csrA, 3′)qRT-PCRTTTAGGTGCATTGACGCCCA
P11 (alaS-csrA, 5′)Strain surveyGCAAGATCAAGGAAAGGTCTTGCT
P12 (galU, 3′)Strain surveyGCTTTAGTAGCCGGAAGCATTCGT
P13csrA mutagenesisCAAGATCAAGGAAAGGTCTTGCTATATTTTACAAACAAGGTGGTATAATGATTCCGGGGATCCGTCGACC
P14csrA mutagenesisCAGGAATAATGACTTTCATTACGTAATCCTTATACTGATTCCGGTATATTTGTAGGCTGGAGCTGCTTCG
P15csrA mutagenesisATATATACTAGTTGCACAAGCAGGTGCTGAATTG
P16csrA mutagenesisATATATACTAGTCGGGTGCAACCATAATTTGACT
P17csrA mutagenesisCTCATCTCTGAAAGTGCGGTAGCA
P18csrA mutagenesisGGCTGTTTCTCCTGCACGAATGTT
P19 (galU, 5′)qRT-PCRCGTGGGTAAAGAGCCATTTGCAGT
P20 (galU, 3′)qRT-PCRGGCACGGGTGCAACCATAATTTGA
P21Trans complementationATATATGAATTCCAATTAGCAAGATCAAGGAAAGGTCT
P22Trans complementationATATATGAATTCCCTTATACTGATTCCGGTATATTATCTGCT
P23 (flp1, 5′)qRT-PCRGGCTTAATTGCAGTCGCAGTTGCT
P24 (flp1, 3′)qRT-PCRGTGCCATTAGCGCTACTTATACCAG
P25 (tadA, 5′)qRT-PCRAATCAATGCCTTGCGTATGCGTCC
P26 (tadA, 3′)qRT-PCRTGTATTGGCGTGCAGGGTAGACAT
P27 (groEL, 5′)qRT-PCRTAGCCGGTGGTGTGGCAGTTATTA
P28 (groEL, 3′)qRT-PCRTGGAGTGCATCATCCACACGATCT
P29 (oxyR, 5′)qRT-PCRCTTGTTGAACAGGCCAAAGCGGTA
P30 (oxyR, 3′)qRT-PCRGTGCAATGGGCCAGACATTTCCTT
P31 (sodC, 5′)qRT-PCRGGCCATTGGGATCCAAAGCAAACT
P32 (sodC, 3′)qRT-PCRCAGGCGTTGTTGCTGAACCATCAT
P33 (bcp, 5′)qRT-PCRCTGTACGACTCAAGCATGCGGTTT
P34 (bcp, 3′)qRT-PCRATCTGGGCTAATGCCAAGCACAAC
P35 (rpoE, 5′)qRT-PCRGCGCGAGTTAGAAGGATTAAGCTACG
P36 (rpoE, 3′)qRT-PCRAATATTAACTCTGTTGCATCAGTGGATTG
  • a Boldfaced text represents sequences with homology to the mutagenic cassette. Underlining indicates regions corresponding to restriction enzyme sites as mentioned in the text. H. ducreyi sequences are from GenBank accession no. AE017143.