TABLE 2.

Oligonucleotides used as primers and probes for PCR assays for plasmid sequences

Gene or ORFPrimerbSequence (5′→3′)LocationLength (bp)Source or reference
acpA (partial)acpA2FAGC-CGA-AAA-ATT-GAT-TTG-TTA-AAT-ATC-CTA-ATT68924-689561,653This study
acpA5RCAC-TCC-TGG-TAA-TAT-CAT-CGG-AAA-TCG-GTT-AT70546-70577This study
acpA3FaGAA-TTG-TAG-GGG-ATG-AAT-TTC-AAA-TTA-TAC-TAA-TG68324-68358This study
acpA3RaTTC-CCC-CTC-TTT-GTA-AAG-TAC-TAA-TTC-TTC-TTG69731-69763This study
acpA (partial)acpA1FGTT-ATG-TTT-GAT-ATC-CCC-TGA-TGT-TAC-CAA-TT68536-685671,657This study
acpA4RCTC-CTA-CAA-ATT-TTA-ATT-GAT-CGC-CAT-AAC-G70163-70193This study
acpA3FaGAA-TTG-TAG-GGG-ATG-AAT-TTC-AAA-TTA-TAC-TAA-TG68324-68358This study
acpA3RaTTC-CCC-CTC-TTT-GTA-AAG-TAC-TAA-TTC-TTC-TTG69731-69763This study
capA capA1FCAA-CAT-TTG-CAA-TCA-TGA-ATA-TTT-ATT-ACT-TAT55630-556621,291This study
capA2RAGT-TGT-TGT-CTC-CAC-TGA-TAC-TTG-ATT-TTC54381-54410This study
capA2FaCGG-ATT-ATG-GTG-CTA-AGG-GAA-CTA-AAG-A55135-55162This study
capCRaCGC-AGC-TAT-TAA-TAT-AAC-TGC-GAT-AAG55494-55520This study
capB capB1FCTT-AAT-AAG-CAA-GAA-ATC-GAA-AAG-CAG-GAA-GG57294-573252,204This study
capA1RAGG-CCT-TTA-TTG-TAT-CTT-TAG-TTC-CCT-TAG55121-55150This study
capB1RaCAA-GCG-ATG-CAT-TAT-CTG-GGA-AGA-CCA56631-56657This study
capCFaGGA-AGA-ACA-AAT-TGG-CAA-AAA-GC56106-56128This study
capC capB2FGGT-CTT-CCC-AGA-TAA-TGC-ATC-GCT-TG56631-566561,535This study
capA1RAGG-CCT-TTA-TTG-TAT-CTT-TAG-TTC-CCT-TAG55121-55150This study
capA1FaCAA-CAT-TTG-CAA-TCA-TGA-ATA-TTT-ATT-ACT-TAT57294-57325This study
capC capCFGGA-AGA-ACA-AAT-TGG-CAA-AAA-GC56106-56128635This study
capCRCGC-AGC-TAT-TAA-TAT-AAC-TGC-GAT-AAG55494-55520This study
capB2RaTTC-TTT-CTG-TAA-AAA-TAA-GGC-TCA-GTG-TAA-CTC-CT56005-56039This study
capC RcapCFACT-CGT-TTT-TAA-TCA-GCC-CG55942-5596126423
RcapCRGGT-AAC-CCT-TGT-CTT-TGA-AT55698-5571723
capA1FaCAA-CAT-TTG-CAA-TCA-TGA-ATA-TTT-ATT-ACT-TAT57294-57325This study
capD dep1FCGA-ACG-TTT-AAA-GGT-CCC-CAT-TGT52697-527201,600This study
dep4RTTG-CGG-TTG-AGG-AAG-GTA-TGA-AA54190-54212This study
dep2FaATC-GTT-TCC-CCA-TCT-TTC-TTT-AAT-ACA-GTG53114-23143This study
dep3RaCAT-ATT-GGA-GTA-CCC-GGA-TTT-GTG-G53892-54006This study
capR capR1FGGC-GGG-TTT-TCC-TTT-GTT-CC35917-359362,408This study
repA1RTGG-CAA-ACT-ATC-AGC-AAA-CAT-TTC-TCG-TA33528-33556This study
capR1RaATG-GCT-AGC-GAT-TAT-GTT-CTT-GTT-GC35507-35532This study
capR2FaATC-GCT-AGC-CAT-TGC-AGA-ACT-TTT-T35494-35518This study
IS1627IS1627FTAA-ACG-GGG-CAC-CTA-TTA-AAA-CAC-CTA-AA39718-39746479This study
IS1627RTTG-AAG-CGT-CAG-TCC-CAA-ATG-AAA-AG40171-40196This study
ORF43-1aGGA-TAC-TTT-TGT-TAC-CTT-TTG-TGA-ATA-GAA39814-39843This study
ORF43-2aGAT-GAA-GAC-AGT-AAA-ACA-AGT-AAT-GAG-AGG40016-40045This study
PromoterprocapFAAA-TAA-TTG-CAA-TCT-TTG-GAT-CAG-AAT-CTA-A58104-58134443This study
procapRAAG-AAA-AAC-GCA-ATT-TAC-AGA-ACT-CCT-CT57684-57722This study
procap-1aCTA-AGA-ATA-GAT-TTC-AAT-TTA-AAG-GGG-GTG57894-57923
ORF 48ORF48-FGGA-GGA-CAA-AGC-ATG-ACT-AAA-GTT-GAT-AAG-GTA-A44465-44498669This study
ORF48-RAAT-GTC-TCC-CCC-TCA-TAA-ACA-GAA-GAT-ACT-TTT-T45130-45163This study
ORF48-1aGCC-TAC-GAC-AAA-AGT-GGT-GAG-ATT-ATG-TGG44645-44674This study
ORF 61ORF61-FCTT-TCT-CTG-TCT-TTA-CCG-ACC-TTT-TAT-ACT-CA62793-62824459This study
ORF61-RAGA-AAT-CAA-ATG-CCT-TCT-TTG-TCG-AT63221-63426This study
ORF61-3aCTT-AAC-CAA-TGC-TTG-GTA-TTG-CTG-TAA-ATC62910-62939This study
repA repA1FGAA-GAT-TTA-AGG-GCT-AAG-TTT-GGG-ACT-CG33913-339411,350This study
repA4RGCC-CTT-CCA-ATA-TGC-CGT-ATA-GTG-TTT-C32591-32618This study
repA2RaTGA-AAA-CAC-GCT-AAA-GAA-AGG-GTG-AAA-AT33211-33239This study
repA4FaGCC-CTT-CCA-ATA-TGC-CGT-ATA-GTG-TTT-C33006-33026This study
  • a Oligonucleotide probes were internal to, and specific for, the target sequence as determined by N-blast with the NCBI library. Probes were used alone or with other oligonucleotide in a “cocktail” for optimal results. Oligonucleotides were end labeled with digoxigenin by following the manufacturer's directions. Probes were also used for DNA-DNA hybridization of dot blots made from either genomic or plasmid DNA.

  • b The position and orientation of each primer can be noted in Fig. 1.