Table 2.

Oligonucleotide primers

PrimerSequence 5′-3′Comments; priming orientationFunction
FP GTT TTC CCA GTC ACG AC pUC18/19; ←a fliIand fliQ mutagenesis
SP002 CAA ATC ATC GCC CTC TAC TAG C InternalfliI; ← fliI probe preparation;fliI transcript detection
SP003 ATC CGC ACT TTC CTT ATT GCC InternalfliI; → fliI probe preparation; fidelity test pSP102
SP009 CCC ATC AAT GCT CTT CAC C InternalfliI; ← virB11 mutagenesis; conservation studies
SP010 GTG CCG ATT TTC ACA CTG C NearmurB 5′ end; ←Fidelity test pSP102; transcript analysis
SP013 GTG CTT AAC CCT TTA GGG C InternalfliI; →Operon conservation studies; characterization of H. pylori fliI mutants; fliI transcript detection
SP014 GCA CGA TCA CAT CAA TCG C NearvirB11 3′ end; ←Characterization of H. pylori virB11 mutants; virB11 transcript detection
SP015 GTG TGC CTA GGC TTA AGC InternalvirB11; → fliQ mutagenesis; transcript analysis; virB11 transcript detection
SP016 GCA CAC GGA TGT TGA GCG InternalvirB11; ←Transcript analysis
SP019 GAA ACG CCA GCA TTC ACG Near ileS 3′ end; → fliI mutagenesis; genotype characterization ofH. pylori virB11 mutants
SP020 CCA AAC CAG AAT GAT GGC C Near ORF02 5′ end; →Transcript analysis
SP021 CCA TCG TGG ATC CGG GCT GCA TGA CAG GCG CTA ATC GC InternalfliI; ←; 5′ tail sticky to SP022, BamHI site fliI mutagenesis
SP022 GCA GCC CGG ATC CAC GAT GGG ACA TCA TCA GCG AGT CTC InternalfliI; →; 5′ tail sticky to SP021, BamHI site fliI mutagenesis
SP023 CCA TCG TAG ATC TGG GCT GCG CGA GTT TCA TGA GTT GTG NearfliQ 5′ end; ←; 5′ tail sticky to SP024, BglII site fliQ mutagenesis; characterization of H. pylori flil mutants
SP024 GCA GCC CAG ATC TAC GAT GGA CCG GTA TTA CTA GCG GG NearfliQ 5′ end; →; 5′ tail sticky to SP023, BglII site fliQ mutagenesis
SP027 GGA ATG AGC TTG ATT AAG G Near fliQ 3′ end; ←Transcript analysis; characterization of H. pylori fliQ mutants; fliQ transcript detection
SP028 CAC AAC TCA TGA AAC TCG C Near fliQ 5′ end; →Transcript analysis; characterization of H. pylori fliQ mutants; fliQ transcript detection
SP032 CAT CGT AGA TCT GGG CTG CGT TGC TCG CAA AAC CTC AGC InternalvirB11; ←; 5′ tail sticky to SP033, BglII site virB11 mutagenesis
SP033 GCA GCC CAG ATC TAC GAT GGA TGA AAG GGT GGT GAG CG InternalvirB11; →; 5′ tail sticky to SP032, BglII site virB11 mutagenesis
SP034 AGG GAG CGA TCA GCA TAG G InternalileS; → virB11 mutagenesis; transcript analysis; conservation studies
SP035 GCA GCC CAG ATC TAC GAT GGG GCG AAT GAT TTA GAG GG InternalmurB; →; 5′ BglII site murBtranscript detection
SP036 TGC TCT TTG GCA AAG CCC Internal murB; ←Transcript analysis; murB transcript detection; conservation studies
SP039 GTG GGT TTA GTG AAG CGG Near ORF03 5′ end; →Transcript analysis
SP040 TCT TCG CAT GAT CTC GGC Near ileS 5′ end; ←Transcript analysis
SP043 AGC AAC CCT ACT TAT GGG Near TIGR HP1417 3′ end; ←Conservation studies
SP048 AAC GCG CCG CTT CAC TAA ACC Near ORF03 5′ end; ←Primer extension
SP050 ACT AGC CTT AGC GCA ACT CCC Internal ORF03; ←Primer extension
SP051 TGG TTG TGT TTA AGT TTA GGG TGT C NearileS 5′ end; ←Primer extension
  • a Priming orientation (relative to Fig.1).