Table 1.

Primer sequences and DNA amplification conditions for each selected region

Amplified regionaPrimerPrimer sequence (5′→3′)Size of amplified fragment (bp)Annealing step (temp [°C], time [min])b
cagA (5′ end)* D008 ATA ATG CTA AAT TAG ACA ACT TGA GCG A 29851, 1.5
R008 TTA GAA TAA TCA ACA AAC ATC ACG CCA T
cagA (5′ end) cagA1 GAT AAC AGG CAA CGT TTT CAG GGA 39460, 1
cagA2 CCG AAC GGA TCA AAA ATT CAT GG
cagA (3′ end)* Ys ACC CTA GTC GGT AAT GGG TTA 59562, 1.5
A6 GGC TGT TAG TAG CGT AAT TGT C
cagC FURF GCG TAA GCA AAA ACA GTC GCC TGA 41251, 1.5
RURF1 AAG AAA AAT GGT TGG GAC AAG TAG
cagC FURF See above 24152, 1
cagC-R CAA GAA TCA CTG ACA GCT ACA AG
virB4/cagF CRB CAC TCT CAA TGA ACC CGT TAT GAA 2,67550, 1.5
5B10 CTT TGT CAA GTC ATT TCT CAG
virB4 CRB See above 59460, 1
cagE-R CTG CCT AGC GTA ATA TCA CC
cagF 5B10 See above 26160, 1
cagF-R CCT CGC TTA TGT TGT TAT TG
cagL/cagN/cagM 5BRB TAT TGT CTG TTT TGA TGG CAG AAG 1,80348, 1.5
H12S TGA TGA GCG ACA AAA CAA CTA TGC
cagL 5BRB See above 35460, 1
cagL-R CGG ATA TTC CGC ATT GTT GC
cagN cagN-F CGC CAC TAA CGC TTT GAG 27760, 1
cagN-R CGG AGC AGC AGG TTT CAC
cagM cagM-F GCA TGG CGA TTG ATA AGA TC 25460, 1
cagM-R CAT AGG ATC GCT ATC TAC G
cagP/cagQ/cagR ARTF2 TAT TGC CTC GTT GAT CAA ACA AAG CTC TGC 1,32747, 1.5
HR1 GAT TTG GAG TTA GAT TAG GGT GGT
cagP cagP-F AGC CTT TAT TAT AGG CTG TTC 26058, 1
cagP-R AAC CAA TTT TGC CAT TGA GTC
cagQ cagQ-F TGC TTC CTA CTA AAA CAC GC 30958, 1
cagQ-R CAA CCA AAG CAG ATC CCA TG
cagS/virB7 B2L1 AAG TGC ATG CAG TAA TTA TGC GAA 1,62747, 1.5
E64Q TCT AAA GAG AAA CCA AAT CCA TTG
cagS cagS-F GGG AGC GTT AGA TAA GGT TC 27958, 1
cagS-R GTG GGA GCT TAG TGC CAT AC
virB7 cagT-F CTG ATA GAG AAG TAT AGT GAG 33758, 1
cagT-R GCA ACA CAT CAA AGG TCT G
virB9 HP528F GTT GGC TGT TTC TGT CTT GG 33960, 1
HP528R GTA ATC TCT TGT CAT TAG GGC
virB10 HP527F GAT GAA ATC CAA ATA AGG CAA G 37660, 1
HP527R CCA CTT GAA CTT TTT GTT GG
virD4/virB11 HP525F1 TAC CTA GCA AAA CAA CCT ATC CTC 1,95548, 1.5
HP525R1 TCC ACA TGT TTC TAG TAG CAG GAC
virB11 HP525F2 ATG ACT GAA GAC AGA TTG AG 50658, 1
HP525R2 GCA ATA CCA TCT TTA ATC GC
virD4 HP524F2 CTT TGG CTT TTG GTT GCA AG 51358, 1
HP524R2 CTA GTA GGA GCA ATC AAG C
IS605 H12H TCA TCG CTC CAT AAC TAG C 1,48654, 1.5
E64U GGT GGC TAT CTC ATC TAT AAC AGA
Empty site HP519 GCT TGC TTG TAT TGG CCT TG 32458, 1
HP549 GCA TGC ACA TTC CCT AAA GTG
JHP rrn16S HS1 GTG CTT ATT CGT TAG ATA CCG TCA T CTA GCA AGC 39955, 1
HS2 TAG AAG CTT CAT CGT T
  • a ∗, Primers used for PCR amplification (direct analysis of cag PAI in clinical strains by PCR and probe obtention for dot blot hybridization). The sequence of these primers was derived from the published sequence of cag PAI region of H. pylori NCTC 11638 (GenBank accession numbersU60176, U60177, and AC000108) (2, 5). †, Primers used for RT-PCR analysis of cag PAI genes; their sequences were derived from the published sequence of the H. pylori strains NCTC 11638 (GenBank accession numbers U60176, U60177, and AC000108) (2, 5), J99 (http://scriabin.astrazeneca-boston.com/hpylori), and 26695 (http://www.tigr.org). ‡, Primers used for PCR amplification and sequencing.

  • b Annealing step for each cycle. The cycling programs were preceeded by one step at 94°C for 5 min; 35 cycles were applied; each consisted of 1 min at 94°C, annealing as specified in the table, and 72°C for a time dependent on the expected product size (1 min per kb). Finally, an elongation step at 72°C for 7 min was added.