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Table 1 Oligonucleotide primers used in typing of H. pylori cag A and vac A alleles

From: Distribution of Helicobacter pylorivirulence markers in patients with gastroduodenal diseases in Pakistan

Region Amplified

Primer designation

Primer sequence (5' to 3')

Size of PCR product

PCR cycles

CagA

    

C-5'

D008

GGTCAAAATGCGGTCATGG

297-bp 19

1 cycle of 94°C for 5 min, 35 cycles of 94°C for 1 min, 55°C for 1 min and 72°C for 90 sec, 1 cycle of 72°C for 5 min

 

R008

TTAGAATAATCAACAAACATCACGCCAT

  

Vac A alleles

    

S1a

SS1-F

GTCAGCATCACACCGCAAC

190-bp 19

1 cycle of 95°C for 5 min; 35 cycles of 95°C for 1 min, 52°C for 1 min and 72°C for 1 min; 1 cycle of 72°C for 5 min

 

VA1-R

CTGCTTGAATGCGCCAAAC

  

S1b

SS3-F

AGCGCCATACCGCAAGAG

187-bp 19

 
 

VA1-R

CTGCTTGAATGCGCCAAAC-

  

S2

SS2-F

GCTAACACGCCAAATGATCC

199-bp19

 
 

VA1-R

CTGCTTGAATGCGCCAAAC

  

m1

VA3-F

GGTCAAAATGCGGTCATGG

290- bp 19

 
 

VA3-R

CCATTGGTACCTGTAGAAAC3'

  

m2

VA4-F

GGAGCCCCAGGAAACATTG

352- bp 19

 
 

VA4-R

CATAACTAGCGCCTTGCAC

  

i1

Vac-F1

GTTGGGATTGGGGGAATGCCG

426- bp14

1 cycle of 95°C for 90 sec; 35 cycles of 95°C for 30 sec, 53°C for 60 sec and 72°C for 30 sec; 1 cycle of 72°C for 5 min

 

C1R

TTAATTTAACGCTGTTTGAAG'

  

i2

Vac-F1

GTTGGGATTGGGGGAATGCCG

432- bp14

 
 

C2R

GATCAACGCTCTGATTTGA