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Table 1 PCR amplification of urease structural (ureA, ureB, ureC) and the accessory (ureE, ureF, ureG, ureD) genes and the intergenic regions thereof, in Y. enterocolitica biovar 1A strain.

From: Molecular and biochemical characterization of urease and survival of Yersinia enterocolitica biovar 1A in acidic pH in vitro

Primer

Sequence (5' - 3')

Target

Accession no.

Region amplified

Amplicon length (bp)

PCR conditions (°C, s)*

      

Den

Ann

Ext

U1

U2

GCAGCCGTTTGGTCACGG

CTATGCCACGCATCCCGACC

ureA-ureC

DQ350880

AM286415

Z18865

275...2896

1075847...1078426

325...2907

2622

2580

2582

94, 60

62.0, 110

72, 110

ureA1

ureA2

GGAGGGCTTATGCAGCTCACCCCAAG

TTGCCATCTCTGGCCCCTTCCA

ureA

DQ350880

AM286415

Z18865

1...161

1075573...1075733

51...211

161

161

161

94, 60

61.4, 60

72, 60

ureAB1

ureAB2

CAATGGAAGGGGCCAGAGATGG

GTAAGCCGCAGCACGGTCAAACTC

ureA-ureB

DQ350880

AM286415

Z18865

137...579

1075709...1076210

187...688

443

502

502

94, 60

60.3, 60

72, 60

ureAB3

ureAB4

GCAGCTCACCCCAAGAGAAGTTGA

AATTTGAGGCATCTGTCGCTCCTT

ureA-ureB

DQ350880

AM286415

Z18865

12...1015

1075584...1076608

62...1086

1004

1025

1025

95, 60

56.9, 110

72, 60

ureB1

ureB2

ATTGCAGAGGATTAAAGCATGAGC

AGCGGAACTTCGGTTTCATCACC

ureB

DQ350880

AM286415

Z18865

349...650

1075920...1076281

398...759

302

362

362

94, 60

60.0, 60

72, 60

ureBC1

ureBC2

TGCGGCTTACGGAAAAAGGCTGAATA

GCCGAGAAATTTGAGGCATCTGTCG

ureB-ureC

DQ350880

AM286415

Z18865

570...1022

1076201...1076615

679...1093

453

415

415

94, 60

60.3, 60

72, 60

ureC1

ureC2

AAAGGAGCGACAGATGCCTCAAA

GAAACCTGAATATCCATTTCATCCGCCAT

ureC

DQ350880

AM286415

Z18865

991...1749

1076584...1077342

1062...1823

759

759

762

94, 60

63.2, 60

72, 60

ureC3

ureC4

GGCTATAAAGTTCACGAAGACTG

CAAAGAAATAGCGCTGGTTCA

ureC

DQ350880

AM286415

Z18865

1661...2717

1077254...1078310

1735...2791

1057

1057

1057

94, 60

52.9, 60

72, 60

ureC1

ureC4

AAAGGAGCGACAGATGCCTCAAA

CAAAGAAATAGCGCTGGTTCA

ureC

DQ350880

AM286415

Z18865

991...2717

1076584...1078310

1062...2791

1727

1727

1730

94, 60

50.0, 60

72, 120

ureCE1

ureCE2

GCGCTGGATGACGGTGTGAAAGAG

ATGTAAGCCGGAGCCATGAGGTTC

ureC-ureE, ureE

DQ350880

AM286415

2504...3552

1078097...1079082

1019

986

94, 60

61.0, 60

72, 60

ureE1

ureE2

ACCATGATGGATTCCGTGATGAGA

GTGAAGGCCCCGACCGGCAGTACG

ureE-ureF

DQ350880

AM286415

3364...3734

1078894...1079270

371

377

95, 60

58.7, 60

72, 60

ureF1

ureF2

TGAATGCATCAGATCTGATTCGTA

ACATCCACAATAGGGACATAAGA

ureF

DQ350880

AM286415

3668...4304

1079204...1079840

637

637

95, 60

50.0, 60

72, 60

ureFG1

ureFG2

CAATATGGCGTGGCGATGACAAT

CCACCGGGCCACCAATACCAA

ureF-ureG

DQ350880

AM286415

4132...4535

1079668...1080070

403

401

95, 60

55.7, 60

72, 60

ureG1

ureG2

GAATAGCCATTCAACCGATAAAC

CGCATAATCATATCCACCAAC

ureG

DQ350880

AM286415

4474...5091

1080009...1080626

618

618

95, 60

51.3, 60

72, 60

ureG1

ureD2

GAATAGCCATTCAACCGATAAAC

TTCCGGCAATGTCACACCGAGAAT

ureG-ureD, ureD

DQ350880

AM286415

4474...6099

1080009...1081634

1626

1626

95, 60

50.4, 60

72, 120

ureD1

ureD2

AGCCAGAATATCGTGGAAACTCCT

TTCCGGCAATGTCACACCGAGAAT

ureD

DQ350880

AM286415

5146...6099

1080681...1081634

954

954

95, 60

50.0, 60

72, 60

ureD3

ureD4

TTGTTAACCCCCAAAGAGCATCAT

CTGCCGGATTCCCTTCGCCATAG

ureD-yut

DQ350880

AM286415

5884...6416

1081419...1081950

533

532

95, 60

58.0, 60

72, 60

Yut1

Yut2

CGCGGCTGTGCTCAAGTC

GTGCTGGCATCACATCTTTATTAGG

yut

AM286415

1081851...1082745

895

95, 60

50.0, 60

72, 60

  1. The primer details and the PCR conditions used are given.
  2. DQ350880:Y. enterocolitica IP27403 (bioserovar 1A/O:6,30); AM286415: Y. enterocolitica 8081 (bioserovar 1B/O:8); Z18865: Y. enterocolitica 6471/76 (bioserovar 4/O:3)
  3. Nucleotides sequences in bold are different in biovar 1A strain (DQ350880)
  4. *PCRs were performed with initial denaturation step of 94°C for 10 min, 30 cycles each of denaturation (Den), annealing (Ann) and extension (Ext) as indicated and a final extension of 10 min at 72°C