Table 2

Number of fragments detected by BOX-PCR and F-BOX-PCR analysis using agarose and capillary electrophoresis separation and ratios between the number of fluorochrome-labeled fragments detected by capillary electrophoresis and the number of unlabeled fragments detected by agarose electrophoresisa.

Strain

DNA extractiona

PCRa

Gel/Injectiona

Number of observed fragment

RHb

RFc


On agarose gel

On AbiPrism 310



Non fluorescent

HEX

6-FAM

HEX

6-FAM


B. cereus BC360

1

1

1

7

1

1

34

36

4.9

5.1

1

1

2

8

n.d.e

n.d.

34

36

4.3

4.5

1

2

1

3

1

1

34

36

11.3

12.0

1

2

2

3

n.d.

n.d.

34

36

11.3

12.0

2

1

1

10

1

5

34

36

3.4

3.6

2

1

2

7

n.d.

n.d.

34

36

4.9

5.1

2

2

1

7

1

1

33

36

4.7

5.1

2

2

2

5

n.d.

n.d.

33

36

6.6

7.2

CI1 23

1

1

1

13

8

11

n.d.

72

n.a.

5.5

1

1

2

13

n.d.

n.d.

n.d.

72

n.a.

5.5

1

2

1

16

6

10

n.d.

70

n.a.

4.4

1

2

2

13

n.d.

n.d.

n.d.

70

n.a.

5.4

CI2 13

1

1

1

9

5

6

34

41

3.8

4.6

1

1

2

9

n.d.

n.d.

34

41

3.8

4.6

1

2

1

10

5

7

28

41

2.8

4.1

1

2

2

9

n.d.

n.d.

29

41

3.2

4.6

2

1

1

11

5

6

34

40

3.1

3.6

2

1

2

11

n.d.

n.d.

33

40

3.0

3.6

2

2

1

10

6

7

34

39

3.4

3.9

2

2

2

11

n.d.

n.d.

34

40

3.1

3.6

CI2 17

1

1

1

10

7

10

26

50

2.6

5.0

1

1

2

9

n.d.

n.d.

26

49

2.9

5.4

1

2

1

18

4

10

27

52

1.5

2.9

1

2

2

13

n.d.

n.d.

26

51

2.0

3.9

CI2 23

1

1

1

8

4

5

44

49

5.5

6.1

1

1

2

12

n.d.

n.d.

44

49

3.7

4.1

1

2

1

10

6

7

44

48

4.4

4.8

1

2

2

11

n.d.

n.d.

44

48

4.0

4.4

2

1

1

11

4

6

45

49

4.1

4.5

2

1

2

11

n.d.

n.d.

45

49

4.1

4.5

2

2

1

9

4

6

43

47

4.8

5.2

2

2

2

12

n.d.

n.d.

44

47

3.7

3.9

CO2 33

1

1

1

12

3

5

n.d.

46

n.a.

3.8

1

1

2

10

n.d.

n.d.

n.d.

46

n.a.

4.6

1

2

1

9

3

5

n.d.

45

n.a.

5.0

1

2

2

11

n.d.

n.d.

n.d.

45

n.a.

4.1

DS3

1

1

1

14

6

7

35

34

2.5

2.4

1

1

2

13

6

6

35

34

2.7

2.6

1

2

1

7

5

7

33

34

4.7

4.9

1

2

2

6

4

5

33

34

5.5

5.7

2

1

1

16

6

8

34

30

2.1

1.9

2

1

2

13

6

7

33

31

2.5

2.4

2

2

1

13

6

7

33

32

2.5

2.5

2

2

2

8

6

6

33

32

4.1

4.0

E. coli DSM50902

1

1

1

19

10

13

26

57

1.4

3.0

1

1

2

17

n.d.

n.d.

26

57

1.5

3.4

1

2

1

18

3

9

24

57

1.3

3.2

1

2

2

14

n.d.

n.d.

25

57

1.8

4.1

2

1

1

19

8

14

26

58

1.4

3.1

2

1

2

16

n.d.

n.d.

26

57

1.6

3.6

2

2

1

15

9

15

26

60

1.7

4.0

2

2

2

15

n.d.

n.d.

26

60

1.7

4.0


a The comparison between BOX-PCR analysis and F-BOX-PCR analysis separated in agarose gel electrophoresis or in capillary electrophoresis was done considering eight strains belonging to B. cereus (G+C content 35%), to the family Geodermatophilaceae (G+C content 60%) and to E. coli (G+C content 50%). The analysis was done in duplicate considering two independent DNA extractions (numbered 1, 2), two independent PCR amplifications (1, 2) and two independent agarose gel runs or sample injection in the sequencer (1, 2)

b The numbers express the ratio of HEX-labeled amplicons detected by capillary electrophoresis versus unlabeled amplicons detected on agarose gels

c The numbers express the ratio of 6-FAM-labeled amplicons detected by capillary electrophoresis versus unlabeled amplicons detected on agarose gels

n.d. not determined.

n.a. not applicable.

Brusetti et al. BMC Microbiology 2008 8:220   doi:10.1186/1471-2180-8-220

Open Data