Table 1

Primers and amplification conditions for the different PCR based screening of genes that encode for antibiotics

Gene and primer set

Primer sequence

Reference

Amplification conditions


PCA (C, D)

PCA2a

PCA3b

5'-TGCCAAGCCTCGCT CCAAC-3'

5'-CGCGTTGTTCCTCGTTCAT-3'

77

Initial denaturation 94°C for 3 min, 30 cycles of 94°C for 60 s, 58°C for 45 s, and 72°C for 60 s. Final extension at 72°C for 10 min.

PCA (X, Y)

30–84/1

30–84/2

5'-CAGTTCATCCGGCGGGCTGCAG-3'

5'-CCCGTTTCAGTAAGTCTTCCATG-

ATGCG-3'

77

Initial denaturation 94°C for 3 min, 30 cycles of 94°C for 60 s, 58°C for 45 s, and 72°C for 60 s, Final extension at 72°C for 10 min.

PCN

PhzH-up

PhzH-low

5'-CGCACGGATCCTTTCAGAATGT-

TC-3'

5'-GCCACGCCAAGCTTCACGCTCA-3'

78

Initial denaturation 94°C for 30 s, 30 cycles of 94°C for 30 s, 64°C for 30 s, and 72°C for 7 min. Final extension at 72°C for 10 min.

DAPG

Phl2a

Phl2b

5'-GAGGACGTCGAAGACCACCA-3'

5'-ACC GCAGCATCGTGTATGAG-3'

79

Initial denaturation 94°C for 90 s, 35 cycles of 94°C for 35 s, 53°C for 30 s, and 72°C for 45 s. Final extension at 72°C for 10 min.

PLT

PltBf

PltBr

5'-CGGAGCATGGACCCCCAGC-3'

5'-GTGCCCGATATTGGTCTTGACCG-

AG-3'

79

Initial denaturation 94°C for 2 min, 29 cycles of 94°C for 1 min, 58°C for 45 s, and 72°C for 1 min, Final extension at 72°C for 10 min.

PRN

Prncf

Prncr

5'-CCACAA GCCCGGCCAGGAGC-3'

5'-GAGAAGAGCGGGTCGATGAAG-

CC-3'

79

Initial denaturation 94°C for 2 min, 30 cycles of 94°C for 1 min, 58°C for 45 s, and 72°C for 1 min. Final extension at72°C for 10 min.


Naik et al. BMC Microbiology 2008 8:230   doi:10.1186/1471-2180-8-230

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