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Table 2 Oligonucleotide primers designed and used in this study

From: Branching of the p-nitrophenol (PNP) degradation pathway in burkholderia sp. Strain SJ98: Evidences from genetic characterization of PNP gene cluster

Target ORF

Primer name

Primer sequence (5’ → 3’)

Application/purpose

PnpE1

pnpE1_F

GGGGACAAGTTTGTACAAAAAAGCAGGCTTAATGGGCCGACATCTGCAT

HqD Large subunit amplification

 

pnpE1_R

GGGGACCACTTTGTACAAGAAAGCTGGGTATTAGAACGCGACCGGATA

 

PnpE2

pnpE2-F

GGGGACAAGTTTGTACAAAAAAGCAGGCTTAATGGAGACAGACATGCAA

HqD Small subunit amplification

 

pnpE2-R

GGGGACCACTTTGTACAAGAAAGCTGGGTATTACTGGATGCAGATGTC

 

PnpE1

pnpE1-RT_F

TCTACGGCTGGGTCAATTTC

HqD large subunit RT-PCR primer

 

pnpE1-RT_R

CTTCGTTCACCCAGTCCTTC

 

PnpE2

pnpE2-RT_F

CGCATTACGTGATGTCCAAC

HqD Small subunit RT-PCR primer

 

pnpE2-RT_R

GTTTCACCGAGCCTTCGATA

 

PnpD

HqD_F

AGGAGTTCATCCTGCT(G/C)(A/T)G

Partial BtD gene amplification

 

HqD_R

CGCAC(GC)CCGAACAC(A/T)GCGTC