Table 3

Oligonucleotides used in the study

Primer Name

Nucleic acid sequence

End modification of the kanamycin resistance gene

KanaSal1

5'-AGCGTCGCATACAAGGGGTGTTATGAGCCAT-3'

KanaHind3

5'-ACCCAAGCTTAATCGGGGGCTCCCTTTAGG-3'

3Kana3 junction from the kanamycin resistance gene

KanaJunc1

5'-TCATCTGTATAACATCATTGGC-3'

KanaJunc2

5'-CATGGTGATTTCTCACTTG-3'

Stuffer fragments amplified from DpAV4 sequence referenced as AJ279812

3primeXba1

5'-GCTCTAGACGGACGTCCAATACATGATG-3'

5primeXba1-F1

5'-GCTCTAGACCGAAAAGATAGACAGTGTG-3'

5primeXba1-F2

5'-GCTCTAGAAACGTGACGCACATGGCTAT-3'

5primeXba1-F3

5'-GCTCTAGAAAACATCCTTCGCCCTGAAC-3'

5primeXba1-F4

5'-GCTCTAGAAGGATTGGTGGGATTTTCCG-3'

5primeXba1-F5

5'-GCTCTAGAACGGCAACTTTCGGAACTAC-3'

Test-orient-F

5'-GCGAATTGGCCCCTAGATTT-3'

Insertion site analyses in the ccdB gene

ccdBup

5'-AGTCGTTCGGCTTCATCTGG-3'

ccdBdown

5'-ATCAGGAAGGGATGGCTGAG-3'

ITR cloning for circular permutation

5'ITRup

5'-AGCTCGTTTACCAGGTGTACAAGTAGGGAATGTCGGTTCCC-3'

5'ITRdw

5'-GGGAACCGACATTCCCTACTTGTACACCTGGTAAACGAGCT-3'

3'ITRup

5'-AGCTCGTTTATCAGGTGTACAAGTATGAAATGTCGTTTCCC-3'

3'ITRdw

5'-GGGAAACGACATTTCATACTTGTACACCTGATAAACGAGCT-3'

Fragments for circular permutation

O1

5'-GGGTTTTCCCAGTCACG-3'

O1R

5'-AACGACATTTCATACTTGTA-3'

O2

5'-ACGTTGTAAAACGACGGC-3'

O2R

5'-CTAGAGCGGCCGCGG-3'

O3

5'-CCAGTGAGCGCGCGTA-3'

O3R

5'-CGGGGGATCCACTAGTT-3'

O4

5'-TACGACTCACTATAGGGC-3'

O4R

5'-ATCGAATTCCTGCAGCCC-3'

O5

5'-CGAATTGGAGCTCGTTTAT-3

O5R

5'-GTATCGATAAGCTTGATATC-3'

O6

5'-ATCAGGTGTACAAGTATGAA-3'

O6R

5'-TTCCCTCGAGGTCGACG-3'

Sinzelle et al. BMC Molecular Biology 2008 9:106   doi:10.1186/1471-2199-9-106