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' |