TABLE 3.
Oligonucleotides used in this study
| Primer use and name | Sequence (description) |
|---|---|
| Mutant construction | |
| Cthe0210up-f-4AMG550Bam | TGATCCACTAGTAAGCTTACCCCTGCGAATACTGAGATTT |
| Cthe0210up-r-for0210down | GATTTTAAGTTGAGACAAATCAGTTTTCTTTGTATTT |
| Cthe0210down-f-for0210up | ATTTGTCTCAACTTAAAATCAGCCTTTTAAGTAAAGAA |
| Cthe0210down-r-4AMG550Bam | GGCCTCGCGAAGGAGTTCTTCCGTCGTAACGT |
| Cthe0210in-f-4AMG550Eco | CCTTTTGTTTTGGTACCGTCAAGCAATAATTCAATCGAGC |
| Cthe0210in-r-4AMG550Eco | AAACGCTGAGGCGCGCCGATCGTCGGAGTTTCAAGAAG |
| Cthe2505up-f-4AMG550Bam | GATCCACTAGTAAGCTTGCCTATGGTTCCGCAACTTTC |
| Cthe2505up-r-for2505down | TCAGCCTATTCGCTTTACTGACATTGTGACTTTCTTTGCCATT |
| Cthe2505down-f-for2505up | AAGAAAGTCACAATGTCAGTAAAGCGAATAGGCTGAT |
| Cthe2505down-r-4MG550Bam | ACTGGCCGGCCTCGCGAGTTGGGAACATTTCTGTGAATTC |
| Cthe2505in-f-4AMG550EcoRI | CCTTTTGTTTTGGTACCGAGCAAGTCAAATTCAAGAACCG |
| Cthe2505in-r-4AMG550EcoRI | AAACGCTGAGGCGCGCCGTCATCGGGAACGGATATACC |
| Ct2808down-r-4AMG550 | ATTGATACACCCATGTCAGAATACTGGCCGGCCTCGCGAGGATCCGATTTAACGACAACACTTTCAACC |
| Ct2808down-f-42808up | TAATTTAAAAAATACAACAGCTGTTGATTGATTGTTTTATAATCATCCAAAGATGTACTC |
| Ct2808up-f- 4AMG550 | GGCGCTACAGGGCGCGTGGGGATGATCCACTAGTAAGCTTGGATCCATTACGGAGAAGGACATTGAAACTATT |
| Ct2808up-r- 42808down | ACATCTTTGGATGATTATAAAACAATCAATCAACAGCTGTTGTATTTTTTAAATTACAAA |
| Ct2808in-f- 4AMG550(Smal) | TCCTTTTATAGGCGTTTTGAAACCTGAAATGTACAGCTAAGGAGGTGGGCCCATGACCAGTGAAGAAATAGCAAAATTAT |
| Ct2808in-r- 4AMG550(Smal) | AAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTCTCGAGGTCAGAATTCCAAAGCCCTCTTGGT |
| Mutant verification | |
| F_AAACCTGTCTCGCAAGAATTG | AAACCTGTCTCGCAAGAATTG (upstream of Che_2808) |
| R_CGCGTTTCCTCTTTTACGTT | CGCGTTTCCTCTTTTACGTT (reverse within Cthe_2808) |
| R_GTACGGATATTGGCGACCAG | GTACGGATATTGGCGACCAG (downstream at end of Cthe_2809) |
| F_CTTGTTTACCGCATCTGCAA | CTTGTTTACCGCATCTGCAA (5′ of Cthe_2505) |
| R_AATTCCTCAACTGCCCACAG | AATTCCTCAACTGCCCACAG (reverse within Cthe_2505) |
| R_TTTGCCTGCATTACAACAGC | TTTGCCTGCATTACAACAGC (3′ of Cthe_2505) |
| F_TTTCATGGCCTTCATGTTGA | TTTCATGGCCTTCATGTTGA (5′ of Cthe_0210) |
| R_CATGGCTATCGGAGCATACA | CATGGCTATCGGAGCATACA (reverse within Cthe_0210) |
| R_AACACTTCAGCAAAGCTCCTG | AACACTTCAGCAAAGCTCCTG (3′ of Cthe_0210) |
| Cloning | |
| F_pTXB1 Clo1313_2023/0210 | TAATTTTGTTTAACTTTAAGAAGGAGATATACAATGAACAGCAAGGATATAGC |
| R_pTXB1_CLO1313_2023/0210 | GGGTAGGGCAACTAGTGCATCTCCCGTGATGCAGACAATTTTTTTACATGAATTACGC |
| F_pTXB1_CLO1313_0089/2505 | TAATTTTGTTTAACTTTAAGAAGGAGATATACAATGGCAAAGAAAGTCACAATG |
| R_pTXB1_Clo1313_0089/2505 | GGGTAGGGCAACTAGTGCATCTCCCGTGATGCATATTCGCTTTACTGAC |
| F_pTXB1_Clo1313_0396/2808 | TAATTTTGTTTAACTTTAAGAAGGAGATATACAATGACCAGTGAAGAAATAGC |
| R_pTXB1_Clo1313_0396/2808 | GGGTAGGGCAACTAGTGCATCTCCCGTGATGCAGAATTCCAAAGCCCTCTTG |
| F_pTXB1 across insertion | TAATACGACTCACTATAGGG |
| R_pTXB1 across insertion | GTAGGGCAACTAGTGCATCT |
| R. pTXB1 A up of insertion | TGTATATCTCCTTCTTAAAG |
| F. pTXB1 A down of insertion | ATCACGGGAGATGCACTAGT |
| Fluorescent EMSA | |
| F_EMSA_288bp_2022 | GCAAAGCTCCTGTAACAATTCA |
| R_EMSA_288bp_2022 | TGCCACACCACCTTCATATCA |
| F_EMSA_100bp_0395 | CCGAATAAAAACTGGACAGAG |
| R_EMSA_100bp_0395 | TGAAACCATTTAACACTGGATTAT |
| F_EMSA_refined_int1397:98 | TTCAATAAAGCGGAATTTGAAGA |
| R_EMSA in refined 1398 | CGGAGGACTTGTGTCGGTT |
| Chemiluminescent EMSA | |
| F_EMSA refined_int1397:98Biotin | TTCAATAAAGCGGAATTTGAAGA |
| R_EMSA in refined 1398 | CGGAGGACTTGTGTCGGTT |
| F_EMSA 288bp_2022 | GCAAAGCTCCTGTAACAATTCA |
| R_EMSA_2022_6_Biotin | TAGTTGACAATCTGAAGTTTA |
| SNP detection | |
| F_Clo1313_0908_1058322_1058 | CAAGGAGGATTTAACATGGATTT |
| R_Clo1313_0908_1058322_1058 | ACCACCCTTTGACCCTTTTT |
| F_Clo1313_1891_2208653_2208 | TAGCATCCGGACTGGTTTTT |
| R_Clo1313_1891_2208653_2208 | ATGAATGAAAACAATCTAAATA |
| F_Clo1313_0145_159861_15986 | CAGATCCCAGTTGGTTTGGA |
| R_Clo1313_0145_159861_15986 | CAGGAAAATACAGGCTGTTGG |
| F_Clo1313_0185_199883_19988 | GTTGGCAAAATCGGTGAGAT |
| R_Clo1313_0185_199883_19988 | CATCGGATCGAGCACTACAA |