TABLE 2.
Oligonucleotides used in this study
| Gene/protein/domain | Oligonucleotide | Sequencea | Plasmid |
|---|---|---|---|
| ΔtraJ constructed by recombineering | ΔTraJ_For | 5′-CTGGGAACCAAAAAAGGAGCGCTGACCATGGGTTGGGTAACGCCAGGGTTTTCC-3′ | pKM101ΔtraJ |
| ΔTraJ_Rev | 5′-TGGCGGGTAATCGTGGTTATATCAACCATGGCACACAGGAAACAGCTATGACCATGATTAC-3′ | ||
| TraJ | TraJ_For | 5′-CAGTAGCCATGGACGATAGAGAAAGA-3′ | pTB26 |
| TraJ_Rev | 5′-ACAATTGGTACCTCAGATCTCCCTCAG-3′ | ||
| TraJ′ (residues 1–75) | NW1_For | 5′-CATACCATGGACGATAGAGAAAGAGGCTTAGCATTTTTATTTG-3′ | pNW1 |
| NW1_Rev | 5′-GTATCTCGAGTATATATCATATGATAAATGATAAAAGCGATCAGACCGCCAAC-3′ | ||
| VirD4At | NW5_For | 5′-CGGTGAACATATGAATTCCAGCAA-3′ | pNW5 |
| NW5_Rev | 5′-AGTTCTCGAGCTACTTTTCAGGATCGTACGG-3′ | ||
| VirD4ΔCTDAt | VirD4AtΔ553_For | 5′-CGGTGAACATATGAATTCCAGCAA-3′ | pTB37 |
| VirD4AtΔ553_Rev | 5′-CTATTAGGTACCTCAGGGCTCAGGCAGAGA-3′ | ||
| VirD4Ap | VirD4Ap_For | 5′-AGTCGTCATATGCATAGTTCCAATCAT-3′ | pTB7 |
| VirD4Ap_Rev | 5′-TTAGTGCTCGAGCTACTTTAGTCTTCC-3′ | ||
| VirD4Wp | VirD4Wp_For | 5′-TAAGCGATCACCATGGGTCATAGC-3′ | pTB12 |
| VirD4Wp_Rev | 5′-GCTAGCTCGGGTACCTTACTTTCC-3′ | ||
| SDVirD4ΔCTDAt | NW4_For | 5′- CATATATATACATATGAATCAGAAGCATCACGGGACGG-3′ | pNW4 |
| NW4_Rev | 5′- GTTCTCGAGTCAAGGGTGCGGGCTCAGGCAG-3′ | ||
| CTDVirD4At | CTD_For | 5′-AAAAAAGAATTCCATCATCATCATCATCACAG CAGC-3′ | pNW12 |
| CTD_Rev | 5′-AAAAAAAAGCTTTCAAAAGCTGTTGACGCTTTG-3′ | ||
| TraJ/VirD4ΔCTDAp | TraJ/VirD4ApΔ574_For | 5′-TTCCGGGTCATAAGGTTCTTGG-3′ | pTB50 |
| TraJ/VirD4ApΔ574_Rev | 5′-TAAATTCGTGGTGGTGTTGAAGG-3′ | ||
| TraJ/VirD4Wp | NW1_For | 5′-CATACCATGGACGATAGAGAAAGAGGCTTAGCATTTTTATTTG-3′ | pTB51 |
| TB51_For1 | 5′-GATTATTCTTTCTCTATAAATGATAAAAGCGATCAGACCGCCAAC-3′ | ||
| TB51Rev1 | 5′-GCTTTTATCATTTATAGAGAAAGAATAATCGAGTGGCGGCC-3′ | ||
| TB51_Rev | 5′-GTATCTCGAGTTACTTTCCATTACTTTTTGGTTTATCACCATCATCTTCATC-3′ | ||
| TraJ/VirD4ΔCTDWp | NW1_For | 5′-CATACCATGGACGATAGAGAAAGAGGCTTAGCATTTTTATTTG-3′ | pTB52 |
| TB51_For1 | 5′-GATTATTCTTTCTCTATAAATGATAAAAGCGATCAGACCGCCAAC-3′ | ||
| TB51Rev1 | 5′-GCTTTTATCATTTATAGAGAAAGAATAATCGAGTGGCGGCC-3′ | ||
| TB52_Rev5′ | 5′-CTATCTCGAGTTATGGGTCATATGGCTCCTGTGTAGGTACATAAGTC-3′ | ||
| His6-VirE1/FLAG-VirE2 | VirE1_For | 5′-GGAGAGAACATATGGCCATCATC-3′ | pPC2049 |
| VirE1_RevFLAG | 5′-TTTGTCGTCGTCGTCTTTGTAGTCCATCGTCTCACTGGTTGTGAC-3′ | ||
| VirE2_ForFLAG | 5′-ATGGACTACAAAGACGACGACGACAAAATGGATCTTTCTGGCAAT-3′ | ||
| VirE2_Rev | 5′-TATCCTCGAGTCAAAAGCTGTTGA-3′ | ||
| VirE2CT100 | E2CT100_For | 5′ TAACTGCAGGCATATGTTGCGTGACATCCATGAC-3′ | pPC2040 |
| VirE2_Rev | 5′-TATCCTCGAGTCAAAAGCTGTTGA-3′ | pTB70 | |
| Cre | Cre_For | 5′-GATAGAGCTCAGGAGGTATTCACCATGTCCAATTTACTGACCGTACACCAAAATTTGC-3′ | pTB33 |
| Cre_Rev | 5′-CATGGTACCTATATATCATATGATCGCCATCTTCCAGCAGGC-3′ | ||
| VirE3 | VirE3_For | 5′-GATGCATATGGTGAGCACTACGAAG | pTB53 |
| VirE3_Rev | 5′-GATCGGTACCTTAGAAACCTCTGGAGG | ||
| VirF | VirF_For | 5′-GCACCATATGAGAAATTCGAGTTTGCG | pTB54 |
| VirF_Rev | 5′-GATATTGGTACCTCATAGACCGCGCGTTG | ||
| Ats-1 | Ats-1_For | 5′-GTGCTCCATATGCTAATAAGAAGAATTCTG-3′ | pTB40 |
| Ats-1_Rev | 5′-GTAATTGGTACCCTCGAGTTACCTCGTACCTTTACC-3′ | ||
| Ats-1 CT100 | AtsCT_For | 5′-GTACTTCATATGGAACGCATTTTCTCATTG-3′ | pTB42 |
| AtsCT_Rev | 5′-GTAATTGGTACCCTCGAGTTACCTCGTACCTTTACC-3′ | ||
| WD0636 | WD0636_For | 5′-GCCGAGCATATGAGTAAAAAAGAAAAAGAG-3′ | pTB43 |
| WD0636_Rev | 5′-CACGGTACCTCATAATTTCTCAAATAACTTTTC-3′ | ||
| WD0811 | WD0811_For | 5′-GTCCATATGATGATATCCAATAATTCT-3′ | pTB44 |
| WD0811_Rev | 5′-GATGGTACCTCAATTCATTTGTAA-3′ | ||
| WD0830 | WD0830_For | 5′-TCGTAGCATATGAAACAAGGAGATAAG-3′ | pTB45 |
| WD0830_Rev | 5′-GTAGGTACCTTACACTGTTCCTGGAGT |
a
Restriction sites for cloning are underlined.