Table 2.
Oligonucleotides used in this work.
| Strain or Plasmid | Description |
|---|---|
| Intron retargeting* | |
| Cdi-dnaK-722a -IBS | AAAAAAGCTTATAATTATCCTTAAATTCCTTCTTAGTGCGCCCAGATAGGGTG |
| Cdi-dnaK-722a -EBS1d | CAGATTGTACAAATGTGGTGATAACAGATAAGTCTTCTTAGCTAACTTACCTTTCTTTGT |
| Cdi-dnaK-722a -EBS2 | TGAACGCAAGTTTCTAATTTCGATTGAATTTCGATAGAGGAAAGTGTCT |
| Cdi-hrcA-285s -IBS | AAAAAAGCTTATAATTATCCTTACTTATCGAACAAGTGCGCCCAGATAGGGTG |
| Cdi-hrcA-285s -EBS1d | CAGATTGTACAAATGTGGTGATAACAGATAAGTCGAACAATGTAACTTACCTTTCTTTGT |
| Cdi-hrcA-285s -EBS2 | TGAACGCAAGTTTCTAATTTCGATTATAAGTCGATAGAGGAAAGTGTCT |
| Cdi-hrcA-200a -IBS | AAAAAAGCTTATAATTATCCTTACTTTTCCAGATGGTGCGCCCAGATAGGGTG |
| Cdi-hrcA-200a -EBS1d | CAGATTGTACAAATGTGGTGATAACAGATAAGTCCAGATGGATAACTTACCTTTCTTTGT |
| Cdi-hrcA-200a -EBS2 | TGAACGCAAGTTTCTAATTTCGGTTAAAAGTCGATAGAGGAAAGTGTCT |
| Cdi-groEL-601s -IBS | AAAAAAGCTTATAATTATCCTTATTTGTCTCTGCAGTGCGCCCAGATAGGGTG |
| Cdi-groEL-601s -EBS1d | CAGATTGTACAAATGTGGTGATAACAGATAAGTCTCTGCATATAACTTACCTTTCTTTGT |
| Cdi-groEL-601s -EBS2 | TGAACGCAAGTTTCTAATTTCGATTACAAATCGATAGAGGAAAGTGTCT |
| Cdi-groEL-689a -IBS | AAAAAAGCTTATAATTATCCTTACTGGTCATAATTGTGCGCCCAGATAGGGTG |
| Cdi-groEL-689a -EBS1d | CAGATTGTACAAATGTGGTGATAACAGATAAGTCATAATTCTTAACTTACCTTTCTTTGT |
| Cdi-groEL-689a -EBS2 | TGAACGCAAGTTTCTAATTTCGGTTACCAGTCGATAGAGGAAAGTGTCT |
| EBS universal | CGAAATTAGAAACTTGCGTTCAGTAAAC |
| ClosTron sequencing | |
| cspfdx-seq-F1 | GATGTAGATAGGATAATAGAATCCATAGAAAATATAGG |
| pMTL007-R1 | AGGGTATCCCCAGTTAGTGTTAAGTCTTGG |
| Screening of clones | |
| Cdi-dnaK-F | CTACAGCTGGTAACAATAGATTAGGT |
| Cdi-dnaK-R | CTGTAGCAGTTATGAAAGGTAAGTT |
| Cdi-groEL-F | AGTCTCAAACTATGAATACTGAATTAGATG |
| Cdi-groEL-R | GCTTTTTACCTTGTTGAACTATTTGT |
| Cdi-hrcA-F | TAGGGTATTTAATTCAGCCTCATACTTC |
| Cdi-hrcA-R | TGCTACAGTTGTATAGTTTGTTAGTTGC |
| ErmRAM-F | ACGCGTTATATTGATAAAAATAATAATAGTGGG |
| ErmRAM-R | ACGCGTGCGACTCATAGAATTATTTCCTCCCG |
*Introns were inserted after the indicated number of bases in the sense (s) or the antisense (a) orientation from the start of the open reading frame (ORF) of the target gene. Cdi, C. difficile; IBS, intron-binding sites; EBS, exon-binding sites; ErmRAM, erythromycin retrotransposition-activated selectable marker.