TABLE 3.
Oligonucleotide sequences and descriptions
| Oligonucleotide name | Sequencea | Description |
|---|---|---|
| ΔrecJ-P1 | GGTTCGTCGTCAATCCTGAA | Primer to interrupt Nm8013 recJ by replacing recJ with kan |
| ΔrecJ-P2 | GCAGGTCGACTCTAGAGGATCAACGTGGAACTTTACAGTGCGGGT | Primer to interrupt Nm8013 recJ by replacing recJ with kan |
| ΔrecJ-P3(Kan) | ACCCGCACTGTAAAGTTCCACGTTGATCCTCTAGAGTCGACCTGC | Primer to interrupt Nm8013 recJ by replacing recJ with kan |
| ΔrecJ-P4(Kan) | CGCTTCCCAGTAGTCGATATAAAGTCAGAAGAACTCGTCAAGAAGGCG | Primer to interrupt Nm8013 recJ by replacing recJ with kan |
| ΔrecJ-P5 | CGCCTTCTTGACGAGTTCTTCTGACTTTATATCGACTACTGGGAAGCG | Primer to interrupt Nm8013 recJ by replacing recJ with kan |
| ΔrecJ-P6 | CCGACCACATAAGCCTGAAA | Primer to interrupt Nm8013 recJ by replacing recJ with kan |
| Δrep-P1 | CCGTGTTCGGACGGTTATTA | Primer to interrupt Nm8013 rep by replacing recJ with kan |
| Δrep-P2 | GCAGGTCGACTCTAGAGGATCGTTTTGATGCCGTCTGAAATC | Primer to interrupt Nm8013 rep by replacing recJ with kan |
| Δrep-P3(Kan) | GATTTCAGACGGCATCAAAACGATCCTCTAGAGTCGACCTGC | Primer to interrupt Nm8013 rep by replacing recJ with kan |
| Δrep-P4(Kan) | CATTGCGGCTCCGGTTTAATCTCAGAAGAACTCGTCAAGAAGGCG | Primer to interrupt Nm8013 rep by replacing recJ with kan |
| Δrep-P5 | CGCCTTCTTGACGAGTTCTTCTGAGATTAAACCGGAGCCGCAATG | Primer to interrupt Nm8013 rep by replacing recJ with kan |
| Δrep-P6 | CGGCGAACTCTTAAACCATTTC | Primer to interrupt Nm8013 rep by replacing recJ with kan |
| ΔrecQ-P1 | GGGACAATTGGAACGCTTTG | Forward primer to amplify the recQ::erm region from the FA1090 recQ mutant |
| ΔrecQ-P2 | GCAACACCCAATCGTTCAAG | Reverse primer to amplify the recQ::erm region from the FA1090 recQ mutant |
| ΔrecJ-colony PCR1 | ACCCGCACTGTAAAGTTCCACGTT | Forward primer to verify recJ interruption |
| ΔrecJ-colony PCR2 | CGCTTCCCAGTAGTCGATATAAAG | Reverse primer to verify recJ interruption |
| Δrep-colony PCR1 | GATTTCAGACGGCATCAAAAC | Forward primer to verify rep interruption |
| Δrep-colony PCR2 | CATTGCGGCTCCGGTTTAATC | Reverse primer to verify rep interruption |
| 454-8013-P1 | CCATCTCATCCCTGCGTGTCTCCGACTCAGACGAGTGCGTTCGCCCTTCCTGCTTATCAA | Forward primer to amplify the pilE region for 454 sequencing, with MID for Nm8013 parent strain grown on solid medium for 11 h |
| 454-P2 | CCTATCCCCTGTGTGCCTTGGCAGTCTCAGCGTGGAAAATCACTTACCGC | Reverse primer to amplify the pilE region for 454 sequencing |
| 454-recA-P1 | CCATCTCATCCCTGCGTGTCTCCGACTCAGAGTATACATATCGCCCTTCCTGCTTATCAA | Forward primer to amplify the pilE region for 454 sequencing, with MID for Nm8013 recA mutant grown on solid medium for 15 h |
| 454-recX-P1 | CCATCTCATCCCTGCGTGTCTCCGACTCAGCGTCTAGTACTCGCCCTTCCTGCTTATCAA | Forward primer to amplify the pilE region for 454 sequencing, with MID for Nm8013 recX mutant grown on solid medium for 13 h |
| 454-recQ-P1 | CCATCTCATCCCTGCGTGTCTCCGACTCAGAGCACTGTAGTCGCCCTTCCTGCTTATCAA | Forward primer to amplify the pilE region for 454 sequencing, with MID for Nm8013 recQ mutant grown on solid medium for 11 h |
| 454-recJ-P1 | CCATCTCATCCCTGCGTGTCTCCGACTCAGTGTACTACTCTCGCCCTTCCTGCTTATCAA | Forward primer to amplify the pilE region for 454 sequencing, with MID for Nm8013 recJ mutant grown on solid medium for 13 h |
| 454-rep-P1 | CCATCTCATCCCTGCGTGTCTCCGACTCAGTACGAGTATGTCGCCCTTCCTGCTTATCAA | Forward primer to amplify the pilE region for 454 sequencing, with MID for Nm8013 rep mutant grown on solid medium for 15 h |
| 454-8013-P1-17h | CCATCTCATCCCTGCGTGTCTCCGACTCAGACGACAGCTCTCGCCCTTCCTGCTTATCAA | Forward primer to amplify the pilE region for 454 sequencing, with MID for Nm8013 parent strain grown on solid media for 17 h |
| 454-recA-P1-21h | CCATCTCATCCCTGCGTGTCTCCGACTCAGTAGCTCTATCTCGCCCTTCCTGCTTATCAA | Forward primer to amplify the pilE region for 454 sequencing, with MID for Nm8013 recA mutant grown on solid medium for 21 h |
| 454-recX-P1-21h | CCATCTCATCCCTGCGTGTCTCCGACTCAGACTCATCTACTCGCCCTTCCTGCTTATCAA | Forward primer to amplify the pilE region for 454 sequencing, with MID for Nm8013 recX mutant grown on solid medium for 21 h |
| 454-recQ-P1-21h | CCATCTCATCCCTGCGTGTCTCCGACTCAGTGATGTGTACTCGCCCTTCCTGCTTATCAA | Forward primer to amplify the pilE region for 454 sequencing, with MID for Nm8013 recQ mutant grown on solid medium for 21 h |
| 454-recJ-P1-21h | CCATCTCATCCCTGCGTGTCTCCGACTCAGAGAGCGTCACTCGCCCTTCCTGCTTATCAA | Forward primer to amplify the pilE region for 454 sequencing, with MID for Nm8013 recJ mutant grown on solid medium for 21 h |
| 454-rep-P1-17h | CCATCTCATCCCTGCGTGTCTCCGACTCAGAGCGACTAGCTCGCCCTTCCTGCTTATCAA | Forward primer to amplify the pilE region for 454 sequencing, with MID for Nm8013 rep mutant grown on solid medium for 17 h |
a
The MID for each sample is underlined.