Table 3.
Oligonucleotides.
| Oligonucleotide | Sequence (5′–3′) | Relevant properties | Use (plasmid generated) |
|---|---|---|---|
| Rpa1CF DS | GTTCGAGGTACCGTTCGGGGAGC | Δrpa1 external downstream primer, KpnI site | pTA1141 |
| Rpa1CR DS | AGGTGCGCATATGAGCGCCTCGC | Δrpa1 internal downstream primer, NdeI site | pTA1141 |
| Rpa1 CR US | TACTACGTCTAGACGGACCTGTTCG | Δrpa1 external upstream primer, XbaI site | pTA1141 |
| Rpa1 CF US | GGTCGAGTTCCATATGGTCGGGATTCGCC | Δrpa1 internal upstream primer, NdeI site | pTA1141 |
| Rpa3KpnI F | GCCGGTGGTACCACAGCCTC | Δrpa3 external upstream primer, KpnI site | pTA1142 |
| Rpa3NdeIR | GCAAATCAGTCATATGCTACCTCGCC | Δrpa3 internal upstream primer, NdeI site | pTA1142 |
| Rpa3EcoRIR | GACGGTGGAATTCGGCCGTCG | Δrpa3 external downstream primer, EcoRI site | pTA1142 |
| Rpa3NdeI FC | GCGAGGTCGATGCATATGAGTTCCAACG | Δrpa3 internal downstream primer, NdeI site | pTA1142 |
| trpANdeIF | CTCTGCACATATGTCGCTCGAAGACGC | trpA forward primer containing NdeI site | pTA1166 |
| trpANdeIR | TGCATGCCATATGCGTTATGTGCG | trpA reverse primer containing NdeI | pTA1166 |
| RPAP11kpnIus | CCGCGAGTGGTACCGCAAGCCCG | Δrpap1 external upstream primer, KpnI site | pTA1170 |
| RPAP11nsiIus | CGACGACCGGCGATGCATTCATGCGCGC | Δrpap1 internal upstream primer, NsiI site | pTA1170 |
| RPAP11sphIds | GCTGAAGGGCATGCGAGGCCGTGC | Δrpap1 internal downstream primer, SphI site | pTA1170 |
| RPAP11ecoRIds | CGGCGAGAGAATTCCCTGCCCGGG | Δrpap1 external downstream primer, EcoRI site | pTA1170 |
| PEecorI F | GCCCGAATTCCGTCTGATTG | Δrpa1 operon external downstream primer, EcoRI site | pTA1189 |
| Rpa1CR US | TACTACGTCTAGACGGACCTGTTCG | Δrpa1 operon external upstream primer, XbaI site | pTA1189 |
| RPEndeI R DS | CTACCGGAACATATGACTCGGGTCG | Δrpa1 operon internal downstream primer, NdeI site | pTA1189 |
| Rpa1ndeI F2 | GTTGGACCCATATGTCGAACGACG | Δrpa1 operon internal upstream primer, NdeI site | pTA1189 |
| RPAP11SphI US | GCGATTTCCCGCATGCCGACGACCG | Δrpap1 internal upstream primer, SphI site | pTA1217 |
| RPAP11 kpnI us | CCGCGAGTGGTACCGCAAGCCCG | Δrpap1 external upstream primer, KpnI site | pTA1217 |
| Rpa3BspHI F | AGGTAGATCATGACTGATTTGC | rpa3 forward primer, BspHI site | pTA1218 |
| Rpa3 RAsel | CGAGTGGGGAATTCGTTGGAATTAATTTACATC | rpa3 reverse primer, AseI site | pTA1218 |
| Rpa1F NcoI | CCCGACTCCATGGAACTCGACC | rpa1 forward primer, NcoI site | pTA1222 |
| Rpa1AseI/EcoRI | CGGCGGCGAATTCGCGGTAGGCGATTAATCGCGTGC | rpa1 reverse primer, AseI and EcoRI sites | pTA1222 |
| pTA1327 | |||
| RPAP1F BspHI | GGTGCGCTCATGAGCGCCTCG | rpap1 forward primer, BspHI site | pTA1223 |
| RPAP1BamHI | CGTTCGGGGGATCCGCGCCTGC | rpap1 reverse primer, BamHI site | pTA1223 |
| pTA1326 | |||
| RPAP3BspHI F | GTCGATGTTCATGAGTTCCAACG | rpap3 forward primer, BspHI site | pTA1224 |
| RPAP3EcoRI R | CGGTCGGAATTCAGGCCGAC | rpap3 reverse primer, EcoRI site | pTA1224 |
| pTA1280 | |||
| HsaCdc48F | GTTCTTGGCATATGACCGAGGCTCTC | Forward primer for Hsa-cdc48d, NdeI site | pTA1240, Probe Figure 5B |
| HsaCdc48R | CTGACAGATCTCGCAGTCACAGC | Reverse primer for Hsa-cdc48d, BgIII site | pTA1240, Probe Figure 5B |
| Rpa3BstEII | GATGCGCGGTGACCTCGTGG | rpap3 forward primer, native BstEII site | pTA1280 |
| Rpa3NdeI | CGAGGTAGCATATGACTGATTTGCG | rpa3 forward primer, NdeI site | pTA1281 |
| RPAP3 gitF | CTCCCAATGGGTACCAAGGTGGAGGC | Δrpap3 internal upstream primer, NdeI site | pTA1282 |
| RPAP3 gitR | TCGTTGGACATATGTTACATCGACCTCGC | Δrpap3 external upstream primer, KpnI site | pTA1282 |
| RPAP3 F DS | CTCGCTGAATTCGGTGGGTGC | Δrpap3 external downstream primer, EcoRI site | pTA1282 |
| RPAP3 R DS | CTGAGCGCATATGCGGGCGTCTCG | Δrpap3 internal downstream primer, NdeI site | pTA1282 |
| cdc48dUF | ACGGGTACCCACGTTGCTGG | Hvo-cdc48d external upstream primer, KpnI site | pTA1294 |
| cdc48dDR | GCCGAATTCGAGCCGAGGTGG | Hvo-cdc48d external downstream primer, EcoRI site | pTA1294 |
| cdc48d-CtrR | CGGCGCGCTAGCCGGACCGGTTACGC | Internal reverse primer to generate C-terminally truncated Hvo-cdc48d, NheI site at cdc48d stop codon | pTA1294 |
| cdc48d-CtrF | CTGTGGTGCTAGCCGTCGTCCGACCCCG | Internal forward primer to generate C-terminal truncated Hvo-cdc48d, NheI site at cdc48d stop codon | pTA1294 |
| cdc48dSeqF | GGAAAAAGGGGCAGATGGTG | Forward primer to downstream flanking region of Hvo-cdc48d | PCR Figure 5C |
| cdc48dHvSeqR | CGACGACATCTCGCTGATTCG | Reverse primer to Hvo-cdc48d gene | PCR Figure 5C |
| cdc48dHsalSeqR | GGTCAACACGCTGCTGAAGTCC | Reverse primer to Hsa-cdc48d gene | PCR Figure 5C |
| Rpa1BstEII | CCGGCACGGTGACCGCCATCC | rpap1 forward primer, native BstEII site | pTA1326 |
| Rpa1NdeI | CCCGACCATATGGAACTCGACC | rpa1 forward primer, NdeI site | pTA1327 |