Table 1 Plasmids.
From: The mechanism of replication stalling and recovery within repetitive DNA
Plasmid | Insert | Backbone | Vector | Vector sites | Insert sites | Derivation of insert | Source |
|---|---|---|---|---|---|---|---|
Replication templates—empty vectors | |||||||
pZN3 | Â | Â | Â | Â | Â | Â | Taylor and Yeeles5 |
pGC504 | BamHI/PacI/BbvCI/NotI/PstI linker | pZN3 | pZN3 | BamHI PstI | BamHI PstI | Annealed oligo GC497/GC498 | This study |
pGC542 | pGC504 - BsaI sites removed | pZN3 | pGC504 | Â | Â | HiFi mutagenesis with primers GC510/GC511/GC512/GC513 | This study |
pGC558 | BamHI/NotI/BbvCI/PacI/PstI linker | pZN3 | pGC542 | BamHI PstI | BamHI PstI | Annealed oligos GC520/GC521 | This study |
pSMART HC-Amp | Â | Â | Â | Â | Â | Â | Lucigen Cat. 40041-2 |
pGC481 | pSMART HC with SalI NheI linker | pSMART | pSMART HC-Amp | Blunt | Blunt | Annealed oligos GC419/GC420 | This study |
pGC483 | pSMART HC - BsaI site removed | pSMART | pGC481 | Â | Â | Mutagenesis with primers GC421/GC422 | This study |
Replication templates—Homopolymers | |||||||
pGC491 | 30xA | pSMART | pGC483 | SalI NheI | SalI NheI | Annealed oligos GC365/GC366 | This study |
pGC499 | 60xA | pSMART | pGC491 | NotI Esp3I | NotI BsaI | Annealed oligos GC367/GC368 | This study |
pGC523 | 114xA | pSMART | pGC499 | NotI Esp3I | NotI BsaI | pGC499 | This study |
pGC526 | 222xA | pSMART | pGC523 | NotI Esp3I | NotI BsaI | pGC523 | This study |
pGC536 | 222xA | pZN3 | pGC504 | PacI NotI | PacI NotI | pGC526 | This study |
pGC601 | 222xT | pZN3 | pGC558 | PacI NotI | PacI NotI | pGC536 | This study |
pGC554 | 10xG | pZN3 | pGC504 | PacI NotI | PacI NotI | Annealed oligos GC516/GC517 | This study |
pGC606 | 13xG | pZN3 | pGC542 | PacI NotI | PacI NotI | Annealed oligos GC583/GC584 | This study |
pGC607 | 16xG | pZN3 | pGC542 | PacI NotI | PacI NotI | Annealed oligos GC585/GC586 | This study |
pGC556 | 20xG | pZN3 | pGC504 | PacI NotI | PacI NotI | Annealed oligos GC518/GC519 | This study |
pGC543 | 30xG | pZN3 | pGC542 | PacI NotI | PacI NotI | Annealed oligos GC369/GC370 | This study |
pGC547 | 40xG | pZN3 | pGC543 | NotI Esp3I | Â | Annealed oligos GC514/GC515 | This study |
pGC548 | 50xG | pZN3 | pGC547 | NotI Esp3I | Â | Annealed oligos GC514/GC515 | This study |
pGC581 | 10xC | pZN3 | pGC558 | PacI NotI | PacI NotI | pGC554 | This study |
pGC608 | 13xC | pZN3 | pGC558 | PacI NotI | PacI NotI | Annealed oligos GC583/GC584 | This study |
pGC609 | 16xC | pZN3 | pGC558 | PacI NotI | PacI NotI | Annealed oligos GC585/GC586 | This study |
pGC582 | 20xC | pZN3 | pGC558 | PacI NotI | PacI NotI | pGC556 | This study |
pGC583 | 30xC | pZN3 | pGC558 | PacI NotI | PacI NotI | pGC543 | This study |
pGC584 | 40xC | pZN3 | pGC558 | PacI NotI | PacI NotI | pGC547 | This study |
pGC585 | 50xC | pZN3 | pGC558 | PacI NotI | PacI NotI | pGC548 | This study |
Replication templates—dinucleotides | |||||||
pGC605 | 6xCG | pZN3 | pGC542 | BamHI PstI | BamHI PstI | Annealed oligos GC581/GC582 | This study |
pGC604 | 8xCG | pZN3 | pGC542 | BamHI PstI | BamHI PstI | Annealed oligos GC579/GC580 | This study |
pGC603 | 10xCG | pZN3 | pGC542 | BamHI PstI | BamHI PstI | Annealed oligos GC577/GC578 | This study |
pGC602 | 12xCG | pZN3 | pGC542 | BamHI PstI | BamHI PstI | Annealed oligos GC575/GC576 | This study |
pGC566 | 14xCG | pZN3 | pGC542 | BamHI PstI | BamHI PstI | Annealed oligos GC544/GC545 | This study |
pGC593 | 24xCG | pZN3 | pGC566 | NotI Esp3I | Â | Annealed oligos GC546/GC547 | This study |
pSW23 | 24xCG Scramble 1 | pZN3 | pGC542 | PacI NotI | PacI NotI | Annealed oligos SW015/SW016 | This study |
pSW24 | 24xCG Scramble 2 | pZN3 | pGC542 | PacI NotI | PacI NotI | Annealed oligos SW017/SW018 | This study |
pGC567 | 14xCA | pZN3 | pGC542 | BamHI PstI | Â | Annealed oligos GC548/GC549 | This study |
pGC594 | 25xCA | pZN3 | pGC567 | NotI Esp3I | Â | Annealed oligos GC550/GC551 | This study |
pGC565 | 15xTA | pZN3 | pGC542 | BamHI PstI | Â | Annealed oligos GC540/GC541 | This study |
pGC634 | 25xTG | pZN3 | pGC558 | BamHI PstI | Â | pGC594 | This study |
pGC633 | 25xGA | pZN3 | pGC542 | BamHI PstI | Â | Annealed oligos GC641/GC642 | This study |
Replication templates—trinucleotides | |||||||
pGC570 | 11xCTG | pZN3 | pGC542 | BamHI PstI | Â | Annealed oligos GC560/GC561 | This study |
pGC597 | 21xCTG | pZN3 | pGC570 | NotI Esp3I | Â | Annealed oligos GC562/GC563 | This study |
pSW01 | 41xCTG | pZN3 | pGC597 | NotI Esp3I | NotI BsaI | pGC597 | This study |
pSW02 | 81xCTG | pZN3 | pSW01 | NotI Esp3I | NotI BsaI | pSW01 | This study |
pSW03 | 161xCTG | pZN3 | pSW02 | NotI Esp3I | NotI BsaI | pSW02 | This study |
pSW08 | 161xCAG | pZN3 | pGC558 | PacI NotI | PacI NotI | pSW03 | This study |
pGC489 | 11xCGG | pSMART | pGC483 | SalI NheI | SalI NheI | Annealed oligos GC363/364 | This study |
pGC497 | 21xCGG | pSMART | pGC489 | NotI Esp3I | NotI BsaI | Annealed oligos GC363/364 | This study |
pGC503 | 41xCGG | pSMART | pGC497 | NotI Esp3I | NotI BsaI | pGC497 | This study |
pGC541 | 61xCGG | pSMART | pGC503 | pGC503 | NotI BsaI | pGC497 | This study |
pGC507 | 11xCGG | pZN3 | pGC504 | PacI NotI | PacI NotI | pGC489 | This study |
pGC610 | 14xCGG | pZN3 | pGC542 | PacI NotI | PacI NotI | Annealed oligos GC587/GC588 | This study |
pGC611 | 17xCGG | pZN3 | pGC542 | PacI NotI | PacI NotI | Annealed oligos GC589/GC590 | This study |
pGC515 | 21xCGG | pZN3 | pGC504 | PacI NotI | PacI NotI | pGC497 | This study |
pGC544 | 41xCGG | pZN3 | pGC542 | PacI NotI | PacI NotI | pGC503 | This study |
pGC545 | 61xCGG | pZN3 | pGC504 | PacI NotI | PacI NotI | pGC541 | This study |
pGC549 | 81xCGG | pZN3 | pGC544 | NotI Esp3I | NotI BsaI | pGC544 | This study |
pGC551 | 101xCGG | pZN3 | pGC549 | NotI Esp3I | NotI BsaI | pGC497 | This study |
pGC552 | 121xCGG | pZN3 | pGC549 | NotI Esp3I | NotI BsaI | pGC544 | This study |
pGC553 | 161xCGG | pZN3 | pGC549 | NotI Esp3I | NotI BsaI | pGC549 | This study |
pMdm10 | 21xCGG Scramble 1 | pZN3 | pGC542 | PacI NotI | PacI NotI | Annealed oligos pMDM10F/pMDM10R | This study |
pMdm11 | 21xCGG Scramble 2 | pZN3 | pGC542 | PacI NotI | PacI NotI | Annealed oligos pMDM11F/pMDM11R | This study |
pGC571 | 11xCCG | pZN3 | pGC558 | PacI NotI | PacI NotI | pGC507 | This study |
pGC612 | 14xCCG | pZN3 | pGC558 | PacI NotI | PacI NotI | Annealed oligos GC587/GC588 | This study |
pGC613 | 17xCCG | pZN3 | pGC558 | PacI NotI | PacI NotI | Annealed oligos GC589/GC590 | This study |
pGC572 | 21xCCG | pZN3 | pGC558 | PacI NotI | PacI NotI | pGC515 | This study |
pGC573 | 41xCCG | pZN3 | pGC558 | PacI NotI | PacI NotI | pGC503 | This study |
pGC574 | 61xCCG | pZN3 | pGC558 | PacI NotI | PacI NotI | pGC545 | This study |
pGC487 | 11xGAA | pSMART | pGC483 | SalI NheI | SalI NheI | Annealed oligos GC361/GC362 | This study |
pGC495 | 21xGAA | pSMART | pGC487 | NotI Esp3I | NotI BsaI | Annealed oligos GC361/GC362 | This study |
pGC522 | 41xGAA | pSMART | pGC495 | NotI Esp3I | NotI BsaI | pGC495 | This study |
pGC525 | 81xGAA | pSMART | pGC522 | NotI Esp3I | NotI BsaI | pGC522 | This study |
pGC535 | 161xGAA | pSMART | pGC525 | NotI Esp3I | NotI BsaI | pGC525 | This study |
pGC538 | 161xGAA | pZN3 | pGC504 | PacI NotI | PacI NotI | pGC535 | This study |
pGC580 | 161xTTC | pZN3 | pGC558 | PacI NotI | PacI NotI | pGC538 | This study |
Protein expression | |||||||
pGEX-4T1 Sld2 | GST-Thrombin-Sld2 | pGEX-4T-1 | pGEX-4T-1 | EcoRI XhoI | EcoRI XhoI | Budding yeast Sld2 PCR amplified from genomic DNA | Diffley lab (stock 1680) |
pGC441 | GST-PreScission-Sld2 | pGEX-6P-1 | pGEX-6P-1 | EcoRI XhoI | EcoRI XhoI | pGEX-4T1 Sld2 | This study |
pAJ6 | Pol2-Gal1,10-Dpb4-TEV-CBP | pRS304 | Â | Â | Â | Â | Yeeles et al.36 |
pSW62 | Pol2-P301R-Gal1,10-Dpb4-TEV-CBP | pRS304 | pAJ6 | BlpI MscI | BlpI MscI | HiFi cloning of a synthetic gBlock fragment | This study |
