TABLE 2.
Oligonucleotide primers and probes
| Function and name | Sequence (5′–3′ [modification])a | Target | Reference or source |
|---|---|---|---|
| Primers for plasmid construction | |||
| capHis-pBUS1-F | TGCAGCTAGCATATGATAAACCTCCTATTTTCCTTTCTTGTTTTCCATTATATATAATCCCCTGTATATTTTGCAAACTCTGGTACCACGCGTTGCGCTCAC | pBUS1 | This study |
| capHis-pBUS1-R | TTTATCATATGCTAGCTGCAGGAATTCTCTGACTAGTCGACCGAAAGCTTTGCTGGATCCGCATGCTCGAGAGGTTCTCATCACCATCACCATCACTAATCTAGAGCGGCCGCCACCG | pBUS1 | This study |
| pBUS1-oriL-F | AATGTTGTACAGAAAACCTCTGACACATGCAG | pBUS1, pBUS1-Pcap, pBJW13 | This study |
| pBUS1-oriL-R | AGTTAAGATCTAGGATCAATTTTGAACTCTCTCC | pBUS1, pBUS1-Pcap, pBJW13 | This study |
| oriL-BsrGI-F | TGAATTGTACACTTCCAAGTAAAGTATAACACAC | pUB110 | This study |
| oriL-BglII-R | TTAGAAGATCTGCGATTGCTGAATAAAAGATACG | pUB110 | This study |
| pBUS1-BsrGI-F | TTAGTTGTACAGGCCATATTGTTGTATAAGTGATG | pBUS1, pBUS1-Pcap, pBJW13 | This study |
| pBlueScript-BglII-R | AGTTAAGATCTATGACCAAAATCCCTTAACGTG | pBUS1, pBUS1-Pcap, pBJW13 | This study |
| pT181-BglII-F | AGATAAGATCTATAGAACATGCATTTATGCCGAG | pVPF5 | This study |
| pT181-BsrGI-R | TAATATGTACACTATTTCCAAAATTTAAATTCATG | pVPF5 | This study |
| mut-repC-F | AAAGCTCCACAGAAATTCCAGAACAAAATATAAGAATTTG | pTSSC, pTSSC-Pcap | This study |
| mut-repC-R | AATTTCTGTGGAGCTTTCCCCATTCTTCTTCATC | pTSSC, pTSSC-Pcap | This study |
| Primers and probes for qPCR | |||
| nuc263-F | AAAGCGATTGATGGTGATACGGTT | nuc | 38 |
| nuc355-R | TGCTTTGTTTCAGGTGTATCAACCA | nuc | 38 |
| nuc294-P | ATGTACAAAGGTCAACCAATGACATTCAGA (Cy5, BHQ2) | nuc | 38 |
| qPCR-tetL-F | GGCTTTCGTTCACCAAAACAGT | tet(L) | This study |
| qPCR-tetL-R | TGGTAAAGTTAAGCAAACTCATTCCA | tet(L) | This study |
| FAM-tetL-TAMRA | TTGTTTCAAGTAGCTTGAAACAGCAGGAAGCTG (FAM, TAMRA) | tet(L) | This study |
a
Bases binding to the template are underlined. Restriction sites used for cloning are in boldface italics. Complementary 5′ ends of cloning and mutagenesis primers are in italics. In mutagenesis primers, mismatched bases are in boldface. Cy5, cyanine fluorescein 5; BHQ2, black hole quencher 2; FAM, 6-carboxyfluorescein; TAMRA, tetramethylrhodamine.