TABLE 2.
PCR primers used in this study
| Target | Primer or probe | Sequence (5′-3′)a | Reference or source |
|---|---|---|---|
| Primers | |||
| M13 | 1211 | GTTGTAAAACGACAACCAGT | Clontech |
| aad9 | aad9 R1 | CCCGTGTCCATAGTTAA | This study |
| aad9L2-bglII | gcgcagatctGGGTGACTAAATAGTGAGGAG | This study | |
| aad9R2-bglII | gcgcagatctGGCATGTGATTTTCC | This study | |
| ccpA | ccpA-L2 | AAAGTGCGCTTAGCAGGT | This study |
| ccpA-L5 | TATTTGGTGATGAATGGT | This study | |
| ccpA-PCRS#1 | CTACTTGAGCAGCTGTTACACCTGGTTT | This study | |
| ccpA-PCRS#2 | ATGCTAACAagatctATTCATTTTTTATCTTCC | This study | |
| ccpA-PCRS#3 | agatctTGTTAGCATGCGGATGTT | This study | |
| ccpA-PCRS#4 | CAGAGCTTCTATAAAACCTGGTATATCGG | This study | |
| ccpA-R1 | CCCTAAGGCTGATTTTACTATT | 2 | |
| ccpA-R2 | GTCAACATCCGCATGCTA | This study | |
| PccpA-L1 | GCCAATTCAGCTCCCTTT | 2 | |
| PccpA-R1 | CTTCACGGGCAACATCAT | 2 | |
| HPr | ptsH-L2 | ggctcgagGTCTTATGCCAATCC | This study |
| ptsH-R2 | gggccatggCTTCAAAAGACTTTC | This study | |
| HPr kinase | HprK-NcoI-L | ggccatggCAACCGTTACTGTAAAGA | This study |
| HprK-XhoI-R | gcctcgagTCATTGACTCACCTCA | This study | |
| Luciferase | LucL | gcaggagagTTCAGATGGGAGCTCGAATTCCAGCTTGGCA | This study |
| LucR | acgcgtcgacTTACAATTTGGACTTTCCGC | This study | |
| LucR1 | CGCACTTTGAATTTTGTA | This study | |
| sagAp | M1_sagA-cre L | GACATTTCTACTTGATTG | This study |
| M1_sagA-cre R | AAGTAACTGATAAGAACG | This study | |
| PsagA-L1-B | gcggatccGACATTTCTACTTGATTG | This study | |
| PsagA-R1-X | gcctcgagAAGTAACTGATTAAGAACG | This study | |
| PsagA Left-L | GAGGCTACTAAAGTATTA | This study | |
| PsagA Left-R | CTTTTTAATATTATCAAA | This study | |
| PsagA Right-L | TATTAATCATTTTTTACTATAA | This study | |
| PsagA Right-R | AATTACCACTTCCAGTAG | This study | |
| sagB | sagB-L | ATACAAACCACTTGTCCTT | This study |
| sagB-R | ATGCCGATAACACCTTA | This study | |
| Spy0515 | Spy0515-L | GCATGGGCATTCTACAGA | This study |
| Spy0515-R | CATCAATTCCTTTCCTCA | This study | |
| Oligonucleotide cre probes | |||
| ccpAp | 5′PccpACRE | TTAATTTTTGAAAACTTTTTCAAAAATTAA | 2 |
| 3′PccpACRE | TTAATTTTTGAAAAAGTTTTCAAAAATTAA | 2 | |
| ccpAp Scr | PccpA Scr Sense | ATAAATTATTTTAGAATTCTATTAACTTAA | 2 |
| PccpA Scr Antisense | TTAAGTTAATAGAATTCTAAAATAATTTAT | 2 | |
| mgap | 5′PmgaCRE | TTAGCTCTTGAAAACGTTTCTACGATGTTT | 2 |
| 3′′PmgaCRE | AAACATCGTAGAAACGTTTTCAAGAGCTAA | 2 | |
| sagAp | PsagACRESense | TATTAAAAAGAAAGGGTTTACATATTAATC | This study |
| PsagACREAntisense | GATTAATATGTAAACCCTTTCTTTTTAATA | This study | |
| rivR | ralp4CRESense | CCAATCTTTGATAACGGTTTCAAGCTTATC | This study |
| ralp4CREAntisense | GATAAGCTTGAAACCGTTATCAAAGATTGG | This study | |
| Real-time RT-PCR probes | |||
| amyA | amyA M1 RT L | GTTTGGGTACTTGGCAATGG | This study |
| amyA M1 RT R | TGGGTGATGTTTTTGAGATGG | This study | |
| arcA | arcA M1 RT L | GAAAATGGTGGTCAGCACGTTA | This study |
| arcA M1 RT R | CGTCTTCGCCGTTCATGAT | This study | |
| atpB | atpB M1 RT L | AATCTGGCTTTTGACCTTGC | This study |
| atpB M1 RT R | TAGCCAAACGTTTCAAATGG | This study | |
| bglP | bglP M1 RT L | ACTGCGACGATTGTGTTAGC | This study |
| bglP M1 RT R | GCAACACTCACTTGCTTTGG | This study | |
| ccpA | ccpA M1 RT L | CGGCTTGTTTGAAGCAGGTAA | 39 |
| ccpA M1 RT R | GTGAATCGTTGCTGGTGATGAT | 39 | |
| celC | celC M1 RT L | TGGTCGTCATCAAGTGATCC | This study |
| celC M1 RT R | CTTGCCCAAGAAGCTAGTGG | This study | |
| covS | covS M1 RT L | CATCTCCTGGCTTGCATGGT | This study |
| covS M1 RT R | GGAAAACCCACGATACTGATCTTC | This study | |
| gyrA | gyrA M1 RT L | CGACTTGTCTGAACGCCAAAGT | 39 |
| gyrA M1 RT R | ATCACGTTCCAAACCAGTCAAAC | 39 | |
| hasA | hasA M1 RT L | CGACTTGTCTGAACGCCAAAGT | 39 |
| hasA M1 RT R | ATCACGTTCCAAACCAGTCAAAC | 39 | |
| malX | malX M1 RT L | CCATAACCGGCAATTAAACC | This study |
| malX M1 RT R | TTTGCTTTTGCCTCTGAACC | This study | |
| ptsA | ptsA M1 RT L | TTTTTTAAAACCAGGCGAAGC | This study |
| ptsA M1 RT R | TTGTCTCAGGGACCAAATCC | This study | |
| pyk | pyk M1 RT L | GGAAGGCAGATGAATCTAAACG | This study |
| pyk M1 RT R | TACCCGGTTGAATCTGTTCG | This study | |
| rivR | rivR M1 RT L | GACGGCCTGTGTCATAAAGC | This study |
| rivR M1 RT R | GATCAATATCAAGGCAACATGC | This study | |
| rofA | rofA M1 RT L | CGAAGAGTGGATGGCCAAAC | 39 |
| rofA M1 RT R | CTCGACATAGTGGCAAAAAAGATG | 39 | |
| sagA | sagA M1 RT L | GCTACTAGTGTAGCTGAAACAACTCAA | This study |
| sagA M1 RT R | AGCAACAAGTAGTACAGCAGCAA | This study | |
| slo | slo M1 RT L | TTGTTGAGGATAATGTAAGAATGTTTAG | This study |
| slo M1 RT R | TCCTGGCTTGCAACTGATTG | This study | |
| Spy1680 | Spy1680 M1 RT L | GGCAAGCCCTACTAAAAGAGG | This study |
| Spy1680 M1 RT R | GGAAACGGATTTCAGTCAGC | This study |
a
Underlining indicates restriction sites, italics indicate regions of overlap, and lowercase letters indicate noncomplementary sequences.