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. 2012 Sep;32(18):3743–3755. doi: 10.1128/MCB.00032-12

Table 1.

Oligonucleotide primers used in this study

Primer Gene Nucleotide sequencea Use
Plasmids for gene disruption
    ndxA5-f ndxA 5′-GCGGCCGCCAAGTGCTGGACCTGTACGA-3′ 5′ region of ndxA
    ndxA5-r 5′-GCGGCCGCGGTATCGGGTGGAGATGAGA-3′
    ndxA3-f 5′-GAATTCACCCGCTACGATGTTACCTG-3′ 3′ region of ndxA
    ndxA3-r 5′-CTCGAGAATATGGAAGCGTCCTCACG-3′
    ndxB5-f ndxB 5′-GCGGCCGCGTTAGATCCGCTCACCGAAG-3′ 5′ region of ndxB
    ndxB5-r 5′-GCGGCCGCAAGCGAATCTCAAGCGACAT-3′
    ndxB3-f 5′-GAATTCCCGTAAGGACTGCCCATTTA-3′ 3′ region of ndxB
    ndxB3-r 5′-CTCGAGCAAAGGTCAGCGCACATCTA-3′
    ndxC5-f ndxC 5′-GCGGCCGCCTCGAAAGGGAATGAACCAA-3′ 5′ region of ndxC
    ndxC5-r 5′-GCGGCCGCTCTTGCCTGCAGAAAACTCA-3′
    ndxC3-f 5′-GAATTCCGTGGACCCAACTTCTGTATATC-3′ 3′ region of ndxC
    ndxC3-r 5′-CTCGAGGAACTCCAACTGTGGTTGATAGG-3′
    sirA5-f sirA 5′-GCGGCCGCGCTCGATCTCAAAACGGAAG-3′ 5′ region of sirA
    sirA5-r 5′-TCTAGATCTTCGACATTGCTGTCGTC-3′
    sirA3-f 5′-GAATTCATCCTTGCCCAACAGATCAC-3′ 3′ region of sirA
    sirA3-r 5′-CTCGAGGGAAGCTCCGTCCATCAATA-3′
    ndxA3-f2 ndxA 5′-CTGCAGACCCGCTACGATGTTACCTG-3′ 3′ region of ndxA (for insertion into pPyrG plasmid)
    ndxA3-r2 5′-GAATTCAATATGGAAGCGTCCTCACG-3′
Plasmids for GFP-fused protein production
    gpdpro-f gpdA 5′-CCAATGCATTGGAAAAGTCACACAACACAAGC-3′ gpdA gene promoter
    gpdpro-r 5′-GCGGCCGCTGTGATGTCTGCTCAAGC-3′ GFP-NdxC fusion
    gfpN-f gfp 5′-GCGGCCGCATGGTGAGCAAGGGCGAGGAGCTG-3′
    gfpN-r 5′-TCTAGACTTGTACAGCTCGTCCAT-3′ NdxA- or NdxB-GFP fusion
    gfpC-f gfp 5′-TCTAGAATGGTGAGCAAGGGCGAGGAGCTG-3′ NdxA-GFP fusion
    gfpC-r 5′-GGATCCTTACTTGTACAGCTCGTCCAT-3′
    gndxA-f ndxA 5′-GCGGCCGCATGCCCACAGAGACAAAATCCGTTCGCGTT-3′ NdxB-GFP fusion
    gndxA-r 5′-TCTAGAGTTCAAAACAGGCTGAAAA-3′
    gndxB-f ndxB 5′-GCGGCCGCATGTCAGATCCAATGTACGCCAGGTCAAA-3′ GFP-NdxC fusion
    gndxB-r 5′-TCTAGAGAGCTTCAGTTTCTTCGCC-3′
    gndxC-f ndxC 5′-TCTAGAATGTCCAATAATTCACAAATCC-3′ DsRed-SKM
    gndxC-r 5′-GGATCCCTACATCTTCGACTTGTCTGCAAG-3′
    ds-red-f ds-red 5′-GCGGCCGCATGGCCTCCTCCGAGGACGT-3′
    ds-red-r 5′-GGATCCCTACATCTTCGACAGGAACAGGTGGTGGCGG-3′
Plasmids for recombinant protein production
    rndxA-f ndxA 5′-CATATGCCGACCGAAACCAAATCCGTTCGCGTT-3′ pETndxA
    rndxA-r 5′-AAGCTTTCAGTTCAAAACAGGCTGAAAA-3′
    rndxB-f ndxB 5′-CATATGTCAGATCCGATGTACGCCCGCTCAAA-3′ pETndxB
    rndxB-r 5′-AAGCTTTCAGAGCTTCAGTTTCTTCGCC-3′
    rndxC-f ndxC 5′-CATATGTCCAATAATTCACAAATCC-3′ pETndxC
    rndxC-r 5′-AAGCTTCTACATCTTCGACTTGTCTGCAAG-3′
    rndxD-f ndxD 5′-GGATCCGTGGACCAGG TTCGTTCAAT-3′ pETndxD
    rndxD-r 5′-GCGGCCGCCTATCTCTTCATGGAACTTC-3′
    rSirA-f sirA 5′-CGGGATCCATGGACCTTGCTTCAGCGCCCCGTGGGGAGA-3′ pETsirA
    rSirA-r 5′-GCGGCCGCTCCGCTAACCTTGAATACATGTCGTGA-3′
Site-directed mutagenesis
    E57Q-f ndxA 5′-TGCGCGGCTCGCCAATTAATAGAAGAA-3′ pETndxA-E57Q
    E57Q-r 5′-TTCTTCTATTAATTGGCGAGCCGCGCA-3′
    E61Q-f ndxA 5′-GAATTAATAGAACAAACGGGGGTACAT-3′ pETndxA-E61Q
    E61Q-r 5′-ATGTACCCCCGTTTGTTCTATTAATTC-3′
    H286N-f sirA 5′-ATTGTACAGTGCAACGGCTCTTTTGCC-3′ pETsirA-H286N
    H286N-r 5′-GGCAAAAGAGCCGTTGCACTGTACAAT-3′
Plasmids for expressing ndxA and sirA in A. nidulans
    ndxA-f ndxA 5′-GCGGCCGCTGACAGGGTACCAATGCAAA-3′ pBSndxA, pBSndxA-E57Q
    ndxA-r 5′-GCGGCCGCAGCTCGCAGTTTTGTCCAAT-3′ pBSsirA, pBSsirA-H286N
    sirA-f sirA 5′-GCGGCCGCTCTCCCGAGCCTCTTATCAA-3′
    sirA-r 5′-GCGGCCGCTTCAGTATAGCCCCGCACTC-3′
Quantitative PCR
    RTactA-f actA 5′-GAAGTCCTACGAACTGCCTGATG-3′
    RTactA-r 5′-AAGAACGCTGGGCTGGAA-3′
    RTndxA-f ndxA 5′-GGACGGGAAGCACTACGTTA-3′
    RTndxA-r 5′-CAGCTTCGACCTGCTTTTTC-3′
    RTndxB-f ndxB 5′-CGTGAGCTCAAGGAGGAGAC-3′
    RTndxB-r 5′-AGTTGTGGCTTGGGATTTTG-3′
    RTndxC-f ndxC 5′-AGCAACAACACAATGCGAAG-3′
    RTndxC-r 5′-AGTAGCTGTTGCGGGTGTTC-3′
    RTaflR-f aflR 5′-CTGCCTTGCGAGTATATGGTTTC-3′
    RTaflR-r 5′-TTGGTGATGGTGCTGTCTTG-3′
    RTstcU-f stcU 5′-CATTTCCATTCAAGCCGATGT-3′
    RTstcU-r 5′-CCAGGTATCCGAAGTGCTCAA-3′
    RTipnA-f ipnA 5′-CAGCGTGATTGATCCATTTG-3′
    RTipnA-r 5′-CTAAATCCAACTCCCGTCCA-3′
    RTpenD-f penDE 5′-AATGGGCGGATAGTGCATAC-3′
    RTpenD-r 5′-CCGTCAAAACCAGAGAGGAG-3′
    RTsirA-f sirA 5′-CGCATTCAGGAATCAAACCT-3′
    RTsirA-r 5′-GCGTGTTCCCTGAAAACATT-3′
ChIP assay
    ipnA #1-f ipnA #1 5′-TAATCCACGCAATCCACTGA-3′ 5′ region of ipnA
    ipnA #1-r 5′-CCGGTGCATAATGACAAGTG-3′
    ipnA #2-f ipnA #2 5′-TGAGAGCTACGCTTCCCATT-3′ 5′ region of ipnA
    ipnA #2-r 5′-AGTTCTCCAAAGCTGGCTCA-3′
    ipnA #3-f ipnA #3 5′-CGTGCCTACAACAAAGAGCA-3′ ipnA
    ipnA #3-r 5′-AGTTGTGGCTTGGGATTTTG-3′
    aflR #4-f aflR #4 5′-GACTCCTAGACCCCGACAGG-3′ 5′ region of aflR
    aflR #4-r 5′-TACTGCGGGCTAGAACTGGT-3′
    aflR #5-f aflR #5 5′-ATCTCCTCATGGCGAATCTC-3′ 5′ region of aflR
    aflR #5-r 5′-TATTCCCGCAGGGATTACAG-3′
    aflR #6-f aflR #6 5′-GCTCCAGATCCAAGGTCAAG-3′ aflR
    aflR #6-r 5′-CGTATTCGTCGGTGTTGTTG-3′
    actApro-f actA 5′-TACTCCGCCTACCGCTACAA-3′ 5′ region of actA
    actApro-r 5′-GGAAGGGAGGAGGAGAGATG-3′
Producing SirA-HA protein
    SirAHA-f sirA-HA 5′-ATAAGAATGCGGCCGCATGGACCTTGCTTCAGCGCCCCGT-3′ pSirA-HA
    SirAHA-r 5′-CTCGAGCTACGCATAGTCCGGGACGTCATAGGGATAGGATCCCGCATAGTCAGGAACATCGTATGGGTAATAGCCCGCATAGTCAGGAACATCGTATGGGTATCCGCTAACCTTGAATACATGTCGTGA-3′
a

Restriction sites are underlined. Silent mutations are double underlined.