TABLE 1.

Oligonucleotides used in this study

Purpose and gene and/or tRNADesignationSequence
Hybridization probes
    pgtE (tRNAArgW)pgtE-for5′-ACTTCATCACCTCTCCAG-3′
    pgtE-rev5′-CTAGAAGCGGTACTGCAAC-3′
    nupC (tRNAArgW)nupC-for5′-ATGGACCGCGTCCTTCATT-3′
    nupC-rev5′-CAGACTTACAGTACCAGC-3′
    apeE (tRNAArgU)apeE-for5′-GCAATATCTCTGTCGGAT-3′
    apeE-rev5′-TTGCCGACTGGCGAAATC-3′
    STM0557 (tRNAArgU)STM0557-for5′-GTGCATTGCGACTTCTTG-3′
    STM0557-rev5′-GGAATAGGTATTCTTGGGG-3′
    sspH2 (tRNAProL)sspH2-for5′-CACGCGGAAGGGGCATC-3′
    sspH2-rev5′-GCTGGTCAGTTGATTACC-3′
    msgA (tRNAProL)msgA-for5′-TTTCGTCAGGCTTGCATC-3′
    msgA-rev5′-TCATTTACCTGCCACTGC-3′
    vexA (tRNAProL)vexE-for5′-CCAAATCCCACCGGAAAG-3′
    vexE-rev5′-CAACCACCCTACTCAAAC-3′
    pilV (tRNAPheU)pilV-for5′-ACATGATGGCGGCTTTGTG-3′
    pilV-rev5′-GCCAGGTAAGTTCAAACAG-3′
    recArecA-for5′-ATGGCTATCGACGAAAAC-3′
    recA-rev5′-CGTTAGTTTCTGCTACGC-3′
    gyrBgyrB-for5′-AAAGTCCTGAAAGGGCTG-3′
    gyrB-rev5′-CGATATTCGCCGCTTTCA-3′
DeletionspgtE-Red-Del-for5′-TCGGCCGGTTATGACCGATGACAT CCCGATGTGGTCTAGTGTAGGCTGGAGCTGCTTC-3′
pgtP-Red-Del-rev5′-AATGTCGGCGCTTCTGTTCCCCAG GAAGGCTAATCGTTTCATATGAATATCCTCCTTAG-3′
ykgD-Red-Del-for5′-CGCCTGGTGTACAACCGAATTC ACGGACAAAAGCTTTGGTGTAGGCTGGAGCTGCTTC-3′
apeE-Red-Del-rev5′-GTCATCAAAATCGGGCGCT AAACCCAACGTTATAACGGGCATATGAATATCCTCCTTAG-3′
tRNA insertion site detection
    tRNAArgUtRNA-ArgU-for5′-GAGTGACTTTGTCTGCTC-3′
    tRNA-ArgU-rev5′-GATGTCCCAAATATGTCCC-3′
    tRNAArgWtRNA-ArgW-for5′-CTGGAGCGACTTTCTCTG-3′
    tRNA-ArgW-rev5′-CGTATTTTGGTGGCGATG-3′
    tRNAProLtRNA-ProL-for5′-CGACAGGTATGGTAATC-3′
    tRNA-ProL-rev5′-GTAACAGGCTGGTTCTTC-3′
    tRNAPheUtRNA-PheU-for5′-CATAGGCTGGGTTTTCTG-3′
    tRNA-PheU-rev5′-CCACTCGACACATTACAG-3′