TABLE 1.
KD values of SarA target DNAsa
| DNA target | KD (pM) | Sequence |
|---|---|---|
| spa | 308 ± 27 | GCGTTTAAATTTAATTATAAATATAGATTTTAGTATTGCAATACATAACG |
| fnbB | 269 ± 117 | GCTGTTCAAGAGCTTTGTATGCAATATATATGTGAGTTTCAAATAATACG |
| fnbA | 228 ± 47 | GCGTTTCTGATGACTTGAATACAATTTATAGGTATATTTCAAATAATACG |
| sspA | 180 ± 82 | ATTTTTATTGTTATATTTAACTTGTAAATAAATTTTTTGGAGGTTTTTAG |
| agr | 145 ± 63 | GCATTTATTTTCCAATTTTTCTTAACTAGTCGTTTTTTATTCTTAACTGT |
| hla | 91 ± 25 | GCATATATAGTTAATTTTTATTTAATAGTTAATTAATTGATTTAATTCCG |
| cna1 | 182 ± 6 | ATGCACTTGTATTCGTTATACTGTATATATTTTGCATAATAAAATAATAA |
| cna2 | 104 ± 26 | TATATTTTGCATAATAAAATAATAATATGAATTTTTGATAAATTTCATTG |
| cna3 | 162 ± 68 | TATGAATTTTTGATAAATTTCATTGAATAAGAACTAAATTAGTTTATAAT |
| cna4 | 196 ± 13 | AATAAGAACTAAATTAGTTTATAATTTATTATTAGTATCCTGTGGATATG |
| cna5 | 541 ± 28 | TTATTATTAGTATCCTGTGGATATGACATAGAGTATAAGGAGGGGTTTTT |
| SELEX 1 | 118 ± 40 | TATGGGAGCATATACTATTCTATGATATTTCTATGCAATTCAAGAGTCTA |
| SELEX 2 | 134 ± 2 | CGTCTTGCATAATATAAAATTTTGTTTTGAGTTGTAATCGAATGCGGTCT |
| SELEX 3 | 162 ± 68 | GAAGTAGCATGAACATATACCCGTTGACTCAATTTTATTTTAGTCCAACA |
| SELEX 4 | 194 ± 30 | AGCATATAGTATAAAATTATCATATTGGTGTACGTGTACGGGGTACTTTT |
| trp | 524 ± 34 | CAATTAATCATCGAACTAGTTAACTAGTACGCAAGTTCACGTAAAAAGGG |
a
All oligonucleotides were synthesized with the same 24-bp extensions to allow amplification of the target region. The sequence of the 5′ extension was GACCTGTGAACTGCGTAGTCCCTG. The sequence of the 3′ extension was GGAAGCTTAGACCGTCAACGTCGG. Putative SarA boxes associated with spa, fnbA, fnbB, sspA, and hla (5, 11) are shown in boldface type. The agr target corresponds to the A1-A2 binding site identified by Rechtin et al. (34). Relative locations of the cna targets are shown in Fig. 1. Sites that match the ATTTTAT motif with no more than a single mismatch are underlined, and a double underline indicates that the motif is located on the opposite strand of the DNA target.