When we attempted this assay with the Dri.SSS.ΔC construct, we found that the peptide bound poorly to the oligonucleotide even at 50 mM salt. Because the ARID proteins show a generally higher affinity for longer pieces of DNA, we attempted the assay with a longer oligonucleotide, containing eight repeats of the consensus sequence rather than three. The Dri.SSS.ΔC peptide bound well to this probe (Figure 9B). Wild-type Dri showed the same behavior on this probe as on the shorter one: it was displaced more readily by the true consensus sequence than by the altered sequence (Figure 9B, panel 1). The Dri.SSS.ΔC peptide showed less specificity than wild-type Dri, but a weak selectivity was still evident (Figure 9B, panel 2), consistent with the behavior seen in Figure 8.
