The lambda DNA restriction fragment pool was used as the target DNA in order to offer a wide range of sequence possibilities to the ARID proteins used in this survey. This allowed for the possibility that some family members, or some mutant variants, would show sequence preference, but for a previously unrecognized sequence. However, a disadvantage of the lambda DNA restriction fragment pool is that the complex restriction pattern precludes the identification of individual restriction fragments, or the actual sequence of the selected fragments. To obtain a more quantitative measurement of sequence specificity, selected mutants were probed in an oligonucleotide competition assay, where their affinity for a Dri consensus binding site (CCAATTAATCCC) was compared with their affinity for an altered consensus site (CCAATTGCTCCC). The consensus sites were synthesized as three tandem repeats. This assay was performed in low salt (50 mM) conditions, so that the effect of increasing salt concentrations on the conformation of the protein would not be a factor in the assay. The results are shown in Figure 9A. The Dri peptide shows a clear preference for its
