Because amino acid identity within the ARID consensus is so high within subfamilies, originally a single member of each subfamily was selected to test for sequence specificity. Recombinant GST-fusion proteins were constructed using sequences that include the ARID domain of each protein examined. The sequence specificity of each protein was then examined in a DNA pull-down assay. This assay allows each protein access to a pool of Lambda DNA restriction fragments of varying size and sequence. As shown in Figure 3, Dri (the Drosophila counterpart of ARID3A) and MRF2 (ARID5B) bind in a sequence-specific manner in this assay, selectively binding to some fragments and not others. Selectivity for specific fragments becomes more pronounced in more stringent binding conditions (i.e. increased salt concentrations). Slight differences in the selected fragments between Dri and MRF2 probably reflect the fact that the two proteins select slightly different consensus sites in vitro (3,4,6). The major bands consistently selected by Dri in this assay are indicated by markers to the right of the Dri panel in Figure 3. In contrast to Dri, p270 (ARID1A) binds in
