The domains in the ARID1, ARID3 and ARID5 subfamilies retain DNA-binding affinity up to at least 200 mM KCl concentration (Figure 3). DNA affinity columns likewise indicate that p270 and Dri have similar DNA-binding affinities [(11) and Figure 8]. ARID1B, which is closely related overall to p270, retains DNA binding up to about 175 mM KCl [(20) and additional data not shown]. JARID1 subfamily domains also retain binding to at least 175 mM KCl (Figure 4). However, the data in Figure 4 indicate that ARID domains of the ARID2, ARID4 and JARID2 subfamilies have relatively low DNA-binding affinity. While this assay is not a direct measure of affinity, the results suggest that there are three distinguishable categories in the ARID family with regard to DNA-binding: sequence non-specific with low affinity, sequence non-specific with high affinity and sequence specific with high affinity. Previously, we showed that Saccharomyces cerevisieae SWI1 has relatively low affinity DNA-binding behavior that correlates with atypical sequence in the Loop 2 and Helix 5 region (11). Current results indicate that DNA-binding affinity of ARID family members can be low for reasons not easily apparent from inspection of the ARID sequence.
