Robust specificity determinants observed in the selected HDs. (A) Canonical recognition pattern for HD–DNA interaction. At the 5′ end of the binding site (bases 1, 2, and 3), positions on the recognition helix (solid boxes) and the N-terminal arm (dashed boxes) contribute to specificity, where the position(s) of the contributing determinants are indicated to the left of the base pair. At the 3′ end of the binding site (bases 4, 5, and 6), homeodomain specificity is primarily defined by positions 47, 50, and 54, where these determinants have overlapping regions of influence. (Solid arrows) Primary positions of interaction; (dotted arrows) secondary influences on specificity. (B) New specificity determinants (blue) and previously described specificity determinants (black) for HDs containing the conserved N51 are broken down by position and trends in base preference within the 3 bp at the 3′ end of the target site. Note that there are exceptions within our characterized HDs to these specificity preferences, likely reflecting the overlapping influence of these determinants.
