Recognition of multiple patterns of DNA sites by Drosophila homeodomain protein bicoid

Our previous studies demonstrated that the Drosophila homeodomain protein, Bicoid (Bcd), binds DNA cooperatively. In this study, we determined the pat terns of adjacent DNA sites required for cooperative recognition by Bcd. Ou r in vitro selection and biochemical experiments demonstrated that Bcd bind s preferentially to both head-to-head and tail-to-tail symmetric sites that are separated by short spacing, An increase in the spacing reduces the str ict requirement of symmetric patterns of adjacent sites, permitting Bcd to recognize tandem repeat sites cooperatively. Our further experiments in viv o showed that the only pair of optimally spaced symmetric Bcd sites in a hu nchback (hb) enhancer element contributes the most to transcriptional activ ation by Bcd, demonstrating the biological importance of the binding site p atterns revealed by our in, vitro selection studies.