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Many Drosophila developmental genes contain a DNA binding domain encoded by the homeobox. This homeodomain contains a region distantly homologous to the helix-turn-helix motif present in several pmlcsryotic DNA binding proteins. We investigated the nature of homeodomain-DNA interactions by making a series of mutations in the helix-turn-helix motif of the Drosophila homeodomain protein Paired (Prd). This protein does not recognize sequences bound by the homeodomain proteins Fushi taraxu (Ftz) or Bicoid@ cd). We show that changing a single amino acid at the C-terminus of the recognition hei! x is both necessary and sufficient to confer the DNA blnding specificity of either Ftz or Bed on Prd. This simple rule indicates that the amino acids that determine the specificity of homeodomains are different fmm those mediating protein-DNA contacts in pmkaryotic proteins. We further show that Prd contains …