The sine oculis (so) gene is required for the development of the Drosophila visual system. The 416 amino acid SO protein contains a 40 amino acid region homologous to the helix-turn-helix (HtH) region of the homeodomain. Three HtH-containing peptides ranging in size from 63 to 93 amino acids (SO(218-279), SO(204-279), and SO(188-279)) were expressed in Escherichia coli and characterized in vitro. These fragments show circular dichroism spectra characteristic of helical proteins and cooperative unfolding transitions. Derivatization of these three peptides with the chemical nuclease 1,10-phenanthroline:copper (OP-Cu) allowed the identification of specific DNA-binding sites within the 3.1 kb pUC119 plasmid. Similar cleavage patterns with similar relative affinities were obtained for all three peptides. Nucleotide resolution mapping of the predominant cleavage area identified two primary cleavage sites with a similar core sequence. The DNA cleavage sites were confirmed by DNase I footprinting with both native and OP-Cu-conjugated SO HtH peptides. This study identifies a 63 amino acid peptide as sufficient for specific DNA binding.