Doublesex (dsx) is a transcription factor in Drosophila that regulates somatic sexual differentiation. Maleand female-specific splicing isoforms of DSX share a novel DNA-binding domain, designated the DM motif. Broadly conserved among metazoan sex-determining factors, the DM domain contains a nonclassical zinc module and binds in the DNA minor groove. Here, we characterize the DM motif by site-directed and random mutagenesis using a yeast one-hybrid (Y1H) system and extend this analysis by chemogenetic complementation in vitro. The Y1H system is based on a sex-specific Drosophila enhancer element and validated through studies of intersexual dsx mutations. We demonstrate that the eight motif-specific histidines and cysteines engaged in zinc coordination are each critical and cannot be interchanged; folding also requires conserved aliphatic side chains in the hydrophobic core. Mutations that impair DNA binding tend to occur at conserved positions, whereas neutral substitutions occur at nonconserved sites. Evidence for a specific salt bridge between a conserved lysine and the DNA backbone is obtained through the synthesis of nonstandard protein and DNA analogs. Together, these results provide molecular links between the structure of the DM domain and its function in the regulation of sexual dimorphism.Sexual dimorphism is regulated by diverse molecular mechanisms (18). In mammals, male development is initiated by a gene on the Y chromosome that is designated Sry (sex-determining region of the Y chromosome) (7,30,41,42). Alternative genetic mechanisms operate in Drosophila melanogaster (and Caenorhabditis elegans), wherein sex is determined by the X-to-autosome ratio, a process linked to X-dosage compensation (Fig. 1A) (19, 59). The sex-determining hierarchy of Drosophila defines an RNA-splicing cascade through the actions of Sex Lethal (SXL) and the TRA factors (18). Doublesex (dsx) functions downstream of this cascade to define one branch of a ramifying pathway (Fig. 1A) (29,59). The sex-specific isoforms of DSX (DSX M and DSX F ; Fig. 1B) regulate most aspects of somatic sexual dimorphism in D. melanogaster. These isoforms share an N-terminal DNA-binding domain, designated the DM motif (Fig. 1C). In this article, we present a mutational analysis of the DSX DM domain to identify key determinants of folding and DNA recognition.The Wilkins-Wolf hypothesis posits that sex-determining pathways have evolved in a reverse order from bottom (most broadly conserved) to top (least conserved) (65, 66). This viewpoint is supported by the ubiquity of DM genes among metazoan sex-determining pathways (35, 59). Such genes encode a newly recognized class of transcription factors (for a review, see reference 59). DM sequences are broadly conserved in metazoans, including nematodes, fish, reptiles, birds, and mammals (Fig. 1D). The deletion of human DM genes on chromosome 9p is associated with intersexual development (6,27,31,49,55,59,63). Although originally described in relation to sex-determining pathways (67), an extended family...