The MyoD family of transcription factors regulates muscle-specific gene expression in vertebrates. In the adult rat, MyoD mRNA accumulates predominately in fast-twitch muscle, in particular type IIb and/or IIx fibers, whereas Myogenin mRNA is restricted to slow-twitch type I muscle fibers. Transgenic mice expressing the avian v-ski oncogene from the murine sarcoma virus (MSV) promoter-enhancer display preferential hypertrophy of type IIb fast-twitch muscle apparently because of the restricted expression of the transgene. We tested the hypothesis that preferential interactions of MyoD, as a heterodimer with E12, with the MSV enhancer, which has six E-box targets for MyoD family proteins, could contribute to v-ski gene expression in IIb muscle fibers. A series of quantitative binding studies was performed using an electrophoretic mobility shift assay to test MyoD-E12 versus Myogenin-E12 binding to the MSV enhancer. Our results indicate that MyoD-E12 binds the MSV enhancer with higher affinity and higher cooperativity than Myogenin-E12. Interestingly, MyoD-E12 bound all of the individual E-boxes tested with positive cooperativity indicating DNA-mediated dimerization of the protein subunits.