A high affinity interaction between a protein and the guanine tetrad nucleic acid structure is described. Recombinant MyoD, a transcription factor that can initiate myogenesis, specifically bound to helical structures formed by stacks of guanine residues in square planar arrays. The N-7 methylation of a set of consecutive dG residues in a single-stranded probe of the creatine kinase enhancer interfered with the formation of this nucleic acid structure and prevented protein binding. Recombinant MyoD also bound to a guanine tetrad formed with a telomeric DNA probe, and it had a higher affinity for the four-stranded structure than for the double-stranded E-box-binding site. These data are the first report of a direct interaction between a protein and this nucleic acid conformation. The potential biological significance of this finding is discussed.