We explored the effect of alpha-helical stabilization upon the binding of short peptides to DNAs. The short peptides were designed according to the binding domains of DNA-binding proteins and were cross-linked between their side chains with diacetylenic or isophthalic cross-linking agents to keep stable alpha-helices. The binding abilities of the peptides to DNAs were evaluated by fluorescence resonance energy transfer analysis. When a cross-linked peptide based on the homeodomain of the transcription factor was titrated with a target DNA duplex, its dissociation constant (K-d) was calculated to be similar to 0.5 nM. This value was the double-digit smaller than that of the corresponding non-cross-linked peptide. The cross-linked peptide showed high substrate specificity for DNAs at the same level as the original DNA-binding protein.