In our search for new dsDNA-binding ligands, combinatorial chemistry was first applied to select unnatural oligopeptides with moderate affinity for dsDNA. To enhance the binding affinity of a heptapeptide lead structure, Ac-Arg-Ual-Sar-Chi-Chi-Tal-Arg-NH2 (K-d = 4.9. 10(-4) M), the compound was conjugated to different heteropolyaromatic moieties by means of a variety of linker arms. Glycine, beta-alanine, glycyl-glycine, glycyl-beta-alanine, gamma-aminobutyric acid, and 6-aminocaproic acid were used as spacers, representing different lengths and/or flexibilities. The intercalators coupled to the oligopeptide were acridine, fluorenone, anthracene, anthraquinone, and 3,8-diamino-5-methyl-6-phenylphenantridinium (methidium). The binding capacities of these new hybrid molecules to dsDNA have been investigated by gel retardation and footprinting assays. The results show that, by conjugating the unnatural oligopeptide to intercalators; the affinity for dsDNA could be enhanced more than 100-fold. For methidium-beta-alanyl-glycyl-Arg-Ual-Sar-Chi-Chi-Tal-Arg-NH2 (K-d of 2.1. 10(-6) M), the interaction with dsDNA was dominated by the intercalator in such a way that the sequence specificity of the heptapeptide was changed. The interaction with dsDNA of hybrid molecules of other intercalators was mainly governed by the oligopeptide, since the sequence selectivity of the heptapeptide was conserved. In general, the linker arm glycine (shortest spacer) and glycine-beta-alanine were preferred over beta-alanine, glycyl-glycine and the more-flexible spacers gamma-aminobutyric acid and 6-aminocaproic acid. This way new hybrid molecules endowed with dsDNA affinities of ca. 10(-6) M and displaying different sequence selectivities have been developed. Therefore, combinations of such unnatural peptides with intercalators can be used to broaden the knowledge about the sequence-selective recognition of dsDNA.