We report the synthesis of an asymmetric Troger base containing the two well characterised DNA binding chromophores. proflavine and phenanthroline. The mode of interaction of the hybrid molecule A as investigated by circular and linear dichroism experiments and a biochemical assay using DNA topoisomerase 1. The data are compatible with a model in which the proflavine moiety intercalates between DNA base pairs and the phenanthroline ring occupies the DNA groove. DNase I cleavage experiments were carried out to investigate the sequence preference of the hybrid ligand and a well resolved footprint was detected at a site encompassing two adjacent 5'-GTC-5-GAC triplets. The sequence preference of the asymmetric molecule is compared to that of the symmetric analogues. (C) 2002 Editions scientifiques et medicales Elsevier SAS. All rights reserved.