A major challenge in the use of oligonucleotides in an anti-gene strategy is to stabilize triple helix formation under physiological conditions. A benzo[e]pyridoindole derivative was shown earlier to stabilize triple-helical better than double-helical complexes (Mergny, J. L. et al. Science 1992, 256, 1681-1684). New derivatives of the benzopyridoindole family were synthesized, and their ability to stabilize triple helices was investigated by thermal denaturation experiments using UV absorption spectroscopy. The stabilizing effects of all the available derivatives were compared and allowed us to infer some general rules regarding the role of the geometry of the molecule and of its various substituents. The melting temperature (T-m) of the tripler-to-duplex transition is increased from 18 to 49 degrees C (Delta T-max = +31 degrees C) upon binding of 3-methoxy-10-methyl-7-[3-(N-methyl-N-3-aminopropyl)propyl]amino-11H-benzo[g]pyrido[4,3-b]indole (BgPI), in a 10 mM sodium cacodylate buffer (pH 6.2) containing 0.1 M NaCl. Sequence-specific effects were also investigated. Benzo[e]- and benzo[g]pyrido[4,3-b]indole derivatives exhibited different properties regarding the role of the alkylamine side chain attached to the pyridine ring. Effects of these compounds on the melting of duplex DNA were also sensitive to changes in the chemical nature of the alkylamine side chain. Results are discussed in terms of respective affinities for tripler and duplex structures. A model is proposed to explain the different roles played by the alkylamine side chain for both types of molecules. For the benzo[e]pyridoindole derivatives, the chain is suggested to lie in the major groove of the triple helix, whereas for the benzo[g]pyridoindole derivatives, it lies in the minor groove. These results provide an experimental and theoretical basis for understanding intercalation of dyes in triple helices and should help to conceive more specific triple helix ligands and to design oligonucleotide-intercalator conjugates for stable triple helix formation.