DNA triple helix stabilisation by a naphthylquinoline dimer

We have used DNase I footprinting to examine the effect of a novel naphthyl quinoline dimer, designed as a triplex-specific bis-intercalator, on the st ability of intermolecular DNA triplexes. We find that this compound efficie ntly promotes tripler formation between the 9-mer oligonucleotide 5'-TTTTTT CTT and its oligopurine duplex target at concentrations as low as 0.1 mu M, enhancing the tripler stability by at least 1000-fold. This compound, whic h is the first reported example of a tripler bis-intercalator, is about 30 times more potent than the simple monofunctional ligand. (C) 1999 Federatio n of European Biochemical Societies.