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.