Sequence-dependent binding of bis-amidine carbazole dications to DNA

The conventional wisdom argues that DNA intercalators possess a condensed p olyaromatic ring whereas DNA minor groove binders generally contain unfused aromatic heterocycles, frequently separated by amide bonds. Recently, this view has been challenged with the discovery of powerful intercalating agen ts formed by unfused aromatic molecules and groove binders containing a pol yaromatic nucleus. Bis-amidinocarbazoles belong to this later category of d rugs having a planar chromophore and capable of reading the genetic informa tion acessible within the minor groove of AT-rich sequences [Tanious, F.A., Ding, D., Patrick, D.A., Bailly, C., Tidwell, R.R. & Wilson, W.D. (2000) B iochemistry 39, 12091-12101]. But in addition to the tight binding to AT si tes, we show here that bis-amidinocarbazoles can also interact with GC site s. The extent and mode of binding of 2,7 and 3,6 substituted amidinocarbazo les to AT and GC sequences were investigated by complementary biochemical a nd biophysical methods. Absorption, fluorescence, melting temperature and s urface plasmon resonance (SPR) measurements indicate that the position of t he two amidine groups on the carbazole ring influences significantly the dr ug-DNA interaction. SPR and DNase I footprinting data confirm the AT-prefer ence of the compounds and provide useful information on their additional in teraction with GC sequences. The 3,6-carbazole binds approximately twice as strongly to the GC-containing hairpin oligomer than the 2,7-regioisomer. T he high tendency of the 3,6 compound to intercalate into different types of DNA containing G.C base pairs is shown by electric linear dichroism. This work completes our understanding of the sequence-dependent DNA binding prop erties of carbazole dications.