Studies on the binding geometry of intercalation of 4-(2-diethylamino-ethylamino)-8-oxo-8H-acenaphtho[1,2-b] pyrrole-9-carbonitrile to DNA by molecular spectra

The binding geometry of a heterocyclic compound, 4-(2-diethylamino-ethylamino)-8-oxo-8H-aee-naphtho [1,2-b] pyrrole-9-carbonitrile (A1) to CT DNA was studied by using molecular spectroscopy. Deduced from SYBR Green-DNA melt curve, fluorescence spectroscopy, UV-Vis spectroscopy and circular dichroism(CD), there were two different interaction mechanisms involved in the whole interaction process depending on the molar ratios of Al to CT DNA base pairs. The binding geometry of A1 to CT DNA was investigated by the induced CD spectroscopy based on the different n(A1)/n(CT DNA) ratio. The value n(A1)/n(CT DNA) =0.20 was the turning point; when n(A1)/n(CT DNA) ≤ 0.20, the intercalation orientation of Al to the dyad axis of DNA double helix was heterogeneous and stacking of Al on the surface helix of DNA was available when n (A1)/n (CT DNA) > 020.