Water-soluble amino derivatives of free-base dppz - syntheses and DNA binding studies

The syntheses of two water soluble dipyrido-[3,2-a:2',3'-c]-phenazine analogues containing one or two appended amino/amide chains are reported. Steady state optical studies on the two new compounds reveal high-energy dppz-based luminescence in water and non-aqueous solvents. Optical titrations with duplex DNA show that the luminescence is quenched on the addition of DNA. Binding curves constructed from absorption and emission changes indicate that, while one of the compounds display negligible binding properties, the other binds DNA with relatively high affinity (>10(5) M-1). Isothermal calorimetry experiments, designed to investigate the higher binding compound in more detail, reveals that its interaction with CT-DNA is actually biphasic with one tight (>105 M-1) and one weaker binding site (similar to 105 M-1). In both cases binding is entropically driven. Further calorimetry studies involving the interaction of the new compound with a variety of polynucleotides were carried out. To aid comparisons, similar experiments involving a previously reported bipyridyldiylium derivative of dppz were also carried out. These studies reveal that the bipyridyldiylium derivative binds all these sequences monophasically with relatively low affinities (similar to 10(4) M-1). However, while the amino/amide chain appended derivative binds to Poly(dA).poly(dT) monophasically with relatively low affinities, it binds all the other polynucleotide studied biphasically, with affinities ranging from <10(6) M-1 to >10(8) M-1. The ITC data reveals that for both compounds thermodynamic signatures for binding are dependent on the sequence being bound. In both cases, the data for Poly(dA). poly(dT) is particularly anomalous. An analysis of the data shows that binding is selective, with affinities at flexible sequences being several orders of magnitude higher than those at more rigid sequences.