DNA-ligand interactions : a biophysical study of 9-hydroxyellipticine, Hoechst 33258 and a meso-substituted porphyrin derivative binding to DNA
The binding of 9-hydroxyellipticine (9-OHE), Hocchst-33258 (Hoechst) and trans-bis-(4- N-methylpyridiniumyl)diphenylporphyrin (t-112P) to DNA has been studied by means of spectroscopic techniques. The binding modes of t-H2P to calf thymus DNA (ct-DNA), poly[d(G-C)12 and poly[d(A-T)12 were dependent on ionic strength, ligand load on DNA and the base composition at the binding site. At low ionic strength, flow linear dichroism (LD) data suggested t-H2P binds to ct-DNA and poly[d(A-T)12 in an orientation consistent with groove binding and to poly[d(G-C)12 in an orientation consistent with partial intercalation. Interpretation of the spectroscopic data was facilitated by molecular modelling. At high ionic strength, circular dichroism (CD) and resonance light scattering (RLS) measurements indicated the formation of extended t-H2P aggregates on DNA. In addition, the approximate, average transition moment polarisations of t-H2P were assigned from stretched film LD data to facilitate interpretation of the flow LD data. The interaction of Hoechst with poly[d(G-C)12 and poly[d(A-T)12 was studied with CD, LD, RLS and fluorescence spectroscopy. The mode of Hoechst binding to poly[d(G-C)]2 was ligand load independent. The collective spectroscopic data suggested abinding mode in which part of the molecule intercalates and part lies extensively stacked in the poly[d(G-C)12 major groove. Hoechst binding to poly[d(A-T)12 was ligand load dependent. The molecule was observed to bind as dimers or small oligomers at the lower ligand loads studied, with extended aggregates being formed as the concentration of bound Hoechst was increased. LD measurements suggested a binding orientation inconsistent with minor groove binding thus it was concluded that the molecule stacked in the major groove. 9-OHE binding to ct-DNA, poly[d(G-C)12 and poly[d(A-T)12 was studied with LD, RLS and normal absorption spectroscopy. Binding by intercalation was shown to occur with each of the three DNAs. The intercalated mode was shown to be complemented at high ligand load by a stacked binding mode. LD data pertaining to the stacked mode were inconsistent with minor groove binding in which the 9-OHE plane lies at 45' to the helix axis, thus it was concluded that the stacking occurred in the major groove. The stacked binding mode occurred most readily on poly[d(G-C)12. The flow LD data were complemented with film LD measurements from which the approximate, average transition moment polarisations were assigned.