Ab initio molecular orbital and force field calculations on the interaction of daunomycin with GC base-pair and intercalation within DNA

The intercalativc binding of daunomycin within dG-dC oligonucleotidcs has been reported but the contribution of stacking interaction is not clearly known. So the stacking interaction between aglycon ring and GC base pair has been studied. The intercalated structure of daunomycin within dG-dC oligonucleotides is also studied by force field calculation. The stacking energy is found to be not so significant for the stabilization of aglycon ring within GC sequences. Both the stacked structure and the intercalated structure are stabilized at the non steric orientations and the approach of drug towards minor groove is found to be favourable for both the stacking interaction and the intercalation.