The Intercalation of Various Forms of Daunomycin within Sequences of DNA

The anticancer drug, daunomycin undergoes various chemical processes such as reduction of chromophore, proton transfer inside chromophore and elimination of sugar moiety before binding with DNA sequences. Various chemical processes of daunomycin might be relevant for analyzing the sequence specific binding of this drug. The sequence specific DNA binding has been analyzed by force field studies. The electrostatic interaction energies and van der Waals interaction energies of different sequence combinations are not equal. The drug binding ability within the inner and end portion of DNA is also different. The preference of chromophore intercalation towards the major and minor grooves of DNA is distinctly shown. The entry of drug towards the minor or major groove is found to be entirely depend on the nature of chromophore (Chrom-A or Chrom-C). Also the drug preferably binds within the inner sequences of DNA due to the additional contribution from the side chain (sugar).