Theoretical Studies on the Intercalation of Actinomycin between Nucleic Acid Base Pairs

Department of Biosciences and Biotechnology, University of Roorkee, Roorkee-247 667 Chemical Physics Group, Tata Institute of Fundamental Research, Homi Bhabha Road, Bombay-400 005 Manuscript received 30 September 1993 Energies associated with the actinomycin chromophore sandwiched between base pairs of dinucleotide model systems have been calculated using classical potential functions. The energy values are partitioned into contributions from . electrostatic, polarisation, dispersion and repulsion terms. The results indicate that contributions from dispersion term dominate the calculated energy values. The energy is minimised by varying rotational angle of drug moiety about helix axis and translation along the X, Y and Z axis relative to the base pairs. The helical angle between two base pairs is also varied and the optimised values are found to lie in the range -7° to -8° for all model systems. The stacked geometries of drug chromophore intercalated between base pairs corresponding to the minimum energy, have been obtained. The effect of base sequence on stacking energy, and unwinding angle have been discussed