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Articles

Vol. 1 No. 1 (2010): January-March 2010

The Stacking Ability of Daunomycin with Base Pairs of DNA: A Theoretical ab Initio (HF) and MP2 Studies

DOI
https://doi.org/10.37285/ijddd.1.1.4
Submitted
November 18, 2024
Published
2010-02-15

Abstract

The description of the intercalative mode of DNA binding of daunomycin is important to understand the sequence selectivity of this drug. Indirectly, DNA sequence specific intercalation can be assessed from the stacking stabilization of chromophore with AT and GC base pairs. For both the stacked complexes of chromophore with AT and GC base pairs, the interaction of certain molecular parts are essentially related to the base pair specificity of this drug. The observed variation in the stacking interactions of molecular parts of chromophore and base pairs have been determined from the interactions of rings A,B and C of chromophore with base pairs. Unlike the other aromatic rings, the ring D is not favourable for stacking interaction. The differences in the structures and interaction energies are used to rationalize the regions of stacking stabilization as well as repulsive interaction due to steric hindrance for certain stacked positions of chromophore. The favorable interaction is found only within the non steric orientations of chromophore in the stacked structures. The interaction energies of chromophore and AT are different from that of GC, and also there observed differences between the interaction energies of drug and base pairs for major and minor groove orientations.

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