Ab initio study on the nature of stacking between azaacridine-4-carboxamides with base pairs of DNA

The stacking interactions between 9-amino azaacridine-4-carboxamide and Watson Crick base pairs have been explored to understand the recognition of a particular sequence in DNA intercalation. Three types of 9-amino azaacridine-4-carboxamides are taken for calculating interaction energies. The MP2 method with 6-31+G(d,p) basis set has been used to study interaction of Aza-1-acridine-4-carboxamide(AZN1), Aza-2-acridine-4-carboxamide (AZN2) and Aza-3-acridine-4-carboxamide (AZN3) with base pairs. The variation of interaction energies of these drugs is small. The optimum stacked structures are stabilized due to the π-π and the heavy atoms interactions. The aromatic rings are found completely stacked within GC and AT base pairs in the optimum stacked structures. The positions of AZN1, AZN2 and AZN3 in the optimum stacked of these structures are not exactly the same, and the relative positions of heavy atoms present in the aromatic rings of these drugs and base pairs are important for stabilizing these structures.