Monitoring the sequence specific intercalation in nucleic acids by 9-substituted acridine-4-carboxamides

Abstract

The anticancer drug, 9-substituted acridine-4-carboxamide, intercalates with sequences in nucleic acids. Some analogues of this drug with substituents at 9-position are chosen for studying the intercalative abilities with Watson Crick base pairs, AT, TA, GC and CG. <i>Ab-initio </i>HF/6-3l G** and B3LYP methods are used for calculating interaction energies of

drug-sequence complexes and the sequence specificity of drugs are analysed from the interaction energies. The computed interaction energies of various drugs with CG and GC sequences are significantly lower than those of others. Hence, these drugs acquire high specificity for GC and CG sequences. Moreover, stacking interaction of heavy atoms present in sequence and drug stabilizes the optimum structures.