A series of 1,4-dihydropyridines have been prepared from a three-component one-pot condensation reaction of β-diketonates, an aromatic aldehyde, and ammonium acetate under microwave irradiation. The reaction is performed using crystalline nano-ZnO in ethanol under microwave irradiation (CEM discover). A wide range of functional groups was tolerated in the developed protocol. The present methodology offers several advantages such as simple procedure, greener condition, excellent yields and short reaction time. The synthesized compounds were evaluated for DNA photocleavage, SAR analysis and molecular docking studies. The compound (4b, 4c, 4 h, 4i, 4n and 4o) showed potent DNA cleavage activities compared to other derivatives. The molecular interactions of the active compounds within the binding site of B-DNA were studied through molecular docking simulations; the compound (4b, 4c, 4 h, 4i, 4n and 4o) showed good docking interaction with minimum binding energies. All synthetic compounds were characterized by different spectroscopic techniques.