First-Principles Study of Nanoparticle–Biomolecular Interactions: Anchoring of a (ZnO)₁₂ Cluster on Nucleobases

Abstract

We report the results of theoretical calculations on interaction of the nucleotide bases of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) with a (ZnO)12 cluster, carried out within density-functional theory framework. In all cases, (ZnO)12 prefers to bind with a ring nitrogen atom having a lone electron pair relative to the other possible binding sites of the bases. The degree of hybridization between Zn-d and N-p orbitals determines the relative interaction strength at the N-site of individual nucleobases with (ZnO)12 in contrast to the cases of interaction of metallic clusters and carbon nanostructures with nucleobases where either electrostatic or van der Waals interactions dominates the bonding characteristics of the conjugate complexes. The predicted site-preference of (ZnO)12 toward the nucleobases appears to be similar to that of the metal clusters, which indicates that the metal clusters retain their site-preference even in their oxidized state.