Exploration on the mechanism of DNA adsorption on graphene and graphene oxide via molecular simulations

Abstract

Several studies have shown that the fundamental principle of biosensors for DNA detection based on graphene oxide (GO) is the preferential adsorption of single-stranded DNA (ssDNA) over double-stranded DNA (dsDNA) on GO. However, the interactions between DNA and GO at the atomic level are poorly understood, and molecular dynamics (MD) simulation can be used to further explore these interactions. In the current study, we performed MD simulations to investigate the dynamic process of both ssDNA and dsDNA adsorption onto GO and pristine graphene (PG). We found that ssDNA was firmly adsorbed and lay flat on the surface of PG and GO, whereas dsDNA was preferentially oriented upright on both surfaces, resulting in weaker adsorption energies. Exploration of the mechanism of DNA segments binding to PG and GO indicated that π–π stacking interaction was the dominant force in the adsorption of DNA segments on PG, while both π–π stacking and hydrogen bonding contributed to the binding affinity between DNA segments and GO. These findings are of significant importance to the understanding of the interactions between DNA and GO, and the optimization of DNA and GO-based biosensors.