Zipper-Like Unfolding of dsDNA Caused by Graphene Wrinkles

Abstract

Wrinkles have been frequently observed in a graphene nanosheet. Such structural corrugations can influence graphene's characteristics and have received considerable attention recently. However, the impact of these wrinkles on the critical graphene interactions with biomolecules remains unclear. Here, we investigate the interaction of a double-stranded DNA (dsDNA) segment with a wrinkled graphene nanosheet using molecular dynamics simulations. We find that dsDNA experiences severe structural deformation upon binding to a wrinkled graphene surface, whereas it tends to maintain its native structure upon binding to an idealized graphene nanosheet. Further analysis reveals that it is energetically advantageous for the terminal bases to bind to the wrinkled area, serving as anchors on the nanosheet. Consequently, movement of the remaining part of the dsDNA generates a "centripetal stretching" force to the anchoring bases, causing the breakage of the interbase hydrogen bonds and local unfolding. Like a slider opening up a zipper, the local unfolding proceeds sequentially from the first base pair to the next until the end. This zipper-like unfolding subsequently exposes more DNA bases to contact with the wrinkled area, thus accelerating the dsDNA deformation. These findings highlight the importance of wrinkles in the interaction of graphene with biomolecules and deepen our understanding of graphene nanotoxicity in general.