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.

Screening 2D Materials for Their Nanotoxicity toward Nucleic Acids and Proteins: An In Silico Outlook

“…78,79 To deduce the effect of large wrinkles on the nanotoxicity of 2D materials, Zhou and co-workers studied the adsorption of a dsDNA on a graphene sheet containing a large wrinkle (Figure 5(a)). 80 It was found that, whenever the dsDNA was adsorbed on the flat section of graphene, the terminal base pairs were unwound, as also reported by us. 58,62 Contrarily, if the dsDNA was adsorbed on the wrinkled domain of the material, it suffered from nearly complete unwinding (Figure 5(b)).…”

A wrinkled nanosurface causes accelerated protein unfolding revealing its critical role in nanotoxicity

“…1G-I). In a previous study of the binding process of doublestranded DNA (dsDNA) with wrinkled graphene, 66 we also noticed 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. Thus, the denaturing behavior of the wrinkle in nanomaterials to bio-molecules could be an inherent character that should be pay more attentions when utilized in biological and medical areas.…”

Direct and Indirect Genotoxicity of Graphene Family Nanomaterials on DNA—A Review

“…The zipper-like unfolding of double-stranded DNA caused by graphene wrinkles has been investigated by using molecular dynamics simulations. The results show that the zipper pattern brings more DNA bases into contact with the wrinkled region, resulting in accelerated deformation of double-stranded DNA [75]. The GO combining with copper ions can intercalate into DNA molecules and cleave DNA fragments, and the system of this DNA cleavage is oxidative and hydrolytic [76].…”

“…The planar structure of GFNs may also have an effect on DNA damage. The dsDNA bases have a stronger binding affinity with wrinkled GFNs and even cause more DNA damage than with planar GFNs [75]. Given these discordant results, it is necessary to clarify the size-and structure-related genotoxicity of GFNs.…”