*2.2. Interaction Mechanisms between DNA and GFNs*

Interaction between GFNs and DNA is critical for understanding and assessing direct genotoxicity. DNA is a biological macromolecule with a repetitive nucleotide structure that controls biological functions. The backbone of DNA is a regular sequence of deoxyribose sugar and phosphate groups. DNA is always negatively charged at most pH values [73]. The oxidized domains of GO are rich in oxygen-containing groups (e.g., epoxides, hydroxyl, carboxyl, and carbonyl groups). The negatively charged carboxyl groups would electrostatically repel negatively charged DNA and use hydrogen bonding as the main attraction force [47]. The GFNs mainly interact with DNA via H-bonding and π–π stacking, casing the DNA distortion and even DNA cleavage. The DNA damaging mechanism of GQDs depends on their size. The small GQDs easily enter the DNA molecule leading to DNA base mismatch. Large GQDs tend to stick to the ends of the DNA molecule, causing the DNA to unfold [74]. 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]. Unlike AuNPs, which rely on stronger DNA base coordination, the adsorption of GO is weak, owing to the weak binding affinity [77]. Furthermore, the GO surface shows great heterogeneity for DNA adsorption and hydrophobic regions for exclusion of DNA. Thus, both the external environment and the physicochemical property (e.g., oxidized degree and size) have a strong influence on the adsorption capacity of GO [47,76–78]. Further research into the direct effects of GFNs on DNA or genetic material is important to explain GFN-mediated targeted genotoxicity.
