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Functional nanoscale structures consisting of a DNA molecule coupled to graphene or graphene oxide (GO) have great potential for applications in biosensors, biomedicine, nanotechnology, and materials science. Extensive studies using the most sophisticated experimental techniques and theoretical methods have still not clarified the dynamic process of single-stranded DNA (ssDNA) adsorbed on GO surfaces. Based on a molecular dynamics simulation, this work shows that an ssDNA segment could be stably adsorbed on a GO surface through hydrogen bonding and π-π stacking interactions, with preferential binding to the oxidized rather than to the unoxidized region of the GO surface. The adsorption process shows a dynamic cooperation adsorption behavior; the ssDNA segment first captures the oxidized groups of the GO surface by hydrogen bonding interaction, and then the configuration relaxes to maximize the π-π stacking interactions between the aromatic rings of the nucleobases and those of the GO surface. We attributed this behavior to the faster forming hydrogen bonding interaction compared to π-π stacking; the π-π stacking interaction needs more relaxation time to regulate the configuration of the ssDNA segment to fit the aromatic rings on the GO surface. [ABSTRACT FROM AUTHOR]

Recent experiments have shown the coexistence of both large unoxidized and oxidized regions on graphene oxide (GO), but the underlying mechanism for the formation of the GO atomic structure remains unknown. Now, using density functional calculations, 52 oxidation pathways for local pyrene structures on GO were identified, and a kinetic profile for graphene oxidation with a high correlation between oxidation loci was proposed, which is different from the conventional view, which entails a random distribution of oxidation loci. The high correlation is an essential nature of graphene oxidation processes and can be attributed to three crucial effects: 1) breaking of delocalized π bonds, 2) steric hindrance, and 3) hydrogen-bond formation. This high correlation leads to the coexistence of both large unoxidized and oxidized regions on GO. Interestingly, even in oxidized regions on GO, some small areas of sp2-hybridized domains, similar to 'islands', can persist because of steric effects. [ABSTRACT FROM AUTHOR]

Recent experiments have shown the coexistence of both large unoxidized and oxidized regions on graphene oxide (GO), but the underlying mechanism for the formation of the GO atomic structure remains unknown. Now, using density functional calculations, 52 oxidation pathways for local pyrene structures on GO were identified, and a kinetic profile for graphene oxidation with a high correlation between oxidation loci was proposed, which is different from the conventional view, which entails a random distribution of oxidation loci. The high correlation is an essential nature of graphene oxidation processes and can be attributed to three crucial effects: 1) breaking of delocalized π bonds, 2) steric hindrance, and 3) hydrogen-bond formation. This high correlation leads to the coexistence of both large unoxidized and oxidized regions on GO. Interestingly, even in oxidized regions on GO, some small areas of sp2-hybridized domains, similar to 'islands', can persist because of steric effects. [ABSTRACT FROM AUTHOR]

Abstract: Using all-atom molecular dynamics (MD) simulation, we have investigated the adsorption of protein GA module (GA53) onto graphene oxide (GO), compared with similar adsorption onto pristine graphene (PG). We find that: (1) the protein GA53 can be easily and firmly adsorbed onto the surface of GO and PG, but the binding sites are not specific; the main difference is that the secondary structure of GA53 can be well preserved in protein–GO system, while GA53 will partially lose its secondary structure after adsorbed on PG. (2) in protein–GO system, hydroxyl and epoxy groups increase the distance between protein and GO, which weaken their vdW interactions, meanwhile, hydrogen bonds and electrostatic interactions enhance their binding affinity. In protein–PG system, strong vdW interactions between residues of GA53 and PG have destroyed its secondary structure. (3) π–π stacking interactions still exist between aromatic residues and both the basal plane of GO and PG. In comparison with PG, our results suggest that GO presents better biocompatibility to preserve protein secondary structure when simultaneously absorbing protein. [Copyright &y& Elsevier]