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Effect of octadecylamine surfactant on DNA interactions with graphene surfaces.

Understanding of how to integrate DNA molecules with graphene materials is important for the development of bio-sensors and biomolecular logic circuits. For some of these applications, controlling DNA structural conformation on the graphene substrate is critically important and can be achieved through the use of self-assembled monolayers. Here, we performed all-atom molecular dynamics simulations to understand how various 1-octadecylamine (ODA) coatings of graphene surface affect the conformation of double-stranded (dsDNA) on the surface. The simulation results demonstrated that dsDNA structures become more stable as ODA concentration increases due to formation of DNA-ODA hydrogen bonds and reduction of DNA - surface interactions, which aid in retaining internal DNA interactions. Specifically, the interaction of ODA molecules with DNA prevents nucleobases from forming pi-pi stacking interactions with the surface. Some dsDNA conformations, such as sharp kinks or unwinding, can happen more frequently in DNA with A-T sequences due to weaker pairing interactions than G-C sequences. Furthermore, our results conclude that both DNA sequence and ODA concentration play an essential role in experimentally observed conformational changes of DNA on the graphene surface.