Simulation study of non-covalent hybridization of carbon nanotubes by single-stranded DNA in water

Solubilization and separation is an important step in utilizing both the unique mechanical and electrical properties of carbon nanotubes (CNTs). Due to different possible chiralities of CNTs, which can have drastically different electrochemical properties, it is also necessary to have a method of separation that will distinguish between these different species. Recent discovery of single-stranded DNA (ssDNA) absorption onto CNTs have shown high affinity towards forming soluble hybrids in polar solvents. The interactions between the ssDNA and CNTs as well as the geometry of the hybrid structure are not well understood. In order to study these phenomena we have implemented multiple all-atom replica exchange simulations. Simulations are carried out in an aqueous environment and vary in single-stranded decamer composition as well as nanotube chirality. The oligonucleotides readily adsorb onto the carbon nanotube surface and immediately following begin a slow structural rearrangement. Dependent upon both oligonucleotide composition and nanotube chirality, the ssDNA is found to form several unique backbone geometries as defined by both local and global order parameters. In contrast to the multiple geometries the backbone may form to, the nucleotide bases are found to organize themselves into either parallel or anti-parallel conformation with a high degree of orientational order. Binding appears to be mainly driven by pi-stacking interactions between DNA bases onto the carbon nanotube surface, equilibrium of the structures is also controlled by a complex mixture of forces including DNA conformational strain and solvent interactions. The result of this is the free energy landscape is found to have multiple minima occupied at room temperature which are separated by high energy barriers.