A study of DNA tube formation mechanisms using 4-, 8-, and 12-helix DNA nanostructures

This paper describes the design and characterization of a new family of rectangular-shaped DNA nanostructures (DNA tiles) containing 4, 8, and 12 helices. The self-assembled morphologies of the three tiles were also investigated. The motivation for designing this set of DNA nanostructures originated from the desire to produce DNA lattices containing periodic cavities of programmable dimensions and to investigate the mechanism of DNA tube formation. Nine assembly scenarios have been investigated through the combination of the three different tiles and three sticky end association strategies. Imaging by atomic force microscopy (AFM) revealed self-assembled structures with varied cavity sizes, lattice morphologies, and orientations. Six samples show only tube formation, two samples show both 2D lattices (>2 microm) and tubes, and one sample shows only 2D lattices without tubes. We found that a lower tile dimensional anisotropy, weaker connection, and corrugated design favor the large 2D array formation, while the opposite (higher tile anisotropy, stronger connection, and uncorrugated design) favors tube formation. We discuss these observations in terms of an energy balance at equilibrium and the kinetic competition between diffusion-limited lateral lattice growth versus fluctuation of the lattice to form tubes at an early stage of the assembly. The DNA nanostructures and their self-assembly demonstrated herein not only provide a new repertoire of scaffolds to template the organization of nanoscale materials, but may also provide useful information for investigating other self-assembly systems.