This communication reports a strategy for solid surface-mediated DNA self-assembly. DNA molecules weakly interact with solid surfaces; thus are confined to solid surfaces. The confinement reduces the flexibility of DNA nanomotifs and promotes the DNA 2D crystals to grow on solid surfaces. As a demonstration, periodic DNA nanoarrays have been directly assembled onto mica surfaces. Such in situ assembly eliminates the sample transfer process between assembly and characterization and possible applications.

This Communication reports complementary strategies to control the face geometry during the self-assembly of DNA polyhedra from branched DNA nanomotifs (tiles). In these approaches, the final DNA polyhedra contain two types of DNA tiles. They are different by either sequence or orientation in the final structures. DNA tiles can associate with each other between the two types of different tiles, but not with the same type of tiles. Thus, each face must contain an even number of tiles. As a demonstration, DNA cubes, whose faces are squares that contain four tiles, have been assembled through these approaches. The cube structures have been confirmed by multiple techniques including polyacrylamide gel electrophoresis (PAGE), dynamic light scattering (DLS), cryogenic electron microscopy (cryo-EM) imaging, and single particle three-dimensional (3D) reconstruction.DNA has been shown as a superb molecular system in selfassembly toward bottom-up nanofabrication. 1 In the last two decades, a range of DNA motifs have been developed, and complicated 1D, 2 2D, 3 and 3D 4 large nanostructures have been fabricated. Recently, we have shown that one-component starshaped DNA motifs can assemble into a range of geometrically well-defined polyhehedra including tetrahedra, dodecahedra, and buckyballs from 3-point-star motifs, 5 and icosahedra and large nanocages from 5-point-star motifs. 6 It is achieved by carefully balancing the flexibilities and the rigidities of the motifs and controlling the DNA concentrations. Each vertex consists of a star tile and the separation between any two adjacent vertices is integral numbers of turns. With such a separation, all tiles face to the same side and the tiles' intrinsic curvatures accumulate at the same direction, which promotes the formation of closed structures instead of extended sheets. One face of the polyhedra can contain any number of vertices. It is straightforward to expand the list of the structures we can achieve by using different building blocks, for example, assembling octahedral structures from four-point-star motifs. However, to further expand the structural scope, novel assembly strategies, in addition to controlling the flexibility and the concentration of DNA tiles, are needed. Herein, we report such strategies to restrict polyhedral faces to consist of only even numbers of vertices and use such strategies to assemble DNA cubes, the symbol for DNA nanotechnology. 4a A cube consists of eight vertices and each vertex can be represented by a three-point-star tile. Each face is a square and consists of four three-point-star tiles. This requirement cannot be met by simply changing the concentration and the flexibility of the DNA tiles. To overcome this problem, we exploit the helical nature of the DNA double helix structure. When being separated by odd numbers of half-turns, two objects along a DNA duplex will be on the opposite sides of the DNA duplex and are related by a 2-fold rotational symmetry. When any two three-point-star tiles are associated through hybridization of...

DNA has recently been used as a programmable ‘smart’ building block for the assembly of a wide range of nanostructures. It remains difficult, however, to construct DNA assemblies that are also functional. Incorporating RNA is a promising strategy to circumvent this issue as RNA is structurally related to DNA but exhibits rich chemical, structural and functional diversities. However, only a few examples of rationally designed RNA structures have been reported. Herein, we describe a simple, general strategy for the de novo design of nanostructures in which the self-assembly of RNA strands is programmed by DNA strands. To demonstrate the versatility of this approach, we have designed and constructed three different RNA–DNA hybrid branched nanomotifs (tiles), which readily assemble into one-dimensional nanofibres, extended two-dimensional arrays and a discrete three-dimensional object. The current strategy could enable the integration of the precise programmability of DNA with the rich functionality of RNA.

Molecularly directed self-assembly has the potential to become a nanomanufacturing technology if the critical factors governing the kinetics and yield of defect-free self-assembled structures can be understood and controlled. The kinetics of streptavidin-functionalized quantum dots binding to biontinylated DNA origami are quantitatively evaluated and to what extent the reaction rate and binding efficiency are controlled by the valency of the binding location, the biotin linker length, and the organization, and spacing of the binding locations on the DNA is shown. Yield improvement is systematically determined as a function of the valency of the binding locations and as a function of the quantum dot spacing. In addition, the kinetic studies show that the binding rate increases with increasing linker length, but that the yield saturates at the same level for long incubation times. The forward and backward reaction rate coefficients are determined using a nonlinear least squares fit to the measured binding kinetics, providing considerable physical insight into the factors governing this type of self-assembly process. It is found that the value of the dissociation constant, K d , for the DNA-nanoparticle complex considered here is up to seven orders of magnitude larger than that of the native biotinstreptavidin complex. This difference is attributed to the combined effect that the much larger size of the DNA origami and the quantum dot have on the translational and rotational diffusion constants.