Creation of ordered 3D tubes out of DNA origami lattices.

Hierarchical self-assembly of nanostructures with addressable complexity has been a promising route for realizing novel functional materials. Traditionally, the fabrication of such structures on a large scale has been achievable using top-down methods but with the cost of complexity of the fabrication equipment versus resolution and limitation mainly to 2D structures. More recently bottom-up methods using molecules like DNA have gained attention due to the advantages of low fabrication costs, high resolution and simplicity in an extension of the methods to the third dimension. One of the more promising bottom-up techniques is DNA origami due to the robust self-assembly of arbitrarily shaped nanostructures with feature sizes down to a few nanometers. Here, we show that under specific ionic conditions of the buffer, the employed plus-shaped, blunt-ended Seeman tile (ST) origami forms elongated, ordered 2D lattices, which are further rolled into 3D tubes in solution. Imaging structures on a surface by atomic force microscopy reveals ribbon-like structures, with single or double layers of the origami lattice. Further studies of the double-layered structures in a liquid state by confocal microscopy and cryo-TEM revealed elongated tube structures with a relatively uniform width but with a varying length. Through meticulous study, we concluded that the assembly process of these 3D DNA origami tubes is heavily dependent on the concentration of both mono- and divalent cations. In particular, nickel seems to act as a trigger for the formation of the tubular assemblies in liquid.

Biosensing with a scanning planar Yagi-Uda antenna.

We investigate a model bioassay in a liquid environment using a z-scanning planar Yagi-Uda antenna, focusing on the fluorescence collection enhancement of ATTO-647N dye conjugated to DNA (deoxyribonucleic acid) molecules. The antenna changes the excitation and the decay rates and, more importantly, the emission pattern of ATTO-647N, resulting in a narrow emission angle (41°) and improved collection efficiency. We efficiently detect immobilized fluorescently-labeled DNA molecules, originating from solutions with DNA concentrations down to 1 nM. In practice, this corresponds to an ensemble of fewer than 10 ATTO-647N labeled DNA molecules in the focal area. Even though we use only one type of biomolecule and one immobilization technique to establish the procedure, our method is versatile and applicable to any immobilized, dye-labeled biomolecule in a transparent solid, air, or liquid environment.

Few-Molecule Strong Coupling with Dimers of Plasmonic Nanoparticles Assembled on DNA.

Hybrid nanostructures, in which a known number of quantum emitters are strongly coupled to a plasmonic resonator, should feature optical properties at room temperature such as few-photon nonlinearities or coherent superradiant emission. We demonstrate here that this coupling regime can only be reached with dimers of gold nanoparticles in stringent experimental conditions, when the interparticle spacing falls below 2 nm. Using a short transverse DNA double-strand, we introduce five dye molecules in the gap between two 40 nm gold particles and actively decrease its length down to sub-2 nm values by screening electrostatic repulsion between the particles at high ionic strengths. Single-nanostructure scattering spectroscopy then evidence the observation of a strong-coupling regime in excellent agreement with electrodynamic simulations. Furthermore, we highlight the influence of the planar facets of polycrystalline gold nanoparticles on the probability of observing strongly coupled hybrid nanostructures.

Constructing Large 2D Lattices Out of DNA-Tiles.

The predictable nature of deoxyribonucleic acid (DNA) interactions enables assembly of DNA into almost any arbitrary shape with programmable features of nanometer precision. The recent progress of DNA nanotechnology has allowed production of an even wider gamut of possible shapes with high-yield and error-free assembly processes. Most of these structures are, however, limited in size to a nanometer scale. To overcome this limitation, a plethora of studies has been carried out to form larger structures using DNA assemblies as building blocks or tiles. Therefore, DNA tiles have become one of the most widely used building blocks for engineering large, intricate structures with nanometer precision. To create even larger assemblies with highly organized patterns, scientists have developed a variety of structural design principles and assembly methods. This review first summarizes currently available DNA tile toolboxes and the basic principles of lattice formation and hierarchical self-assembly using DNA tiles. Special emphasis is given to the forces involved in the assembly process in liquid-liquid and at solid-liquid interfaces, and how to master them to reach the optimum balance between the involved interactions for successful self-assembly. In addition, we focus on the recent approaches that have shown great potential for the controlled immobilization and positioning of DNA nanostructures on different surfaces. The ability to position DNA objects in a controllable manner on technologically relevant surfaces is one step forward towards the integration of DNA-based materials into nanoelectronic and sensor devices.

Dual-color nanoscale assemblies of structurally stable, few-atom silver clusters, as reported by fluorescence resonance energy transfer.

We develop approaches to hold fluorescent silver clusters composed of only 10-20 atoms in nanoscale proximity, while retaining the individual structure of each cluster. This is accomplished using DNA clamp assemblies that incorporate a 10 atom silver cluster and a 15 or 16 atom silver cluster. Thermally modulated fluorescence resonance energy transfer (FRET) verifies assembly formation. Comparison to Förster theory, using measured spectral overlaps, indicates that the DNA clamps hold clusters within roughly 5 to 6 nm separations, in the range of the finest resolutions achievable on DNA scaffolds. The absence of spectral shifts in dual-cluster FRET pairs, relative to the individual clusters, shows that select few-atom silver clusters of different sizes are sufficiently stable to retain structural integrity within a single nanoscale DNA construct. The spectral stability of the cluster persists in a FRET pair with an organic dye molecule, in contrast to the blue-shifted emission of the dye.

Evidence for rod-shaped DNA-stabilized silver nanocluster emitters.

Fluorescent DNA-stabilized silver nanoclusters contain both cationic and neutral silver atoms. The absorbance spectra of compositionally pure solutions follow the trend expected for rod-shaped silver clusters, consistent with the polarized emission measured from individual nanoclusters. The data suggest a rod-like assembly of silver atoms, with silver cations mediating attachment to the bases.