A facile, modular and high yield method to assemble three-dimensional DNA structures.

We describe a rapid and quantitative method to generate DNA cages of deliberately designed geometry from readily available starting strands. Balancing the incorporation of sequence uniqueness and symmetry in a face-centered approach to 3D construction can result in triangular (TP), rectangular (RP), and pentagonal prisms (PP) without compromising the potential for nanostructure addressability.

Organization of intracellular reactions with rationally designed RNA assemblies.

The rules of nucleic acid base-pairing have been used to construct nanoscale architectures and organize biomolecules, but little has been done to apply this technology in vivo. We designed and assembled multidimensional RNA structures and used them as scaffolds for the spatial organization of bacterial metabolism. Engineered RNA modules were assembled into discrete, one-dimensional, and two-dimensional scaffolds with distinct protein-docking sites and used to control the spatial organization of a hydrogen-producing pathway.

Self-assembly of metal-DNA triangles and DNA nanotubes with synthetic junctions.

The site-specific insertion of organic and inorganic molecules into DNA nanostructures can provide unique structural and functional capabilities. We have demonstrated the inclusion of two types of molecules. The first is a diphenylphenanthroline (dpp, 1) molecule that is site specifically inserted into DNA strands and which can be used as a template to create metal-coordinating pockets.

Loading and selective release of cargo in DNA nanotubes with longitudinal variation.

Nanotubes hold promise for a number of biological and materials applications because of their high aspect ratio and encapsulation potential. A particularly attractive goal is to access nanotubes that exert well-defined control over their cargo, such as selective encapsulation, precise positioning of the guests along the nanotube length and triggered release of this cargo in response to specific external stimuli. Here, we report the construction of DNA nanotubes with longitudinal variation and alternating larger and smaller capsules along the tube length.

A structurally tunable DNA-based extracellular matrix.

The principles of DNA nanotechnology and protein engineering have been combined to generate a new class of artificial extracellular matrices. The potential of this material for ex vivo cellular scaffolding was demonstrated using experiments in which human cervical cancer cells were found to adhere strongly, stay alive, and grow with high migration rates. The use of DNA in our DNA/protein-based matrices makes these structures inherently amenable to structural tunability.

Long-range assembly of DNA into nanofibers and highly ordered networks using a block copolymer approach.

A simple method to introduce the long-range order achieved by block copolymers into DNA structures is described. This results in the hierarchical assembly of short DNA strands into a new one-dimensional material, with high aspect ratio and the ability to further align into highly ordered surfaces over tens of micrometers. Fibers derived from biological materials have a wide range of potential applications, such as scaffolds for nanowires and one-dimensional (1D) materials, templates for tissue growth, and ligand display tools for multivalent biological interactions.

Metal-nucleic acid cages.

Metal-nucleic acid cages are a promising new class of materials. Like metallo-supramolecular cages, these systems can use their metals for redox, photochemical, magnetic and catalytic control over encapsulated cargo. However, using DNA provides the potential to program pore size, geometry, chemistry and addressability, and the ability to symmetrically and asymmetrically position transition metals within the three-dimensional framework.

Modular construction of DNA nanotubes of tunable geometry and single- or double-stranded character.

DNA nanotubes can template the growth of nanowires, orient transmembrane proteins for nuclear magnetic resonance determination, and can potentially act as stiff interconnects, tracks for molecular motors and nanoscale drug carriers. Current methods for the construction of DNA nanotubes result in symmetrical and cylindrical assemblies that are entirely double-stranded. Here, we report a modular approach to DNA nanotube synthesis that provides access to geometrically well-defined triangular and square-shaped DNA nanotubes.

Assembling materials with DNA as the guide.

DNA's remarkable molecular recognition properties and structural features make it one of the most promising templates to pattern materials with nanoscale precision. The emerging field of DNA nanotechnology strips this molecule from any preconceived biological role and exploits its simple code to generate addressable nanostructures in one, two, and three dimensions. These structures have been used to precisely position proteins, nanoparticles, transition metals, and other functional components into deliberately designed patterns.

Effect of ligand density on the spectral, physical, and biological characteristics of CdSe/ZnS quantum dots.

Chemical modification of the surface of CdSe/ZnS quantum dots (QDs) with small molecules or functional ligands often alters the characteristics of these particles. For instance, dopamine conjugation quenches the fluorescence of the QDs, which is a property that can be exploited for sensing applications if the conjugates are taken up into living cells. However, different sizes and/or preparations of mercaptocarboxylic acid solubilized QDs show very different properties when incubated with cells.