A team of researchers led by Oleg Gang of Columbia University has demonstrated how DNA can be used to organize quantum dots, enzymes, and other nanoscale objects into three-dimensional (3D) arrays. Previous efforts to do this have been limited by the need to design custom scaffolds for each object. In an article published in Nature Materials, Gang and his co-workers describe a new approach that overcomes this challenge, positioning DNA as a universal scaffolding with significant potential in nanoscale engineering.

“My deep interest is in establishing how we can make complex materials according to our design consideration with different functions at very small scales,” says Gang. “If we want to create three-dimensional materials, we cannot do it with conventional methods...and that’s what we’re working on here.” Toward this end, Gang’s team has been working on a possible solution, one they describe as DNA-prescribed and valence-controlled material voxels. The use of voxels in this context alludes to the techniques functionality in building 3D structures—in graphic design, pixels are used to render a two-dimensional digital image and voxels are used to build 3D images.

The technique uses DNA origami—a process in which nanoscale objects are formed through DNA self-assembly—to build 3D polyhedral structures (such as tetrahedra, octahedra, and cubes). At the structures’ vertices are protrusions of single-stranded DNA which provide each polyhedron with a structure-specific valence, defined in this context as one polyhedron’s capacity for binding to other polyhedra through complementary base-pairing. When bound together, polyhedral structures form a lattice upon which nanoparticles can be arranged.

To facilitate nanoparticle binding, each polyhedron is outfitted with a set of eight single-stranded DNA protrusions that extend toward the structure’s interior and which serve as docking sites for any nanoparticles that carry complementary strands of DNA. In this way, the DNA polyhedra behave like voxels—each representing a defined unit of 3D space which can be empty or occupied. Due to this similarity, Gang dubbed these polyhedra “valence-controlled material voxels.”

“They’ve identified and solved a problem that we’ve been aware of for a long time,” says Matthew Jones, assistant professor of chemistry at Rice University. Previous techniques for organizing nanoparticles required researchers to design structures that accommodated for a nanoparticle’s specific size, shape, and reactivity. “The identity of a particle changes how it will assemble. So a cube [shaped particle] is going to pack into a different structure than a sphere,” Jones says. Because of this, the assembly of 3D materials into shapes that are independent of the nanoparticle’s properties has not been feasible. 

Gang’s approach, however, enables the same structure to be used for a myriad of nanoparticles, so long as those nanoparticles can be made to present strands of DNA that are complimentary to those found in the DNA voxels.

Gang suggests that the power of this approach is that “the voxel carries the capability for self-assembly in a very deterministic way,” regardless of what is inside. “It works the same way for nanoparticles and enzymes.”

To demonstrate this functionality, Gang and his colleagues showed that super-lattices formed from valence-controlled material voxels could be used to arrange gold nanoparticles, quantum dots, and even proteins. Furthermore, using this technique, the researchers found that the photoluminescent yield of a quantum dot array could be improved by adjusting the distance between dots. This is significant in light of ongoing efforts to develop materials containing quantum dots for biomedical imaging and advanced image display technologies. Current techniques for quantum dot incorporation rely on the formation of layers or films; however, this positions dots in close proximity to one another and enables energy transfer between them, resulting in a decrease in photoluminescent yield. With voxels, the spacing between dots can be modified and their yield improved.

Similarly, the proximity of two enzymes that work in tandem—glucose oxidase (GOx) and horseradish peroxidase (HRP), where GOx’s product serves as a substrate for HRP—affects the efficiency of this enzyme cascade. This insight, the researchers note, could not have been produced in a free-floating solution.

DNA-prescribed and valence-controlled material voxels appear to be a valuable tool for research at the nanoscale. As Jones puts it, the work presented here is a “real tour de force” for the field of nanoengineering and may prove to be a significant step toward the fabrication of 3D materials.

Read the abstract in Nature Materials.