Encoding Hierarchical 3D Architecture through Inverse Design of Programmable Bonds

Abstract

The ability to fabricate materials and devices by-design at small scales, largely based in advances in lithographic and additive manufacturing methods, has led to the tremendous technological progress of the last decades. However, the growing need to structure 3D nanoscale matter for emergent functions, according to design and in a massively parallel manner, requires new means of material fabrication. Here, we demonstrate the concept and experimental realization of the encoded assembly of nanoparticles into prescribed, hierarchically ordered 3D organizations using DNA programmable bonds. Our information-constrained inverse design approach allows for encoding of targeted 3D hierarchical architectures with programmable bonds through identification of repeating mesoscale motifs and their elemental blocks, nanoscale voxels, that can also carry encoded nano-cargo. Using intrinsic symmetries of mesoscale motifs in targeted 3D architectures, we reduce the amount of information required for encoding bonds and incorporate this into the inverse design assembly strategy. As examples of this approach, we assemble spatially ordered, low-dimensional arrays with coupled plasmonic and photonic scales, a nanoscale analog of face-perovskite lattice, and a hierarchically organized lattice of spiral motifs. Detailed x-ray scattering and electron microcopy methods confirm the correspondence between the designed and realized architectures. The presented approach paves the road for establishing a by-design assembly platform for the fabrication of 3D architectures from diverse types of nanocomponents.

Economical routes to size-specific assembly of self-closing structures

“…1D ). Using sticky-end hybridization allows us to encode many low cross-talk interactions ( 15 , 35 , 37 – 39 ) without changing any internal routing of the DNA origami, which could otherwise have unintended effects on the monomer structure ( 19 , 20 , 40 ). Last, we assemble tubules at a constant temperature chosen such that the intersubunit interactions are weak and reversible (section S1).…”

“…More complex geometries, such as capsids or gyroids, require considering local point symmetries of the structure ( 16 , 19 , 43 , 45 ) to encode the correct interactions, while fully addressable clusters often reveal their allowed colorings through detailed searches of all possible interactions ( 46 ). Recent efforts have also shown that colorings can be used to encode hierarchical structures into crystalline self-assemblies ( 15 ). As assembly structures become more complex, finding the right scheme to encode large libraries of interactions may require new methods, such as SAT-assembly ( 47 , 48 ).…”

“…The design and control of self-assembly pathways is a promising route for creating complex, functional nanomaterials (1). Recent successes in colloidal self-assembly focus primarily on synthesizing spatially unbounded, dense crystalline materials or spatially limited architectures, like clusters, membranes, and filaments, whose dimensions are specified by the building block sizes (2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15). However, Nature is brimming with examples from a different class of structures that have self-regulated cavity sizes that are much larger than the size of the individual building blocks.…”

Symmetry-Guided Inverse Design of Self-Assembling Multiscale DNA Origami Tilings

“…We assemble tilings with up to 12 species, containing as many as 72 triangles in a unit cell, significantly larger than other recent examples reported in the literature. 34 Finally, by conjugating DNAgrafted gold nanoparticles onto a small number of species, we fabricate various gold nanoparticle supracrystals with periodicities reaching hundreds of nanometers (Figure 1D,E). Fourier transforms of the gold nanoparticles exhibit distinct low-spatial-frequency features, demonstrating order on length scales larger than the gold nanoparticles themselves.…”

“…To show that our design scheme works in practice, we synthesize DNA origami subunits with programmable interactions (Figure A). We assemble tilings with up to 12 species, containing as many as 72 triangles in a unit cell, significantly larger than other recent examples reported in the literature . Finally, by conjugating DNA-grafted gold nanoparticles onto a small number of species, we fabricate various gold nanoparticle supracrystals with periodicities reaching hundreds of nanometers (Figure D,E).…”