Programmable self-assembly of complex 2D manifolds using DNA origami colloids
Creators: name: Hayakawa, Daichi
Publisher: name: Brandeis University
Year: 2024
Subjects: DNA nanotechnology
Inverse design
Self-assembly
Supracrystal
Tiling

description: Nature is replete with self-assembled materials with complex geometries that give rise to its functionalities, including shells, tubules, and fibers. Despite significant advances in synthesizing nanometer- and micrometer-scale particles, the programmable assembly of similar architectures from synthetic components has remained largely out of reach for two reasons. First, there is a nearly boundless design space, which calls for design principles for defining the mutual interactions between multiple particle species to target a user-specified complex structure or pattern. Second, synthesizing building blocks that can simultaneously tune the valence, binding angle, and interaction specificity is still difficult.To address the first point, we develop a symmetry-based method to generate the interaction matrices that specify the assembly of two-dimensional tilings, which we illustrate using equilateral triangles. By exploiting the allowed 2D symmetries, we develop an algorithmic approach by which any periodic 2D tiling can be generated from an arbitrarily large number of subunit species. To demonstrate the utility of our design approach, we encode specific interactions between triangular subunits synthesized by DNA origami and show that we can guide their self-assembly into tilings with a wide variety of symmetries, using up to 12 unique species of triangles. Next, we design a DNA origami triangle with programmable binding angles and study their assembly into tubules of programmable width and helicity. Notably, the tubules we assemble are always polymorphic, an attribute inherent to self-closing structures with cavities; assembled tubules end up with a distribution of widths and helicities due to fluctuations of binding angles between subunits. To compensate for this finite ‘geometric specificity’ of the subunits, we turn to the interaction specificity of the assembly system to enhance the selectivity of the geometry of the assembled tubules. Through theory and experiments, we show that the specificity of the tubule geometry increases by increasing the number of unique triangles in the system. Finally, we drastically broaden the classes of geometries that can be assembled by introducing a DNA origami platform whose interface can simultaneously and modularly encode for the interaction specificity and binding angle. Our approach utilizes equilateral triangle building blocks that interact through DNA hybridization via extruded overhangs, whose relative length can be tuned to encode for the binding angles. We leverage the combined programmability of bevel angle and interaction specificity of DNA sequences to build various low-symmetry capsids and a hollow toroid. Taken together, the three breakthroughs discussed in this work -- the inverse design, the systematic strategy to reduce failure modes, and the modular particle platform -- offer new avenues not only to mimic Nature's sophisticated assemblies but also to assemble geometries of unprecedented complexity.