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DNA nanotechnology leverages the molecular design resolution of the DNA double helix to fold and tile matter into designer architectures. Recent advances in bioinorganic chemistry have exploited the affinity of soft nucleobase functional groups for silver ions in order to template the growth of silver nanoclusters by templated reduction. The coupling of the spatial resolution of DNA nanotechnology and the atomic precision of DNA-based nanocluster synthesis has not been realized. Here we develop a method using 3D DNA crystals to employ silver-ion-mediated base pairs as nucleation sites for atomically-precise nanocluster growth. By leveraging the topology of DNA tensegrity triangles, we provide a mesoporous 3D lattice that is robust to reducing conditions, enabling precise spatial templating. Use of in situ confocal fluorescence microscopy allows for the direct observation of reaction kinetics and reconstruction of the optical bandgap. Control over reaction time and stoichiometry, base pair identity, and buffer composition enable precise tuning of the atomic composition and optical properties of the ensuing nanoclusters. The resulting crystals are of diffraction quality, yielding molecular structures of Ag4 and Ag6 in 3D. Inter-cluster distances of less than 2 nm show strong plasmonic coupling, with red shifting observed relative to literature standards. We anticipate that these results will yield advances in materials synthesis, DNA-based plasmonic crystals, and optically-active nanoelectronics. 

Tertiary chirality describes the handedness of supramolecular assemblies and relies not only on the primary and secondary structures of the building blocks but also on topological driving forces that have been sparsely characterized. Helical biopolymers, especially DNA, have been extensively investigated as they possess intrinsic chirality that determines the optical, mechanical, and physical properties of the ensuing material. Here, we employ the DNA tensegrity triangle as a model system to locate the tipping points in chirality inversion at the tertiary level by X-ray diffraction. We engineer tensegrity triangle crystals with incremental rotational steps between immobile junctions from 3 to 28 base pairs (bp). We construct a mathematical model that accurately predicts and explains the molecular configurations in both this work and previous studies. Our design framework is extendable to other supramolecular assemblies of helical biopolymers and can be used in the design of chiral nanomaterials, optically active molecules, and mesoporous frameworks, all of which are of interest to physical, biological, and chemical nanoscience. 

Abstract The successful self‐assembly of tensegrity triangle DNA crystals heralded the ability to programmably construct macroscopic crystalline nanomaterials from rationally‐designed, nanoscale components. This 3D DNA tile owes its “tensegrity” nature to its three rotationally stacked double helices locked together by the tensile winding of a center strand segmented into 7 base pair (bp) inter‐junction regions, corresponding to two‐thirds of a helical turn of DNA. All reported tensegrity triangles to date have employed turn inter‐junction segments, yielding right‐handed, antiparallel, “J1” junctions. Here a minimal DNA triangle motif consisting of 3‐bp inter‐junction segments, or one‐third of a helical turn is reported. It is found that the minimal motif exhibits a reversed morphology with a left‐handed tertiary structure mediated by a locally‐parallel Holliday junction—the “L1” junction. This parallel junction yields a predicted helical groove matching pattern that breaks the pseudosymmetry between tile faces, and the junction morphology further suggests a folding mechanism. A Rule of Thirds by which supramolecular chirality can be programmed through inter‐junction DNA segment length is identified. These results underscore the role that global topological forces play in determining local DNA architecture and ultimately point to an under‐explored class of self‐assembling, chiral nanomaterials for topological processes in biological systems.