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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.