A general approach to DNA-programmable atom equivalents

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The ability to predictably control the coassembly of multiple nanoscale building blocks, especially those with disparate chemical and physical properties such as biomolecules and inorganic nanoparticles, has far-reaching implications in catalysis, sensing, and photonics, but a generalizable strategy for engineering specific contacts between these particles is an outstanding challenge. This is especially true in the case of proteins, where the types of possible interparticle interactions are numerous, diverse, and complex. Herein, we explore the concept of trading protein-protein interactions for DNA-DNA interactions to direct the assembly of two nucleic-acid-functionalized proteins with distinct surface chemistries into six unique lattices composed of catalytically active proteins, or of a combination of proteins and DNA-modified gold nanoparticles. The programmable nature of DNA-DNA interactions used in this strategy allows us to control the lattice symmetries and unit cell constants, as well as the compositions and habit, of the resulting crystals. This study provides a potentially generalizable strategy for constructing a unique class of materials that take advantage of the diverse morphologies, surface chemistries, and functionalities of proteins for assembling functional crystalline materials.nanoscience | biomaterials | self-assembly | superlattice | DNA-programmable assembly D NA-mediated assembly strategies (1-3) that take advantage of rigid building blocks, functionalized with oriented oligonucleotides to create entities with well-defined "valencies," have emerged as powerful new ways for programming the formation of crystalline materials (4, 5). With such methods, one can make architectures with well-defined lattice parameters (6-12), symmetries (4,8,10,12), and compositions (10, 12, 13), but to date they have been confined primarily to the use of hard inorganic nanoparticles (NPs) or highly branched pure nucleic-acid materials (2, 14, 15). In contrast, Nature's most powerful and versatile nanostructured building blocks are proteins and are used to effect the vast majority of processes in living systems (16). Unlike most inorganic NP systems, proteins can be made in pure and perfectly monodisperse form, making them ideal synthons for supramolecular assemblies. However, the ability to engineer lattices composed of multiple proteins, or of proteins and inorganic nanomaterials, has been limited, and the choice of protein building blocks is often restricted by structural constraints, which limits the catalytic functionalities that can be incorporated into these structures. Currently, the primary methods for making protein lattices have relied on the use of natural protein-protein interactions (17), interactions between proteins and ligands on the surfaces of inorganic NPs (17, 18), metal coordination chemistry (19), small molecule ligand-protein interactions (20-23), genetically fusing protein complexes with specific symmetries (24, 25), or DNA-mediated assembly of viruses (26,27). Here, we introduce a new...

Section: Resultssupporting

confidence: 84%

Section: Resultssupporting

confidence: 69%

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confidence: 99%

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DNA-mediated engineering of multicomponent enzyme crystals

Brodin

Auyeung

Mirkin

2015

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128

138

“…At the colloidal scale, such interactions have a range that is much shorter than the size of the particles. The use of DNA labeling to control binding specificity was originally pioneered for assembling nanoparticles (14)(15)(16)(17) into infinite crystals (18)(19)(20)(21)(22)(23)(24), where recently it was demonstrated that with two species with differing particle radii and DNA linker length a zoo of different crystal morphologies can be created (25). Work at the colloidal scale has begun to bear fruit (13,17,(26)(27)(28)(29)(30).…”

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confidence: 99%

Size limits of self-assembled colloidal structures made using specific interactions

Zeravcic

Manoharan

Brenner

2014

We establish size limitations for assembling structures of controlled size and shape out of colloidal particles with short-ranged interactions. Through simulations we show that structures with highly variable shapes made out of dozens of particles can form with high yield, as long as each particle in the structure binds only to the particles in their local environment. To understand this, we identify the excited states that compete with the ground-state structure and demonstrate that these excited states have a completely topological characterization, valid when the interparticle interactions are short-ranged. This allows complete enumeration of the energy landscape and gives bounds on how large a colloidal structure can assemble with high yield. For large structures the yield can be significant, even with hundreds of particles.assembly | DNA-coated particles | local minima | short-ranged interactions N ature uses hierarchical assembly of complicated building blocks to make highly functional structures such as biomolecules, virus shells, and microtubules without any external influence and with high fidelity. Mimicking this would not only give more insight into biological mechanisms but would also help realize the dream of "bottom-up" assembly that has been a central theme of nanotechnology for many decades (1).As in biology, the information needed for assembling arbitrary macroscopic structures can be stored in the building blocks through the design of their interactions and interaction rules. Over the years great advances have been made by synthesizing new building blocks differing in geometry, composition, and interactions (2-10), allowing for study of more complex objects. However, basic rules necessary for robust and efficient assembly of a desired structure in a scalable fashion and reasonable time scales are still not understood. A number of schemes for approaching this "inverse" statistical mechanics problem have been proposed (11-13), but a general framework and systematic studies are still missing. One of the essential underlying questions, having both practical and conceptual impact, is whether any desired macroscopic structure can be assembled with a high yield, out of a given set of building blocks. Or are there fundamental constraints limiting the structures that can be effectively built?In this paper we address these general questions using the model system of DNA-coated particles, itself of considerable recent interest. We consider an isolated system of N spherical colloidal particles, each of which is isotropically coated with DNA strands to control interparticle interactions. At the colloidal scale, such interactions have a range that is much shorter than the size of the particles. The use of DNA labeling to control binding specificity was originally pioneered for assembling nanoparticles (14-17) into infinite crystals (18-24), where recently it was demonstrated that with two species with differing particle radii and DNA linker length a zoo of different crystal morphologies can be created (25). ...

“…DNA-guided nanoparticle colloidal crystallization provides remarkable control over the assembly of nanoparticles into superlattices (9,10), enabling the deliberate tailoring of crystal symmetry (9), lattice constant (11), and particle composition (12). Furthermore, structures with geometrically well-defined 3D crystal habits (10), when locked into the solid state via silica embedding procedures (13), open up potential applications in the field of optics.…”

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confidence: 99%

Directional emission from dye-functionalized plasmonic DNA superlattice microcavities

Park

Sun

et al. 2017

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Three-dimensional plasmonic superlattice microcavities, made from programmable atom equivalents comprising gold nanoparticles functionalized with DNA, are used as a testbed to study directional light emission. DNA-guided nanoparticle colloidal crystallization allows for the formation of micrometer-scale single-crystal bodycentered cubic gold nanoparticle superlattices, with dye molecules coupled to the DNA strands that link the particles together, in the form of a rhombic dodecahedron. Encapsulation in silica allows one to create robust architectures with the plasmonically active particles and dye molecules fixed in space. At the micrometer scale, the anisotropic rhombic dodecahedron crystal habit couples with photonic modes to give directional light emission. At the nanoscale, the interaction between the dye dipoles and surface plasmons can be finely tuned by coupling the dye molecules to specific sites of the DNA particle-linker strands, thereby modulating dye-nanoparticle distance (three different positions are studied). The ability to control dye position with subnanometer precision allows one to systematically tune plasmon-excition interaction strength and decay lifetime, the results of which have been supported by electrodynamics calculations that span length scales from nanometers to micrometers. The unique ability to control surface plasmon/ exciton interactions within such superlattice microcavities will catalyze studies involving quantum optics, plasmon laser physics, strong coupling, and nonlinear phenomena.DNA programmable assembly | directional emission | anisotropic 3D microcavity | nanoparticle surface plasmon | fluorescence enhancement M icrocavities are important photonic architectures that can be used to couple dipole emitters with optical modes and enhance light-matter interactions typically with long cavity lifetimes (high Q factors). They have been used to understand phenomena in cavity quantum electrodynamics (1, 2), and to enable molecular sensing (3) and lasing (4) technologies. In recent years, researchers have developed strategies for incorporating plasmonic nanostructures into microcavity structures to enhance light-matter interactions via strong light confinement (small mode volume, V), resulting in materials that are capable of plasmon lasing (5-7). These plasmonic microcavities exploit two different aspects of the architectures simultaneously: guided optical modes that resonate or scatter light (via the microcavity geometry) and near-field-driven optical confinement (via the metallic nanostructure). Such hybrid photonic structures are desirable because they can lead to high Q factors and strong light confinement within a single architecture, significantly enhancing light-matter interactions by a large cavity figure of merit, Q/V. However, most of the plasmonic microcavities have been limited to 1D or 2D microcavity geometries and plasmonic mode confinement (7) (metallic nanostructures) due to limitations in fabrication methods (6,8). Importantly, 3D counterparts of these 1D and 2D a...