Oligonucleotide Flexibility Dictates Crystal Quality in DNA‐Programmable Nanoparticle Superlattices

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Bottom-up assemblies of plasmonic nanoparticles exhibit unique optical effects such as tunable reflection, optical cavity modes, and tunable photonic resonances. Here, we compare detailed simulations with experiment to explore the effect of structural inhomogeneity on the optical response in DNA-gold nanoparticle superlattices. In particular, we explore the effect of background environment, nanoparticle polydispersity (>10%), and variation in nanoparticle placement (∼5%). At volume fractions less than 20% Au, the optical response is insensitive to particle size, defects, and inhomogeneity in the superlattice. At elevated volume fractions (20% and 25%), structures incorporating different sized nanoparticles (10-, 20-, and 40-nm diameter) each exhibit distinct far-field extinction and near-field properties. These optical properties are most pronounced in lattices with larger particles, which at fixed volume fraction have greater plasmonic coupling than those with smaller particles. Moreover, the incorporation of experimentally informed inhomogeneity leads to variation in far-field extinction and inconsistent electric-field intensities throughout the lattice, demonstrating that volume fraction is not sufficient to describe the optical properties of such structures. These data have important implications for understanding the role of particle and lattice inhomogeneity in determining the properties of plasmonic nanoparticle lattices with deliberately designed optical properties.T he rational arrangement of nanoparticles in multiple dimensions is a promising means for creating materials with novel properties not found in nature. Noble metal nanoparticles are interesting material building blocks due to their ability to amplify local fields by orders of magnitude and scatter light well below the diffraction limit. These efficient interactions with visible light are due to localized surface plasmon resonances (LSPRs), the collective oscillation of conduction electrons (1). Hierarchical arrangements of plasmonic nanoparticles have become the basis for colorimetric sensors (2, 3), subdiffraction limited waveguides (4), visible light metamaterials (5), and nanoscale lasing devices (6, 7), and the ability to adjust architecture in such materials has led to a wide variety of structures with tunable and unusual optical properties (8-12). Many of these technologies leverage the scalability and modularity of bottom-up assembly techniques, which use chemically synthesized colloidal nanoparticles as building blocks (13,14). Unfortunately, all nanoparticle assembly techniques result in materials with structural defects across multiple length scales, including imprecise particle placement, grain boundaries, and variation in crystallite size. In addition, the nanoparticles used in these systems are inherently inhomogeneous: varying in size, shape, and radius of curvature. Although the effects of inhomogeneity have been investigated at the individual nanoparticle level (15, 16), the effects of inhomogeneity on plasmonic assemblies are...

Section: Resultsmentioning

confidence: 94%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Defect tolerance and the effect of structural inhomogeneity in plasmonic DNA-nanoparticle superlattices

Ross

Blaber

et al. 2015

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“…If these results were extended to lower-symmetry particles (e.g., tetrahedra), one would imagine an even smaller zone of anisotropy and richer phase diagram, including the possibility of quasicrystal or diamond lattices (20,30,36,39). Due to the highly modular and programmable nature of nucleic acids, the location of these phase transitions can likely be tuned depending on the desired structure, via modulation of the design (e.g., flexibility) (40) or the type of nucleic acid used (e.g., locked nucleic acid or RNA) (41). Beyond defining the zone of anisotropy, this work also establishes a strategy to assemble nonspherical building blocks into a rich set of different phases based on the interplay of the particle and ligand structure.…”

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confidence: 99%

Exploring the zone of anisotropy and broken symmetries in DNA-mediated nanoparticle crystallization

O’Brien

Girard

Lin

et al. 2016

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In this work, we present a joint experimental and molecular dynamics simulations effort to understand and map the crystallization behavior of polyhedral nanoparticles assembled via the interaction of DNA surface ligands. In these systems, we systematically investigated the interplay between the effects of particle core (via the particle symmetry and particle size) and ligands (via the ligand length) on crystallization behavior. This investigation revealed rich phase diagrams, previously unobserved phase transitions in polyhedral crystallization behavior, and an unexpected symmetry breaking in the ligand distribution on a particle surface. To understand these results, we introduce the concept of a zone of anisotropy, or the portion of the phase space where the anisotropy of the particle is preserved in the crystallization behavior. Through comparison of the zone of anisotropy for each particle we develop a foundational roadmap to guide future investigations.ver the past decade, major advances in the control of nanoparticle interactions have led to powerful methods to assemble colloidal crystals (1-9). A high degree of structural control can be achieved in these methods if surface-bound ligands are used as nanoscale bonding elements to control the specificity, spacing, and strength of interactions. DNA has emerged as a particularly versatile ligand whose chemically and structurally defined nature can be used to program the symmetry, lattice parameters, and habit of colloidal crystals (1,2,7,(10)(11)(12)(13)(14)(15)(16)(17)(18)(19). The shape of the underlying nanoparticle influences the directionality of DNA interactions, which can result in correlated nanoparticle orientations and predictable crystal symmetries based on geometric considerations (7,13,16,19,20). However, predictive control can be lost if the DNA shell does not preserve the anisotropy of the particle core (13), and thus key questions pertain to (i) the phase space over which predictable directional interactions persist and (ii) the nature of the phase transitions that occur as the anisotropy of the particle disappears. Identifying this "zone of anisotropy" and the broken symmetries that form are critical to establish design rules for work with nonspherical particles and to develop nanostructured materials with controlled properties.Herein, we systematically investigate the phase space encoded by particle symmetry, particle size (L), and DNA length (D) to understand and map where directional interactions persist (Fig. 1). We show that particle symmetry dictates the crystalline states that can be accessed and how easily changes in L and D affect phase transitions between these states, which include transitions in Bravais lattice (i.e., the symmetry of how the particles are arranged within the unit cell) and particle orientation. The concepts introduced herein provide a roadmap to understand and predict particle crystallization behavior toward the construction of functional nanoparticle-based materials.To map the zone of anisotropy in DNA-mediated nan...

“…In these systems, however, the identity of the atom and its bonding behavior cannot be independently controlled, limiting our ability to tune material properties at will. In contrast, when a nanoparticle is modified with a dense shell of upright, oriented DNA, it can behave as a programmable atom equivalent (PAE) (1, 2) that can be used to synthesize diverse crystal structures with independent control over composition, scale, and lattice symmetry (3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14). The thermodynamic product of this crystallization process has been extensively studied by both experimental and theoretical means, and thus a series of design rules has been proposed and validated with a simple geometric model known as the complementary contact model (CCM).…”

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Importance of the DNA “bond” in programmable nanoparticle crystallization

Macfarlane

Thaner

Brown

et al. 2014

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If a solution of DNA-coated nanoparticles is allowed to crystallize, the thermodynamic structure can be predicted by a set of structural design rules analogous to Pauling's rules for ionic crystallization. The details of the crystallization process, however, have proved more difficult to characterize as they depend on a complex interplay of many factors. Here, we report that this crystallization process is dictated by the individual DNA bonds and that the effect of changing structural or environmental conditions can be understood by considering the effect of these parameters on free oligonucleotides. Specifically, we observed the reorganization of nanoparticle superlattices using time-resolved synchrotron small-angle X-ray scattering in systems with different DNA sequences, salt concentrations, and densities of DNA linkers on the surface of the nanoparticles. The agreement between bulk crystallization and the behavior of free oligonucleotides may bear important consequences for constructing novel classes of crystals and incorporating new interparticle bonds in a rational manner.DNA materials | self assembly | nanostructure M aterials scientists have accomplished much by studying the way atoms and molecules crystallize. In these systems, however, the identity of the atom and its bonding behavior cannot be independently controlled, limiting our ability to tune material properties at will. In contrast, when a nanoparticle is modified with a dense shell of upright, oriented DNA, it can behave as a programmable atom equivalent (PAE) (1, 2) that can be used to synthesize diverse crystal structures with independent control over composition, scale, and lattice symmetry (3-14). The thermodynamic product of this crystallization process has been extensively studied by both experimental and theoretical means, and thus a series of design rules has been proposed and validated with a simple geometric model known as the complementary contact model (CCM). These rules allow one to predict the thermodynamically favored structure as the arrangement of particles that maximizes complementary contacts and therefore DNA hybridization (2, 6). These efforts have been very successful in predicting the thermodynamically favored product; recent studies have even demonstrated that PAEs can form single-crystal Wulff polyhedra that are analogous to those formed in atomic systems with the same crystallographic symmetry (15). However, the fact that there is a crystalline thermodynamic product does not mean that any choice of DNA and nanoparticles will result in crystalline systems in practice (3, 4). For example, crystallization has been observed for a relatively narrow class of PAEs (16) and in a manner that is primarily dependent upon the length of the DNA linker and temperature at which assembly occurs (8). Thus, absent from our understanding of these systems is a connection between the crystallization process and the properties of the DNA bonds that form the foundation of these structures.Here, we study the crystallization process and find t...