Controlling the Lattice Parameters of Gold Nanoparticle FCC Crystals with Duplex DNA Linkers

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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...

Section: Significancementioning

confidence: 99%

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confidence: 99%

Importance of the DNA “bond” in programmable nanoparticle crystallization

Macfarlane

Thaner

Brown

et al. 2014

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“…With such methods, one can make architectures with well-defined lattice parameters (6)(7)(8)(9)(10)(11)(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).…”

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confidence: 99%

DNA-mediated engineering of multicomponent enzyme crystals

Brodin

Auyeung

Mirkin

2015

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127

138

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...

“…Despite the success of these theories in providing insights into the ground-state free energy, they are generally limited to enumerating interactions at the twoparticle level. They also ignore any entropic effects relevant to this self-assembly process (9)(10)(11)(12)(17)(18)(19)(20)(21). Molecular dynamics simulations avoid these difficulties and extend this analysis to superlattice self-assembly so as to provide a detailed understanding of the effects of kinetics (13), DNA sequence (14), and electrostatics (15,16,22) on lattice stability.…”

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confidence: 99%

Stoichiometric control of DNA-grafted colloid self-assembly

Venkatasubramanian

Kumar

et al. 2015

There has been considerable interest in understanding the selfassembly of DNA-grafted nanoparticles into different crystal structures, e.g., CsCl, AlB 2 , and Cr 3 Si. Although there are important exceptions, a generally accepted view is that the right stoichiometry of the two building block colloids needs to be mixed to form the desired crystal structure. To incisively probe this issue, we combine experiments and theory on a series of DNA-grafted nanoparticles at varying stoichiometries, including noninteger values. We show that stoichiometry can couple with the geometries of the building blocks to tune the resulting equilibrium crystal morphology. As a concrete example, a stoichiometric ratio of 3:1 typically results in the Cr 3 Si structure. However, AlB 2 can form when appropriate building blocks are used so that the AlB 2 standard-state free energy is low enough to overcome the entropic preference for Cr 3 Si. These situations can also lead to an undesirable phase coexistence between crystal polymorphs. Thus, whereas stoichiometry can be a powerful handle for direct control of lattice formation, care must be taken in its design and selection to avoid polymorph coexistence. colloidal interactions | functional particle | superlattice engineering | molecular design | modeling O ver the past several decades, there has been increasing interest in programmable self-assembly for materials fabrication. Rather than using traditional methods of shaping bulk materials, the emerging concept is to focus on the design of nanoscale building blocks that self-organize into desired structures. This "design" philosophy has led to the development of novel techniques such as DNA origami, where specific interactions are used to direct the folding of oligonucleotides into a variety of assemblies (1-6). Another vein of research is to focus on the directed assembly of DNA-grafted nanoparticles (DNA-NPs) into superlattices with well-defined crystal morphologies. These systems have unusual photonic and plasmonic properties with applications in spectroscopy, surface imaging, and optical sensors (7,8).A large number of theories and simulations have been developed to delineate the hybridization interactions between two interacting DNA-NPs (9-20). Despite the success of these theories in providing insights into the ground-state free energy, they are generally limited to enumerating interactions at the twoparticle level. They also ignore any entropic effects relevant to this self-assembly process (9-12, 17-21). Molecular dynamics simulations avoid these difficulties and extend this analysis to superlattice self-assembly so as to provide a detailed understanding of the effects of kinetics (13), DNA sequence (14), and electrostatics (15, 16, 22) on lattice stability. We particularly highlight the work of Li et al. (16), who explicitly considered the role of stoichiometry on the crystal morphology formed. They selected several stoichiometries, i.e., 1:1, 2:1, and 3:1. We focus here on one specific case, 2:1. As the size and linker ratios of ...