Assembly and organization processes in DNA-directed colloidal crystallization

Abstract

We present an analysis of the key steps involved in the DNAdirected assembly of nanoparticles into crystallites and polycrystalline aggregates. Additionally, the rate of crystal growth as a function of increased DNA linker length, solution temperature, and self-complementary versus non-self-complementary DNA linker strands (1-versus 2-component systems) has been studied. The data show that the crystals grow via a 3-step process: an initial ''random binding'' phase resulting in disordered DNA-AuNP aggregates, followed by localized reorganization and subsequent growth of crystalline domain size, where the resulting crystals are well-ordered at all subsequent stages of growth.DNA materials ͉ SAXS ͉ self assembly T he chemical and physical properties of most materials are determined by the placement of individual atoms relative to one another (1-4). These atom-atom interactions include forces such as covalent and ionic bonds, Van der Waals forces and London dispersion forces. However, in the field of nanomaterials, the length scales of particle assembly are significantly larger and the assembly process is governed by a more complicated set of interactions (5-7). The tailorable arrangement of nanoscale materials through directed-mechanisms has proven to be the most practical method to create ordered arrangements of nanoparticles in solution (8-15); crystalline nanoparticle aggregates have potential implications for the development of materials with unique plasmonic (16, 17), photonic (18, 19), electrical (20), and magnetic properties (21). Previous strategies developed to create well-ordered nanoscale assemblies have used electrostatic interactions (11, 12), hydrogen bonding networks (10, 13), and peptide recognition properties (9). Over a decade ago, we introduced the concept of synthetically programmable particle assembly through the use of DNA and polyvalent oligonucleotide nanoparticle conjugates (22). Recently, we (23,24) and the Gang group (25) independently used these principles to construct highly-ordered nanoparticle crystallites via DNA hybridization, where crystal type and lattice parameters can be programmed through design of DNA linker.The formation of these crystals involves multiple types of molecular interactions that are highly dependent and predictable based on the DNA base sequence (22,(26)(27)(28), where the hybridization of the DNA linkers drives the crystallization process. Moreover, the ultimate structure formed is typically the one that maximizes the number of hybridization events, and therefore, if enough thermal energy is provided, the system will typically equilibrate to this structure (23,25,29,30). Indeed, only highly-ordered crystalline aggregates present the thermodynamically most stable arrangement of nanoparticles, because they allow for a maximum of nearestneighbor complementary DNA interactions.Previous work has shown that the complexity of the nanoparticle systems studied thus far necessitates significant thermal annealing to create the thermodynamically favorable crystal structu...

Importance of the DNA “bond” in programmable nanoparticle crystallization

“…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).…”

“…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.…”

Clicking DNA to gold nanoparticles: poly-adenine-mediated formation of monovalent DNA-gold nanoparticle conjugates with nearly quantitative yield

“…4,41 It is also envisioned that these DNA-AuNPs can be further exploited to assemble high-ordered structures, for example, hydrogel or crystals with better control and homogeneity. [14][15][16] In addition, because we have obtained high yields of well-defined and uniform Au nanostructures, we expect that this system holds great promise for DNAregulated plasmonic applications 42,43 and biomolecular imaging. [44][45][46][47] …”

“…[9][10][11][12][13] During the past two decades, we have witnessed dramatic advances in such functional nanosystems, including the formation of molecule-like crystal structures and the assembly of dynamic nanodevices. [14][15][16][17][18] Despite the rapid progress, most of these applications used polyvalent DNA-AuNP conjugates without knowing the exact number of loaded DNA strands. Although polyvalent DNA-AuNPs possess unique merits, such as signal amplification and cellular internalization; [19][20][21] such inaccuracy may introduce potential imperfectness in the artificially constructed nanosystems.…”

Introduction to the Molecular Recognition and Self-Assembly Special Feature

“…The article by Macfarlane et al (14), ''DNA-directed colloidal crystal formation: Assembly and reorganization,'' applies the recognition involved in dsDNA to the directed assembly of nanoparticles into aggregates. These are used to elucidate processes involved in crystal growth and reveal the mechanism of growth for DNA gold nanoparticles.…”