DNA‐Linked Nanoparticle Building Blocks for Programmable Matter

Abstract

Programmable matter is a distributed system of agents that act cooperatively to configure themselves into arbitrary shapes with arbitrary functions. Molecular self-assembled structures containing many nanoparticles are candidates for programmable matter. Programmability implies that system designers are able to control the properties of assembly products. The system should be able to assemble into arbitrary, anisotropic shapes, like an electronic circuit, with the capability of incorporating different materials at specific locations within the structure. Defects or errors should be minimized, and 3D assembly should be possible. In self-assembly, component parts, or building blocks, interact locally to produce a coherent and organized whole. At the molecular level, the interactions are determined by “patches” that react between building blocks. Frequently, the assemblies exhibit collective properties that are distinct from those of their constituent components. These properties often depend upon the shape of the structure. Thus, the difficulty of programmability is really the difficulty of controlling the shape of resulting nanostructures. The ability to program the shape of a final assembly is computationally difficult and subject to frequent errors. Nevertheless, through careful design and implementation of building blocks, desired shapes and properties might be achieved. To maximize programmability (i.e., control), there should be a large number of types of patches available. Otherwise, there is no variety of interactions to assemble complicated shapes. The placement and relative orientation of patches on the surface of the building block should be controlled. Different types of patches should be able to be placed on the same building block to diversify the shapes available. Finally, the chemistry for patch conjugation to the building block should be relatively simple and sustainable, and it should be able to be used with a variety of materials. Because of its unique molecular recognition properties, structural features, and ease of manipulation, beginning with seminal work by Seeman and Chen, DNA has been considered as a promising material to achieve programmable assembly of nanostructures. Nanoparticle (NP) building blocks with different surface functionalities for DNA linkers have been reported. DNA computing verified the programmability of DNA-based nanotechnology and, in fact, demonstrated that DNA self-assembly was computationuniversal. DNA programmability has demonstrated the ability to assemble a variety of shapes 9] and, when NPs are incorporated, to control the position of NPs in linear, 2D, and 3D assemblies, including those based upon origami techniques. 10] Nevertheless, the rational self-assembly of functional structures with arbitrary shapes in all dimensions and at all scales that can incorporate many different NPs into a variety of final geometries remains difficult to attain. Herein we present a strategy to control the number, placement, and relative orientation of DNA linkers on the surface of a colloidal NP building block to maximize its programmability and realize enhanced control over the shape and function of final self-assembled structures. Figure 1 shows a schematic illustration of the assembly sequence to produce the DNA-linked colloidal gold NP building blocks (termed nBLOCKs). A measure of control was achieved by the sequential ligand replacement approach and stiff DNA linkers, which were shorter than the persistence length of double-stranded DNA. In the assembly reaction, the electrostatic repulsions and steric hindrances of DNA molecules influence the layout of DNA on a NP. The net charge of DNA at a pH value above its isoelectric point (i.e., pH 5) is negative, so it would tend to position on a NP to minimize its mutual electrostatic repulsions, in analogy to the valence shell electron pair repulsion model, thus contributing to the molecular geometry. Also, mutual steric hindrance could be another factor to further constrain the overall geometry, particularly using small NPs. In our strategy, a Au NP is functionalized by DNA strand by strand: for example, a NP with one DNA strand is the starting material for the second DNA attachment, a NP with two DNA strands is the starting material for the third DNA attachment, etc. (Figure 1; see Figure S1 in the Supporting Information). With this constraint, the position of DNA attachment would be chosen to minimize the electrostatic and steric interactions with existing DNA on the NP, yielding the optimal arrangement of DNA on a NP with up to sixfold symmetry, that is, linear (one and two DNA strands), T-shaped (three DNA strands), square planar (four DNA strands), square pyramidal (five DNA [*] Prof. J.-W. Kim, Dr. J.-H. Kim Bio/Nano Technology Laboratory Department of Biological and Agricultural Engineering and Institute for Nanoscience and Engineering University of Arkansas, Fayetteville, AR 72701 (USA) E-mail: jwkim@uark.edu