Parallel molecular computations of pairwise exclusive-or (XOR) using DNA "string tile" self-assembly

Self-assembling DNA nanostructures are an efficient means of executing parallel molecular computations. However, previous experimental demonstrations of computations by DNA tile self-assembly only allowed for one set of distinct input to be processed at a time. Here, we report the multibit, parallel computation of pairwise exclusive-or (XOR) using DNA "string tile" self-assembly. A set of DNA tiles encoding the truth table for the XOR logical operation was constructed. Parallel tile self-assembly and ligation led to the formation of reporter DNA strands which encoded both the input and the output of the computations. These reporter strands provided a molecular look-up table containing all possible pairwise XOR calculations up to a certain input size. The computation was readout by sequencing the cloned reporter strands. This is the first experimental demonstration of a parallel computation by DNA tile self-assembly in which a large number of distinct input were simultaneously processed.     

Subtractive assembly of DNA nanoarchitectures driven by fuel strand displacement

Herein we demonstrate that flexible DNA architectures with larger cavities can be efficiently constructed by first assembling a relatively more rigid DNA tile architecture and subsequently subtracting a center tile through fuel strand displacement; such structures are otherwise difficult to obtain if the center tile is missing in the beginning, proving a new strategy for DNA self-assembly.     

Direct atomic force microscopy observation of DNA tile crystal growth at the single-molecule level

While the theoretical implications of models of DNA tile self-assembly have been extensively researched and such models have been used to design DNA tile systems for use in experiments, there has been little research testing the fundamental assumptions of those models. In this paper, we use direct observation of individual tile attachments and detachments of two DNA tile systems on a mica surface imaged with an atomic force microscope (AFM) to compile statistics of tile attachments and detachments. We show that these statistics fit the widely used kinetic Tile Assembly Model and demonstrate AFM movies as a viable technique for directly investigating DNA tile systems during growth rather than after assembly.     

Direct visualization of transient thermal response of a DNA origami

The DNA origami approach enables the construction of complex objects from DNA strands. A fundamental understanding of the kinetics and thermodynamics of DNA origami assembly is extremely important for building large DNA structures with multifunctionality. Here both experimental and theoretical studies of DNA origami melting were carried out in order to reveal the reversible association/disassociation process. Furthermore, by careful control of the temperature cycling via in situ thermally controlled atomic force microscopy, the self-assembly process of a rectangular DNA origami tile was directly visualized, unveiling key mechanisms underlying their structural and thermodynamic features.     

Single-chain antibodies against DNA aptamers for use as adapter molecules on DNA tile arrays in nanoscale materials organization

Complex DNA nanostructures have been developed as structural components for the construction of nanoscale objects. Recent advances have enabled self-assembly of organized DNA nanolattices and their use in patterning functional bio-macromolecules and other nanomaterials. Adapter molecules that bind specifically to both DNA lattices and nanomaterials would be useful components in a molecular construction kit for patterned nanodevices. Herein we describe the selection from phage display libraries of single-chain antibodies (scFv) for binding to a specific DNA aptamer and their development as adapter molecules for nanoscale construction. We demonstrate the decoration of various DNA tile structures with aptamers and show binding of the selected single-chain antibody as well as the self-assembly of mixed DNA-protein biomolecular lattices.     

A study of DNA tube formation mechanisms using 4-, 8-, and 12-helix DNA nanostructures

This paper describes the design and characterization of a new family of rectangular-shaped DNA nanostructures (DNA tiles) containing 4, 8, and 12 helices. The self-assembled morphologies of the three tiles were also investigated. The motivation for designing this set of DNA nanostructures originated from the desire to produce DNA lattices containing periodic cavities of programmable dimensions and to investigate the mechanism of DNA tube formation. Nine assembly scenarios have been investigated through the combination of the three different tiles and three sticky end association strategies. Imaging by atomic force microscopy (AFM) revealed self-assembled structures with varied cavity sizes, lattice morphologies, and orientations. Six samples show only tube formation, two samples show both 2D lattices (>2 microm) and tubes, and one sample shows only 2D lattices without tubes. We found that a lower tile dimensional anisotropy, weaker connection, and corrugated design favor the large 2D array formation, while the opposite (higher tile anisotropy, stronger connection, and uncorrugated design) favors tube formation. We discuss these observations in terms of an energy balance at equilibrium and the kinetic competition between diffusion-limited lateral lattice growth versus fluctuation of the lattice to form tubes at an early stage of the assembly. The DNA nanostructures and their self-assembly demonstrated herein not only provide a new repertoire of scaffolds to template the organization of nanoscale materials, but may also provide useful information for investigating other self-assembly systems.     

A master-equation approach to simulate kinetic traps during directed self-assembly

Robust directed self-assembly of non-periodic nanoscale structures is a key process that would enable various technological breakthroughs. The dynamic evolution of directed self-assemblies towards structures with desired geometries is governed by the rugged potential energy surface of nanoscale systems, potentially leading the system to kinetic traps. To study such phenomena and to set the framework for the directed self-assembly of nanoparticles towards structures with desired geometries, the development of a dynamic model involving a master equation to simulate the directed self-assembly process is presented. The model describes the probability of each possible configuration of a fixed number of nanoparticles on a domain, including parametric sensitivities that can be used for optimization, as a function of time during self-assembly. An algorithm is presented that solves large-scale instances of the model with linear computational complexity. Case studies illustrate the influence of several degrees of freedom on directed self-assembly. A design approach that systematically decomposes the ergodicity of the system to direct self-assembly of a targeted configuration with high probability is illustrated. The prospects for extending such an approach to larger systems using coarse graining techniques are also discussed.     

DNA-templated three-branched nanostructures for nanoelectronic devices

Three-branched DNA molecules have been designed and assembled from oligonucleotide components. These nucleic acid constructs contain double- and single-stranded regions that control the hybridization behavior of the assembly. Specific localization of a single streptavidin molecule at the center of the DNA complex has been investigated as a model system for the directed placement of nanostructures. Highly selective silver and copper metallization of the DNA template has also been characterized. Specific hybridization of these DNA complexes to oligonucleotide-coupled nanostructures followed by metallization should provide a bottom-up self-assembly route for the fabrication and characterization of discrete three-terminal nanodevices.     

Constructing Large 2D Lattices Out of DNA-Tiles

The predictable nature of deoxyribonucleic acid (DNA) interactions enables assembly of DNA into almost any arbitrary shape with programmable features of nanometer precision. The recent progress of DNA nanotechnology has allowed production of an even wider gamut of possible shapes with high-yield and error-free assembly processes. Most of these structures are, however, limited in size to a nanometer scale. To overcome this limitation, a plethora of studies has been carried out to form larger structures using DNA assemblies as building blocks or tiles. Therefore, DNA tiles have become one of the most widely used building blocks for engineering large, intricate structures with nanometer precision. To create even larger assemblies with highly organized patterns, scientists have developed a variety of structural design principles and assembly methods. This review first summarizes currently available DNA tile toolboxes and the basic principles of lattice formation and hierarchical self-assembly using DNA tiles. Special emphasis is given to the forces involved in the assembly process in liquid-liquid and at solid-liquid interfaces, and how to master them to reach the optimum balance between the involved interactions for successful self-assembly. In addition, we focus on the recent approaches that have shown great potential for the controlled immobilization and positioning of DNA nanostructures on different surfaces. The ability to position DNA objects in a controllable manner on technologically relevant surfaces is one step forward towards the integration of DNA-based materials into nanoelectronic and sensor devices.     

DNA directed self-assembly of anisotropic plasmonic nanostructures

Programmable positioning of one-dimensional (1D) gold nanorods (AuNRs) was achieved by DNA directed self-assembly. AuNR dimer structures with various predetermined inter-rod angles and relative distances were constructed with high efficiency. These discrete anisotropic metallic nanostructures exhibit unique plasmonic properties, as measured experimentally and simulated by the discrete dipole approximation method.     

Design and construction of double-decker tile as a route to three-dimensional periodic assembly of DNA

DNA is a useful material for nanoscale construction. Due to highly specific Watson-Crick base pairing, the DNA sequences can be designed to form small tiles or origami. Adjacent helices in such nanostructures are connected via Holliday junction-like crossovers. DNA tiles can have sticky ends which can then be programmed to form large one-dimensional and two-dimensional periodic lattices. Recently, a three-dimensional DNA lattice has also been constructed. Here we report the design and construction of a novel DNA cross tile, called the double-decker tile. Its arms are symmetric and have four double helices each. Using its sticky ends, large two-dimensional square lattices have been constructed which are on the order of tens of micrometers. Furthermore, it is proposed that the sticky ends of the double-decker tile can be programmed to form a three-dimensional periodic lattice with large cavities that could be used as a scaffold for precise positioning of molecules in space.     

Effect of DNA hairpin loops on the twist of planar DNA origami tiles

The development of scaffolded DNA origami, a technique in which a long single-stranded viral genome is folded into arbitrary shapes by hundreds of short synthetic oligonucleotides, represents an important milestone in DNA nanotechnology. Recent findings have revealed that two-dimensional (2D) DNA origami structures based on the original design parameters adopt a global twist with respect to the tile plane, which may be because the conformation of the constituent DNA (10.67 bp/turn) deviates from the natural B-type helical twist (10.4 bp/turn). Here we aim to characterize the effects of DNA hairpin loops on the overall curvature of the tile and explore their ability to control, and ultimately eliminate any unwanted curvature. A series of dumbbell-shaped DNA loops were selectively displayed on the surface of DNA origami tiles with the expectation that repulsive interactions among the neighboring dumbbell loops and between the loops and the DNA origami tile would influence the structural features of the underlying tiles. A systematic, atomic force microscopy (AFM) study of how the number and position of the DNA loops influenced the global twist of the structure was performed, and several structural models to explain the results were proposed. The observations unambiguously revealed that the first generation of rectangular shaped origami tiles adopt a conformation in which the upper right (corner 2) and bottom left (corner 4) corners bend upward out of the plane, causing linear superstructures attached by these corners to form twisted ribbons. Our experimental observations are consistent with the twist model predicted by the DNA mechanical property simulation software CanDo. Through the systematic design and organization of various numbers of dumbbell loops on both surfaces of the tile, a nearly planar rectangular origami tile was achieved.     

Selective, controllable, and reversible aggregation of polystyrene latex microspheres via DNA hybridization

The directed three-dimensional self-assembly of microstructures and nanostructures through the selective hybridization of DNA is the focus of great interest toward the fabrication of new materials. Single-stranded DNA is covalently attached to polystyrene latex microspheres. Single-stranded DNA can function as a sequence-selective Velcro by only bonding to another strand of DNA that has a complementary sequence. The attachment of the DNA increases the charge stabilization of the microspheres and allows controllable aggregation of microspheres by hybridization of complementary DNA sequences. In a mixture of microspheres derivatized with different sequences of DNA, microspheres with complementary DNA form aggregates, while microspheres with noncomplementary sequences remain suspended. The process is reversible by heating, with a characteristic "aggregate dissociation temperature" that is predictably dependent on salt concentration, and the evolution of aggregate dissociation with temperature is observed with optical microscopy.     

环糊精与表面活性剂主客体作用诱导的金纳米棒可控自组装

The self-assembly of colloidal nanocrystals has emerged as a powerful strategy for the bottom-up fabrication of functional materials and nanodevices. Recently, the self-assembly of gold nanorods (GNRs) has attracted significant attention because of their unique plasmonic properties, but the realization of their adjustable self-assembly of GNRs through facile and effective approaches remains challenging. In this work, the controllable self-assembly of GNRs in aqueous solution was realized through the host-guest interactions of cyclodextrins (CDs) and the cetyltrimethylammonium bromide (CTAB) molecules adsorbed on the surface of the GNRs. The self-assembly of GNRs was readily achieved by the addition of aqueous α-CD solutions with varied concentrations into aqueous dispersions of CTAB-stabilized GNRs. At a relatively low α-CD concentration, slow aggregation of the GNRs occurred, resulting in their side-by-side assembly. This was revealed by the blue shift of the longitudinal surface plasmon resonance (LSPR) band in the absorption spectra and confirmed by transmission electron microscopy (TEM) observations. On the other hand, when a higher concentration of α-CD was added, fast aggregation of the GNRs occurred, resulting in their end-to-end assembly. This was revealed by the red shift in the LSPR band together with the TEM observations. If β-CD was employed instead of α-CD, the self-assembly of GNRs could also be induced, although a relatively higher concentration of β-CD was required to achieve the extent of aggregation similar to that induced by α-CD, indicating that the supramolecular host–guest interaction between CDs and the surfactant CTAB was crucial to the directed self-assembly of GNRs. Furthermore, the α-CD-induced assembly was inhibited on addition of excess CTAB, confirming that the supramolecular interaction of α-CD and CTAB played a key role in directing the self-assembly of the GNRs. Based on these experimental results, a possible mechanism for the α-CD-induced self-assembly of GNRs was proposed as follows: at a lower α-CD concentration, the gradual formation of the host-guest inclusion complex α-CD/CTAB led to the partial replacement of the highly charged CTAB bilayers adsorbed on the GNRs by the less charged complex, which resulted in a slow side-by-side assembly of the GNRs; at a higher α-CD concentration, the CTAB bilayers were quickly replaced by the α-CD/CTAB complex, and the CTAB molecules adsorbed at both ends of the GNRs were almost completely replaced, resulting in a fast end-to-end assembly of the GNRs. Additionally, on the basis of the hydrolysis of α-cyclodextrin catalyzed by α-amylase, the self-assembly of GNRs directed by the host-guest interaction could be used to realize the feasible detection of α-amylase in solutions. This self-assembly strategy mediated by the host-guest interaction may be extendable to other colloidal systems involving surfactants adsorbed on the surface of nanoparticles, and may open new avenues for the controllable self-assembly of non-spherical nanoparticles.     

Nucleic acid functionalized graphene for biosensing

There is immense demand for complex nanoarchitectures based on graphene nanostructures in the fields of biosensing or nanoelectronics. DNA molecules represent the most versatile and programmable recognition element and can provide a unique massive parallel assembly strategy with graphene nanomaterials. Here we demonstrate a facile strategy for covalent linking of single stranded DNA (ssDNA) to graphene using carbodiimide chemistry and apply it to genosensing. Since graphenes can be prepared by different methods and can contain various oxygen containing groups, we thoroughly investigated the utility of four different chemically modified graphenes for functionalization by ssDNA. The materials were characterized in detail and the different DNA functionalized graphene platforms were then employed for the detection of DNA hybridization and DNA polymorphism by using impedimetric methods. We believe that our findings are very important for the development of novel devices that can be used as alternatives to classical techniques for sensitive and fast DNA analysis. In addition, covalent functionalization of graphene with ssDNA is expected to have broad implications, from biosensing to nanoelectronics and directed, DNA programmable, self-assembly.     

Self‐Assembly of Complex DNA Tessellations by Using Low‐Symmetry Multi‐arm DNA Tiles

Modular DNA tile‐based self‐assembly is a versatile way to engineer basic tessellation patterns on the nanometer scale, but it remains challenging to achieve high levels of structural complexity. We introduce a set of general design principles to create intricate DNA tessellations by employing multi‐arm DNA motifs with low symmetry. We achieved two novel Archimedean tiling patterns, (4.8.8) and (3.6.3.6), and one pattern with higher‐order structures beyond the complexity observed in Archimedean tiling. Our success in assembling complicated DNA tessellations demonstrates the broad design space of DNA structural motifs, enriching the toolbox of DNA tile‐based self‐assembly and expanding the complexity boundaries of DNA tile‐based tessellation.     

DNA折纸术研究进展

DNA折纸术是近年来提出的一种全新的DNA自组装的方法,是DNA纳米技术与DNA自组装领域的一个重大进展。与传统的DNA自组装技术不同,DNA折纸术通过将一条长的DNA单链（通常为基因组DNA）与一系列经过设计的短DNA片段进行碱基互补,能够可控地构造出高度复杂的纳米图案或结构,在新兴的纳米领域中具有广泛的潜在应用。本文在介绍DNA折纸术相关原理的基础上,就DNA折纸术的起源、发展及其在DNA芯片、纳米元件与材料等领域的潜在应用进行了概述,探讨了DNA折纸术未来可能的发展方向。     

Kinetics of receptor directed assembly of multisegment nanowires

We demonstrate the receptor directed end-to-end assembly of multisegment Au/Ni/Au nanowires under agitation in ethanol. The gold end-segments were functionalized with biotin-terminated thiol thereby restricting aggregation to end-to-end attachment via an avidin linkage. On mixing biotin-terminated nanowires with avidin-terminated nanowires, the average chain length is shown to increase linearly with time. The rate constant was independent of the nanowire concentration. Kinetic Monte Carlo simulations were used to model the self-assembly process, and we show that the directed end-to-end assembly of nanowires is similar to the polycondensation of linear polymers.     

Template-directed self-assembly of 10-microm-sized hexagonal plates

This article presents a strategy for the fabrication of ordered microstructures using concepts of design inspired by molecular self-assembly and template-directed synthesis. The self-assembling components are 4-microm-thick hexagonal metal plates having sides 10 microm in length ("hexagons"), and each template consists of a 4-microm-thick circular metal plate surrounding a central cavity, the perimeter of which is complementary in shape to the external edges of a two-dimensional, close-packed array of hexagons. The hexagons and templates (collectively, "pieces") were fabricated via standard procedures and patterned into hydrophobic and hydrophilic regions using self-assembled monolayers (SAMs). Templated self-assembly occurs in water through capillary interactions between thin films of a nonpolar liquid adhesive coating the hydrophobic faces of the pieces. The hexagons tile the cavities enclosed by the templates, and the boundaries of the cavities determine the sizes and shapes of the assemblies. Curing the adhesive with ultraviolet light furnishes mechanically stable arrays having well-defined morphologies. By allowing control over the structures of the resulting aggregates, this work represents a step toward the development of practical methods for microfabrication based on self-assembly.