Environment-Resistant DNA Origami Crystals Bridged by Rigid DNA Rods with Adjustable Unit Cells

Crystalline Assemblies of DNA Nanostructures and Their Functional Properties

Self-assembly presents a remarkable approach for creating intricate structures by positioning nanomaterials in precise locations, with control over molecular interactions. For example, material arrays with interplanar distances similar to the wavelength of light can generate structural color through complex interactions like scattering, diffraction, and interference. Moreover, enzymes, plasmonic nanoparticles, and luminescent materials organized in periodic lattices are envisioned to create functional materials with various applications. Focusing on structural DNA nanotechnology, here, we summarized the recent developments of two- and three-dimensional lattices made purely from DNA nanostructures. We review DNA-based monomer design for different lattices, guest molecule assembly, and inorganic material coating techniques and discuss their functional properties and potential applications in photonic crystals, nanoelectronics, and bioengineering as well as future challenges and perspectives.

Fast synthesis of DNA origami single crystals at room temperature

Structural DNA nanotechnology makes the programmable design and assembly of DNA building blocks into user-defined microstructures feasible. However, the formation and further growth of these microstructures requires slow heat treatment in precise instruments, as otherwise amorphous aggregates result. Here, we used an organic solute, urea, as the catalyst for the crystallization of DNA origami building blocks to achieve the fast synthesis of DNA origami single crystals with a cubic Wulff shape at room temperature. The ordered assemblies can be formed within 4 hours at room temperature, which further grew into cubic microcrystals with an average size of about 5 micrometers within 2 days. Furthermore, the phase diagram provides an inverse logic that allows users to proactively customize the melting temperature (T m) of crystallization according to the target temperature conditions, rather than requiring de novo design of DNA sequences or painstakingly difficult trial-and-error attempts. On this basis, even under random fluctuating outdoor temperature conditions, DNA origami crystals can still grow and maintain high quality and high yield comparable to those of crystals synthesized in precise instruments, creating a basis for the development of adaptive self-assemblies and the industrialization of functional DNA microstructures.

Diamond-lattice photonic crystals assembled from DNA origami

Colloidal self-assembly allows rational design of structures on the micrometer and submicrometer scale. One architecture that can generate complete three-dimensional photonic bandgaps is the diamond cubic lattice, which has remained difficult to realize at length scales comparable with the wavelength of visible or ultraviolet light. In this work, we demonstrate three-dimensional photonic crystals self-assembled from DNA origami that act as precisely programmable patchy colloids. Our DNA-based nanoscale tetrapods crystallize into a rod-connected diamond cubic lattice with a periodicity of 170 nanometers. This structure serves as a scaffold for atomic-layer deposition of high-refractive index materials such as titanium dioxide, yielding a tunable photonic bandgap in the near-ultraviolet.

DNA-Based Gold Nanoparticle Assemblies: From Structure Constructions to Sensing Applications

Gold nanoparticles (Au NPs) have become one of the building blocks for superior assembly and device fabrication due to the intrinsic, tunable physical properties of nanoparticles. With the development of DNA nanotechnology, gold nanoparticles are organized in a highly precise and controllable way under the mediation of DNA, achieving programmability and specificity unmatched by other ligands. The successful construction of abundant gold nanoparticle assembly structures has also given rise to the fabrication of a wide range of sensors, which has greatly contributed to the development of the sensing field. In this review, we focus on the progress in the DNA-mediated assembly of Au NPs and their application in sensing in the past five years. Firstly, we highlight the strategies used for the orderly organization of Au NPs with DNA. Then, we describe the DNA-based assembly of Au NPs for sensing applications and representative research therein. Finally, we summarize the advantages of DNA nanotechnology in assembling complex Au NPs and outline the challenges and limitations in constructing complex gold nanoparticle assembly structures with tailored functionalities.

Exploring the Potential of Three-Dimensional DNA Crystals in Nanotechnology: Design, Optimization, and Applications

DNA has been used as a robust material for the building of a variety of nanoscale structures and devices owing to its unique properties. Structural DNA nanotechnology has reported a wide range of applications including computing, photonics, synthetic biology, biosensing, bioimaging, and therapeutic delivery, among others. Nevertheless, the foundational goal of structural DNA nanotechnology is exploiting DNA molecules to build three-dimensional crystals as periodic molecular scaffolds to precisely align, obtain, or collect desired guest molecules. Over the past 30 years, a series of 3D DNA crystals have been rationally designed and developed. This review aims to showcase various 3D DNA crystals, their design, optimization, applications, and the crystallization conditions utilized. Additionally, the history of nucleic acid crystallography and potential future directions for 3D DNA crystals in the era of nanotechnology are discussed.

Programming the morphology of DNA origami crystals by magnesium ion strength

Harnessing the programmable nature of DNA origami for controlling structural features in crystalline materials affords opportunities to bring crystal engineering to a remarkable level. However, the challenge of crystallizing a single type of DNA origami unit into varied structural outcomes remains, given the requirement for specific DNA designs for each targeted structure. Here, we show that crystals with distinct equilibrium phases and shapes can be realized using a single DNA origami morphology with an allosteric factor to modulate the binding coordination. As a result, origami crystals undergo phase transitions from a simple cubic lattice to a simple hexagonal (SH) lattice and eventually to a face-centered cubic (FCC) lattice. After selectively removing internal nanoparticles from DNA origami building blocks, the body-centered tetragonal and chalcopyrite lattice are derived from the SH and FCC lattices, respectively, revealing another phase transition involving crystal system conversions. The rich phase space was realized through the de novo synthesis of crystals under varying solution environments, followed by the individual characterizations of the resulting products. Such phase transitions can lead to associated transitions in the shape of the resulting products. Hexagonal prism crystals, crystals characterized by triangular facets, and twinned crystals are observed to form from SH and FCC systems, which have not previously been experimentally realized by DNA origami crystallization. These findings open a promising pathway toward accessing a rich phase space with a single type of building block and wielding other instructions as tools to develop crystalline materials with tunable properties.

DNA origami-designed 3D phononic crystals

Moulding the flow of phononic waves in three-dimensional (3D) space plays a critical role in controlling the sound and thermal properties of matter. To this end, 3D phononic crystals (PnCs) have been considered the gold standard because their complete phononic bandgap (PnBG) enables omnidirectional inhibition of phononic wave propagation. Nevertheless, achieving a complete PnBG in the high-frequency regime is still challenging, as attaining the correspondingly demanded mesoscale 3D crystals consisting of continuous frame networks with conventional fabrications is difficult. Here, we report that a DNA origami-designed-3D crystal can serve as a hypersonic 3D PnC exhibiting the widest complete PnBG. DNA origami crystallization can unprecedentedly provide 3D crystals such that continuous frame 3D crystals at the mesoscale are realizable. Furthermore, their lattice symmetry can be molecularly programmed to be at the highest level in a hierarchy of symmetry groups and numbers, which can facilitate the widening of the PnBG. More importantly, conformal silicification can render DNA origami-3D crystals rigid. Overall, we predict that the widest hypersonic PnBG can be achieved with DNA origami-designed 3D crystals with optimal lattice geometry and silica fraction; our work can provide a blueprint for the design and fabrication of mesoscale 3D PnCs with a champion PnBG.

Reconfigurable pH-Responsive DNA Origami Lattices

DNA nanotechnology enables straightforward fabrication of user-defined and nanometer-precise templates for a cornucopia of different uses. To date, most of these DNA assemblies have been static, but dynamic structures are increasingly coming into view. The programmability of DNA not only allows for encoding of the DNA object shape but also it may be equally used in defining the mechanism of action and the type of stimuli-responsiveness of the dynamic structures. However, these "robotic" features of DNA nanostructures are usually demonstrated for only small, discrete, and device-like objects rather than for collectively behaving higher-order systems. Here, we show how a large-scale, two-dimensional (2D) and pH-responsive DNA origami-based lattice can be assembled into two different configurations ("open" and "closed" states) on a mica substrate and further switched from one to the other distinct state upon a pH change of the surrounding solution. The control over these two configurations is achieved by equipping the arms of the lattice-forming DNA origami units with "pH-latches" that form Hoogsteen-type triplexes at low pH. In short, we demonstrate how the electrostatic control over the adhesion and mobility of the DNA origami units on the surface can be used both in the large lattice formation (with the help of directed polymerization) and in the conformational switching of the whole lattice. To further emphasize the feasibility of the method, we also demonstrate the formation of pH-responsive 2D gold nanoparticle lattices. We believe this work can bridge the nanometer-precise DNA origami templates and higher-order large-scale systems with the stimuli-induced dynamicity.

Dynamically Reconfigurable DNA Origami Crystals Driven by a Designated Path Diagram

Constructing adaptable and switchable crystal structures renders it possible to dynamically control the properties and functions of adaptive materials, thereby expanding the potential application of these structures in fields such as optics, biology, and catalysis. Recently, researchers have developed various dynamic crystals possessing phase transition abilities. However, manufacturing switchable crystals with multiple-phase-transition ability by integrating various responsive behaviors into different dimensions of a single lattice remains considerably challenging. Herein, we built a set of dynamically reconfigurable DNA origami crystals by orthogonally integrating multiple dynamic effectors into the prescribed dimensions of the octahedral DNA origami frames. Further, we independently manipulated and logically combined the dynamic behaviors of the effectors in different dimensions. The initial mother phase and three derived daughter phases were interconnected into a path diagram by six elementary paths. Furthermore, these paths could be superimposed under multiple stimulus instructions by design to obtain the desired intricate transition routes. Moreover, finer manipulations were also applied to these paths to obtain extra new phase stations for the path diagram. To conveniently detect these phase transitions, a color-based visualization strategy was developed that converted the microscopic symmetry transformation of the lattices into macroscopic color changes that could be observed via a fluorescence microscope. Hence, this strategy lays the foundation for artificially constructing biomimetic functional crystals.

DNA as grabbers and steerers of quantum emitters

The chemically synthesizable quantum emitters such as quantum dots (QDs), fluorescent nanodiamonds (FNDs), and organic fluorescent dyes can be integrated with an easy-to-craft quantum nanophotonic device, which would be readily developed by non-lithographic solution process. As a representative example, the solution dipping or casting of such soft quantum emitters on a flat metal layer and subsequent drop-casting of plasmonic nanoparticles can afford the quantum emitter-coupled plasmonic nanocavity (referred to as a nanoparticle-on-mirror (NPoM) cavity), allowing us for exploiting various quantum mechanical behaviors of light-matter interactions such as quantum electrodynamics (QED), strong coupling (e.g., Rabi splitting), and quantum mirage. This versatile, yet effective soft quantum nanophotonics would be further benefitted from a deterministic control over the positions and orientations of each individual quantum emitter, particularly at the molecule level of resolution. In this review, we will argue that DNA nanotechnology can provide a gold vista toward this end. A collective set of exotic characteristics of DNA molecules, including Watson-Crick complementarity and helical morphology, enables reliable grabbing of quantum emitters at the on-demand position and steering of their directors at the single molecular level. More critically, the recent advances in large-scale integration of DNA origami have pushed the reliance on the distinctly well-formed single device to the regime of the ultra-scale device arrays, which is critical for promoting the practically immediate applications of such soft quantum nanophotonics.

Dynamics of DNA Origami Lattices

Hierarchical assembly of programmable DNA frameworks─such as DNA origami─paves the way for versatile nanometer-precise parallel nanopatterning up to macroscopic scales. As of now, the rapid evolution of the DNA nanostructure design techniques and the accessibility of these methods provide a feasible platform for building highly ordered DNA-based assemblies for various purposes. So far, a plethora of different building blocks based on DNA tiles and DNA origami have been introduced, but the dynamics of the large-scale lattice assembly of such modules is still poorly understood. Here, we focus on the dynamics of two-dimensional surface-assisted DNA origami lattice assembly at mica and lipid substrates and the techniques for prospective three-dimensional assemblies, and finally, we summarize the potential applications of such systems.

A universal way to enrich the nanoparticle lattices with polychrome DNA origami "homologs"

DNA origami technology has rapidly developed into an ideal means to programmably crystallize nanoparticles. However, most existing DNA origami three-dimensional platforms normally used a single type of DNA origami unit, which greatly limits the types of nanoparticle superlattices that can be synthesized. Here, we report a universal strategy to vastly enrich the library of nanoparticle superlattices, based on multiple-unit (≥4 units) DNA origami platforms, which were constructed by programmably cocrystallizing three different DNA origami octahedral "homologs." Through selectively inserting nanoparticles into DNA origami monomers, numerous nanoparticle superlattices can be synthesized on the basis of the same platform. In this work, we obtained 85 types of DOF/AuNP (DNA origami frame/gold nanoparticle) superlattices using three different DNA origami platforms as examples. We believe that our strategy can provide possible access to fabricate virtually endless types of nanoparticle superlattices and promote the construction of functional materials with special properties.

Two-Stage Assembly of Nanoparticle Superlattices with Multiscale Organization

Self-assembly processes, while promising for enabling the fabrication of complexly organized nanomaterials from nanoparticles, are often limited in creating structures with multiscale order. These limitations are due to difficulties in practically realizing the assembly processes required to achieve such complex organizations. For a long time, a hierarchical assembly attracted interest as a potentially powerful approach. However, due to the experimental limitations, intermediate-level structures are often heterogeneous in composition and structure, which significantly impacts the formation of large-scale organizations. Here, we introduce a two-stage assembly strategy: DNA origami frames scaffold a coordination of nanoparticles into designed 3D nanoclusters, and then these clusters are assembled into ordered lattices whose types are determined by the clusters' valence. Through modulating the nanocluster architectures and intercluster bindings, we demonstrate the successful formation of complexly organized nanoparticle crystals. The presented two-stage assembly method provides a powerful fabrication strategy for creating nanoparticle superlattices with prescribed unit cells.