Core-Shell and Layer-by-Layer Assembly of 3D DNA Crystals

Precision Self-assembly of 3D DNA Crystals Using Microfluidics

Controlling the uniformity in size and quantity of macroscopic three-dimensional (3D) DNA crystals is essential for their integration into complex systems and broader applications. However, achieving such control remains a major challenge in DNA nanotechnology. Here, we present a novel strategy for synthesizing monodisperse 3D DNA single crystals using microfluidic double-emulsion droplets as nanoliter-scale microreactors. These uniformly sized droplets can shrink and swell without leaking their inner contents, allowing the concentration of the DNA solution inside to be adjusted. The confined volume ensures that, once a crystal seed forms, it rapidly consumes the available DNA material, preventing the formation of additional crystals within the same droplet. This approach enables precise control over crystal growth, resulting in a yield of one DNA single crystal per droplet, with a success rate of up to 98.6% ± 0.9%. The resulting DNA crystals exhibit controlled sizes, ranging from 19.3 ± 0.9 μm to 56.8 ± 2.6 μm. Moreover, this method can be applied to the controlled growth of various types of DNA crystals. Our study provides a new pathway for DNA crystal self-assembly and microengineering.

Engineered 3D DNA Crystals: A Molecular Design Perspective

Recent advances in biomolecular self-assembly have transformed material science, enabling the creation of novel materials with unparalleled precision and functionality. Among these innovations, 3D DNA crystals have emerged as a distinctive class of macroscopic materials, engineered through the bottom-up approach by DNA self-assembly. These structures uniquely combine precise molecular ordering with high programmability, establishing their importance in advanced material design. This review delves into the molecular design of engineered 3D DNA crystals, classifying current crystal structures based on "crystal bond orientations" and examining key aspects of in-silico molecular design, self-assembly, and crystal modifications. The functionalization of 3D DNA crystals for applications in crystallization scaffolding, biocatalysis, biosensing, electrical and optical devices, as well as in the emerging fields of DNA computing and data storage are explored. Finally, the ongoing challenges are addressed and future directions to advance the field of engineered 3D DNA crystals are proposed.

Pursuing excitonic energy transfer with programmable DNA-based optical breadboards

DNA nanotechnology has now enabled the self-assembly of almost any prescribed 3-dimensional nanoscale structure in large numbers and with high fidelity. These structures are also amenable to site-specific modification with a variety of small molecules ranging from drugs to reporter dyes. Beyond obvious application in biotechnology, such DNA structures are being pursued as programmable nanoscale optical breadboards where multiple different/identical fluorophores can be positioned with sub-nanometer resolution in a manner designed to allow them to engage in multistep excitonic energy-transfer (ET) via Förster resonance energy transfer (FRET) or other related processes. Not only is the ability to create such complex optical structures unique, more importantly, the ability to rapidly redesign and prototype almost all structural and optical analogues in a massively parallel format allows for deep insight into the underlying photophysical processes. Dynamic DNA structures further provide the unparalleled capability to reconfigure a DNA scaffold on the fly in situ and thus switch between ET pathways within a given assembly, actively change its properties, and even repeatedly toggle between two states such as on/off. Here, we review progress in developing these composite materials for potential applications that include artificial light harvesting, smart sensors, nanoactuators, optical barcoding, bioprobes, cryptography, computing, charge conversion, and theranostics to even new forms of optical data storage. Along with an introduction into the DNA scaffolding itself, the diverse fluorophores utilized in these structures, their incorporation chemistry, and the photophysical processes they are designed to exploit, we highlight the evolution of DNA architectures implemented in the pursuit of increased transfer efficiency and the key lessons about ET learned from each iteration. We also focus on recent and growing efforts to exploit DNA as a scaffold for assembling molecular dye aggregates that host delocalized excitons as a test bed for creating excitonic circuits and accessing other quantum-like optical phenomena. We conclude with an outlook on what is still required to transition these materials from a research pursuit to application specific prototypes and beyond.

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.

The Formation and Displacement of Ordered DNA Triplexes in Self-Assembled Three-Dimensional DNA Crystals

Reconfigurable structures engineered through DNA hybridization and self-assembly offer both structural and dynamic applications in nanotechnology. Here, we have demonstrated that strand displacement of triplex-forming oligonucleotides (TFOs) can be translated to a robust macroscopic DNA crystal by coloring the crystals with covalently attached fluorescent dyes. We show that three different types of triplex strand displacement are feasible within the DNA crystals and the bound TFOs can be removed and/or replaced by (a) changing the pH from 5 to 7, (b) the addition of the Watson-Crick complement to a TFO containing a short toehold, and (c) the addition of a longer TFO that uses the duplex edge as a toehold. We have also proved by X-ray diffraction that the structure of the crystals remains as designed in the presence of the TFOs.

Programmable 3D Hexagonal Geometry of DNA Tensegrity Triangles

Non-canonical interactions in DNA remain under-explored in DNA nanotechnology. Recently, many structures with non-canonical motifs have been discovered, notably a hexagonal arrangement of typically rhombohedral DNA tensegrity triangles that forms through non-canonical sticky end interactions. Here, we find a series of mechanisms to program a hexagonal arrangement using: the sticky end sequence; triangle edge torsional stress; and crystallization condition. We showcase cross-talking between Watson-Crick and non-canonical sticky ends in which the ratio between the two dictates segregation by crystal forms or combination into composite crystals. Finally, we develop a method for reconfiguring the long-range geometry of formed crystals from rhombohedral to hexagonal and vice versa. These data demonstrate fine control over non-canonical motifs and their topological self-assembly. This will vastly increase the programmability, functionality, and versatility of rationally designed DNA constructs.

The wending rhombus: Self-assembling 3D DNA crystals

In this perspective, we provide a summary of recent developments in self-assembling three-dimensional (3D) DNA crystals. Starting from the inception of this subfield, we describe the various advancements in structure that have led to an increase in the diversity of macromolecular crystal motifs formed through self-assembly, and we further comment on the future directions of the field, which exploit noncanonical base pairing interactions beyond Watson-Crick. We then survey the current applications of self-assembling 3D DNA crystals in reversibly active nanodevices and materials engineering and provide an outlook on the direction researchers are taking these structures. Finally, we compare 3D DNA crystals with DNA origami and suggest how these distinct subfields might work together to enhance biomolecule structure solution, nanotechnological motifs, and their applications.

Self-Assembled Micro-Sized Hexagons Built from Short DNA in a Crowded Environment

DNA programmable structures of various morphologies have attracted extensive attention due to their potential for materials science and biomedical applications. Here, we report the formation of micro-sized hexagons via assembly of only one pair of short double-stranded DNA in buffer-salt poly(ethylene glycol) solution. Each DNA strand had complementary bases with a two-base overhang. The procedure of heating and subsequent cooling of blunt-ended double-stranded DNA resulted in different assemblies. These results indicated that end-to-end adhesion at the terminals induced by complementary overhangs were required to construct the hexagonal DNA assemblies. The stable formation of the hexagons was highly dependent on heating temperature. In addition, concentration adjustments of DNA and poly(ethylene glycol) were essential. Circular dichroism spectral measurements and polarization microscopy observations indicated parallel alignment of double-stranded DNA in the hexagonal platelet. Self-assembled micro-sized hexagons composed of simple building blocks may have great potential for future biomedical device development.

Inclusion of organic species in exfoliated montmorillonite nanolayers towards hierarchical functional inorganic-organic nanostructures

Montmorillonite (Mt) can readily undergo spontaneous delamination or exfoliation into nanolayers by various physical and chemical processes, which allow various strategies to engineer hierarchical functional inorganic-organic nanostructures. This review aims to discuss the recent progress in the liquid-phase exfoliation of Mt into individual nanolayers and the inclusion chemistry of functional organic species, ions, or molecules into the exfoliated Mt nanolayers to produce hierarchical functional inorganic-organic nanostructures. The exfoliation methods include mechanical force, ultrasonication, and intercalation-assisted exfoliation. Techniques for quickly assessing the quality of the exfoliated Mt nanolayers are still needed. Layer-by-layer (LbL) deposition, template, and evaporation-induced inclusions are examined to fabricate hierarchical Mt-organic species nanocomposites with unique functionalities and properties. The nanocomposites can be produced as multilayered porous films, brick-and-mortar coatings, hydrogels with a house-of-cards structure, core-shell materials, and hollow and mesoporous spherical nanocomposites, which exhibit significant potential for adsorption, catalysis, targeted delivery and controlled drug release, highly sensitive sensors, flame retardant coatings, and thermal energy storage and release (i.e. phase change materials). Finally, the challenges and prospects for the future development of hierarchical nanocomposites of exfoliated Mt nanolayers and organic species, particularly in hierarchical supramolecular nanostructured composites, are highlighted.

Porous crystals as scaffolds for structural biology

Molecular scaffolds provide routes to otherwise inaccessible organized states of matter. Scaffolds that are crystalline can be observed in atomic detail using diffraction, along with any guest molecules that have adopted coherent structures therein. This approach, scaffold-assisted structure determination, is not yet routine. However, with varying degrees of guest immobilization, porous crystal scaffolds have recently been decorated with guest molecules. Herein we analyze recent milestones, compare the relative advantages and challenges of different types of scaffold crystals, and weigh the merits of diverse guest installation strategies.

Building machines with DNA molecules

In nature, DNA molecules carry the hereditary information. But DNA has physical and chemical properties that make it attractive for uses beyond heredity. In this Review, we discuss the potential of DNA for creating machines that are both encoded by and built from DNA molecules. We review the main methods of DNA nanostructure assembly, describe recent advances in building increasingly complex molecular structures and discuss strategies for creating machine-like nanostructures that can be actuated and move. We highlight opportunities for applications of custom DNA nanostructures as scientific tools to address challenges across biology, chemistry and engineering.

Making Engineered 3D DNA Crystals Robust

Engineered 3D DNA crystals are promising scaffolds for bottom-up construction of three-dimensional, macroscopic devices from the molecular level. Nevertheless, this has been hindered by the highly constrained conditions for DNA crystals to be stable. Here we report a method to prepare robust 3D DNA crystals by postassembly ligation to remove this constraint. Specifically, sticky ends at crystal contacts were enzymatically ligated, and the covalent bonds significantly enhanced crystal stability, e.g., being stable at 65 °C. This method also enabled the fabrication of DNA crystals with complex architectures including crystal shell, core-shell, and matryoshka dolls. Furthermore, we have demonstrated the applications of the robust DNA crystals in biocatalysis and protein entrapment. Our study removes one key obstacle for the applications of DNA crystals and offers many new opportunities in DNA nanotechnology.

Molecular tectonics: control of crystalline sequences

Isostructural and almost isometric crystals that differ in their colour may be welded in solution and under mild conditions into crystalline materials with imposed sequences.