Construction and Structure Determination of a Three-Dimensional DNA Crystal

Engineering tertiary chirality in helical biopolymers

Tertiary chirality describes the handedness of supramolecular assemblies and relies not only on the primary and secondary structures of the building blocks but also on topological driving forces that have been sparsely characterized. Helical biopolymers, especially DNA, have been extensively investigated as they possess intrinsic chirality that determines the optical, mechanical, and physical properties of the ensuing material. Here, we employ the DNA tensegrity triangle as a model system to locate the tipping points in chirality inversion at the tertiary level by X-ray diffraction. We engineer tensegrity triangle crystals with incremental rotational steps between immobile junctions from 3 to 28 base pairs (bp). We construct a mathematical model that accurately predicts and explains the molecular configurations in both this work and previous studies. Our design framework is extendable to other supramolecular assemblies of helical biopolymers and can be used in the design of chiral nanomaterials, optically active molecules, and mesoporous frameworks, all of which are of interest to physical, biological, and chemical nanoscience.

Programming crystallization kinetics of self-assembled DNA crystals with 5-methylcytosine modification

Self-assembled DNA crystals offer a precise chemical platform at the ångström-scale for DNA nanotechnology, holding enormous potential in material separation, catalysis, and DNA data storage. However, accurately controlling the crystallization kinetics of such DNA crystals remains challenging. Herein, we found that atomic-level 5-methylcytosine (5mC) modification can regulate the crystallization kinetics of DNA crystal by tuning the hybridization rates of DNA motifs. We discovered that by manipulating the axial and combination of 5mC modification on the sticky ends of DNA tensegrity triangle motifs, we can obtain a series of DNA crystals with controllable morphological features. Through DNA-PAINT and FRET-labeled DNA strand displacement experiments, we elucidate that atomic-level 5mC modification enhances the affinity constant of DNA hybridization at both the single-molecule and macroscopic scales. This enhancement can be harnessed for kinetic-driven control of the preferential growth direction of DNA crystals. The 5mC modification strategy can overcome the limitations of DNA sequence design imposed by limited nucleobase numbers in various DNA hybridization reactions. This strategy provides a new avenue for the manipulation of DNA crystal structure, valuable for the advancement of DNA and biomacromolecular crystallography.

Structure determination of a DNA crystal by MicroED

Microcrystal electron diffraction (MicroED) is a powerful tool for determining high-resolution structures of microcrystals from a diverse array of biomolecular, chemical, and material samples. In this study, we apply MicroED to DNA crystals, which have not been previously analyzed using this technique. We utilized the d(CGCGCG)2 DNA duplex as a model sample and employed cryo-FIB milling to create thin lamella for diffraction data collection. The MicroED data collection and subsequent processing resulted in a 1.10 Å resolution structure of the d(CGCGCG)2 DNA, demonstrating the successful application of cryo-FIB milling and MicroED to the investigation of nucleic acid crystals.

Mechanics of dynamic and deformable DNA nanostructures

In DNA nanotechnology, DNA molecules are designed, engineered, and assembled into arbitrary-shaped architectures with predesigned functions. Static DNA assemblies often have delicate designs with structural rigidity to overcome thermal fluctuations. Dynamic structures reconfigure in response to external cues, which have been explored to create functional nanodevices for environmental sensing and other applications. However, the precise control of reconfiguration dynamics has been a challenge due partly to flexible single-stranded DNA connections between moving parts. Deformable structures are special dynamic constructs with deformation on double-stranded parts and single-stranded hinges during transformation. These structures often have better control in programmed deformation. However, related deformability and mechanics including transformation mechanisms are not well understood or documented. In this review, we summarize the development of dynamic and deformable DNA nanostructures from a mechanical perspective. We present deformation mechanisms such as single-stranded DNA hinges with lock-and-release pairs, jack edges, helicity modulation, and external loading. Theoretical and computational models are discussed for understanding their associated deformations and mechanics. We elucidate the pros and cons of each model and recommend design processes based on the models. The design guidelines should be useful for those who have limited knowledge in mechanics as well as expert DNA designers.

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.

Divergence and Convergence: Complexity Emerges in Crystal Engineering from an 8-mer DNA

Biology provides plenty of examples on achieving complicated structures out of minimal numbers of building blocks. In contrast, structural complexity of designed molecular systems is achieved by increasing the numbers of component molecules. In this study, the component DNA strand assembles into a highly complex crystal structure via an unusual path of divergence and convergence. This assembly path suggests a route to minimalists for increasing structural complexity. The original purpose of this study is to engineer DNA crystals with high resolution, which is the primary motivation and a key objective for structural DNA nanotechnology. Despite great efforts in the last 40 years, engineered DNA crystals have not yet consistently reached resolution better than 2.5 Å, limiting their potential uses. Our research has shown that small, symmetrical building blocks generally lead to high resolution crystals. Herein, by following this principle, we report an engineered DNA crystal with unprecedented high resolution (2.17 Å) assembled from one single DNA component: an 8-base-long DNA strand. This system has three unique characteristics: (1) It has a very complex architecture, (2) the same DNA strand forms two different structural motifs, both of which are incorporated into the final crystal, and (3) the component DNA molecule is only an 8-base-long DNA strand, which is, arguably, the smallest DNA motif for DNA nanostructures to date. This high resolution opens the possibility of using these DNA crystals to precisely organize guest molecules at the Å level, which could stimulate a range of new investigations.

Structure determination of a DNA crystal by MicroED

Microcrystal electron diffraction (MicroED) is a powerful tool for determining high-resolution structures of microcrystals from a diverse array of biomolecular, chemical, and material samples. In this study, we apply MicroED to DNA crystals, which have not been previously analyzed using this technique. We utilized the d(CGCGCG) 2 DNA duplex as a model sample and employed cryo-FIB milling to create thin lamella for diffraction data collection. The MicroED data collection and subsequent processing resulted in a 1.10 Å resolution structure of the d(CGCGCG) 2 DNA, demonstrating the successful application of cryo-FIB milling and MicroED to the investigation of nucleic acid crystals.

Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations

Holliday junction (HJ) is a noncanonical four-way DNA structure with a prominent role in DNA repair, recombination, and DNA nanotechnology. By rearranging its four arms, HJ can adopt either closed or open state. With enzymes typically recognizing only a single state, acquiring detailed knowledge of the rearrangement process is an important step toward fully understanding the biological function of HJs. Here, we carried out standard all-atom molecular dynamics (MD) simulations of the spontaneous opening-closing transitions, which revealed complex conformational transitions of HJs with an involvement of previously unconsidered "half-closed" intermediates. Detailed free-energy landscapes of the transitions were obtained by sophisticated enhanced sampling simulations. Because the force field overstabilizes the closed conformation of HJs, we developed a system-specific modification which for the first time allows the observation of spontaneous opening-closing HJ transitions in unbiased MD simulations and opens the possibilities for more accurate HJ computational studies of biological processes and nanomaterials.

Recent Advances in DNA Origami-Engineered Nanomaterials and Applications

DNA nanotechnology is a unique field, where physics, chemistry, biology, mathematics, engineering, and materials science can elegantly converge. Since the original proposal of Nadrian Seeman, significant advances have been achieved in the past four decades. During this glory time, the DNA origami technique developed by Paul Rothemund further pushed the field forward with a vigorous momentum, fostering a plethora of concepts, models, methodologies, and applications that were not thought of before. This review focuses on the recent progress in DNA origami-engineered nanomaterials in the past five years, outlining the exciting achievements as well as the unexplored research avenues. We believe that the spirit and assets that Seeman left for scientists will continue to bring interdisciplinary innovations and useful applications to this field in the next decade.

Designing the Self-Assembly of Arbitrary Shapes Using Minimal Complexity Building Blocks

The design space for self-assembled multicomponent objects ranges from a solution in which every building block is unique to one with the minimum number of distinct building blocks that unambiguously define the target structure. We develop a pipeline to explore the design spaces for a set of structures of various sizes and complexities. To understand the implications of the different solutions, we analyze their assembly dynamics using patchy particle simulations and study the influence of the number of distinct building blocks, and the angular and spatial tolerances on their interactions, on the kinetics and yield of the target assembly. We show that the resource-saving solution with a minimum number of distinct blocks can often assemble just as well (or faster) than designs where each building block is unique. We further use our methods to design multifarious structures, where building blocks are shared between different target structures. Finally, we use coarse-grained DNA simulations to investigate the realization of multicomponent shapes using DNA nanostructures as building blocks.

The Rule of Thirds: Controlling Junction Chirality and Polarity in 3D DNA Tiles

The successful self-assembly of tensegrity triangle DNA crystals heralded the ability to programmably construct macroscopic crystalline nanomaterials from rationally-designed, nanoscale components. This 3D DNA tile owes its "tensegrity" nature to its three rotationally stacked double helices locked together by the tensile winding of a center strand segmented into 7 base pair (bp) inter-junction regions, corresponding to two-thirds of a helical turn of DNA. All reported tensegrity triangles to date have employed ( Z + 2 / 3 ) \[\left( {Z{\bm{ + }}2{\bf /}3} \right)\] turn inter-junction segments, yielding right-handed, antiparallel, "J1" junctions. Here a minimal DNA triangle motif consisting of 3-bp inter-junction segments, or one-third of a helical turn is reported. It is found that the minimal motif exhibits a reversed morphology with a left-handed tertiary structure mediated by a locally-parallel Holliday junction-the "L1" junction. This parallel junction yields a predicted helical groove matching pattern that breaks the pseudosymmetry between tile faces, and the junction morphology further suggests a folding mechanism. A Rule of Thirds by which supramolecular chirality can be programmed through inter-junction DNA segment length is identified. These results underscore the role that global topological forces play in determining local DNA architecture and ultimately point to an under-explored class of self-assembling, chiral nanomaterials for topological processes in biological systems.

Engineering DNA Crystals toward Studying DNA-Guest Molecule Interactions

Sequence-selective recognition of DNA duplexes is important for a wide range of applications including regulating gene expression, drug development, and genome editing. Many small molecules can bind DNA duplexes with sequence selectivity. It remains as a challenge how to reliably and conveniently obtain the detailed structural information on DNA-molecule interactions because such information is critically needed for understanding the underlying rules of DNA-molecule interactions. If those rules were understood, we could design molecules to recognize DNA duplexes with a sequence preference and intervene in related biological processes, such as disease treatment. Here, we have demonstrated that DNA crystal engineering is a potential solution. A molecule-binding DNA sequence is engineered to self-assemble into highly ordered DNA crystals. An X-ray crystallographic study of molecule-DNA cocrystals reveals the structural details on how the molecule interacts with the DNA duplex. In this approach, the DNA will serve two functions: (1) being part of the molecule to be studied and (2) forming the crystal lattice. It is conceivable that this method will be a general method for studying drug/peptide-DNA interactions. The resulting DNA crystals may also find use as separation matrices, as hosts for catalysts, and as media for material storage.

Influence of hydrophobic moieties on the crystallization of amphiphilic DNA nanostructures

Three-dimensional crystalline frameworks with nanoscale periodicity are valuable for many emerging technologies, from nanophotonics to nanomedicine. DNA nanotechnology has emerged as a prime route for constructing these materials, with most approaches taking advantage of the structural rigidity and bond directionality programmable for DNA building blocks. Recently, we have introduced an alternative strategy reliant on flexible, amphiphilic DNA junctions dubbed C-stars, whose ability to crystallize is modulated by design parameters, such as nanostructure topology, conformation, rigidity, and size. While C-stars have been shown to form ordered phases with controllable lattice parameter, response to stimuli, and embedded functionalities, much of their vast design space remains unexplored. Here, we investigate the effect of changing the chemical nature of the hydrophobic modifications and the structure of the DNA motifs in the vicinity of these moieties. While similar design variations should strongly alter key properties of the hydrophobic interactions between C-stars, such as strength and valency, only limited differences in self-assembly behavior are observed. This finding suggests that long-range order in C-star crystals is likely imposed by structural features of the building block itself rather than the specific characteristics of the hydrophobic tags. Nonetheless, we find that altering the hydrophobic regions influences the ability of C-star crystals to uptake hydrophobic molecular cargoes, which we exemplify by studying the encapsulation of antibiotic penicillin V. Besides advancing our understanding of the principles governing the self-assembly of amphiphilic DNA building blocks, our observations thus open up new routes to chemically program the materials without affecting their structure.

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.

Highly Symmetric, Self-Assembling 3D DNA Crystals with Cubic and Trigonal Lattices

The rational design of nanoscopic DNA tiles has yielded highly ordered crystalline matter in 2D and 3D. The most well-studied 3D tile is the DNA tensegrity triangle, which is known to self-assemble into macroscopic crystals. However, contemporary rational design parameters for 3D DNA crystals nearly universally invoke integer numbers of DNA helical turns and Watson-Crick (WC) base pairs. In this study, 24-bp edges are substituted into a previously 21-bp (two helical turns of DNA) tensegrity triangle motif to explore whether such unconventional motif can self-assemble into 3D crystals. The use of noncanonical base pairs in the sticky ends results in a cubic arrangement of tensegrity triangles with exceedingly high symmetry, assembling a lattice from winding helical axes and diamond-like tessellation patterns. Reverting this motif to sticky ends with Watson-Crick pairs results in a trigonal hexagonal arrangement, replicating this diamond arrangement in a hexagonal context. These results showcase that the authors can generate unexpected, highly complex, pathways for materials design by testing modifications to 3D tiles without prior knowledge of the ensuing symmetry. This study expands the rational design toolbox for DNA nanotechnology; and it further illustrates the existence of yet-unexplored arrangements of crystalline soft matter.

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.

DNA-Based Molecular Machines

Artificial molecular machines have found widespread applications ranging from fundamental studies to biomedicine. More recent advances in exploiting unique physical and chemical properties of DNA have led to the development of DNA-based artificial molecular machines. The unprecedented programmability of DNA provides a powerful means to design complex and sophisticated DNA-based molecular machines that can exert mechanical force or motion to realize complex tasks in a controllable, modular fashion. This Perspective highlights the potential and strategies to construct artificial molecular machines using double-stranded DNA, functional nucleic acids, and DNA frameworks, which enable improved control over reaction pathways and motion behaviors. We also outline the challenges and opportunities of using DNA-based molecular machines for biophysics, biosensing, and biocomputing.

Mechanical deformation behaviors and structural properties of ligated DNA crystals

DNA self-assembly has emerged as a powerful strategy for constructing complex nanostructures. While the mechanics of individual DNA strands have been studied extensively, the deformation behaviors and structural properties of self-assembled architectures are not well understood. This is partly due to the small dimensions and limited experimental methods available. DNA crystals are macroscopic crystalline structures assembled from nanoscale motifs via sticky-end association. The large DNA constructs may thus be an ideal platform to study structural mechanics. Here, we investigate the fundamental mechanical properties and behaviors of ligated DNA crystals made of tensegrity triangular motifs. We perform coarse-grained molecular dynamics simulations and confirm the results with nanoindentation experiments using atomic force microscopy. We observe various deformation modes, including untension, linear elasticity, duplex dissociation, and single-stranded component stretch. We find that the mechanical properties of a DNA architecture are correlated with those of its components. However, the structure shows complex behaviors which may not be predicted by components alone and the architectural design must be considered.

Interfacing DNA nanotechnology and biomimetic photonic complexes: advances and prospects in energy and biomedicine

Self-assembled photonic systems with well-organized spatial arrangement and engineered optical properties can be used as efficient energy materials and as effective biomedical agents. The lessons learned from natural light-harvesting antennas have inspired the design and synthesis of a series of biomimetic photonic complexes, including those containing strongly coupled dye aggregates with dense molecular packing and unique spectroscopic features. These photoactive components provide excellent features that could be coupled to multiple applications including light-harvesting, energy transfer, biosensing, bioimaging, and cancer therapy. Meanwhile, nanoscale DNA assemblies have been employed as programmable and addressable templates to guide the formation of DNA-directed multi-pigment complexes, which can be used to enhance the complexity and precision of artificial photonic systems and show the potential for energy and biomedical applications. This review focuses on the interface of DNA nanotechnology and biomimetic photonic systems. We summarized the recent progress in the design, synthesis, and applications of bioinspired photonic systems, highlighted the advantages of the utilization of DNA nanostructures, and discussed the challenges and opportunities they provide.

Structural DNA nanotechnology: Immobile Holliday junctions to artificial robots

DNA nanotechnology marvels the scientific world with its capabilities to design, engineer, and demonstrate nanoscale shapes. This review is a condensed version walking the reader through the structural developments in the field over the past 40 years starting from the basic design rules of the double-stranded building block to the most recent advancements in self-assembled hierarchically achieved structures to date. It builds off from the fundamental motivation of building 3-dimensional (3D) lattice structures of tunable cavities going all the way up to artificial nanorobots fighting cancer. The review starts by covering the most important developments from the fundamental bottom-up approach of building structures, which is the 'tile' based approach covering 1D, 2D, and 3D building blocks, after which, the top-down approach using DNA origami and DNA bricks is also covered. Thereafter, DNA nanostructures assembled using not so commonly used (yet promising) techniques like i-motifs, quadruplexes, and kissing loops are covered. Highlights from the field of dynamic DNA nanostructures have been covered as well, walking the reader through the various approaches used within the field to achieve movement. The article finally concludes by giving the authors a view of what the future of the field might look like while suggesting in parallel new directions that fellow/future DNA nanotechnologists could think about.

Amphiphilic DNA nanostructures for bottom-up synthetic biology

DNA nanotechnology enables the construction of sophisticated biomimetic nanomachines that are increasingly central to the growing efforts of creating complex cell-like entities from the bottom-up. DNA nanostructures have been proposed as both structural and functional elements of these artificial cells, and in many instances are decorated with hydrophobic moieties to enable interfacing with synthetic lipid bilayers or regulating bulk self-organisation. In this feature article we review recent efforts to design biomimetic membrane-anchored DNA nanostructures capable of imparting complex functionalities to cell-like objects, such as regulated adhesion, tissue formation, communication and transport. We then discuss the ability of hydrophobic modifications to enable the self-assembly of DNA-based nanostructured frameworks with prescribed morphology and functionality, and explore the relevance of these novel materials for artificial cell science and beyond. Finally, we comment on the yet mostly unexpressed potential of amphiphilic DNA-nanotechnology as a complete toolbox for bottom-up synthetic biology - a figurative and literal scaffold upon which the next generation of synthetic cells could be built.

3D Hexagonal Arrangement of DNA Tensegrity Triangles

The tensegrity triangle motif utilizes Watson-Crick sticky end cohesion to self-assemble into a rhombohedral crystal lattice using complementary 5'-GA and 5'-TC sticky ends. Here, we report that using noncanonical 5'-AG and 5'-TC sticky ends in otherwise isomorphic tensegrity triangles results in crystal self-assembly in the P6₃ hexagonal space group as revealed by X-ray crystallography. In this structure, the DNA double helices bend at the crossover positions, a feature that was not observed in the original design. Instead of propagating linearly, the tilt between base pairs of each right-handed helix results in a left-handed superstructure along the screw axis, forming a microtubule-like structure composed of three double helices with an unbroken channel at the center. This hexagonal lattice has a cavity diameter of 11 nm and a unit cell volume of 886 000 ų-far larger than the rhombohedral counterpart (5 nm, 330 000 ų).

Structures of artificially designed discrete RNA nanoarchitectures at near-atomic resolution

Although advances in nanotechnology have enabled the construction of complex and functional synthetic nucleic acid–based nanoarchitectures, high-resolution discrete structures are lacking because of the difficulty in obtaining good diffracting crystals. Here, we report the design and construction of RNA nanostructures based on homooligomerizable one-stranded tiles for x-ray crystallographic determination. We solved three structures to near-atomic resolution: a 2D parallelogram, a 3D nanobracelet unexpectedly formed from an RNA designed for a nanocage, and, eventually, a bona fide 3D nanocage designed with the guidance of the two previous structures. Structural details of their constituent motifs, such as kissing loops, branched kissing loops, and T-junctions, that resemble natural RNA motifs and resisted x-ray determination are revealed, providing insights into those natural motifs. This work unveils the largely unexplored potential of crystallography in gaining high-resolution feedback for nanoarchitectural design and suggests a route to investigate RNA motif structures by configuring them into nanoarchitectures.

5'-Phosphorylation Strengthens Sticky-End Cohesions

Sticky-end cohesion plays a critical role in molecular biology and nucleic acid nanotechnology. Although free energy calculations and molecular mechanics can predict these interactions, chemical modification would compromise such predictions. Herein, we have used rationally designed 3D DNA crystals as a tool to experimentally investigate the modulation of 5'-phosphorylation on sticky-end cohesions. We have found that 5'-phosphorylation strengthens the sticky-end cohesion: in a DNA crystal self-assembled exclusively via sticky-end cohesions, 5'-phosphorylation not only promotes the crystallization process, in general, but also accelerates the crystal growth along designed directions. Such a finding allows the fine-tuning of DNA crystallization kinetics and the control of DNA crystal morphology. It also suggests a potential difference in self-assembly kinetics between natural DNA (with 5'-phosphorylation) and synthetic DNA (without 5'-phosphorylation).

DNA Nanodevices as Mechanical Probes of Protein Structure and Function

DNA nanotechnology has reported a wide range of structurally tunable scaffolds with precise control over their size, shape and mechanical properties. One promising application of these nanodevices is as probes for protein function or determination of protein structure. In this perspective we cover several recent examples in this field, including determining the effect of ligand spacing and multivalency on cell activation, applying forces at the nanoscale, and helping to solve protein structure by cryo-EM. We also highlight some future directions in the chemistry necessary for integrating proteins with DNA nanoscaffolds, as well as opportunities for computational modeling of hybrid protein-DNA nanomaterials.

Nanoscopic observation of a DNA crystal surface and its dynamic formation and degradation using atomic force microscopy

We report the direct observation of the formation and degradation of tensegrity triangle DNA crystals using atomic force microscopy (AFM). We observed the crystal surface by AFM and characterized the lattice coordination of the assembled triangle units at a molecular level. We visualized dynamic formation and degradation of the crystals and characterized them at nano-scale resolution.

A complete rule set for designing symmetry combination materials from protein molecules

Diverse efforts in protein engineering are beginning to produce novel kinds of symmetric self-assembling architectures, from protein cages to extended two-dimensional (2D) and three-dimensional (3D) crystalline arrays. Partial theoretical frameworks for creating symmetric protein materials have been introduced, but no complete system has been articulated. Only a minute fraction of the possible design space has been explored experimentally, in part because that space has not yet been described in theory. Here, in the form of a multiplication table, we lay out a complete rule set for materials that can be created by combining two chiral oligomeric components (e.g., proteins) in precise configurations. A unified system is described for parameterizing and searching the construction space for all such symmetry-combination materials (SCMs). In total, 124 distinct types of SCMs are identified, and then proven by computational construction. Mathematical properties, such as minimal ring or circuit size, are established for each case, enabling strategic predictions about potentially favorable design targets. The study lays out the theoretical landscape and detailed computational prescriptions for a rapidly growing area of protein-based nanotechnology, with numerous underlying connections to mathematical networks and chemical materials such as metal organic frameworks.

Near-Atomic Fabrication with Nucleic Acids

Nucleic acids hold great promise for bottom-up construction of nanostructures via programmable self-assembly. Especially, the emerging of advanced sequence design principles and the maturation of chemical synthesis of nucleic acids together have led to the rapid development of structural DNA/RNA nanotechnology. Diverse nucleic acids-based nano objects and patterns have been constructed with near-atomic resolutions and with controllable sizes and geometries. The monodispersed distribution of objects, the up-to-submillimeter scalability of patterns, and the excellent feasibility of carrying other materials with spatial and temporal resolutions have made DNA/RNA assemblies extremely unique in molecular engineering. In this review, we summarize recent advances in nucleic acids-based (mainly DNA-based) near-atomic fabrication by focusing on state-of-the-art design techniques, toolkits for DNA/RNA nanoengineering, and related applications in a range of areas.

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.

Turning DNA Binding Motifs into a Material for Flow Cells

Nanoscale assemblies of DNA strands are readily designed and can be generated in a wide range of shapes and sizes. Turning them into solids that bind biomolecules reversibly, so that they can act as active material in flow cells, is a challenge. Among the biomolecular ligands, cofactors are of particular interest because they are often the most expensive reagents of biochemical transformations, for which controlled release and recycling are desirable. We have recently described DNA triplex motifs that bind adenine-containing cofactors, such as NAD, FAD and ATP, reversibly with low micromolar affinity. We sought ways to convert the soluble DNA motifs into a macroporous solid for cofactor binding. While assemblies of linear and branched DNA motifs produced hydrogels with undesirable properties, long DNA triplexes treated with protamine gave materials suitable for flow cells. Using exchangeable cells in a flow system, thermally controlled loading and discharge were demonstrated. Employing a flow cell loaded with ATP, bioluminescence was induced through thermal release of the cofactor. The results show that materials generated from functional DNA structures can be successfully employed in macroscopic devices.

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.

Programming Structured DNA Assemblies to Probe Biophysical Processes

Structural DNA nanotechnology is beginning to emerge as a widely accessible research tool to mechanistically study diverse biophysical processes. Enabled by scaffolded DNA origami in which a long single strand of DNA is weaved throughout an entire target nucleic acid assembly to ensure its proper folding, assemblies of nearly any geometric shape can now be programmed in a fully automatic manner to interface with biology on the 1-100-nm scale. Here, we review the major design and synthesis principles that have enabled the fabrication of a specific subclass of scaffolded DNA origami objects called wireframe assemblies. These objects offer unprecedented control over the nanoscale organization of biomolecules, including biomolecular copy numbers, presentation on convex or concave geometries, and internal versus external functionalization, in addition to stability in physiological buffer. To highlight the power and versatility of this synthetic structural biology approach to probing molecular and cellular biophysics, we feature its application to three leading areas of investigation: light harvesting and nanoscale energy transport, RNA structural biology, and immune receptor signaling, with an outlook toward unique mechanistic insight that may be gained in these areas in the coming decade.

Modulating Self-Assembly of DNA Crystals with Rationally Designed Agents

This manuscript reports a strategy for controlling the crystallization kinetics and improving the quality of engineered self-assembled 3D DNA crystals. Growing large, high-quality biomacromolecule crystals is critically important for determining the 3D structures of biomacromolecules. It often presents a great challenge to structural biologists. Herein, we introduce a rationally designed agent to modulate the crystallization process. Under such conditions, fewer, but larger, crystals that yield diffraction patterns of modestly higher resolution are produced compared with the crystals from conditions without the modulating agent. We attribute the improvement to a smaller number of nuclei and slow growth rate of crystallization. This strategy is expected to be generally applicable for crystallization of other biomacromolecules.

Layered-Crossover Tiles with Precisely Tunable Angles for 2D and 3D DNA Crystal Engineering

DNA tile-based assembly provides a promising bottom-up avenue to create designer two-dimensional (2D) and three-dimensional (3D) crystalline structures that may host guest molecules or nanoparticles to achieve novel functionalities. Herein, we introduce a new kind of DNA tiles (named layered-crossover tiles) that each consists of two or four pairs of layered crossovers to bridge DNA helices in two neighboring layers with precisely predetermined relative orientations. By providing proper matching rules for the sticky ends at the terminals, these layered-crossover tiles are able to assemble into 2D periodic lattices with precisely controlled angles ranging from 20° to 80°. The layered-crossover tile can be slightly modified and used to successfully assemble 3D lattice with dimensions of several hundred micrometers with tunable angles as well. These layered-crossover tiles significantly expand the toolbox of DNA nanotechnology to construct materials through bottom-up approaches.

Self-Assembly of a 3D DNA Crystal Structure with Rationally Designed Six-Fold Symmetry

Programming self-assembled designer DNA crystals with various lattices and functions is one of the most important goals for nanofabrication using nucleic acids. The resulting porous materials possess atomic precision for several potential applications that rely on crystalline lattices and cavities. Herein, we present a rationally designed and self-assembled 3D DNA crystal lattice with hexagonal symmetry. In our design, two 21-base oligonucleotides are used to form a duplex motif that further assembles into a 3D array. The interactions between the strands are programmed using Watson-Crick base-pairing. The six-fold symmetry, as well as the chirality, is directed by the Holliday junctions formed between the duplex motifs. The rationally designed DNA crystal provides a new avenue that could create self-assembled macromolecular 3D crystalline lattices with atomic precision. In addition, the structure contains a highly organized array of well-defined cavities that are suitable for future applications with immobilized guests.

3D DNA Origami Crystals

3D crystals assembled entirely from DNA provide a route to design materials on a molecular level and to arrange guest particles in predefined lattices. This requires design schemes that provide high rigidity and sufficiently large open guest space. A DNA-origami-based "tensegrity triangle" structure that assembles into a 3D rhombohedral crystalline lattice with an open structure in which 90% of the volume is empty space is presented here. Site-specific placement of gold nanoparticles within the lattice demonstrates that these crystals are spacious enough to efficiently host 20 nm particles in a cavity size of 1.83 × 10⁵ nm³ , which would also suffice to accommodate ribosome-sized macromolecules. The accurate assembly of the DNA origami lattice itself, as well as the precise incorporation of gold particles, is validated by electron microscopy and small-angle X-ray scattering experiments. The results show that it is possible to create DNA building blocks that assemble into lattices with customized geometry. Site-specific hosting of nano objects in the optically transparent DNA lattice sets the stage for metamaterial and structural biology applications.

Facilitation of DNA self-assembly by relieving the torsional strains between building blocks

Paranemic crossover (PX) DNA motifs were designed and used for self-assembly of two dimensional lattices. The PX motifs tested include overwound and underwound ones, and different forms of self-assembled two-dimensional (2D) lattices were generated, demonstrating the correlation between the helical torsional strain within the system and the quality of the lattice formed. Relief of the torsional strain by adjusting the number of base pairs in the JX region adjacent to the PX motifs, facilitates and optimizes DNA self-assembly, which leads to 2D lattices of greater uniformity and higher yield. This study demonstrated that the helical relationship among DNA building blocks is a critical factor for the tile-based self-assembly of large nanostructures.

Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals

The foundational goal of structural DNA nanotechnology-the field that uses oligonucleotides as a molecular building block for the programmable self-assembly of nanostructured systems-was to use DNA to construct three-dimensional (3D) lattices for solving macromolecular structures. The programmable nature of DNA makes it an ideal system for rationally constructing self-assembled crystals and immobilizing guest molecules in a repeating 3D array through their specific stereospatial interactions with the scaffold. In this work, we have extended a previously described motif (4 × 5) by expanding the structure to a system that links four double-helical layers; we use a central weaving oligonucleotide containing a sequence of four six-base repeats (4 × 6), forming a matrix of layers that are organized and dictated by a series of Holliday junctions. In addition, we have assembled mirror image crystals (l-DNA) with the identical sequence that are completely resistant to nucleases. Bromine and selenium derivatives were obtained for the l- and d-DNA forms, respectively, allowing phase determination for both forms and solution of the resulting structures to 3.0 and 3.05 Å resolution. Both right- and left-handed forms crystallized in the trigonal space groups with mirror image 3-fold helical screw axes P3₂ and P3₁ for each motif, respectively. The structures reveal a highly organized array of discrete and well-defined cavities that are suitable for hosting guest molecules and allow us to dictate a priori the assembly of guest-DNA conjugates with a specified crystalline hand.

Crystallization of Amphiphilic DNA C-Stars

Many emerging technologies require materials with well-defined three-dimensional nanoscale architectures. Production of these structures is currently underpinned by self-assembling amphiphilic macromolecules or engineered all-DNA building blocks. Both of these approaches produce restricted ranges of crystal geometries due to synthetic amphiphiles' simple shape and limited specificity, or the technical difficulties in designing space-filling DNA motifs with targeted shapes. We have overcome these limitations with amphiphilic DNA nanostructures, or "C-Stars", that combine the design freedom and facile functionalization of DNA-based materials with robust hydrophobic interactions. C-Stars self-assemble into single crystals exceeding 40 μm in size with lattice parameters exceeding 20 nm.

Limiting the valence: advancements and new perspectives on patchy colloids, soft functionalized nanoparticles and biomolecules

Artistic representation of limited valance units consisting of a soft core (in blue) and a small number of flexible bonding patches (in orange).