Design space for complex DNA structures

Suppressing high-dimensional crystallographic defects for ultra-scaled DNA arrays

While DNA-directed nano-fabrication enables the high-resolution patterning for conventional electronic materials and devices, the intrinsic self-assembly defects of DNA structures present challenges for further scaling into sub-1 nm technology nodes. The high-dimensional crystallographic defects, including line dislocations and grain boundaries, typically lead to the pattern defects of the DNA lattices. Using periodic line arrays as model systems, we discover that the sequence periodicity mainly determines the formation of line defects, and the defect rate reaches 74% at 8.2-nm line pitch. To suppress high-dimensional defects rate, we develop an effective approach by assigning the orthogonal sequence sets into neighboring unit cells, reducing line defect rate by two orders of magnitude at 7.5-nm line pitch. We further demonstrate densely aligned metal nano-line arrays by depositing metal layers onto the assembled DNA templates. The ultra-scaled critical pitches in the defect-free DNA arrays may further promote the dimension-dependent properties of DNA-templated materials.

Regulation of 2D DNA Nanostructures by the Coupling of Intrinsic Tile Curvature and Arm Twist

The overwinding and underwinding of DNA duplexes between junctions have been used in designing left- and right-handed DNA origami nanostructures, respectively. For DNA tubes obtained from self-assembled tiles, only a theoretical approach of the intrinsic curvature of the tiles has been previously used to explain their formation. Details regarding the quantitative and structural descriptions of the tile's intrinsic curvature in DNA nanostructures have so far never been addressed. In this work, we designed three types of tile cores built around a circular scaffold using three- and four-branched junctions. Joining the tile cores with arms having two kinds of inter-tile distances, an odd and an even number of DNA half-turns, tended to form planar 2D lattices and tubes, respectively. Streptavidin bound to biotin was used as a labeling technique to characterize the inside and outside surfaces of the tubes and thereby the tile conformation of dihedrals with addressable faces. DNA tubes with either right- or left-handed chirality were obtained by the coupling of the intrinsic curvature of the tiles with the arm twist. We were able to assign the chiral indices (n,m) to a tube with its structure resolved by AFM at the single-tile level and therefore to estimate the global curvature of the tube (or its component tile) using a regular polygon model that approximated its transverse section. A deeper understanding of the integrated actions of different types of twisting forces on DNA tubes will be extremely helpful in engineering more elaborate DNA nanostructures in the future.

Automated exploration of DNA-based structure self-assembly networks

Finding DNA sequences capable of folding into specific nanostructures is a hard problem, as it involves very large search spaces and complex nonlinear dynamics. Typical methods to solve it aim to reduce the search space by minimizing unwanted interactions through restrictions on the design (e.g. staples in DNA origami or voxel-based designs in DNA Bricks). Here, we present a novel methodology that aims to reduce this search space by identifying the relevant properties of a given assembly system to the emergence of various families of structures (e.g. simple structures, polymers, branched structures). For a given set of DNA strands, our approach automatically finds chemical reaction networks (CRNs) that generate sets of structures exhibiting ranges of specific user-specified properties, such as length and type of structures or their frequency of occurrence. For each set, we enumerate the possible DNA structures that can be generated through domain-level interactions, identify the most prevalent structures, find the best-performing sequence sets to the emergence of target structures, and assess CRNs' robustness to the removal of reaction pathways. Our results suggest a connection between the characteristics of DNA strands and the distribution of generated structure families.

DNA dynamics and computation based on toehold-free strand displacement

We present a simple and effective scheme of a dynamic switch for DNA nanostructures. Under such a framework of toehold-free strand displacement, blocking strands at an excess amount are applied to displace the complementation of specific segments of paired duplexes. The functional mechanism of the scheme is illustrated by modelling the base pairing kinetics of competing strands on a target strand. Simulation reveals the unique properties of toehold-free strand displacement in equilibrium control, which can be leveraged for information processing. Based on the controllable dynamics in the binding of preformed DNA nanostructures, a multi-input-multi-output (MIMO) Boolean function is controlled by the presence of the blockers. In conclusion, we implement two MIMO Boolean functions (one with 4-bit input and 2-bit output, and the other with 16-bit input and 8-bit output) to showcase the controllable dynamics.

Synthetic DNA constructs can to used to recognise and respond to input signals. Here the authors present complex DNA nanostructures with toehold-free strand displacement for generation of ON/OFF switches and Boolean gates.

The hierarchical assembly of a multi-level DNA ring-based nanostructure in a precise order and its application for screening tumor cells

DNA nanotechnology can be used to precisely construct nanostructures of different shapes, sizes and surface chemistry, which is appreciated in a variety of areas such as biomaterials, nanodevices, disease diagnosis, imaging, and drug delivery. Enzymatic degradation resistance and cell-targeting capability are indispensable for the applications of DNA nanostructures in biological and biomedical fields, and is challenging to rationally design the desirable nanoscale DNA materials suitable for the clinical translation by the existing assembly methodologies. Herein, we present a simple and efficient method for the hierarchical assembly of a three-level DNA ring-based nanostructure (DNA h-Nanoring) in a precise order, where DNA compositions at the primary level, the second level and the third level are a single DNA ring, two-ring-hybridized duplex and uniform complex macro-cycle, respectively. Most as-assembled DNA h-Nanorings exhibit the regular two-dimensional cycle-shaped structure characterized by atomic force microscopy (AFM). The Nanoring exhibits a significantly enhanced resistance to enzymatic attack, such that it can remain intact in 10% fetal bovine serum (FBS) for 24 h, and even stably exist in the presence of nuclease at a high concentration. More importantly, it is very easy to modify the DNA h-Nanoring with functional moieties (e.g., targeting ligand aptamer) because there are many single-stranded fragments available for further hybridization. By combining with receptor-targeted Sgc8, the nanoring can be used to accomplish the cell imaging and criminate target CEM cells from control cells, demonstrating a potential platform for in vivo tumor imaging and targeted chemotherapeutics delivery.

Two-layer stacked multi-arm junction tiles and nanostructures assembled with small circular DNA molecules serving as scaffolds

One-layer multi-arm junction (mAJ) motifs have been investigated extensively for many kinds of planar 2D (two-dimension) lattices, surface-curved 3D (three-dimension) polyhedra, and complex 3D wireframe and tensegrity structures. Herein, we report the weaving strategy to achieve two-layer stacked multi-arm junction tiles (abbreviated as mAJ²) of 3AJ² and 4AJ², and several primary tessellation nanostructures of nanocages and 2D rhombus lattices carrying beautifully embossed 4-point stars. Challenges for perfect tessellation are also raised regarding the increase of motif complexity from 2D to 3D.

Design and synthesis of pleated DNA origami nanotubes with adjustable diameters

DNA origami allows for the synthesis of nanoscale structures and machines with nanometre precision and high yields. Tubular DNA origami nanostructures are particularly useful because their geometry facilitates a variety of applications including nanoparticle encapsulation, the construction of artificial membrane pores and as structural scaffolds that can uniquely spatially arrange nanoparticles in circular, linear and helical arrays. Here we report a system of parametrization for the design of radially symmetric DNA origami nanotubes with adjustable diameter, length, crossover density, pleat angle and chirality. The system is implemented into a computational algorithm that provides a practical means to navigate the complex geometry of DNA origami nanotube design. We apply this in the design, synthesis and characterization of novel DNA origami nanotubes. These include structures with pleated walls where the same number of duplexes can form nanotubes with different diameters, and to vary the diameter within the same structure. We also construct nanotubes that can be reconfigured into different chiral shapes. Finally, we explore the effect of strain on the local and global geometry of DNA origami nanotubes and demonstrate how pleated walls can provide a strategy to rigidify nanotubes and to construct closely packed parallel duplexes.

Addressable DNA nanotubes with repetitive components

Extended DNA nanostructures have already been constructed in a repetitive arrangement from millions of building blocks, many more than currently feasible with even the gold standard of addressable self-assembled structures. In order to construct addressable DNA nanostructures with more building blocks, it is desirable to arrange the addressable components repetitively. Accordingly, the overall size of the structure can be multiplied by the level of repetition in the addressable strands. In this study, we present a nanotube system that combines two seemingly conflicting features: addressability and repetitiveness. Based on an understanding of the tubulation resulting from the intrinsic curvature of the components, we produce DNA nanotubes with addressability available along the axial direction of the self-assembled tubes, which are also programmably repetitive along the lateral direction.

DNA nanostructures from double-C-shaped motifs with controllable twist and curvature

We demonstrate twist and curvature engineering in DNA nanostructures from the scaffold-free approach. The DNA 'LEGO' bricks adopted in this study are double-C-shaped motifs, and extended nanostructures are constructed to visualize the structural details of twist or curvature. By systematically deleting and inserting base pairs at certain domains of the component motifs, we are able to study various levels of the twist and curvature of the resulting nanostructures comprehensively.

Complex wireframe DNA nanostructures from simple building blocks

DNA nanostructures with increasing complexity have showcased the power of programmable self-assembly from DNA strands. At the nascent stage of the field, a variety of small branched objects consisting of a few DNA strands were created. Since then, a quantum leap of complexity has been achieved by a scaffolded 'origami' approach and a scaffold-free approach using single-stranded tiles/bricks-creating fully addressable two-dimensional and three-dimensional DNA nanostructures designed on densely packed lattices. Recently, wireframe architectures have been applied to the DNA origami method to construct complex structures. Here, revisiting the original wireframe framework entirely made of short synthetic strands, we demonstrate a design paradigm that circumvents the sophisticated routing and size limitations intrinsic to the scaffold strand in DNA origami. Under this highly versatile self-assembly framework, we produce a myriad of wireframe structures, including 2D arrays, tubes, polyhedra, and multi-layer 3D arrays.

Triangulated Wireframe Structures Assembled Using Single-Stranded DNA Tiles

The field of structural DNA nanotechnology offers a wide range of design strategies with which to build structures with a desired aspect ratio, size, and shape. Compared with traditional close-packed DNA structures, triangulated wireframe structures require less material per surface or volume unit and improve the stability in biologically relevant conditions due to the reduced electrostatic repulsion. Herein, we expand the design space of the DNA single-stranded tile method to cover a range of anisotropic, finite, triangulated wireframe structures as well as a number of one-dimensional crystalline assemblies. These structures are composed of six-arm junctions with a single double helix as connecting edges that assemble in physiologically relevant salinities. For a reliable folding of the structures, single-stranded spacers 2-4 nucleotides long have to be introduced in the junction connecting neighboring arms. Coarse-grained molecular dynamics simulations using the oxDNA model suggests that the spacers prevent the stacking of DNA helices, thereby facilitating the assembly of planar geometries.

Hierarchical Assembly of DNA Nanostructures Based on Four-Way Toehold-Mediated Strand Displacement

Because of its attractive cost and yield, hierarchical assembly, in which constituent structures of lower hierarchy share a majority of components, is an appealing approach to scale up DNA self-assembly. A few strategies have already been investigated to combine preformed DNA nanostructures. In this study, we present a new hierarchical assembly method based on four-way toehold-mediated strand displacement to facilitate the combination of preformed DNA structural units. Employing such a method, we have constructed a series of higher-order structures composed of 5, 7, 9, 11, 13, and 15 preformed units respectively.

Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly

Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculations with oxDNA, a nucleotide-based model of DNA, to parametrize a coarser kinetic model that can reach the time and length scales needed to study the assembly mechanisms of these structures. We test the model by performing a detailed study of the assembly pathways for a two-dimensional target structure made up of 334 unique strands each of which are 42 nucleotides long. Without adjustable parameters, the model reproduces a critical temperature for the formation of the assembly that is close to the temperature at which assembly first occurs in experiments. Furthermore, the model allows us to investigate in detail the nucleation barriers and the distribution of critical nucleus shapes for the assembly of a single target structure. The assembly intermediates are compact and highly connected (although not maximally so), and classical nucleation theory provides a good fit to the height and shape of the nucleation barrier at temperatures close to where assembly first occurs.

Evolution of Structural DNA Nanotechnology

The research field entitled structural DNA nanotechnology emerged in the beginning of the 1980s as the first immobile synthetic nucleic acid junctions were postulated and demonstrated. Since then, the field has taken huge leaps toward advanced applications, especially during the past decade. This Progress Report summarizes how the controllable, custom, and accurate nanostructures have recently evolved together with powerful design and simulation software. Simultaneously they have provided a significant expansion of the shape space of the nanostructures. Today, researchers can select the most suitable fabrication methods, and design paradigms and software from a variety of options when creating unique DNA nanoobjects and shapes for a plethora of implementations in materials science, optics, plasmonics, molecular patterning, and nanomedicine.

DNA nanostructures constructed with multi-stranded motifs

Earlier studies in DNA self-assembly have foretold the feasibility of building addressable nanostructures with multi-stranded motifs, which is fully validated in this study. In realizing this feasibility in DNA nanotechnology, a diversified set of motifs of modified domain lengths is extended from a classic type. The length of sticky ends can be adjusted to form different dihedral angles between the matching motifs, which corresponds to different connecting patterns. Moreover, the length of rigidity core can also be tuned to result in different dihedral angles between the component helices of a certain motif therefore different numbers of component helices. The extended set of motifs is used for self-assembly of complex one dimensional, two dimensional and three dimensional structures.

DNA Origami Reorganizes upon Interaction with Graphite: Implications for High-Resolution DNA Directed Protein Patterning

Although there is a long history of the study of the interaction of DNA with carbon surfaces, limited information exists regarding the interaction of complex DNA-based nanostructures with the important material graphite, which is closely related to graphene. In view of the capacity of DNA to direct the assembly of proteins and optical and electronic nanoparticles, the potential for combining DNA-based materials with graphite, which is an ultra-flat, conductive carbon substrate, requires evaluation. A series of imaging studies utilizing Atomic Force Microscopy has been applied in order to provide a unified picture of this important interaction of structured DNA and graphite. For the test structure examined, we observe a rapid destabilization of the complex DNA origami structure, consistent with a strong interaction of single-stranded DNA with the carbon surface. This destabilizing interaction can be obscured by an intentional or unintentional primary intervening layer of single-stranded DNA. Because the interaction of origami with graphite is not completely dissociative, and because the frustrated, expanded structure is relatively stable over time in solution, it is demonstrated that organized structures of pairs of the model protein streptavidin can be produced on carbon surfaces using DNA origami as the directing material.

Self-assembly of fully addressable DNA nanostructures from double crossover tiles

DNA origami and single-stranded tile (SST) are two proven approaches to self-assemble finite-size complex DNA nanostructures. The construction elements appeared in structures from these two methods can also be found in multi-stranded DNA tiles such as double crossover tiles. Here we report the design and observation of four types of finite-size lattices with four different double crossover tiles, respectively, which, we believe, in terms of both complexity and robustness, will be rival to DNA origami and SST structures.

Rational design of DNA-actuated enzyme nanoreactors guided by single molecule analysis

The control of enzymatic reactions using nanoscale DNA devices offers a powerful application of DNA nanotechnology uniquely derived from actuation. However, previous characterization of enzymatic reaction rates using bulk biochemical assays reported suboptimal function of DNA devices such as tweezers. To gain mechanistic insight into this deficiency and to identify design rules to improve their function, here we exploit the synergy of single molecule imaging and computational modeling to characterize the three-dimensional structures and catalytic functions of DNA tweezer-actuated nanoreactors. Our analysis revealed two important deficiencies--incomplete closure upon actuation and conformational heterogeneity. Upon rational redesign of the Holliday junctions located at their hinge and arms, we found that the DNA tweezers could be more completely and uniformly closed. A novel single molecule enzyme assay was developed to demonstrate that our design improvements yield significant, independent enhancements in the fraction of active enzyme nanoreactors and their individual substrate turnover frequencies. The sequence-level design strategies explored here may aid more broadly in improving the performance of DNA-based nanodevices including biological and chemical sensors.

Effects of co-ordination number on the nucleation behaviour in many-component self-assembly

We report canonical and grand-canonical lattice Monte Carlo simulations of the self-assembly of addressable structures comprising hundreds of distinct component types. The nucleation behaviour, in the form of free-energy barriers to nucleation, changes significantly as the co-ordination number of the building blocks is changed from 4 to 8 to 12. Unlike tetrahedral structures – which roughly correspond to DNA bricks that have been studied in experiments – the shapes of the free-energy barriers of higher co-ordination structures depend strongly on the supersaturation, and such structures require a very significant driving force for structure growth before nucleation becomes thermally accessible. Although growth at high supersaturation results in more defects during self-assembly, we show that high co-ordination number structures can still be assembled successfully in computer simulations and that they exhibit self-assembly behaviour analogous to DNA bricks. In particular, the self-assembly remains modular, enabling in principle a wide variety of nanostructures to be assembled, with a greater spatial resolution than is possible in low co-ordination structures.

Self-assembly protocol design for periodic multicomponent structures

Assembling molecular superstructures with many distinct components will allow unprecedented control over morphology at the nanoscale. Recently, this approach has been used to assemble periodic structures with precisely defined features, such as repeating arrays of pores and channels, using a large number of building blocks. Here we propose a predictive tool that allows us to optimize the nucleation and growth of unbounded, ordered structures. In what follows, we call these structures 'crystals', even though they may only be periodic in one or two dimensions. We find that the nucleation barriers and growth pathways for crystals consisting of many components exhibit generic features that are very different from those of simple crystals. To illustrate the very non-classical nature of the nucleation and growth of such structures, we study the formation of one and two-dimensional crystals with multicomponent unit cells. We find that, whilst the boundaries in the non-periodic dimensions significantly affect the stabilities of these crystals, the nucleation barriers are largely determined by the local connectivity of the associated bulk crystal and are independent of the number of distinct components in the unit cell. We predict that the self-assembly of crystals with complex morphologies can be made to follow specific pathways toward the target structure that successively incorporate key features of the three-dimensional target structure. In contrast with simple crystals, it is possible to tune the kinetics of nucleation and growth separately, thus minimizing defect formation. We show how control over self-assembly pathways can be used to optimize the kinetics of formation of extended structures with arbitrary nanoscale patterns.

Size-controllable DNA nanoribbons assembled from three types of reusable brick single-strand DNA tiles

Precise control of nanostructure is a significant goal shared by supramolecular chemistry, nanotechnology and materials science. In DNA nanotechnology, methods of constructing desired DNA nanostructures using programmable DNA strands have been studied extensively and have become a promising branch of research, but developing universal and low-cost (in the sense of using fewer types of DNA strands) methods remains a challenge. In this work, we propose a novel approach to assemble size-controllable DNA nanoribbons with three types of reusable brick SSTs (single-stranded DNA tiles), where the control of ribbon size is achieved by regulating the concentration ratio between manipulative strands and packed single-stranded DNA tiles. In our method, three types of brick SSTs are sufficient in assembling DNA nanoribbons of different sizes, which is much less than the number of types of unique tile-programmable assembling strategy, thus achieving a universal and low-cost method. The assembled DNA nanoribbons are observed and analyzed by atomic force microscopy (AFM). Experimental observations strongly suggest the feasibility and reliability of our method.

A Compact DNA Cube with Side Length 10 nm

A small and compact DNA cube with zeptoliter volume is constructed by means of a generalized DNA brick concept using short synthetic oligonucleotides with varying lengths. By mimicking design principles from the DNA origami technique, the DNA cube offers higher stability and assembly yields compared to other approaches. Its potential application as nanoscale fluorescent probe is demonstrated using super-resolution imaging.

Rational design of self-assembly pathways for complex multicomponent structures

The field of complex self-assembly is moving toward the design of multiparticle structures consisting of thousands of distinct building blocks. To exploit the potential benefits of structures with such "addressable complexity," we need to understand the factors that optimize the yield and the kinetics of self-assembly. Here we use a simple theoretical method to explain the key features responsible for the unexpected success of DNA-brick experiments, which are currently the only demonstration of reliable self-assembly with such a large number of components. Simulations confirm that our theory accurately predicts the narrow temperature window in which error-free assembly can occur. Even more strikingly, our theory predicts that correct assembly of the complete structure may require a time-dependent experimental protocol. Furthermore, we predict that low coordination numbers result in nonclassical nucleation behavior, which we find to be essential for achieving optimal nucleation kinetics under mild growth conditions. We also show that, rather surprisingly, the use of heterogeneous bond energies improves the nucleation kinetics and in fact appears to be necessary for assembling certain intricate 3D structures. This observation makes it possible to sculpt nucleation pathways by tuning the distribution of interaction strengths. These insights not only suggest how to improve the design of structures based on DNA bricks, but also point the way toward the creation of a much wider class of chemical or colloidal structures with addressable complexity.

DNA brick crystals with prescribed depths

The ability to assemble functional materials with precise spatial arrangements is important for applications ranging from protein crystallography to photovoltaics. Here, we describe a general framework for constructing two-dimensional crystals with prescribed depths and sophisticated three-dimensional features. The crystals are self-assembled from single-stranded DNA components called DNA bricks. We demonstrate the experimental construction of DNA brick crystals that can grow to micrometre size in their lateral dimensions with precisely controlled depths up to 80 nm. They can be designed to pack DNA helices at angles parallel or perpendicular to the plane of the crystal and to display user-specified sophisticated three-dimensional nanoscale features, such as continuous or discontinuous cavities and channels.

Assembly of barcode-like nucleic acid nanostructures

Barcode-like (BC) nanopatterns from programmed self-assembly of nucleic acids (DNA and RNA) are reported. BC nanostructures are generated by the introduction of open spaces at selected sites to an otherwise closely packed, plain, rectangle nucleic acid nanostructure. This strategy is applied to nanostructures assembled from both origami approach and single stranded tile approach.

Numerical evidence for nucleated self-assembly of DNA brick structures

The observation by Ke et al. [Science 338, 1177 (2012)] that large numbers of short, predesigned DNA strands can assemble into three-dimensional target structures came as a great surprise, as no colloidal self-assembling system has ever achieved the same degree of complexity. That failure seemed easy to rationalize: the larger the number of distinct building blocks, the higher the expected error rate for self-assembly. The experiments of Ke et al. have disproved this argument. Here, we report Monte Carlo simulations of the self-assembly of a DNA brick cube, comprising approximately 1000 types of DNA strand, using a simple model. We model the DNA strands as lattice tetrahedra with attractive patches, the interaction strengths of which are computed using a standard thermodynamic model. We find that, within a narrow temperature window, the target structure assembles with high probability. Our simulations suggest that misassembly is disfavored because of a slow nucleation step. As our model incorporates no aspect of DNA other than its binding properties, these simulations suggest that, with proper design of the building blocks, other systems, such as colloids, may also assemble into truly complex structures.

Complex reconfiguration of DNA nanostructures

Nucleic acids have been used to create diverse synthetic structural and dynamic systems. Toehold-mediated strand displacement has enabled the construction of sophisticated circuits, motors, and molecular computers. Yet it remains challenging to demonstrate complex structural reconfiguration in which a structure changes from a starting shape to another arbitrarily prescribed shape. To address this challenge, we have developed a general structural-reconfiguration method that utilizes the modularly interconnected architecture of single-stranded DNA tile and brick structures. The removal of one component strand reveals a newly exposed toehold on a neighboring strand, thus enabling us to remove regions of connected component strands without the need to modify the strands with predesigned external toeholds. By using this method, we reconfigured a two-dimensional rectangular DNA canvas into diverse prescribed shapes. We also used this method to reconfigure a three-dimensional DNA cuboid.