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DNA tensegrity triangles self-assemble into rhombohedral three-dimensional crystals via sticky ended cohesion. Crystals containing two-nucleotide (nt) sticky ends (GA:TC) have been reported previously, and those crystals diffracted to 4.9 Å at beam line NSLS-I-X25. Here, we analyze the effect of varying sticky end lengths and sequences, as well as the impact of 5’- and 3’-phosphates on crystal formation and resolution. Tensegrity triangle motifs having 1-, 2- and 3-nt sticky ends all form crystals. X-ray diffraction data from the same beam line reveal that the crystal resolution for a 1-nt sticky end (G:C) and a 3-nt sticky end (GAT:ATC) were 3.4 Å and 4.2 Å respectively. Resolutions were determined from complete data sets in each case. We also conducted trials that examined every possible combination of 1-nucleotide and 2-nucleotide sticky-ended phosphorylated strands and successfully crystallized all 16 possible combinations of strands. We observed the position of the 5’-phosphate on either the crossover (1), helical (2), or central strand (3) affected the resolution of the self-assembled crystals for the 2-turn monomer (3.0 Å for 1–2P-3P) and 2-turn dimer sticky ended (4.1 Å for 1–2-3P) systems. We have also examined the impact of the identity of the base flanking the sticky ends, as well as the use of 3’-sticky ends. We conclude that crystal resolution is not a simple consequence of the thermodynamics of the direct nucleotide pairing interactions involved in molecular cohesion in this system.

A major challenge in material design is to couple nanoscale molecular and supramolecular events into desired chemical, physical, and mechanical properties at the macroscopic scale. Here, a novel self-assembled DNA crystal actuator is reported, which has reversible, directional expansion and contraction for over 50 μm in response to versatile stimuli, including temperature, ionic strength, pH, and redox potential. The macroscopic actuation is powered by cooperative dissociation or cohesion of thousands of DNA sticky ends at the designed crystal contacts. The increase in crystal porosity and cavity in the expanded state dramatically enhances the crystal capability to accommodate/encapsulate nanoparticles/proteins, while the contraction enables a "sponge squeezing" motion for releasing nanoparticles. This crystal actuator is envisioned to be useful for a wide range of applications, including powering self-propelled robotics, sensing subtle environmental changes, constructing functional hybrid materials, and working in drug controlled-release systems.

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.

64th Annual Biophysical Society Meeting, San Diego, 15 Feb 2020 - 19 Feb 2020; Biophysical journal 118(3), 137a - 138a (2020). doi:10.1016/j.bpj.2019.11.877, Outrunning radiation damage, highly intense femtosecond pulses of X-ray free-electron lasers (XFELs) open up the possibility of structure determination of macromolecules to viruses at room temperature, by aggregating diffraction patterns recorded from uncrystallized single-particles. A key challenge in XFEL single-particle diffractive imaging (SPI) is to either constrain the orientation of the particle or to determine it from each of the very noisy weak diffraction patterns. Here we report a unique approach to address these challenges using structural DNA nanotechnology. A DNA-origami ���rigid tail��� is site-specifically attached to the macromolecule to flow-align it in a thin liquid jet, and also provides a strong holographic reference. In a proof-of-principle study, the computational design and production of the DNA-origami-target construct has been achieved and the experimental results obtained from the Linac Coherent Light Source (LCLS), USA show the alignment of the target single-particle, consistent with simulations, at extremely low concentrations approaching single-molecule in the interaction region with the nanofocus hard X-ray laser beam, in a sum of as few as a thousand single-shots. The results open up the possibility of single-molecule diffractive imaging in solution with XFEL pulses. Acknowledgements: The Human Frontier Science Program (RGP0010/2017)., Published by Soc., Bethesda, Md.

Nature self-assembles functional materials by programming flexible linear arrangements of molecules and then folding them to make 2D and 3D objects. To understand and emulate this process, we have made emulsion droplets with specific recognition and controlled valence. Uniquely monovalent droplets form dimers: divalent lead to polymer-like chains, trivalent allow for branching, and programmed mixtures of different valences enable a variety of designed architectures and the ability to subsequently close and open structures. Our functional building blocks are a hybrid of micrometer-scale emulsion droplets and nanoscale DNA origami technologies. Functional DNA origami rafts are first added to droplets and then herded into a patch using specifically designated "shepherding" rafts. Additional patches with the same or different specificities can be formed on the same droplet, programming multiflavored, multivalence droplets. The mobile patch can bind to a patch on another droplet containing complementary functional rafts, leading to primary structure formation. Further binding of nonneighbor droplets can produce secondary structures, a third step in hierarchical self-assembly. The use of mobile patches rather than uniform DNA coverage has the advantage of valence control at the expense of slow kinetics. Droplets with controlled flavors and valences enable a host of different material and device architectures.

Over the past 35 years, DNA has been used to produce various nanometer-scale constructs, nanomechanical devices, and walkers. Construction of complex DNA nanostructures relies on the creation of rigid DNA motifs. Paranemic crossover (PX) DNA is one such motif that has played many roles in DNA nanotechnology. Specifically, PX cohesion has been used to connect topologically closed molecules, to assemble a three-dimensional object, and to create two-dimensional DNA crystals. Additionally, a sequence-dependent nanodevice based on conformational change between PX and its topoisomer, JX2, has been used in robust nanoscale assembly lines, as a key component in a DNA transducer, and to dictate polymer assembly. Furthermore, the PX motif has recently found a new role directly in basic biology, by possibly serving as the molecular structure for double-stranded DNA homology recognition, a prominent feature of molecular biology and essential for many crucial biological processes. This review discusses the many attrib...

An electro-optical modulator was constructed using a DNA nanostructure scaffold with oligomers of poly(phenylenevinylene) and polyaniline. A molecular device containing one each of the functional molecules was assembled in a DNA origami. The constructs formed an "X" shape and were visualized by atomic force microscopy. In response to redox reconfiguration, the device reversibly altered fluorescence signal output. This molecular self-assembly strategy provides opportunities to make unique material composites that are difficult to achieve by blending. The strategy offers a "plug and play" format that may lead to many new functions.

We describe the half-lap model, a mathematical framework that captures the geometric constraints of rigid tiles that are branched junction molecules used as building blocks for tile-based DNA self-assembly. The model captures not only the combinatorial structures of the sets of cohesive ends on the tiles, but also the specific geometry of the inter-arm angles of the tiles and most critically the relative orientations of adhering tiles. We illustrate the functionality of the model by providing provably optimal DNA self-assembly strategies to construct Platonic and Archimedean 3-regular polyhedral skeletons and computing the minimum number of tile types and bond-edge types for each target structure. We further demonstrate the utility of the model by using it to analyze the benefits and limitations of palindromic rigid tiles. Moreover, we give explicit combinatorial and geometric descriptions of the tiles needed for each construction.

Although stereochemistry has been a central focus of the molecular sciences since Pasteur, its province has previously been restricted to the nanometric scale. We have programmed the self-assembly of micron-sized colloidal clusters with structural information stemming from a nanometric arrangement. This was done by combining DNA nanotechnology with colloidal science. Using the functional flexibility of DNA origami in conjunction with the structural rigidity of colloidal particles, we demonstrate the parallel self-assembly of three-dimensional microconstructs, evincing highly specific geometry that includes control over position, dihedral angles, and cluster chirality.

DNA nanostructures are created by exploiting the high fidelity base-pairing interactions of double-stranded branched DNA molecules. These structures present a convenient medium for the self-assembly of macroscopic 3D crystals. In some self-assemblies in this system, crystals can be formed by lowering the temperature, and they can be dissolved by raising it. The ability to monitor the formation and melting of these crystals yields information that can be used to monitor crystal formation and growth. Here, we describe the development of an inexpensive tool that enables direct observation of the crystal growth process as a function of both time and temperature. Using the hanging-drop crystallization of the well-characterized 2-turn DNA tensegrity triangle motif for our model system, its response to temperature has been characterized visually.

Self-replication and evolution under selective pressure are inherent phenomena in life, and but few artificial systems exhibit these phenomena. We have designed a system of DNA origami rafts that exponentially replicates a seed pattern, doubling the copies in each diurnal-like cycle of temperature and ultraviolet illumination, producing more than 7 million copies in 24 cycles. We demonstrate environmental selection in growing populations by incorporating pH-sensitive binding in two subpopulations. In one species, pH-sensitive triplex DNA bonds enable parent-daughter templating, while in the second species, triplex binding inhibits the formation of duplex DNA templating. At pH 5.3, the replication rate of species I is ∼1.3-1.4 times faster than that of species II. At pH 7.8, the replication rates are reversed. When mixed together in the same vial, the progeny of species I replicate preferentially at pH 7.8; similarly at pH 5.3, the progeny of species II take over the system. This addressable selectivity should be adaptable to the selection and evolution of multi-component self-replicating materials in the nanoscopic-to-microscopic size range.

Self-assembly using DNA origami methods requires determining a route for the scaffolding strand through the targeted structure. Here we provide strategies and software tools for determining optimal routes for reporter or scaffolding strands through graph-like (ball-and-rod) constructs. The approach applies to complex constructs, for example arbitrary geometric embeddings of graphs rather than surface meshes, lattice subsets, and meshes on higher genus surfaces than spheres. The software notably allows the user the flexibility of specifying ranked preferences for augmenting edges and for the possible configurations of branched junctions. The greater topological complexity of arbitrary graph embeddings and meshes on higher genus surfaces can result in scaffolding strand routes that are knotted in 3 space, so we also present necessary caveats for these settings.

We present a computational framework to model RNA based nanostructures and study their microscopic structures. We model hexagonal nanotubes made of 6 dsRNA (RNTs) connected by double crossover (DX) at different positions. Using several hundred nano-second (ns) long all-atom molecular dynamics simulations, we study the atomic structure, conformational change and elastic properties of RNTs in the presence of explicit water and ions. Based on several structural quantities such as root mean square deviation (RMSD) and root mean square fluctuation (RMSF), we find that the RNTs are almost as stable as DNA nanotubes (DNTs). Although the central portion of the RNTs maintain its cylindrical shape, both the terminal regions open up to give rise to a gating like behavior which can play a crucial role in drug delivery. From the bending angle distribution, we observe that the RNTs are more flexible than DNTs. The calculated persistence length of the RNTs is in the micron range which is an order of magnitude higher than that of a single dsRNA. The stretch modulus of the RNTs from the contour length distribution is in the range of 4-7 nN depending on the sequence. The calculated persistence length and stretch modulus are in the same range of values as in the case of DNTs. To understand the structural properties of RNTs at the individual base-pair level we have also calculated all the helicoidal parameters and analyzed the relative flexibility and rigidity of RNTs having a different sequence. These findings emphasized the fascinating properties of RNTs which will expedite further theoretical and experimental studies in this field.

Single-wall carbon nanotubes (SWCNTs) are known to embody many desirable features for nanoelectronic and photonic applications, including excellent electronic and optical properties and mechanical robustness. To utilize these species in a bottom-up nanotechnological approach, it is necessary to be able to place them in precise absolute positions within a larger framework, without disturbing the conduction surface. Although it is well-known how to orient one or two nanotubes on a DNA origami, precise placement has eluded investigators previously. Here, we report a method of attaching a strand of DNA on the reactive end of a SWCNT, and then of using that DNA strand to place the nanotube at a specific site on a 2D DNA origami raft. We demonstrate that it is possible to place one or two nanotubes on such a DNA origami raft.

DNA, when folded into nanostructures of customizable shapes, is capable of spacing and arranging external ligands in a desired geometric pattern with nanometer-precision. This allows DNA to serve as an excellent, biocompatible scaffold for complex spatial pattern-recognizing displays. In this report, we demonstrate that a templated designer DNA nanostructure achieves multi-ligand display with precise spatial pattern-recognition, representing a unique strategy in synthesizing potent viral sensors and inhibitors. Specifically, a star-shaped DNA architecture, carrying five molecular beacon-like motifs, was constructed to display ten dengue virus envelope protein domain-III (ED3)-binding aptamers into a 2D pattern precisely matching the pentagonal arrangement of ED3 clusters on the dengue viral surface. The resulting spatial pattern recognition and multivalent interactions achieve high dengue-binding avidity, conferring direct, highly-sensitive, facile, low-cost, and rapid sensing as well as potent viral inhibition capability. Our molecular-platform design strategy could be adapted to detect and combat other disease-causing pathogens, including bacteria and microbial-toxins, by generating the requisite ligand patterns on customized DNA nanoarchitectures.

Self-replication and exponential growth are ubiquitous in nature but until recently there were few examples of artificial self-replication. Often replication is a templated process where a parent produces a single offspring, doubling the population in each generation. Many species however produce more than one offspring at a time, enabling faster population growth and higher probability of species perpetuation. We have made a system of cross-shaped origami tiles that yields a number of offspring, four to eight or more, depending on the concentration of monomer units to be assembled. The parent dimer template serves as a seed to crystallize a one-dimensional crystal, a ladder. The ladder rungs are then UV–cross-linked and the offspring are then released by heating, to yield a litter of autonomous daughters. In the complement study, we also optimize the growth conditions to speed up the process and yield a 10(3) increase in the growth rate for the single-offspring replication system. Self-replication and exponential growth of autonomous motifs is useful for fundamental studies of selection and evolution as well as for materials design, fabrication, and directed evolution. Methods that increase the growth rate, the primary evolutionary drive, not only speed up experiments but provide additional mechanisms for evolving materials toward desired functionalities.

The PX motif of DNA is a four-stranded structure in which two parallel juxtaposed double-helical domains are fused by crossovers at every point where the strands approach each other. Consequently, its twist and writhe are approximately half of those of conventional DNA. This property has been shown to relax supercoiled plasmid DNA under circumstances in which head-to-head homology exists within the plasmid; the homology can be either complete homology or every-other-half-turn homology, known as PX homology. It is clearly of interest to establish whether the cell contains proteins that interact with this unusual and possibly functional motif. We have examined Escherichia coli extracts to seek such a protein. We find by gel mobility studies that the PX motif is apparently bound by a cellular component. Fractionation of this binding activity reveals that the component is DNA polymerase I (Pol I). Although the PX motif binds to Pol I, we find that PX-DNA is not able to serve as a substrate for the extension of a shortened strand. We cannot say at this time whether the binding is a coincidence or whether it represents an activity of Pol I that is currently unknown. We have modeled the interaction of Pol I and PX-DNA using symmetry considerations and molecular dynamics.

Structural DNA nanotechnology combines branched DNA junctions with sticky-ended cohesion to create self-assembling macromolecular architectures. One of the key goals of structural DNA nanotechnology is to construct three-dimensional (3D) crystalline lattices. Here we present a new DNA motif and a strategy that has led to the assembly of a 3D lattice. We have determined the X-ray crystal structures of two related constructs to 3.1 Å resolution using bromine-derivatized crystals. The motif we used employs a five-nucleotide repeating sequence that weaves through a series of two-turn DNA duplexes. The duplexes are tied into a layered structure that is organized and dictated by a concert of four-arm junctions; these in turn assemble into continuous arrays facilitated by sequence-specific sticky-ended cohesion. The 3D X-ray structure of these DNA crystals holds promise for the design of new structural motifs to create programmable 3D DNA lattices with atomic spatial resolution. The two arrays differ by the use of four or six repeats of the five-nucleotide units in the repeating but statistically disordered central strand. In addition, we report a 2D rhombuslike array formed from similar components.

The tensegrity triangle is a robust DNA motif that can self-assemble to generate macroscopic three-dimensional crystals. However, the stability of these crystals is dependent on the high ionic conditions used for crystal growth. Here we demonstrate that a triplex-forming oligonucleotide can be used to direct the specific intercalation, and subsequent photo-cross-linking, of 4,5',8-trimethylpsoralen to single or multiple loci within or between the tiles of the crystal. Cross-linking between the tiles of the crystal improves their thermal stability. Such an approach is likely to facilitate the removal of crystals from their mother liquor and may prove useful for applications that require greater crystal stability.

The founding of structural DNA nanotechnology is described, birth pangs and all by the originator of the field. The excitement of the invention, the characters, and the roles are evident as a true celebration of scientific research.

Catenation is the process by which cyclic strands are combined like the links of a chain, whereas knotting changes the linking properties of a single strand. In the cell, topoisomerases catalyzing strand passage operations enable the knotting and catenation of DNA so that single- or double-stranded segments can be passed through each other. Here, we use a system of closed DNA structures involving a paranemic motif, called PX-DNA, to bind double strands of DNA together. These PX-cohesive closed molecules contain complementary loops whose linking by Escherichia coli topoisomerase 1 (Topo 1) leads to various types of catenated and knotted structures. We were able to obtain specific DNA topological constructs by varying the lengths of the complementary tracts between the complementary loops. The formation of the structures was analyzed by denaturing gel electrophoresis, and the various topologies of the constructs were characterized using the program Knotilus.

PX-DNA is a four-stranded DNA structure that has been implicated in the recognition of homology, either continuously, or in an every-other-half-turn fashion. Some of the structural features of the molecule have been noted previously, but the structure requires further characterization. Here, we report atomic force microscopic characterization of PX molecules that contain periodically placed biotin groups, enabling the molecule to be labeled by streptavidin molecules at these sites. In comparison with conventional double stranded DNA and with antiparallel DNA double crossover molecules, it is clear that PX-DNA is a more dynamic structure. Furthermore, the spacing between the nucleotide pairs along the helix axis is shorter, suggesting a mixed B/A structure. Circular dichroism spectroscopy indicates unusual features in the PX molecule that are absent in both the molecules to which it is compared.

This manuscript reports an effort to stabilize self-assembled DNA crystals. Owing to their weak inter-unit cohesion, self-assembled DNA crystals are fragile, which limits the potential applications of such crystals. To overcome this problem, another molecule was introduced, which binds to the cohesive sites and stabilizes the inter-unit interactions. The extra interactions greatly improve the stability of the DNA crystals. The original DNA crystals are only stable in solutions of high ionic strength (e.g., ≥1.2 M (NH4)2SO4); in contrast, the stabilized crystals can be stable at ionic strengths as low as that of a 0.02 M solution of (NH4)2SO4. The current strategy is expected to represent a general approach for increasing the stability of self-assembled DNA nanostructures for potential applications, for example, as structural scaffolds and molecular sieves.

DNA nanostructured tiles play an active role in their own self-assembly in the system described herein whereby they initiate a binding event that produces a cascading assembly process. We present DNA tiles that have a simple but powerful property: they respond to a binding event at one end of the tile by passing a signal across the tile to activate a binding site at the other end. This action allows sequential, virtually irreversible self-assembly of tiles and enables local communication during the self-assembly process. This localized signal-passing mechanism provides a new element of control for autonomous self-assembly of DNA nanostructures.

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 P3

Complex structures and devices, both natural and manmade, are often constructed sequentially. From crystallization to embryogenesis, a nucleus or seed is formed and built upon. Sequential assembly allows for initiation, signaling, and logical programming, which are necessary for making enclosed, hierarchical structures. Although biology relies on such schemes, they have not been available in materials science. Here, we demonstrate programmed sequential self-assembly of DNA functionalized emulsions. The droplets are initially inert because the grafted DNA strands are pre-hybridized in pairs. Active strands on initiator droplets then displace one of the paired strands and thus release its complement, which in turn activates the next droplet in the sequence, akin to living polymerization. Our strategy provides time and logic control during the self-assembly process, and offers a new perspective on the synthesis of materials., Natural complex systems are often constructed by sequential assembly but this is not readily available for synthetic systems. Here, the authors program the sequential self-assembly of DNA functionalized emulsions by altering the DNA grafted strands.

A 3D array of organic semiconductors was assembled using a DNA scaffold. An octameric aniline molecule (“octaniline”) was incorporated into a DNA building block based on a dimeric tensegrity triangle. The construct self-assembled to form a 3D crystal. Reversible redox conversion between the pernigraniline and leucoemeraldine states of the octaniline is retained in the crystal. Protonic doping gave emeraldine salt at pH 5, corresponding to the conductive form of polyaniline. Redox cycling within the crystal was visualized by color changes and Raman microscopy. The ease of conversion between the octaniline states suggests that it is a viable electronic switch within a unique 3D structure.

We describe two DNA-templated ligation strategies: native chemical ligation (NCL), and thiol-disulfide exchange. Both systems result in successful ligation in the presence of a DNA template. The stability of the product from the NCL reaction relies on exogenous thiol, while the thiol-disulfide reaction proceeds in a catalyst-free manner.

In this paper we demonstrate the power of a model of tile self-assembly based on active glues which can dynamically change state. We formulate the Signal-passing Tile Assembly Model (STAM), based on the model of Padilla et al. [24] to be asynchronous, allowing any action of turning a glue on or off, attaching a new tile, or breaking apart an assembly to happen in any order. Within this highly generalized model we provide three new solutions to tile self-assembly problems that have been addressed within the abstract Tile Assembly Model and its variants, showing that signal passing tiles allow for substantial improvement across multiple complexity metrics. Our first result utilizes a recursive assembly process to achieve tile-type efficient assembly of linear structures, using provably fewer tile types than what is possible in standard tile assembly models. Our second system of signal-passing tiles simulates any Turing machine with high fuel efficiency by using only a constant number of tiles per computation step. Our third system assembles the discrete Sierpinski triangle, demonstrating that this pattern can be strictly self-assembled within the STAM. This result is of particular interest in that it is known that this pattern cannot self-assemble within a number of well studied tile self-assembly models. Notably, all of our constructions are at temperature 1, further demonstrating that signal-passing confers the power to bypass many restrictions found in standard tile assembly models.

Amyloid fibrils are ordered, insoluble protein aggregates that are associated with neurodegenerative conditions such as Alzheimer’s disease1. The fibrils have a common rod-like core structure, formed from an elongated stack of β-strands, and have a rigidity similar to silk (Young’s modulus of 0.2-14 Gpa)2. They also exhibit high thermal and chemical stability3, and can be assembled in vitro from short synthetic non-disease-related peptides4,5. As a result, they are of significant interest in the development of self-assembled materials for bionanotechnology applications6. Synthetic DNA molecules have previously been used to form intricate structures and organize other materials such as metal nanoparticles7,8, and could in principle be used to nucleate and organize amyloid fibrils. Here we show that DNA origami nanotubes can sheathe amyloid fibrils formed within them. The fibrils are built by modifying the synthetic peptide fragment corresponding to residues 105-115 of the amyloidogenic protein transthyretin (TTR)9, and a DNA origami10 construct is used to form 20-helix DNA nanotubes with sufficient space for the fibrils inside. Once formed, the fibril-filled nanotubes can be organized onto predefined two-dimensional platforms via DNA-DNA hybridization interactions.

The linear, double-helical structure of DNA was initially recognized as beautiful, as well as being informative about the mechanism of heredity. Recently, branched DNA molecules have been used to produce nanoscale objects, crystals and machines, all the products of a new field: structural DNA nanotechnology. The inspiration for much of this work has been art, starting from the notion that Escher's woodcut Depth was analogous to a molecular crystal of branched DNA. The article describes how connecting branched molecules together with the “sticky ends” used by genetic engineers has led to 3D crystals, and how Dalí's Butterfly Landscape illuminates the relationship between wrappings of DNA and the crossings in knots or links. Disparate aesthetic patterns are related to branched DNA motifs and constructions.

DNA is a very useful molecule for the programmed self-assembly of 2D and 3D nanoscale objects.[1] The design of these structures exploits Watson–Crick hybridization and strand exchange to stitch linear duplexes into finite assemblies.[2–4] The dimensions of these complexes can be increased by over five orders of magnitude through self-assembly of cohesive single-stranded segments (sticky ends).[5,6] Methods that exploit the sequence addressability of DNA nanostructures will enable the programmable positioning of components in 2D and 3D space, offering applications such as the organization of nanoelectronics,[7] the direction of biological cascades,[8] and the structure determination of periodically positioned molecules by X-ray diffraction.[9] To this end we present a macroscopic 3D crystal based on the 3-fold rotationally symmetric tensegrity triangle[3,6] that can be functionalized by a triplex-forming oligonucleotide on each of its helical edges.

The simplest practical route to producing precisely designed 3D macroscopic objects is to form a crystalline arrangement by self-assembly, because such a periodic array has only conceptually simple requirements: a motif that has a robust 3D structure, dominant affinity interactions between parts of the motif when it self-associates, and predictable structures for these affinity interactions. Fulfilling these three criteria to produce a 3D periodic system is not easy, but should readily be achieved with well-structured branched DNA motifs tailed by sticky ends (Zheng et al., Nature 461:74-77, 2009). Herein, a brief introduction to designed 3D DNA crystals from tensegrity triangle is presented.

The simplest practical route to producing precisely designed 3D macroscopic objects is to form a crystalline arrangement by self-assembly, because such a periodic array has only conceptually simple requirements: a motif that has a robust 3D structure, dominant affinity interactions between parts of the motif when it self-associates, and predictable structures for these affinity interactions. Fulfilling these three criteria to produce a 3D periodic system is not easy, but should readily be achieved with well-structured branched DNA motifs tailed by sticky ends (Zheng et al., Nature 461:74-77, 2009). Herein, a brief introduction to designed 3D DNA crystals from tensegrity triangle is presented.

Structural DNA nanotechnology finds applications in numerous areas, but the construction of objects, 2D and 3D crystalline lattices and devices is prominent among them. Each of these components has been developed individually, and most of them have been combined in pairs. However, to date there are no reports of independent devices contained within 3D crystals. Here we report a three-state 3D device whereby we change the colour of the crystals by diffusing strands that contain dyes in or out of the crystals through the mother-liquor component of the system. Each colouring strand is designed to pair with an extended triangle strand by Watson-Crick base pairing. The arm that contains the dyes is quite flexible, but it is possible to establish the presence of the duplex proximal to the triangle by X-ray crystallography. We modelled the transition between the red and blue states through a simple kinetic model.

We present an atomistic model of pillared DNA nanotubes (DNTs) and their elastic properties which will facilitate further studies of these nanotubes in several important nanotechnological and biological applications. In particular, we introduce a computational design to create an atomistic model of a 6-helix DNT (6HB) along with its two variants, 6HB flanked symmetrically by two double helical DNA pillars (6HB+2) and 6HB flanked symmetrically by three double helical DNA pillars (6HB+3). Analysis of 200 ns all-atom simulation trajectories in the presence of explicit water and ions shows that these structures are stable and well behaved in all three geometries. Hydrogen bonding is well maintained for all variants of 6HB DNTs. We calculate the persistence length of these nanotubes from their equilibrium bend angle distributions. The values of persistence length are ~10 {\mu}m, which is 2 orders of magnitude larger than that of dsDNA. We also find a gradual increase of persistence length with an increasing number of pillars, in quantitative agreement with previous experimental findings. To have a quantitative understanding of the stretch modulus of these tubes we carried out nonequilibrium Steered Molecular Dynamics (SMD). The linear part of the force extension plot gives stretch modulus in the range of 6500 pN for 6HB without pillars which increases to 11,000 pN for tubes with three pillars. The values of the stretch modulus calculated from contour length distributions obtained from equilibrium MD simulations are similar to those obtained from nonequilibrium SMD simulations. The addition of pillars makes these DNTs very rigid., Comment: Published in ACS Nano

DNA is increasingly used as an important tool in programming the self-assembly of micrometer- and nanometer-scale particles. This is largely due to the highly specific thermoreversible interaction of cDNA strands, which, when placed on different particles, have been used to bind precise pairs in aggregates and crystals. However, DNA functionalized particles will only reach their true potential for particle assembly when each particle can address and bind to many different kinds of particles. Indeed, specifying all bonds can force a particular designed structure. In this paper, we present the design rules for multiflavored particles and show that a single particle, DNA functionalized with many different “flavors,” can recognize and bind specifically to many different partners. We investigate the cost of increasing the number of flavors in terms of the reduction in binding energy and melting temperature. We find that a single 2-μm colloidal particle can bind to 40 different types of particles in an easily accessible time and temperature regime. The practical limit of ∼100 is set by entropic costs for particles to align complementary pairs and, surprisingly, by the limited number of distinct “useful” DNA sequences that prohibit subunits with nonspecific binding. For our 11 base “sticky ends,” the limit is 73 distinct sequences with no unwanted overlaps of 5 bp or more. As an example of phenomena enabled by polygamous particles, we demonstrate a three-particle system that forms a fluid of isolated clusters when cooled slowly and an elastic gel network when quenched.

DNA is a highly effective molecule for controlling nanometer-scale structure. The convenience of using DNA lies in the programmability of Watson-Crick base-paired secondary interactions, useful both to design branched molecular motifs and to connect them through sticky-ended cohesion. Recently, the tensegrity triangle motif has been used to self-assemble three-dimensional crystals whose structures have been determined; sticky ends were reported to be the only intermolecular cohesive elements in those crystals. A recent communication in this journal suggested that tertiary interactions between phosphates and cytosine N(4) groups are responsible for intermolecular cohesion in these crystals, in addition to the secondary and covalent interactions programmed into the motif. To resolve this issue, we report experiments challenging this contention. Gel electrophoresis demonstrates that the tensegrity triangle exists in conditions where cytosine-PO(4) tertiary interactions seem ineffective. Furthermore, we have crystallized a tensegrity triangle using a junction lacking the cytosine suggested for involvement in tertiary interactions. The unit cell is isomorphous with that of a tensegrity triangle crystal reported earlier. This structure has been solved by molecular replacement and refined. The data presented here leave no doubt that the tensegrity triangle crystal structures reported earlier depend only on base pairing and covalent interactions for their formation.

The paper reviews two computing models by DNA self-assembly whose proof of principal have recently been experimentally confirmed. The first model incorporates DNA nano-devices and triple crossover DNA molecules to algorithmically arrange non-DNA species. This is achieved by simulating a finite-state automaton with output where golden nanoparticles are assembled to read-out the result. In the second model, a complex DNA molecule representing a graph emerges as a solution of a computational problem. This supports the idea that in molecular self-assembly computing, it may be necessary to develop the notion of shape processing besides the classical approach through symbol processing.