Single-stranded Tiles Research Articles

Multiple-unit interlocking enhances the single-stranded tiles assembly of DNA nanostructures.

Single-stranded tiles (DNA brick) assembly has provided a simple and modular tool for constructing nanostructures with the potential for numerous applications. However, in this strategy, the short-strand building blocks are susceptible to environmental fluctuations and bring about rapid dissociation during assembly, resulting in instability and prolonged annealing. Thus, developing new strategies which can enhance the stability and accelerate the assembly process of DNA bricks is important. In this study, we applied the kinetically interlocking multiple-unit (KIMU) strategy to tune the process of DNA brick assembly by adopting long DNA strands as building blocks, ranging from tens of to 1000 nucleotides. We constructed a series of DNA structures with improved stability over DNA bricks. Furthermore, the annealing process could be accelerated by increasing the number of units. Our study demonstrated that DNA assembly based on the KIMU strategy using multiple-unit DNA strands could be a promising method for constructing relatively stable DNA nanostructures.

Dynamic Gold Nanostructures Based on DNA Self Assembly.

The combination of DNA nanotechnology and Nano Gold (NG) plasmon has opened exciting possibilities for a new generation of functional plasmonic systems that exhibit tailored optical properties and find utility in various applications. In this review, the booming development of dynamic gold nanostructures are summarized, which are formed by DNA self-assembly using DNA-modified NG, DNA frameworks, and various driving forces. The utilization of bottom-up strategies enables precise control over the assembly of reversible and dynamic aggregations, nano-switcher structures, and robotic nanomachines capable of undergoing on-demand, reversible structural changes that profoundly impact their properties. Benefiting from the vast design possibilities, complete addressability, and sub-10nm resolution, DNA duplexes, tiles, single-stranded tiles and origami structures serve as excellent platforms for constructing diverse 3D reconfigurable plasmonic nanostructures with tailored optical properties. Leveraging the responsive nature of DNA interactions, the fabrication of dynamic assemblies of NG becomes readily achievable, and environmental stimulation can be harnessed as a driving force for the nanomotors. It is envisioned that intelligent DNA-assembled NG nanodevices will assume increasingly important roles in the realms of biological, biomedical, and nanomechanical studies, opening a new avenue toward exploration and innovation.

DNA T-shaped crossover tiles for 2D tessellation and nanoring reconfiguration

DNA tiles serve as the fundamental building blocks for DNA self-assembled nanostructures such as DNA arrays, origami, and designer crystals. Introducing additional binding arms to DNA crossover tiles holds the promise of unlocking diverse nano-assemblies and potential applications. Here, we present one-, two-, and three-layer T-shaped crossover tiles, by integrating T junction with antiparallel crossover tiles. These tiles carry over the orthogonal binding directions from T junction and retain the rigidity from antiparallel crossover tiles, enabling the assembly of various 2D tessellations. To demonstrate the versatility of the design rules, we create 2-state reconfigurable nanorings from both single-stranded tiles and single-unit assemblies. Moreover, four sets of 4-state reconfiguration systems are constructed, showing effective transformations between ladders and/or rings with pore sizes spanning ~20 nm to ~168 nm. These DNA tiles enrich the design tools in nucleic acid nanotechnology, offering exciting opportunities for the creation of artificial dynamic DNA nanopores.

Isothermal self-assembly of multicomponent and evolutive DNA nanostructures

Thermal annealing is usually needed to direct the assembly of multiple complementary DNA strands into desired entities. We show that, with a magnesium-free buffer containing NaCl, complex cocktails of DNA strands and proteins can self-assemble isothermally, at room or physiological temperature, into user-defined nanostructures, such as DNA origamis, single-stranded tile assemblies and nanogrids. In situ, time-resolved observation reveals that this self-assembly is thermodynamically controlled, proceeds through multiple folding pathways and leads to highly reconfigurable nanostructures. It allows a given system to self-select its most stable shape in a large pool of competitive DNA strands. Strikingly, upon the appearance of a new energy minimum, DNA origamis isothermally shift from one initially stable shape to a radically different one, by massive exchange of their constitutive staple strands. This method expands the repertoire of shapes and functions attainable by isothermal self-assembly and creates a basis for adaptive nanomachines and nanostructure discovery by evolution.

DNA Nanostructure-Guided Plasmon Coupling Architectures

DNA Nanostructure-Guided Plasmon Coupling Architectures

DNA origami frame filled with two types of single-stranded tiles.

DNA origami and DNA single-stranded tiles (SSTs) are two basic motifs that are widely used in fabricating DNA nanostructures. Typically, DNA origami is self-folded via a long single phage strand (scaffold strand) and this process is aided by a myriad of short oligonucleotides (staple strand). Unlike DNA origami, SSTs construct nanostructures using many unique strands connected with each other to obtain specific shapes. These motifs are material- and labour-consuming, and require multiple different synthetic oligonucleotides, and DNA SSTs tend to remain kinetically trapped in the form of tubes. In this study, we present a new strategy that combines DNA origami with DNA SSTs to construct a DNA nanostructure with a predesigned shape. A rectangular DNA origami frame with ten dozen helper strands was filled with two types of SSTs assembled repeatedly, which avoided the kinetic trap and used fewer synthetic oligonucleotides. The assembly results were identified using atomic force microscopy. The experimental analysis demonstrated the stability and feasibility of the strategy.

Self-Assembly of Gamma-Modified Peptide Nucleic Acids into Complex Nanostructures in Organic Solvent Mixtures.

Current strategies in DNA and RNA nanotechnology enable the self-assembly of a variety of nucleic acid nanostructures in aqueous or substantially hydrated media. In this article, we describe detailed protocols that enable the construction of nanofiber architectures in organic solvent mixtures through the self-assembly of uniquely addressable, single-stranded, gamma-modified peptide nucleic acid (γPNA) tiles. Each single-stranded tile (SST) is a 12-base γPNA oligomer composed of two concatenated modular domains of 6 bases each. Each domain can bind to a mutually complimentary domain present on neighboring strands using programmed complementarity to form nanofibers that can grow to microns in length. The SST motif is made of 9 total oligomers to enable the formation of 3-helix nanofibers. In contrast with analogous DNA nanostructures, which form diameter-monodisperse structures, these γPNA systems form nanofibers that bundle along their widths during self-assembly in organic solvent mixtures. Self-assembly protocols described here therefore also include a conventional surfactant, Sodium Dodecyl Sulfate (SDS), to reduce bundling effects.

Programming DNA Tube Circumference by Tile Offset Connection.

DNA tubes with prescribed circumferences are appealing for numerous multidisciplinary applications. The DNA single-stranded tiles (SSTs) assembly method has demonstrated an unprecedented capability for programming the circumferences of DNA tubes in a modular fashion. Nevertheless, a distinct set of SSTs is typically required to assemble DNA tube of a specific circumference, with wider tubes requiring higher numbers of tiles of unique sequences, which not only increases the expense and design complexity but also hampers the assembly yield. Herein, we introduce "offset connection" to circumvent such challenges in conventional SST tube assembly. In this new connection scheme, the boundary SST tiles in an SST array are designed to connect in an offset manner. To compensate for the offset, the SST array has to grow wider until the array can close to form a wide tube with a tolerable degree of twist. Using this strategy, we have successfully assembled DNA tubes with prescribed circumferences consisting of 8, 12, 14, 16, 20, 24, 28, 32, 36, 42, 56, or 70 helices from two distinct sets of SSTs composed of 19×4 or 19×14 tiles.

Diverse and robust molecular algorithms using reprogrammable DNA self-assembly.

Molecular biology provides an inspiring proof-of-principle that chemical systems can store and process information to direct molecular activities such as the fabrication of complex structures from molecular components. To develop information-based chemistry as a technology for programming matter to function in ways not seen in biological systems, it is necessary to understand how molecular interactions can encode and execute algorithms. The self-assembly of relatively simple units into complex products1 is particularly well suited for such investigations. Theory that combines mathematical tiling and statistical-mechanical models of molecular crystallization has shown that algorithmic behaviour can be embedded within molecular self-assembly processes2,3, and this has been experimentally demonstrated using DNA nanotechnology4 with up to 22 tile types5-11. However, many information technologies exhibit a complexity threshold-such as the minimum transistor count needed for a general-purpose computer-beyond which the power of a reprogrammable system increases qualitatively, and it has been unclear whether the biophysics of DNA self-assembly allows that threshold to be exceeded. Here we report the design and experimental validation of a DNA tile set that contains 355 single-stranded tiles and can, through simple tile selection, be reprogrammed to implement a wide variety of 6-bit algorithms. We use this set to construct 21 circuits that execute algorithms including copying, sorting, recognizing palindromes and multiples of 3, random walking, obtaining an unbiased choice from a biased random source, electing a leader, simulating cellular automata, generating deterministic and randomized patterns, and counting to 63, with an overall per-tile error rate of less than 1 in 3,000. These findings suggest that molecular self-assembly could be a reliable algorithmic component within programmable chemical systems. The development of molecular machines that are reprogrammable-at a high level of abstraction and thus without requiring knowledge of the underlying physics-will establish a creative space in which molecular programmers can flourish.

A study on a special DNA nanotube assembled from two single-stranded tiles

Single-stranded tile (SST) strategy offers precise control over the circumferences of nanotubes while the kinetic trap in the process of the self-assembly prevents the formation of wider tubes. Here, we report a simple and efficient method to build DNA nanotubes using only 2 SSTs via one-pot annealing. The diameters of the 2-SST nanotubes were much larger than what the kinetic trap theory would predict, indicating a new mechanism was at play in the formation of these nanotubes. Further investigation suggested that the 2-SST nanotubes were assembled through a hierarchical pathway that involved an intermediate formation of 2-SST nano-lines.

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.

Mix‐and‐match nanobiosensor design: Logical and spatial programming of biosensors using self‐assembled DNA nanostructures

The evergrowing need to understand and engineer biological and biochemical mechanisms has led to the emergence of the field of nanobiosensing. Structural DNA nanotechnology, encompassing methods such as DNA origami and single-stranded tiles, involves the base pairing-driven knitting of DNA into discrete one-, two-, and three-dimensional shapes at nanoscale. Such nanostructures enable a versatile design and fabrication of nanobiosensors. These systems benefit from DNA's programmability, inherent biocompatibility, and the ability to incorporate and organize functional materials such as proteins and metallic nanoparticles. In this review, we present a mix-and-match taxonomy and approach to designing nanobiosensors in which the choices of bioanalyte and transduction mechanism are fully independent of each other. We also highlight opportunities for greater complexity and programmability of these systems that are built using structural DNA nanotechnology. This article is categorized under: Implantable Materials and Surgical Technologies > Nanomaterials and Implants Diagnostic Tools > Biosensing Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.

Isothermal approach to assemble spatial DNA nanotubes for drug delivery

// Xiaolong Shi 1 , Haiyan Zhao 1 , Xin Li 2 and Tao Song 3, 4 1 Key Laboratory of Image Information Processing and Intelligent Control, School of Automation, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China 2 Department of Gynecology 2, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei, China 3 College of Computer and Communication Engineering, China University of Petroleum, Qingdao 266580, Shandong, China 4 Departamento de Inteligencia Artificial, Universidad Politécnica de Madrid, Campus de Montegancedo, Boadilla del Monte 28660, Madrid, Spain Correspondence to: Tao Song, email: tsong@upc.edu.cn , t.song@upm.es Keywords: DNA nanotechnology; DNA origami; DNA nanotube; drug cargo Received: October 09, 2017      Accepted: November 13, 2017      Published: January 04, 2018 ABSTRACT DNA Nanostructures assembled from artificial single stranded DNA provided an engineering method to fabricate highly biocompatible spatial objects, which have potentials applications as drug delivery vehicles and templates for the patterning of biological molecules as biosensor for active hepatic targeting drug delivery. Most DNA nanostructures are constructed by annealing process, which means some thermal sensitive drugs and biosensors made from peptides or proteins in the structure will be denatured during fabrication. Fabrication of DNA nanostructure under isothermal condition remains challenging. Herein we report a simple and cost-effective method to form DNA nanotubes in the presence of urea with only two single-stranded tiles (SST) at room temperature. The constructed DNA nanotubes were observed and analyzed by atomic force microscopy (AFM). Experimental results show the feasibility and stability of our method. This method avoids traditional annealing procedure and will provide possibility to further assembly nano-scale structures in vivo .

Fluorescence Resonance Energy Transfer-Based Photonic Circuits Using Single-Stranded Tile Self-Assembly and DNA Strand Displacement.

Structural DNA nanotechnology has great potential in the fabrication of complicated nanostructures and devices capable of bio-sensing and logic function. A variety of nanostructures with desired shapes have been created in the past few decades. But the application of nanostructures remains to be fully studied. Here, we present a novel biological information processing system constructed on a self-assembled, spatially addressable single-stranded tile (SST) nanostructure as DNA nano-manipulation platform that created by SST self-assembly technology. Utilizing DNA strand displacement technology, the fluorescent dye that is pre-assembled in the nano-manipulation platform is transferred from the original position to the destination, which can achieve photonic logic circuits by FRET signal cascades, including logic AND, OR, and NOT gates. And this transfer process is successfully validated by visual DSD software. The transfer process proposed in this study may provide a novel method to design complicated biological information processing system constructed on a SST nanostructure, and can be further used to develop intelligent delivery of drug molecules in vivo.

Self-assembly programming of DNA polyominoes

Fabrication of functional DNA nanostructures operating at a cellular level has been accomplished through molecular programming techniques such as DNA origami and single-stranded tiles (SST). During implementation, restrictive and constraint dependent designs are enforced to ensure conformity is attainable. We propose a concept of DNA polyominoes that promotes flexibility in molecular programming. The fabrication of complex structures is achieved through self-assembly of distinct heterogeneous shapes (i.e., self-organised optimisation among competing DNA basic shapes) with total flexibility during the design and assembly phases. In this study, the plausibility of the approach is validated using the formation of multiple 3×4 DNA network fabricated from five basic DNA shapes with distinct configurations (monomino, tromino and tetrominoes). Computational tools to aid the design of compatible DNA shapes and the structure assembly assessment are presented. The formations of the desired structures were validated using Atomic Force Microscopy (AFM) imagery. Five 3×4 DNA networks were successfully constructed using combinatorics of these five distinct DNA heterogeneous shapes. Our findings revealed that the construction of DNA supra-structures could be achieved using a more natural-like orchestration as compared to the rigid and restrictive conventional approaches adopted previously.

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.

Minimalist Approach to Complexity: Templating the Assembly of DNA Tile Structures with Sequentially Grown Input Strands.

Given its highly predictable self-assembly properties, DNA has proven to be an excellent template toward the design of functional materials. Prominent examples include the remarkable complexity provided by DNA origami and single-stranded tile (SST) assemblies, which require hundreds of unique component strands. However, in many cases, the majority of the DNA assembly is purely structural, and only a small "working area" needs to be aperiodic. On the other hand, extended lattices formed by DNA tile motifs require only a few strands; but they suffer from lack of size control and limited periodic patterning. To overcome these limitations, we adopt a templation strategy, where an input strand of DNA dictates the size and patterning of resultant DNA tile structures. To prepare these templating input strands, a sequential growth technique developed in our lab is used, whereby extended DNA strands of defined sequence and length may be generated simply by controlling their order of addition. With these, we demonstrate the periodic patterning of size-controlled double-crossover (DX) and triple-crossover (TX) tile structures, as well as intentionally designed aperiodicity of a DX tile structure. As such, we are able to prepare size-controlled DNA structures featuring aperiodicity only where necessary with exceptional economy and efficiency.

Analogical China Map Constructed by Single-Stranded DNA Tiles Assembly

Analogical China Map Constructed by Single-Stranded DNA Tiles Assembly

Single-Stranded Tile Stoppers for Interlocked DNA Architectures.

Interlocked DNA architectures are useful for DNA nanotechnology because of their mechanically bonded components, which can move relative to one another without disassembling. We describe the design, synthesis, and characterization of novel single-stranded tile (SST) stoppers for the assembly of interlocked DNA architectures. SST stoppers are shown to self-assemble into a square-shaped rigid structure upon mixing 97 oligodeoxynucleotide (ODN) strands. The structures are equipped with a sticky end that is designed for hybridization with the sticky ends of a dsDNA axle of a DNA rotaxane. Because the diameter of the macrocycle threaded onto the axle is 14 nm, the dimension of the square-shaped stopper was designed to be bulky enough to prevent the dethreading of the macrocycle. An asymmetric rotaxane with a SST- and a ring-shaped stopper featuring two stations for hybridization of the macrocycle to the axle was assembled. The macrocycle can be directed towards one or the other station upon triggering with fuel ODNs.

JoVE - Year in Review: 2015

In January 2015, JoVE Developmental Biology became the newest addition to the JoVE family, and featured a live-imaging protocol for visualizing the developing Drosophila eye. In February, JoVE Medicine showed state-of-the-art cranial ultrasound imaging in neonates. Advances in this technique have improved its diagnostic value, allowing timely therapeutic intervention. In March, JoVE Environment featured dendroecology, the science of using tree rings to study ecological effects of specific environmental factors. In April, JoVE Biology examined a mode of bacterial motility called swarming with a two-phase swarm assay. that can be used to study various aspects of bacterial growth. In May, JoVE Chemistry described the self-assembly of single-stranded DNA tiles into complex 2D shapes. This demonstrated the principles of DNA tiling as an approach for making programmable nanostructures. June 2015 marked the release of JoVE's 100th issue, and in JoVE Behavior, we featured protocols for assessing cognition, including a method of quantifying learning in young infants by tracking leg movements. In July, JoVE Medicine presented a method for measuring halitosis in dogs by taking breath samples, and performing gas chromatography. This assay could be used in trials of dog food formulated to fight bad breath in our canine companions. In August, JoVE Bioengineering contained a protocol for bioengineering kidney tissues. Kidneys are decellularized by perfusion, and repopulated with human renal cells, This promising technology can lead to kidney grafts made from a patient's own cells. In September, JoVE Environment examined herbicide resistance, which threatens commercial crop production. An excised leaf assay determines the rates of herbicide metabolism, which is useful for studying the metabolic basis of resistance. In October, JoVE Neuroscience featured a method for interfacing 3D neuronal cultures to micro-electrode arrays. The complex 3D assemblies closely approximate in vivo neural networks. November's edition of JoVE Behavior showcased the natural human ability to acquire new motor skills, which is central in a structured rehabilitation program for amputees as they learn how to use multifunctional prosthetics. In December, JoVE Immunology & Infection prepared us for the impending flu season with an easy protocol for sampling influenza in pigs. Because swine are important hosts for flu viruses, this method helps to monitor virus evolution and currently circulating strains. This Year in Review was just a sampling of more than 900 video-articles that JoVE published in 2015. Browse the JoVE archives for thousands of other videos, and come back each week to see brand-new material in JoVE: The Journal of Visualized Experiments.