Origami Tiles Research Articles

Control of DNA origami inter-tile connection with vertical linkers.

This communication describes a new method that enables high yield assembly along both of the two-dimensional edges of DNA origami tiles by controlling the Mg(2+) concentration; high Mg(2+) concentrations promote linkage connections between the vertical edges of the tiles. As a demonstration, DNA origami dimers assembled from two rectangular origami along the vertical edges are used as scaffolds for the double sided assembly of gold nanoparticles with different inter-particle spacings.

Designing a Single-Molecule Biophysics Tool for Characterising DNA Damage for Techniques that Kill Infectious Pathogens Through DNA Damage Effects.

Antibiotics such as the quinolones and fluoroquinolones kill bacterial pathogens ultimately through DNA damage. They target the essential type IIA topoisomerases in bacteria by stabilising the normally transient double-strand break state which is created to modify the supercoiling state of the DNA. Here we discuss the development of these antibiotics and their method of action. Existing methods for DNA damage visualisation, such as the comet assay and immunofluorescence imaging can often only be analysed qualitatively and this analysis is subjective. We describe a putative single-molecule fluorescence technique for quantifying DNA damage via the total fluorescence intensity of a DNA origami tile fully saturated with an intercalating dye, along with the optical requirements for how to implement these into a light microscopy imaging system capable of single-molecule millisecond timescale imaging. This system promises significant improvements in reproducibility of the quantification of DNA damage over traditional techniques.

74 Creating combinatorial patterns with DNA origami arrays

DNA origami (Rothemund, 2006) and smaller DNA tiles (Winfree et al., 1998) have been used as effective scaffolds to create complex patterns for organizing molecules with nanometer precision but of a limited size. Arrays of DNA origami (Liu et al., 2011) and DNA tiles have been shown to be capable of creating patterns in a larger scale, either periodically or following a specific set of rules defined by a cellular automaton (Rothemund et al., 2004). Here we aim to create a variety of large-scale complex patterns by using a combinatorial approach with a mathematically simple and elegant rule called Truchet tiling.

DNA Motors: A Bipedal DNA Motor that Travels Back and Forth between Two DNA Origami Tiles (Small 5/2015)

DNA Motors: A Bipedal DNA Motor that Travels Back and Forth between Two DNA Origami Tiles (Small 5/2015)

A bipedal DNA motor that travels back and forth between two DNA origami tiles.

In this work, the successful operation of a dynamic DNA device constructed from two DNA origami building blocks is reported. The device includes a bipedal walker that strides back and forth between the two origami tiles. Two different DNA origami tiles are first prepared separately; they are then joined together in a controlled manner by a set of DNA strands to form a stable track in high yield as confirmed by single-molecule fluorescence (SMF). Second, a bipedal DNA motor, initially attached to one of the two origami units and operated by sequential interaction with "fuel" and "antifuel" DNA strands, moves from one origami tile to another and then back again. The operational yield, measured by SMF, was similar to that of a motor operating on a similar track embedded in a single origami tile, confirming that the transfer across the junction from one tile to the other does not result in dissociation that is any more than that of steps on a single tile. These results demonstrate that moving parts can reliably travel from one origami unit to another, and it demonstrates the feasibility of dynamic DNA molecular machines that are made of more than a single origami building block. This study is a step toward the development of motors that can stride over micrometer distances.

DNA walker circuits: computational potential, design, and verification

Unlike their traditional, silicon counterparts, DNA computers have natural interfaces with both chemical and biological systems. These can be used for a number of applications, including the precise arrangement of matter at the nanoscale and the creation of smart biosensors. Like silicon circuits, DNA strand displacement systems (DSD) can evaluate non-trivial functions. However, these systems can be slow and are susceptible to errors. It has been suggested that localised hybridization reactions could overcome some of these challenges. Localised reactions occur in DNA ‘walker’ systems which were recently shown to be capable of navigating a programmable track tethered to an origami tile. We investigate the computational potential of these systems for evaluating Boolean functions and forming composable circuits. We find that systems of multiple walkers have severely limited potential for parallel circuit evaluation. DNA walkers, like DSDs, are also susceptible to errors. We develop a discrete stochastic model of DNA walker ‘circuits’ based on experimental data, and demonstrate the merit of using probabilistic model checking techniques to analyse their reliability, performance and correctness. This analysis aids in the design of reliable and efficient DNA walker circuits.

Surface-assisted large-scale ordering of DNA origami tiles.

The arrangement of DNA-based nanostructures into extended higher order assemblies is an important step towards their utilization as functional molecular materials. We herein demonstrate that by electrostatically controlling the adhesion and mobility of DNA origami structures on mica surfaces by the simple addition of monovalent cations, large ordered 2D arrays of origami tiles can be generated. The lattices can be formed either by close-packing of symmetric, non-interacting DNA origami structures, or by utilizing blunt-end stacking interactions between the origami units. The resulting crystalline lattices can be readily utilized as templates for the ordered arrangement of proteins.

Nanolithography based on metalized DNA templates for graphene patterning.

DNA self-assembly, such as DNA origami and single-stranded tile (SST) assembly, can create complex nanostructures with prescribed two-dimensional (2-D) and three-dimensional (3-D) shapes. Distinct patterned DNA nanostructures can be used as templates or shadow masks for the lithographic patterning of 2-D thin-film materials for nanodevices. The protocols in this article describe a general procedure of metalized DNA nanolithography based upon DNA metalization and subsequent etching to transfer the shape information from DNA templates to graphene, such that the shape of complex graphene nanostructures can be rationally programmed. Spatial information within the predesigned DNA patterns, such as width, orientation, curvature, and angles, can be successfully transferred to the graphene nanostructures with sub-10 nm resolution. This method could be further generalized to enable patterning of nano-sized modules of graphene and other 2-D electronic materials with predesigned shapes for complex electronic and quantum circuits.

Understanding the Mechanical Properties of DNA Origami Tiles and Controlling the Kinetics of Their Folding and Unfolding Reconfiguration

DNA origami represents a class of highly programmable macromolecules that can go through conformational changes in response to external signals. Here we show that a two-dimensional origami rectangle can be effectively folded into a short, cylindrical tube by connecting the two opposite edges through the hybridization of linker strands and that this process can be efficiently reversed via toehold-mediated strand displacement. The reconfiguration kinetics was experimentally studied as a function of incubation temperature, initial origami concentration, missing staples, and origami geometry. A kinetic model was developed by introducing the j factor to describe the reaction rates in the cyclization process. We found that the cyclization efficiency (j factor) increases sharply with temperature and depends strongly on the structural flexibility and geometry. A simple mechanical model was used to correlate the observed cyclization efficiency with origami structure details. The mechanical analysis suggests two sources of the energy barrier for DNA origami folding: overcoming global twisting and bending the structure into a circular conformation. It also provides the first semiquantitative estimation of the rigidity of DNA interhelix crossovers, an essential element in structural DNA nanotechnology. This work demonstrates efficient DNA origami reconfiguration, advances our understanding of the dynamics and mechanical properties of self-assembled DNA structures, and should be valuable to the field of DNA nanotechnology.

Metallized DNA nanolithography for encoding and transferring spatial information for graphene patterning

The vision for graphene and other two-dimensional electronics is the direct production of nanoelectronic circuits and barrier materials from a single precursor sheet. DNA origami and single-stranded tiles are powerful methods to encode complex shapes within a DNA sequence, but their translation to patterning other nanomaterials has been limited. Here we develop a metallized DNA nanolithography that allows transfer of spatial information to pattern two-dimensional nanomaterials capable of plasma etching. Width, orientation and curvature can be programmed by specific sequence design and transferred, as we demonstrate for graphene. Spatial resolution is limited by distortion of the DNA template upon Au metallization and subsequent etching. The metallized DNA mask allows for plasmonic enhanced Raman spectroscopy of the underlying graphene, providing information on defects, doping and lattice symmetry. This DNA nanolithography enables wafer-scale patterning of two-dimensional electronic materials to create diverse circuit elements, including nanorings, three- and four-membered nanojunctions, and extended nanoribbons.

Develop Spatially‐ Interactive Multienzyme Complex on Selfassembled DNA Nanostructures

Cellular activities are directed by complex, multi‐step synthetic pathways. Many of the enzymes in these pathways are spatially organized to improve both the speed and specificity. This abstracts presents a DNA scaffold‐directed strategy to assemble multienzyme systems with precisely controlled orientations and positions. It has increased our understanding of the enzymology for biological metabolic pathways and also provided the tools and design principles for creating efficient man‐made catalytic complexes.As shown in Figure 1, a two‐enzyme Glucose Oxidase (GOx) ‐ Horseradish Peroxidase (HRP) cascade was assembled on rectangular DNA origami tiles with inter‐enzyme distances ranging from 10 to 65 nm. It was observed that the rate of coupled reactions dramatically increased when the two enzymes were positioned very close together (e.g. 10‐nm in Figure 1B) so that the hydration shells of enzymes overlapped. Further, a protein bridge structure was constructed to facilitate the transfer of intermediates between enzymes (Figure 1C). This opens the door for the design of much more efficient multi‐enzyme systems which should find utility in the development of catalysts for the production of high‐value products in industry and bioenergy, as well as diagnostic applications in biomedicine.

Nano-encrypted Morse code: a versatile approach to programmable and reversible nanoscale assembly and disassembly.

While much work has been devoted to nanoscale assembly of functional materials, selective reversible assembly of components in the nanoscale pattern at selective sites has received much less attention. Exerting such a reversible control of the assembly process will make it possible to fine-tune the functional properties of the assembly and to realize more complex designs. Herein, by taking advantage of different binding affinities of biotin and desthiobiotin toward streptavidin, we demonstrate selective and reversible decoration of DNA origami tiles with streptavidin, including revealing an encrypted Morse code "NANO" and reversible exchange of uppercase letter "I" with lowercase "i". The yields of the conjugations are high (>90%), and the process is reversible. We expect this versatile conjugation technique to be widely applicable with different nanomaterials and templates.

Direct Visualization of Transient Thermal Response of a DNA Origami

The DNA origami approach enables the construction of complex objects from DNA strands. A fundamental understanding of the kinetics and thermodynamics of DNA origami assembly is extremely important for building large DNA structures with multifunctionality. Here both experimental and theoretical studies of DNA origami melting were carried out in order to reveal the reversible association/disassociation process. Furthermore, by careful control of the temperature cycling via in situ thermally controlled atomic force microscopy, the self-assembly process of a rectangular DNA origami tile was directly visualized, unveiling key mechanisms underlying their structural and thermodynamic features.

Interenzyme Substrate Diffusion for an Enzyme Cascade Organized on Spatially Addressable DNA Nanostructures

Spatially addressable DNA nanostructures facilitate the self-assembly of heterogeneous elements with precisely controlled patterns. Here we organized discrete glucose oxidase (GOx)/horseradish peroxidase (HRP) enzyme pairs on specific DNA origami tiles with controlled interenzyme spacing and position. The distance between enzymes was systematically varied from 10 to 65 nm, and the corresponding activities were evaluated. The study revealed two different distance-dependent kinetic processes associated with the assembled enzyme pairs. Strongly enhanced activity was observed for those assemblies in which the enzymes were closely spaced, while the activity dropped dramatically for enzymes as little as 20 nm apart. Increasing the spacing further resulted in a much weaker distance dependence. Combined with diffusion modeling, the results suggest that Brownian diffusion of intermediates in solution governed the variations in activity for more distant enzyme pairs, while dimensionally limited diffusion of intermediates across connected protein surfaces contributed to the enhancement in activity for closely spaced GOx/HRP assemblies. To further test the role of limited dimensional diffusion along protein surfaces, a noncatalytic protein bridge was inserted between GOx and HRP to connect their hydration shells. This resulted in substantially enhanced activity of the enzyme pair.

Effect of DNA hairpin loops on the twist of planar DNA origami tiles.

The development of scaffolded DNA origami, a technique in which a long single-stranded viral genome is folded into arbitrary shapes by hundreds of short synthetic oligonucleotides, represents an important milestone in DNA nanotechnology. Recent findings have revealed that two-dimensional (2D) DNA origami structures based on the original design parameters adopt a global twist with respect to the tile plane, which may be because the conformation of the constituent DNA (10.67 bp/turn) deviates from the natural B-type helical twist (10.4 bp/turn). Here we aim to characterize the effects of DNA hairpin loops on the overall curvature of the tile and explore their ability to control, and ultimately eliminate any unwanted curvature. A series of dumbbell-shaped DNA loops were selectively displayed on the surface of DNA origami tiles with the expectation that repulsive interactions among the neighboring dumbbell loops and between the loops and the DNA origami tile would influence the structural features of the underlying tiles. A systematic, atomic force microscopy (AFM) study of how the number and position of the DNA loops influenced the global twist of the structure was performed, and several structural models to explain the results were proposed. The observations unambiguously revealed that the first generation of rectangular shaped origami tiles adopt a conformation in which the upper right (corner 2) and bottom left (corner 4) corners bend upward out of the plane, causing linear superstructures attached by these corners to form twisted ribbons. Our experimental observations are consistent with the twist model predicted by the DNA mechanical property simulation software CanDo. Through the systematic design and organization of various numbers of dumbbell loops on both surfaces of the tile, a nearly planar rectangular origami tile was achieved.

Hierarchical self assembly of patterns from the Robinson tilings: DNA tile design in an enhanced Tile Assembly Model

We introduce a hierarchical self assembly algorithm that produces the quasiperiodic patterns found in the Robinson tilings and suggest a practical implementation of this algorithm using DNA origami tiles. We modify the abstract Tile Assembly Model, (aTAM), to include active signaling and glue activation in response to signals to coordinate the hierarchical assembly of Robinson patterns of arbitrary size from a small set of tiles according to the tile substitution algorithm that generates them. Enabling coordinated hierarchical assembly in the aTAM makes possible the efficient encoding of the recursive process of tile substitution.

Geometrical self-assembly

DNA origami tiles with complementary shapes have been designed and assembled into large nanostructures through the geometrically controlled stacking of their helices.

Organizing DNA Origami Tiles into Larger Structures Using Preformed Scaffold Frames

Structural DNA nanotechnology utilizes DNA molecules as programmable information-coding polymers to create higher order structures at the nanometer scale. An important milestone in structural DNA nanotechnology was the development of scaffolded DNA origami in which a long single-stranded viral genome (scaffold strand) is folded into arbitrary shapes by hundreds of short synthetic oligonucleotides (staple strands). The achievable dimensions of the DNA origami tile units are currently limited by the length of the scaffold strand. Here we demonstrate a strategy referred to as "superorigami" or "origami of origami" to scale up DNA origami technology. First, this method uses a collection of bridge strands to prefold a single-stranded DNA scaffold into a loose framework. Subsequently, preformed individual DNA origami tiles are directed onto the loose framework so that each origami tile serves as a large staple. Using this strategy, we demonstrate the ability to organize DNA origami nanostructures into larger spatially addressable architectures.

Crystalline two-dimensional DNA-origami arrays.

Nanotechnology aims to organize matter with the highest possible accuracy and control. Such control will lead to nanoelectronics, nanorobotics, programmable chemical synthesis, scaffolded crystals, and nanoscale systems responsive to their environments. Structural DNA nanotechnology1 is one of the most powerful routes to this goal. It combines robust branched DNA species with the control of affinity and structure2 inherent in the programmability of sticky ends. The successes of structural DNA nanotechnology include the formation of objects,3 2D crystals,4 3D crystals,5 nanomechanical devices,6 and various combinations of these species (e.g., ref. 7). DNA origami8 is arguably the most effective way of producing a large addressable area on a 2D DNA surface. This method entails the combination of a long single strand (typically M13 single-stranded form, 7249 nucleotides) with about ~250 staple strands to define its shape and patterning. With a pixilation estimated at about 6 nm,8 it is possible to build patterns with about 100 addressable points within a definable shape in an area of about 10,000 nm2. Many investigators have sought unsuccessfully to increase the useful size of 2D origami units by forming crystals of individual origami tiles.0 Here, we report the 2D crystallization of origami tiles to yield a 2D array with dimensions 2–3 microns on an edge. This size is likely to be large enough to connect bottom-up methods of patterning with top-down approaches.

Molecular behavior of DNA origami in higher-order self-assembly.

DNA-based self-assembly is a unique method for achieving higher-order molecular architectures made possible by the fact that DNA is a programmable information-coding polymer. In the past decade, two main types of DNA nanostructures have been developed: branch-shaped DNA tiles with small dimensions (commonly up to ∼20 nm) and DNA origami tiles with larger dimensions (up to ∼100 nm). Here we aimed to determine the important factors involved in the assembly of DNA origami superstructures. We constructed a new series of rectangular-shaped DNA origami tiles in which parallel DNA helices are arranged in a zigzag pattern when viewed along the DNA helical axis, a design conceived in order to relax an intrinsic global twist found in the original planar, rectangular origami tiles. Self-associating zigzag tiles were found to form linear arrays in both diagonal directions, while planar tiles showed significant growth in only one direction. Although the series of zigzag tiles were designed to promote two-dimensional array formation, one-dimensional linear arrays and tubular structures were observed instead. We discovered that the dimensional aspect ratio of the origami unit tiles and intertile connection design play important roles in determining the final products, as revealed by atomic force microscopy imaging. This study provides insight into the formation of higher-order structures from self-assembling DNA origami tiles, revealing their unique behavior in comparison with conventional DNA tiles having smaller dimensions.