Origami Construction Research Articles

Expanding DNA Origami Design Freedom with De Novo Synthesized Scaffolds.

The construction of DNA origami nanostructures is heavily dependent on the folding of the scaffold strand, which is typically a single-stranded DNA genome extracted from a bacteriophage (M13). Custom scaffolds can be prepared in a number of methods, but they are not widely accessible to a broad user base in the DNA nanotechnology community. Here, we explored new design and construction possibilities with custom scaffolds prepared in our cost- and time-efficient production pipeline. According to the pipeline, we de novo produced a variety of scaffolds of specified local and global sequence characteristics and consequent origami constructs of modular arrangement in morphologies and functionalities. Taking advantage of this strategy of template-free scaffold production, we also designed and produced three-letter-coded scaffolds that can fold into designated morphologies rapidly at room temperature. The expanded design and construction freedom immediately brings in many new research opportunities and invites many more on the horizon.

Behavior of high-performance concrete canvas Miura-origami structures under flexural loading

Rapid construction and reducing building weight have been the favorite objectives of civil engineers in recent years. Canvas concrete is a promising material for rapid construction in which 3D spacer fabric is used for reinforcement and Origami construction has attracted attention for its structural efficiency and low weight in addition to its architectural aspects. The present study investigated the behavior of folded plates with origami patterns made of canvas concrete. The Miura pattern was used as the origami structure that was combined with high-performance concrete reinforced with 3D spacer fabric. Three Miura models were constructed as both non-sandwich and the core of the sandwich specimens. The specimens were subjected to four-point flexural loading, which showed that the Miura models with the same amount of materials increased the load-bearing capacity of a structure. By comparing specimens, the Miura patterns with sharper angles provided greater load-bearing capacity, energy absorption, and maximum load/weight ratios.

Geometric solution of a six order equation by three-fold origami

Robert J. Lang has proposed a theorem that when solving equations using multi-folds origami, general equations of order n can be solved using n-2 simultaneous folds. However, recently Jorge C. Lucero proved that arbitrary five order equations can be solved using two simultaneous folds. Combining this with the fact that one single fold can solve general quartic equations, the writer questions that whether the theorem may be altered into general equations of order n can be solved by n-3 simultaneous folds. Thus, in this paper, a method of geometric graphing -Lills method is used to try to solve six order equations with three simultaneous folds. By conducting case analysis using theoretical knowledge, it can be found that the six order equations can be possibly solved by three simultaneous folds. Besides, a comparison of solving equations with origami constructions and compass-and-straightedge is carried out. The result will encourage more research on using origami to solve higher order equations and inspire people to pay more attention to origami construction, which is more powerful, accurate, and efficient than the compass-and-straightedge people usually use.

High-precision estimation of emitter positions using Bayesian grouping of localizations

Single-molecule localization microscopy super-resolution methods rely on stochastic blinking/binding events, which often occur multiple times from each emitter over the course of data acquisition. Typically, the blinking/binding events from each emitter are treated as independent events, without an attempt to assign them to a particular emitter. Here, we describe a Bayesian method of inferring the positions of the tagged molecules by exploring the possible grouping and combination of localizations from multiple blinking/binding events. The results are position estimates of the tagged molecules that have improved localization precision and facilitate nanoscale structural insights. The Bayesian framework uses the localization precisions to learn the statistical distribution of the number of blinking/binding events per emitter and infer the number and position of emitters. We demonstrate the method on a range of synthetic data with various emitter densities, DNA origami constructs and biological structures using DNA-PAINT and dSTORM data. We show that under some experimental conditions it is possible to achieve sub-nanometer precision.

DNA Origami-Platelet Adducts: Nanoconstruct Binding without Platelet Activation.

Objective. Platelets are small, mechanosensitive blood cells responsible for maintaining vascular integrity and activatable on demand to limit bleeding and facilitate thrombosis. While circulating in the blood, platelets are exposed to a range of mechanical and chemical stimuli, with the platelet membrane being the primary interface and transducer of outside-in signaling. Sensing and modulating these interface signals would be useful to study mechanochemical interactions; yet, to date, no methods have been defined to attach adducts for sensor fabrication to platelets without triggering platelet activation. We hypothesized that DNA origami, and methods for its attachment, could be optimized to enable nonactivating instrumentation of the platelet membrane. Approach and Results. We designed and fabricated multivalent DNA origami nanotile constructs to investigate nanotile hybridization to membrane-embedded single-stranded DNA-tetraethylene glycol cholesteryl linkers. Two hybridization protocols were developed and validated (Methods I and II) for rendering high-density binding of DNA origami nanotiles to human platelets. Using quantitative flow cytometry, we showed that DNA origami binding efficacy was significantly improved when the number of binding overhangs was increased from two to six. However, no additional binding benefit was observed when increasing the number of nanotile overhangs further to 12. Using flow cytometry and transmission electron microscopy, we verified that hybridization with DNA origami constructs did not cause alterations in the platelet morphology, activation, aggregation, or generation of platelet-derived microparticles. Conclusions. Herein, we demonstrate that platelets can be successfully instrumented with DNA origami constructs with no or minimal effect on the platelet morphology and function. Our protocol allows for efficient high-density binding of DNA origami to platelets using low quantities of the DNA material to label a large number of platelets in a timely manner. Nonactivating platelet-nanotile adducts afford a path for advancing the development of DNA origami nanoconstructs for cell-adherent mechanosensing and therapeutic agent delivery.

Submillimeter-scale multimaterial terrestrial robots.

Robots with submillimeter dimensions are of interest for applications that range from tools for minimally invasive surgical procedures in clinical medicine to vehicles for manipulating cells/tissues in biology research. The limited classes of structures and materials that can be used in such robots, however, create challenges in achieving desired performance parameters and modes of operation. Here, we introduce approaches in manufacturing and actuation that address these constraints to enable untethered, terrestrial robots with complex, three-dimensional (3D) geometries and heterogeneous material construction. The manufacturing procedure exploits controlled mechanical buckling to create 3D multimaterial structures in layouts that range from arrays of filaments and origami constructs to biomimetic configurations and others. A balance of forces associated with a one-way shape memory alloy and the elastic resilience of an encapsulating shell provides the basis for reversible deformations of these structures. Modes of locomotion and manipulation span from bending, twisting, and expansion upon global heating to linear/curvilinear crawling, walking, turning, and jumping upon laser-induced local thermal actuation. Photonic structures such as retroreflectors and colorimetric sensing materials support simple forms of wireless monitoring and localization. These collective advances in materials, manufacturing, actuation, and sensing add to a growing body of capabilities in this emerging field of technology.

Origami as A Media for Introduction to Early Mathematics

Early mathematics learning needs to be done in a fun way and adjusted to early childhood development. One of the methods to learn mathematics in early childhood is by using games with attractive visuals or media. In this paper, literature study was done to describe the use of origami for early mathematics learning in early childhood. Origami is generally used for the development of fine motor skills in early childhood learning and the teaching is done using the demonstration method. By modifying origami paper using the Huzita-Justin construction, the learning process can be carried out more easily and simply, without the demonstration method. The aspects that can be achieved by using origami media are logical thinking, symbolic thinking, and visual-spatial thinking. However, it is still not widely used, since origami construction paper is not easy to make.

Preface to the special issue dedicated to Professor Richard P. Van Duyne (1945–2019)

Preface to the special issue dedicated to Professor Richard P. Van Duyne (1945–2019)

Dynamics of deterministically positioned single‐bond surface‐enhanced Raman scattering from DNA origami assembled in plasmonic nanogaps

AbstractWe study the dynamics of single bonds through the surface‐enhanced Raman scattering (SERS) from single SERS‐marker molecules containing a distinctive single alkyl bond. Assembly of the nanogaps and positioning of single molecules inside the electromagnetic hotspot are precisely controlled using DNA origami constructs. The observed SERS intensities and their spectral wandering, together with electromagnetic simulations, all confirm the role of picocavities in this nanogap geometry in allowing observation of SERS signatures from individual vibrating bonds. The strong electromagnetic field around each picocavity and the transient binding of the SERS‐marker molecule reveal significant modifications to bond vibrations and selection rules over time.

Limited trial on origami construction as mathematics learning strategy for early childhood on kindergarten teachers

The aim of this study is to do a limited trial on the hypothetical learning strategy for early childhood mathematics concepts using origami construction. Using the training devices designed for the limited trial, 17 early childhood education teachers in Bandung and its surrounding areas were trained on the learning strategy. The trial pre-test and post-test scores and it shows an improvement in the knowledge of participating teachers of early childhood mathematics learning using origami. The significance of the improvement had been proven using t-paired test. The improvement might be caused by the fact that most of the participants only have high school diploma as education background with lack of training on early childhood mathematics learning, and also with the fact that origami is mainly used for fine motor skills improvement in early childhood education. Thus, the origami construction can be used as an alternative strategy to learn mathematics concept in early childhood.

Counterion-Dependent Mechanisms of DNA Origami Nanostructure Stabilization Revealed by Atomistic Molecular Simulation.

The DNA origami technique has proven to have tremendous potential for therapeutic and diagnostic applications like drug delivery, but the relatively low concentrations of cations in physiological fluids cause destabilization and degradation of DNA origami constructs preventing in vivo applications. To reveal the mechanisms behind DNA origami stabilization by cations, we performed atomistic molecular dynamics simulations of a DNA origami rectangle in aqueous solvent with varying concentrations of magnesium and sodium as well as polyamines like oligolysine and spermine. We explored the binding of these ions to DNA origami in detail and found that the mechanism of stabilization differs between ion types considerably. While sodium binds weakly and quickly exchanges with the solvent, magnesium and spermine bind close to the origami with spermine also located in between helices, stabilizing the crossovers characteristic for DNA origami and reducing repulsion of parallel helices. In contrast, oligolysine of length ten prevents helix repulsion by binding to adjacent helices with its flexible side chains, spanning the gap between the helices. Shorter oligolysine molecules with four subunits are weak stabilizers as they lack both the ability to connect helices and to prevent helix repulsion. This work thus shows how the binding modes of ions influence the stabilization of DNA origami nanostructures on a molecular level.

Tailoring the Mechanical Stiffness of DNA Nanostructures Using Engineered Defects.

As scaffolded DNA origami enables the construction of diverse DNA nanostructures with predefined shapes, precise modulation of their mechanical stiffness remains challenging. We demonstrate a modular design method to widely and precisely control the mechanical flexibility of scaffolded DNA origami nanostructures while maintaining their overall structural integrity and geometric characteristics. Individually engineered defects that are short single-stranded DNA (ssDNA) gaps could reduce up to 70% of the bending stiffness of DNA origami constructs with different cross-sectional shapes. We further developed a computational analysis platform predicting the bending stiffness of a defect-engineered DNA nanostructure quickly during the design process, to offer an efficient way of designing various DNA constructs with required mechanical stiffness in a desired shape for a targeted function.

DNA Origami as Scaffolds for Self-Assembly of Lipids and Proteins.

Since first being reported in 2006, the DNA origami approach has attracted increasing attention due to programmable shapes, structural stability, biocompatibility, and fantastic addressability. Herein, we provide an account of recent developments of DNA origami as scaffolds for templating the selfassembly of distinct biocomponents, essentially proteins and lipids, into a diverse spectrum of integrated supramolecular architectures. First, the historical development of the DNA origami concept is briefly reviewed. Next, various applications of DNA origami constructs in controllable directed assembly of soluble proteins are discussed. The manipulation and self-assembly of lipid membranes and membrane proteins by using DNA origami as scaffolds are also addressed. Furthermore, recent progress in applying DNA origami in cryoelectron microscopy analysis is discussed. These advances collectively emphasize that the DNA origami approach is a highly versatile, fast evolving tool that may be integrated with lipids and proteins in a way that meets future challenges in molecular biology and nanomedicine.

Genetically Encoded, Functional Single-Strand RNA Origami: Anticoagulant.

Nucleic acid aptamers selected for thrombin binding have been previously shown to possess anticoagulant activity; however, problems with rapid renal clearance and short circulation half-life have prevented translation to clinical usefulness. Here, a family of self-folding, functional RNA origami molecules bearing multiple thrombin-binding RNA aptamers and showing significantly improved anticoagulant activity is described. These constructs may overcome earlier problems preventing clinical use of nucleic acid anticoagulants. RNA origami structures are designed in silico and produced by in vitro transcription from DNA templates. Incorporation of 2'-fluoro-modified C- and U-nucleotides is shown to increase nuclease resistance and stability during long-term storage. Specific binding to human thrombin as well as high stability in the presence of RNase A and in human plasma, comparatively more stable than DNA is demonstrated. The RNA origami constructs show anticoagulant activity sevenfold greater than free aptamer and higher than previous DNA weave tiles decorated with DNA aptamers. Anticoagulation activity is maintained after at least 3 months of storage in buffer at 4 °C. Additionally, inhibition of thrombin is shown to be reversed by addition of single-stranded DNA antidotes. This project paves the way for development of RNA origami for potential therapeutic applications especially as a safer surgical anticoagulant.

Origami launcher

The article studies the elastic and locomotive properties of Miura-ori-type paper origami. The mechanics of a single paper crease is studied experimentally, and its non-elastic properties turn out to be crucial. The entire origami construction is then described as a collection of individual creases, its capability to launch small objects is evaluated, and the equation of motion is found. Thus, the height of the launched ball is studied theoretically and experimentally as a function of governing parameters.

Imidazole-modified G-quadruplex DNA as metal-triggered peroxidase.

Four imidazoles, serving as metalloprotein-inspired ligands for complexing a range of transition metal cations, were incorporated into tetramolecular G-quadruplex DNA structures. Modified quadruplexes were found to complex Cu(ii), Ni(ii), Zn(ii) and Co(ii) in a 1 : 1 ratio with unprecedented strong thermal stabilizations of up to ΔT 1/2 = +51 °C. Furthermore, addition of Cu(ii) was found to lead to extraordinarily fast G-quadruplex association rates with k on values being ∼100 times higher compared to unmodified G-quadruplexes. This is ascribed to a template effect of Cu(ii), preorganizing the four single strands via coordination, followed by rapid formation of hydrogen-bonded G-quartets. Native electrospray ionization mass spectrometry (ESI), coupled with trapped ion-mobility spectrometry (timsTOF), supports the proposed 1 : 1 G-quadruplex-metal complexes and could further disclose their ability to bind the iron-porphyrin complex hemin in a 1 : 1 stoichiometry. DNA sequence design allowed us to equip this G-quadruplex-hemin complex, known to function as a horseradish peroxidase mimic, with a metal-dependent trigger. A competitive screen of transition metals revealed a high selectivity for Cu(ii), even in mixtures of several divalent metal cations. Once formed, the Cu(ii)-carrying DNAzyme was shown to be preserved in the presence of EDTA, attributed to its remarkable kinetic stability. Stimuli-responsive G-quadruplexes promise application in DNAzymes with switchable activity, adaptive sensors and dynamic DNA origami constructs.

Study of DNA Origami Dimerization and Dimer Dissociation Dynamics and of the Factors that Limit Dimerization.

Organizing DNA origami building blocks into higher order structures is essential for fabrication of large structurally and functionally diverse devices and molecular machines. Unfortunately, the yields of origami building block attachment reactions are typically not sufficient to allow programed assembly of DNA devices made from more than a few origami building blocks. To investigate possible reasons for these low yields, a detailed single-molecule fluorescence study of the dynamics of rectangular origami dimerization and origami dimer dissociation reactions is conducted. Reactions kinetics and yields are investigated at different origami and ion concentrations, for different ion types, for different lengths of bridging strands, and for the "sticky end" and "weaving welding" attachment techniques. Dimerization yields are never higher than 86%, which is typical for such systems. Analysis of the dynamic data shows that the low yield cannot be explained by thermodynamic instability or structural imperfections of the origami constructs. Atomic force microscopy and gel electrophoresis evidence reveal self-dimerization of the origami monomers, likely via blunt-end interactions made possible by the presence of bridging strands. It is suggested that this mechanism is the major factor that inhibits correct dimerization and means to overcome it are discussed.

Folding DNA Origami Nanolevers From Differently Prepared Scaffold Strands

The use of length‐predefined DNA origami constructs acting as nanolevers in the analysis of protein binding kinetics requires an optimized and cost‐efficient nanolever assembly, and therefore, a customized scaffold strand synthesis. In this paper, a top‐down and a bottom‐up approach for the fabrication of two scaffold strands of customized length for predefined DNA origami structures are presented. Three different origami structures are synthesized and analyzed in terms of accuracy of shape, yield as well as the costs attributed to each fabrication route.

Design and application of 'J-shaped' stress-strain behavior in stretchable electronics: a review.

A variety of natural biological tissues (e.g., skin, ligaments, spider silk, blood vessel) exhibit 'J-shaped' stress-strain behavior, thereby combining soft, compliant mechanics and large levels of stretchability, with a natural 'strain-limiting' mechanism to prevent damage from excessive strain. Synthetic materials with similar stress-strain behaviors have potential utility in many promising applications, such as tissue engineering (to reproduce the nonlinear mechanical properties of real biological tissues) and biomedical devices (to enable natural, comfortable integration of stretchable electronics with biological tissues/organs). Recent advances in this field encompass developments of novel material/structure concepts, fabrication approaches, and unique device applications. This review highlights five representative strategies, including designs that involve open network, wavy and wrinkled morphologies, helical layouts, kirigami and origami constructs, and textile formats. Discussions focus on the underlying ideas, the fabrication/assembly routes, and the microstructure-property relationships that are essential for optimization of the desired 'J-shaped' stress-strain responses. Demonstration applications provide examples of the use of these designs in deformable electronics and biomedical devices that offer soft, compliant mechanics but with inherent robustness against damage from excessive deformation. We conclude with some perspectives on challenges and opportunities for future research.

FRET enhancement close to gold nanoparticles positioned in DNA origami constructs.

Here we investigate the energy transfer rates of a Förster resonance energy transfer (FRET) pair positioned in close proximity to a 5 nm gold nanoparticle (AuNP) on a DNA origami construct. We study the distance dependence of the FRET rate by varying the location of the donor molecule, D, relative to the AuNP while maintaining a fixed location of the acceptor molecule, A. The presence of the AuNP induces an alteration in the spontaneous emission of the donor (including radiative and non-radiative rates) which is strongly dependent on the distance between the donor and AuNP surface. Simultaneously, the energy transfer rates are enhanced at shorter D-A (and D-AuNP) distances. Overall, in addition to the direct influence of the acceptor and AuNP on the donor decay there is also a significant increase in decay rate not explained by the sum of the two interactions. This leads to enhanced energy transfer between donor and acceptor in the presence of a 5 nm AuNP. We also demonstrate that the transfer rate in the three "particle" geometry (D + A + AuNP) depends approximately linearly on the transfer rate in the donor-AuNP system, suggesting the possibility to control FRET process with electric field induced by 5 nm AuNPs close to the donor fluorophore. It is concluded that DNA origami is a very versatile platform for studying interactions between molecules and plasmonic nanoparticles in general and FRET enhancement in particular.