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DOE OSTI2021

Programmable Site‐Specific Functionalization of DNA Origami with Polynucleotide Brushes

Abstract Combining surface‐initiated, TdT (terminal deoxynucleotidyl transferase) catalyzed enzymatic polymerization (SI‐TcEP) with precisely engineered DNA origami nanostructures (DONs) presents an innovative pathway for the generation of stable, polynucleotide brush‐functionalized DNA nanostructures. We demonstrate that SI‐TcEP can site‐specifically pattern DONs with brushes containing both natural and non‐natural nucleotides. The brush functionalization can be precisely controlled in terms of the location of initiation sites on the origami core and the brush height and composition. Coarse‐grained simulations predict the conformation of the brush‐functionalized DONs that agree well with the experimentally observed morphologies. We find that polynucleotide brush‐functionalization increases the nuclease resistance of DONs significantly, and that this stability can be spatially programmed through the site‐specific growth of polynucleotide brushes. The ability to site‐specifically decorate DONs with brushes of natural and non‐natural nucleotides provides access to a large range of functionalized DON architectures that would allow for further supramolecular assembly, and for potential applications in smart nanoscale delivery systems.

Yang, Yunqi↗

DOE OSTI2023

Spatiotemporal Control over Polynucleotide Brush Growth on DNA Origami Nanostructures

Abstract DNA nanotechnology provides an approach to create precise, tunable, and biocompatible nanostructures for biomedical applications. However, the stability of these structures is severely compromised in biological milieu due to their fast degradation by nucleases. Recently, we showed how enzymatic polymerization could be harnessed to grow polynucleotide brushes of tunable length and location on the surface of DNA origami nanostructures, which greatly enhances their nuclease stability. Here, we report on strategies that allow for both spatial and temporal control over polymerization through activatable initiation, cleavage, and regeneration of polynucleotide brushes using restriction enzymes. The ability to site‐specifically decorate DNA origami nanostructures with polynucleotide brushes in a spatiotemporally controlled way provides access to “smart” functionalized DNA architectures with potential applications in drug delivery and supramolecular assembly.

Yang, Yunqi↗

DOE OSTI2021

Programmable Site-Specific Functionalization of DNA Origami with Polynucleotide Brushes

Combining surface-initiated, TdT (terminal deoxynucleotidyl transferase) catalyzed enzymatic polymerization (SI-TcEP) with precisely engineered DNA origami nanostructures (DONs) presents an innovative pathway for the generation of stable, polynucleotide brush-functionalized DNA nanostructures. Here we demonstrate that SI-TcEP can site-specifically pattern DONs with brushes containing both natural and non-natural nucleotides. The brush functionalization can be precisely controlled in terms of the location of initiation sites on the origami core and the brush height and composition. Coarse-grained simulations predict the conformation of the brush-functionalized DONs that agree well with the experimentally observed morphologies. We find that polynucleotide brush-functionalization increases the nuclease resistance of DONs significantly, and that this stability can be spatially programmed through the site-specific growth of polynucleotide brushes. The ability to site-specifically decorate DONs with brushes of natural and non-natural nucleotides provides access to a large range of functionalized DON architectures that would allow for further supramolecular assembly, and for potential applications in smart nanoscale delivery systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Spatiotemporal Control over Polynucleotide Brush Growth on DNA Origami Nanostructures

DNA nanotechnology provides an approach to create precise, tunable, and biocompatible nanostructures for biomedical applications. However, the stability of these structures is severely compromised in biological milieu due to their fast degradation by nucleases. Recently, we showed how enzymatic polymerization could be harnessed to grow polynucleotide brushes of tunable length and location on the surface of DNA origami nanostructures, which greatly enhances their nuclease stability. Here, in this study, we report on strategies that allow for both spatial and temporal control over polymerization through activatable initiation, cleavage, and regeneration of polynucleotide brushes using restriction enzymes. The ability to site‐specifically decorate DNA origami nanostructures with polynucleotide brushes in a spatiotemporally controlled way provides access to “smart” functionalized DNA architectures with potential applications in drug delivery and supramolecular assembly.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Controlling the Self-Assembly of DNA Origami Octahedra via Manipulation of Inter-Vertex Interactions

Recent studies have demonstrated novel strategies for the organization of nanomaterials into three-dimensional (3D) ordered arrays with prescribed lattice symmetries using DNA-based self-assembly strategies. In one approach, the nanomaterial is sequestered into DNA origami frames or “material voxels” and then coordinated into ordered arrays based on the voxel geometry and the corresponding directional interactions based on its valency. While the lattice symmetry is defined by the valency of the bonds, a larger-scale morphological development is affected by assembly processes and differences in energies of anisotropic bonds. To facilely model this assembly process, we investigate the self-assembly behavior of hard particles with six interacting vertices via theory and Monte Carlo simulations and exploration of corresponding experimental systems. We demonstrate that assemblies with different 3D crystalline morphologies, but the same lattice symmetry can be formed depending on the relative strength of vertex-to-vertex interactions in orthogonal directions. We observed three distinct assembly morphologies for such systems: cube-like, sheet-like, and cylinder-like. A simple analytical theory inspired by well-established ideas in the areas of protein crystallization, based on calculating the second virial coefficient of patchy hard spheres, captures the simulation results and thus represents a straightforward means of modeling this self-assembly process. To complement the theory and simulations, experimental studies were performed to investigate the assembly of octahedral DNA origami frames with varying binding energies at their vertices. In conclusion, x-ray scattering confirms the robustness of the formed nanoscale lattices for different binding energies, while both optical and electron microscopy imaging validated the theoretical predictions on the dependence of the distinct morphologies of assembled state on the interaction strengths in the three orthogonal directions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Controlled mechanochemical coupling of anti-junctions in DNA origami arrays

Abstract Allostery is a hallmark of cellular function and important in every biological system. Still, we are only starting to mimic it in the laboratory. Here, we introduce an approach to study aspects of allostery in artificial systems. We use a DNA origami domino array structure which–upon binding of trigger DNA strands–undergoes a stepwise allosteric conformational change. Using two FRET probes placed at specific positions in the DNA origami, we zoom in into single steps of this reaction cascade. Most of the steps are strongly coupled temporally and occur simultaneously. Introduction of activation energy barriers between different intermediate states alters this coupling and induces a time delay. We then apply these approaches to release a cargo DNA strand at a predefined step in the reaction cascade to demonstrate the applicability of this concept in tunable cascades of mechanochemical coupling with both spatial and temporal control.

Science & Technology - Other Topics↗

DOE OSTI2023

Structure, folding and flexibility of co-transcriptional RNA origami

RNA origami is a method for designing RNA nanostructures that can self-assemble through co-transcriptional folding with applications in nanomedicine and synthetic biology. However, to advance the method further, an improved understanding of RNA structural properties and folding principles is required. Here we use cryogenic electron microscopy to study RNA origami sheets and bundles at sub-nanometre resolution revealing structural parameters of kissing-loop and crossover motifs, which are used to improve designs. In RNA bundle designs, we discover a kinetic folding trap that forms during folding and is only released after 10 h. Furthermore, exploration of the conformational landscape of several RNA designs reveal the flexibility of helices and structural motifs. Finally, sheets and bundles are combined to construct a multidomain satellite shape, which is characterized by individual-particle cryo-electron tomography to reveal the domain flexibility. Together, the study provides a structural basis for future improvements to the design cycle of genetically encoded RNA nanodevices.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2021

Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami

Wireframe DNA origami assemblies can now be programmed automatically from the top-down using simple wireframe target geometries, or meshes, in 2D and 3D, using either rigid, six-helix bundle (6HB) or more compliant, two-helix bundle (DX) edges. While these assemblies have numerous applications in nanoscale materials fabrication due to their nanoscale spatial addressability and high degree of customization, no easy-to-use graphical user interface software yet exists to deploy these algorithmic approaches within a single, standalone interface. Further, top-down sequence design of 3D DX-based objects previously enabled by DAEDALUS was limited to discrete edge lengths and uniform vertex angles, limiting the scope of objects that can be designed. Here, we introduce the open-source software package ATHENA with a graphical user interface that automatically renders single-stranded DNA scaffold routing and staple strand sequences for any target wireframe DNA origami using DX or 6HB edges, including irregular, asymmetric DX-based polyhedra with variable edge lengths and vertices demonstrated experimentally, which significantly expands the set of possible 3D DNA-based assemblies that can be designed. ATHENA also enables external editing of sequences using caDNAno, demonstrated using asymmetric nanoscale positioning of gold nanoparticles, as well as providing atomic-level models for molecular dynamics, coarse-grained dynamics with oxDNA, and other computational chemistry simulation approaches.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2014

Deployment Methods for an Origami-Inspired Rigid-Foldable Array

The purpose of this work is to evaluate several deployment methods for an origami-inspired solar array at two size scales: 25-meter array and CubeSat array. The array enables rigid panel deployment and introduces new concepts for actuating CubeSat deployables. The design for the array was inspired by the origami flasher model (Lang, 1997; Shafer, 2001). Figure 1 shows the array prototyped from Garolite and Kapton film at the CubeSat scale. Prior work demonstrated that rigid panels like solar cells could successfully be folded into the final stowed configuration without requiring the panels to flex (Zirbel, Lang, Thomson, & al., 2013). The design of the array is novel and enables efficient use of space. The array can be wrapped around the central bus of the spacecraft in the case of the large array, or can accommodate storage of a small instrument payload in the case of the CubeSat array. The radial symmetry of this array around the spacecraft is ideally suited for spacecraft that need to spin. This work focuses on several actuation methods for a one-time deployment of the array. The array is launched in its stowed configuration and it will be deployed when it is in space. Concepts for both passive and active actuation were considered.

Zirbel, Shannon A.↗

NASA NTRS2013

Accommodating Thickness in Origami-Based Deployable Arrays

The purpose of this work is to create deployment systems with a large ratio of stowed-to-deployed diameter. Deployment from a compact form to a final flat state can be achieved through origami-inspired folding of panels. There are many models capable of this motion when folded in a material with negligible thickness; however, when the application requires the folding of thick, rigid panels, attention must be paid to the effect of material thickness not only on the final folded state, but also during the folding motion (i.e., the panels must not be required to flex to attain the final folded form). The objective is to develop new methods for deployment from a compact folded form to a large circular array (or other final form). This paper describes a mathematical model for modifying the pattern to accommodate material thickness in the context of the design, modeling, and testing of a deployable system inspired by an origami six-sided flasher model. The model is demonstrated in hardware as a 1/20th scale prototype of a deployable solar array for space applications. The resulting prototype has a ratio of stowed-to-deployed diameter of 9.2 (or 1.25 m deployed outer diameter to 0.136 m stowed outer diameter).

flasher↗

NASA NTRS2021

Origami-Inspired Optical Shield for a Starshade Inner Disk Testbed: Design, Fabrication, and Analysis

In 2019, a 10 m-diameter starshade inner disk test article was assembled; this test article demonstrated deployment accuracy sufficient for starshade mission concepts. Here, we describe the design, fabrication, and computational structural analysis of a key inner disk component realized for this effort: the origami-folded optical shield. The optical shield is a 10 m-diameter lightweight cover that makes the inner disk opaque. It stows within a 2.3 m-diameter volume by using an origami-inspired wrapping pattern, and is deployed passively by the inner disk perimeter truss. The fold pattern was generated by a custom algorithm based one existing generative design approaches. This prototype demonstrated critical functions: stowage in a compact volume, static equilibrium when stowed and deployed, and low strain when stowed. Four separate computational structural analysis models of the optical shield were de- veloped, at varying levels of fidelity and using a variety of software solutions: Abaqus, RAPID, and ADAMS. These models were intended to pathfind approaches for modeling the stowage and deployment of the inner disk, and to demonstrate that the optical shield is amenable existing structural modeling approaches. These models were found to adequately capture pertinent stowage and deployment behavior of the optical shield prototype.

Hoffman, Laura↗

NASA NTRSDate not supplied

Preliminary Design of a Deployable Optical Space Array Based on a Thickened Origami Flasher Pattern

Performance of space-based optics could be greatly enhanced by using deployable origami-based arrays, which can offer a large aperture size relative to their stowed volume when compared to traditional technology, thus improving imaging quality. In this work, we select, develop, and adapt the origami flasher pattern to serve as the foundation for a deployable array that shows promise for meeting stringent optical requirements. We apply a novel thickness accommodation technique, outline an approach for implementing the technique, improve stability by adjusting geometric characteristics of the pattern, and create an array of frames for housing optical elements in a co-planar configuration. Problems of non-rigid foldability in the flasher pattern are addressed. A prototype is created and tested. We find that the deployable flasher shows promise as an optical array. By following the guidelines in this work, more efficient and powerful optical arrays can be developed.

Jared Hunter↗

DOE OSTI2026

Effect of Thermodynamic and Environmental Factors on Crystallization of DNA‐Origami Superlattices

The directed self‐assembly of nanoscale materials into ordered superlattices presents a powerful strategy for creating next‐generation materials with programmable mechanical, optical, and photonic properties. Deoxyribonucleic acid (DNA) origami has emerged as a versatile scaffold for encoding nanoscale geometry and guiding the crystallization of complex 3D architectures. However, a systematic understanding of the parameters that govern the efficiency and quality of superlattice formation remains limited. In this study, we utilize octahedral DNA nanoscale frames as a model system to investigate the relative influence of key factors, including buffer composition, ionic strength, frame concentration, and thermal annealing protocols, on the size, order, and reproducibility of the resulting superlattices. Our findings provide a quantitative framework to rationally optimize DNA‐based assembly pathways. Structural characterization via small‐angle x‐ray scattering (SAXS), scanning electron microscopy (SEM), and optical microscopy validates the quality and fidelity of the assembled lattices. Moreover, by templating these DNA frameworks into inorganic replicas, we establish general design principles that extend beyond biomolecular systems, providing a foundation for the synthesis of programmable materials in broader nanofabrication contexts.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2021

Strategies for Constructing and Operating DNA Origami Linear Actuators

Abstract Linear actuators are ubiquitous components at all scales of engineering. DNA nanotechnology offers a unique opportunity for bottom‐up assembly at the molecular scale, providing nanoscale precision with multiple methods for constructing and operating devices. In this paper, DNA origami linear actuators with up to 200 nm travel, based on a rail threading a topologically locked slider, are demonstrated. Two strategies, one‐ and two‐pot assembly, are demonstrated whereby the two components are folded from one or two DNA scaffold strands, respectively. In order to control the position of the slider on the rail, the rail and the inside of the slider are decorated with single‐stranded oligonucleotides with distinct sequences. Two positioning strategies, based on diffusion and capture of signaling strands, are used to link the slider reversibly to determined positions on the rail with high yield and precision. These machine components provide a basis for applications in molecular machinery and nanoscale manufacture including programmed chemical synthesis.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2022

Lifelike metallic structures using origami and compliant mechanisms

In nature, materials and designs are smart i.e., they achieve the desired shape or size to optimize different processes without needing external devices. However, in the design of mechanical metallic structures, gaining such behavior without using special materials or external sources is still a visionary thought. Here the concept of lifelike metallic structures is introduced. Further, the vision is to produce designs where the metallic walls can behave like human muscles. To create such structures, origami-inspired designs in combination with compliant mechanisms are proposed. For fabricating such designs with desired mechanical properties, it is also proposed to leverage additive manufacturing techniques.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Origami Terahertz Detectors Realized by Inkjet Printing of Carbon Nanotube Inks

Terahertz (THz) technology has shown promise for several applications, but limitations in sources and detectors have prevented broader adoption. Existing THz detectors are rigid, planar, and fabricated using complex technology, making it difficult to integrate into systems. Here we demonstrate THz detectors fabricated by inkjet printing on submicrometer thick, ultraflexible substrates. By developing p- and n-type carbon nanotube inks, we achieve optically thick p–n junction and p-type devices, enabling antenna-free pixels for THz imaging. By further designing and folding the printed devices, we realize origami-inspired architectures with improved performance over single devices, achieving a noise-equivalent power of 12 nW/Hz 1/2 at room temperature with no voltage bias. Finally, our approach opens avenues for nonplanar, foldable, deployable, insertable, and retractable THz detectors for applications in nondestructive inspection.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Formation of Linear Plasmonic Heterotrimers Using Nanoparticle Docking to DNA Origami Cages

The fabrication of complex assemblies with interesting collective properties from plasmonic nanoparticles (NPs) is often challenging. While DNA-directed self-assembly has emerged as one of the most promising approaches to forming such complex assemblies, the resulting structures tend to have large variability in gap sizes and shapes, as the DNA strands used to organize these particles are flexible, and the polydispersity of the NPs leads to variability in these critical structural features. Here, we use a new strategy termed docking to DNA origami cages (D-DOC) to organize spherical NPs into a linear heterotrimer with a precisely defined geometrical arrangement. Instead of binding NPs to the exterior of the DNA templates, D-DOC binds the NPs to either the interior or the opening of a 3D cage, which significantly reduces the variability of critical structural features by incorporating multiple diametrically arranged capture strands to tether NPs. Additionally, such a spatial arrangement of the capture strand can work synergistically with shape complementarity to achieve tighter confinement. To assemble NPs via D-DOC, we developed a multistep assembly process that first encapsulates an NP inside a cage and then binds two other NPs to the openings. Microscopic characterization shows low variability in the bond angles and gap sizes. Both UV–vis absorption and surface-enhanced Raman scattering (SERS) measurements showed strong plasmonic coupling that aligned with predictions by electrodynamic simulations, further confirming the precision of the assembly. These results suggest D-DOC could open new opportunities in biomolecular sensing, SERS and fluorescence spectroscopies, and energy harvesting through the self-assembly of NPs into more complex 3D assemblies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Realizing mechanical frustration at the nanoscale using DNA origami

Structural designs inspired by physical and biological systems have been previously utilized to develop mechanical metamaterials with enhanced properties based on clever geometric arrangement of constituent building blocks. Here, we use the DNA origami method to realize a nanoscale metastructure exhibiting mechanical frustration, a counterpart of the well-known phenomenon of magnetic frustration. By selectively actuating reconfigurable struts, it adopts either frustrated or non-frustrated states, each characterized by distinct free energy profiles. While the non-frustrated state distributes the strain homogeneously, the frustrated mode concentrates it at a specific location. Molecular dynamics simulations reconcile the contrasting behaviors and provide insights into underlying mechanics. We explore the design space further by tailoring responses through structural modifications. Our work combines programmable DNA self-assembly with mechanical design principles to overcome engineering limitations encountered at the macroscale to design dynamic, deformable nanostructures with potential applications in elastic energy storage, nanomechanical computation, and allosteric mechanisms in DNA-based nanomachinery.

DNA nanostructures↗