Browse
Submit Data
Databases
API
Help

Dataset Information

23 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

SUBMITTER: Jun H

PROVIDER: S-EPMC8501967 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Automated sequence design of 2D wireframe DNA origami with honeycomb edges.

Project description:Wireframe DNA origami has emerged as a powerful approach to fabricating nearly arbitrary 2D and 3D geometries at the nanometer-scale. Complex scaffold and staple routing needed to design wireframe DNA origami objects, however, render fully automated, geometry-based sequence design approaches essential for their synthesis. And wireframe DNA origami structural fidelity can be limited by wireframe edges that are composed only of one or two duplexes. Here we introduce a fully automated computational approach that programs 2D wireframe origami assemblies using honeycomb edges composed of six parallel duplexes. These wireframe assemblies show enhanced structural fidelity from electron microscopy-based measurement of programmed angles compared with identical geometries programmed using dual-duplex edges. Molecular dynamics provides additional theoretical support for the enhanced structural fidelity observed. Application of our top-down sequence design procedure to a variety of complex objects demonstrates its broad utility for programmable 2D nanoscale materials.

| S-EPMC6882874 | biostudies-literature

Automated Sequence Design of 3D Polyhedral Wireframe DNA Origami with Honeycomb Edges.

Project description:3D polyhedral wireframe DNA nanoparticles (DNA-NPs) fabricated using scaffolded DNA origami offer complete and independent control over NP size, structure, and asymmetric functionalization on the 10-100 nm scale. However, the complex DNA sequence design needed for the synthesis of these versatile DNA-NPs has limited their widespread use to date. While the automated sequence design algorithms DAEDALUS and vHelix-BSCOR apply to DNA-NPs synthesized using either uniformly dual or hybrid single-dual duplex edges, respectively, these DNA-NPs are relatively compliant mechanically and are therefore of limited utility for some applications. Further, these algorithms are incapable of handling DNA-NP edge designs composed of more than two duplexes, which are needed to enhance DNA-NP mechanical stiffness. As an alternative, here we introduce the scaffolded DNA origami sequence design algorithm TALOS, which is a generalized procedure for the fully automated design of wireframe 3D polyhedra composed of edges of any cross section with an even number of duplexes, and apply it to DNA-NPs composed uniformly of single honeycomb edges. We also introduce a multiway vertex design that enables the fabrication of DNA-NPs with arbitrary edge lengths and vertex angles and apply it to synthesize a highly asymmetric origami object. Sequence designs are demonstrated to fold robustly into target DNA-NP shapes with high folding efficiency and structural fidelity that is verified using single particle cryo-electron microscopy and 3D reconstruction. In order to test its generality, we apply TALOS to design an in silico library of over 200 DNA-NPs of distinct symmetries and sizes, and for broad impact, we also provide the software as open source for the generation of custom NP designs.

| S-EPMC6679942 | biostudies-literature

A GRAPPA algorithm for arbitrary 2D/3D non-Cartesian sampling trajectories with rapid calibration.

Project description:PurposeGRAPPA is a popular reconstruction method for Cartesian parallel imaging, but is not easily extended to non-Cartesian sampling. We introduce a general and practical GRAPPA algorithm for arbitrary non-Cartesian imaging.MethodsWe formulate a general GRAPPA reconstruction by associating a unique kernel with each unsampled k-space location with a distinct constellation, that is, local sampling pattern. We calibrate these generalized kernels using the Fourier transform phase shift property applied to fully gridded or separately acquired Cartesian Autocalibration signal (ACS) data. To handle the resulting large number of different kernels, we introduce a fast calibration algorithm based on nonuniform FFT (NUFFT) and adoption of circulant ACS boundary conditions. We applied our method to retrospectively under-sampled rotated stack-of-stars/spirals in vivo datasets, and to a prospectively under-sampled rotated stack-of-spirals functional MRI acquisition with a finger-tapping task.ResultsWe reconstructed all datasets without performing any trajectory-specific manual adaptation of the method. For the retrospectively under-sampled experiments, our method achieved image quality (i.e., error and g-factor maps) comparable to conjugate gradient SENSE (cg-SENSE) and SPIRiT. Functional activation maps obtained from our method were in good agreement with those obtained using cg-SENSE, but required a shorter total reconstruction time (for the whole time-series): 3 minutes (proposed) vs 15 minutes (cg-SENSE).ConclusionsThis paper introduces a general 3D non-Cartesian GRAPPA that is fast enough for practical use on today's computers. It is a direct generalization of original GRAPPA to non-Cartesian scenarios. The method should be particularly useful in dynamic imaging where a large number of frames are reconstructed from a single set of ACS data.

| S-EPMC6894481 | biostudies-literature

Autonomously designed free-form 2D DNA origami.

Project description:Scaffolded DNA origami offers the unique ability to organize molecules in nearly arbitrary spatial patterns at the nanometer scale, with wireframe designs further enabling complex 2D and 3D geometries with irregular boundaries and internal structures. The sequence design of the DNA staple strands needed to fold the long scaffold strand to the target geometry is typically performed manually, limiting the broad application of this materials design paradigm. Here, we present a fully autonomous procedure to design all DNA staple sequences needed to fold any free-form 2D scaffolded DNA origami wireframe object. Our algorithm uses wireframe edges consisting of two parallel DNA duplexes and enables the full autonomy of scaffold routing and staple sequence design with arbitrary network edge lengths and vertex angles. The application of our procedure to geometries with both regular and irregular external boundaries and variable internal structures demonstrates its broad utility for nanoscale materials science and nanotechnology.

| S-EPMC6314877 | biostudies-other

Spatial Regulation of T-Cell Signaling by Programmed Death-Ligand 1 on Wireframe DNA Origami Flat Sheets.

Project description:Programmed Death-1 (PD-1) is a coinhibitory receptor expressed on activated T cells that suppresses T-cell signaling and effector functions. It has been previously shown that binding to its ligand PD-L1 induces a spatial reorganization of PD-1 receptors into microclusters on the cell membrane. However, the roles of the spatial organization of PD-L1 on PD-1 clustering and T-cell signaling have not been elucidated. Here, we used DNA origami flat sheets to display PD-L1 ligands at defined nanoscale distances and investigated their ability to inhibit T-cell activation in vitro. We found that DNA origami flat sheets modified with CD3 and CD28 activating antibodies (FS-α-CD3-CD28) induced robust T-cell activation. Co-treatment with flat sheets presenting PD-L1 ligands separated by ∼200 nm (FS-PD-L1-200), but not 13 nm (FS-PD-L1-13) or 40 nm (FS-PD-L1-40), caused an inhibition of T-cell signaling, which increased with increasing molar ratio of FS-PD-L1-200 to FS-α-CD3-CD28. Furthermore, FS-PD-L1-200 induced the formation of smaller PD-1 nanoclusters and caused a larger reduction in IL-2 expression compared to FS-PD-L1-13. Together, these findings suggest that the spatial organization of PD-L1 determines its ability to regulate T-cell signaling and may guide the development of future nanomedicine-based immunomodulatory therapies.

| S-EPMC7905882 | biostudies-literature

Lab on a Biomembrane: rapid prototyping and manipulation of 2D fluidic lipid bilayers circuits.

Project description:Lipid bilayer membranes are among the most ubiquitous structures in the living world, with intricate structural features and a multitude of biological functions. It is attractive to recreate these structures in the laboratory, as this allows mimicking and studying the properties of biomembranes and their constituents, and to specifically exploit the intrinsic two-dimensional fluidity. Even though diverse strategies for membrane fabrication have been reported, the development of related applications and technologies has been hindered by the unavailability of both versatile and simple methods. Here we report a rapid prototyping technology for two-dimensional fluidic devices, based on in-situ generated circuits of phospholipid films. In this "lab on a molecularly thin membrane", various chemical and physical operations, such as writing, erasing, functionalization, and molecular transport, can be applied to user-defined regions of a membrane circuit. This concept is an enabling technology for research on molecular membranes and their technological use.

| S-EPMC3783038 | biostudies-literature

High-resolution 3D photopolymerization assisted by upconversion nanoparticles for rapid prototyping applications.

Project description:Three-dimensional (3D) rapid prototyping technology based on near-infrared light-induced polymerization of photocurable compositions containing upconversion nanomaterials has been explored. For this aim, the rationally-designed core/shell upconversion nanoparticles NaYF4:Yb3+,Tm3+/NaYF4, with the distinct ultraviolet-emitting lines and unprecedentedly high near-infrared to ultraviolet conversion efficiency of [Formula: see text] have been used. The upconverted ultraviolet photons were capable to efficiently activate photoinitiators contained in light-sensitive resins under moderate intensities of NIR excitation below 10?W?cm-2 and induce generation of radicals and photopolymerization in situ. Near infrared-activated polymerization process, both at the millimeter and sub-micron scales, was investigated. Polymeric macro- and microstructures were fabricated by means of near infrared laser scanning photolithography in the volume of liquid photocurable compositions with focused laser light at 975?nm wavelength. Examination of the polymerization process in the vicinity of the nanoparticles shows strong differences in the rate of polymer shell growth on flat and edge nanoparticle sides. This phenomenon mainly defines the resolution of the demonstrated near infrared - ultraviolet 3D printing technology at the micrometer scale level.

| S-EPMC5832145 | biostudies-literature

Stabilization and structural changes of 2D DNA origami by enzymatic ligation.

Project description:The low thermal stability of DNA nanostructures is the major drawback in their practical applications. Most of the DNA nanotubes/tiles and the DNA origami structures melt below 60°C due to the presence of discontinuities in the phosphate backbone (i.e., nicks) of the staple strands. In molecular biology, enzymatic ligation is commonly used to seal the nicks in the duplex DNA. However, in DNA nanotechnology, the ligation procedures are neither optimized for the DNA origami nor routinely applied to link the nicks in it. Here, we report a detailed analysis and optimization of the conditions for the enzymatic ligation of the staple strands in four types of 2D square lattice DNA origami. Our results indicated that the ligation takes overnight, efficient at 37°C rather than the usual 16°C or room temperature, and typically requires much higher concentration of T4 DNA ligase. Under the optimized conditions, up to 10 staples ligation with a maximum ligation efficiency of 55% was achieved. Also, the ligation is found to increase the thermal stability of the origami as low as 5°C to as high as 20°C, depending on the structure. Further, our studies indicated that the ligation of the staple strands influences the globular structure/planarity of the DNA origami, and the origami is more compact when the staples are ligated. The globular structure of the native and ligated origami was also found to be altered dynamically and progressively upon ethidium bromide intercalation in a concentration-dependent manner.

| S-EPMC8373134 | biostudies-literature

Rapid Prototyping of 3D Biochips for Cell Motility Studies Using Two-Photon Polymerization.

Project description:The study of cellular migration dynamics and strategies plays a relevant role in the understanding of both physiological and pathological processes. An important example could be the link between cancer cell motility and tumor evolution into metastatic stage. These strategies can be strongly influenced by the extracellular environment and the consequent mechanical constrains. In this framework, the possibility to study the behavior of single cells when subject to specific topological constraints could be an important tool in the hands of biologists. Two-photon polymerization is a sub-micrometric additive manufacturing technique that allows the fabrication of 3D structures in biocompatible resins, enabling the realization of ad hoc biochips for cell motility analyses, providing different types of mechanical stimuli. In our work, we present a new strategy for the realization of multilayer microfluidic lab-on-a-chip constructs for the study of cell motility which guarantees complete optical accessibility and the possibility to freely shape the migration area, to tailor it to the requirements of the specific cell type or experiment. The device includes a series of micro-constrictions that induce different types of mechanical stress on the cells during their migration. We show the realization of different possible geometries, in order to prove the versatility of the technique. As a proof of concept, we present the use of one of these devices for the study of the motility of murine neuronal cancer cells under high physical confinement, highlighting their peculiar migration mechanisms.

| S-EPMC8078855 | biostudies-literature

Cryo-EM structure of a 3D DNA-origami object.

Project description:A key goal for nanotechnology is to design synthetic objects that may ultimately achieve functionalities known today only from natural macromolecular complexes. Molecular self-assembly with DNA has shown potential for creating user-defined 3D scaffolds, but the level of attainable positional accuracy has been unclear. Here we report the cryo-EM structure and a full pseudoatomic model of a discrete DNA object that is almost twice the size of a prokaryotic ribosome. The structure provides a variety of stable, previously undescribed DNA topologies for future use in nanotechnology and experimental evidence that discrete 3D DNA scaffolds allow the positioning of user-defined structural motifs with an accuracy that is similar to that observed in natural macromolecules. Thereby, our results indicate an attractive route to fabricate nanoscale devices that achieve complex functionalities by DNA-templated design steered by structural feedback.

| S-EPMC3523823 | biostudies-other

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data