Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Polyhedra self-assembled from DNA tripods and characterized with 3D DNA-PAINT.

ABSTRACT: DNA self-assembly has produced diverse synthetic three-dimensional polyhedra. These structures typically have a molecular weight no greater than 5 megadaltons. We report a simple, general strategy for one-step self-assembly of wireframe DNA polyhedra that are more massive than most previous structures. A stiff three-arm-junction DNA origami tile motif with precisely controlled angles and arm lengths was used for hierarchical assembly of polyhedra. We experimentally constructed a tetrahedron (20 megadaltons), a triangular prism (30 megadaltons), a cube (40 megadaltons), a pentagonal prism (50 megadaltons), and a hexagonal prism (60 megadaltons) with edge widths of 100 nanometers. The structures were visualized by means of transmission electron microscopy and three-dimensional DNA-PAINT super-resolution fluorescent microscopy of single molecules in solution.

SUBMITTER: Iinuma R

PROVIDER: S-EPMC4153385 | biostudies-literature | 2014 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Polyhedra self-assembled from DNA tripods and characterized with 3D DNA-PAINT.

Iinuma Ryosuke R Ke Yonggang Y Jungmann Ralf R Schlichthaerle Thomas T Woehrstein Johannes B JB Yin Peng P

Science (New York, N.Y.) 20140313 6179

DNA self-assembly has produced diverse synthetic three-dimensional polyhedra. These structures typically have a molecular weight no greater than 5 megadaltons. We report a simple, general strategy for one-step self-assembly of wireframe DNA polyhedra that are more massive than most previous structures. A stiff three-arm-junction DNA origami tile motif with precisely controlled angles and arm lengths was used for hierarchical assembly of polyhedra. We experimentally constructed a tetrahedron (20 ...[more]

PMID: 24625926

Similar Datasets

Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT.

Project description:Super-resolution fluorescence microscopy is a powerful tool for biological research, but obtaining multiplexed images for a large number of distinct target species remains challenging. Here we use the transient binding of short fluorescently labeled oligonucleotides (DNA-PAINT, a variation of point accumulation for imaging in nanoscale topography) for simple and easy-to-implement multiplexed super-resolution imaging that achieves sub-10-nm spatial resolution in vitro on synthetic DNA structures. We also report a multiplexing approach (Exchange-PAINT) that allows sequential imaging of multiple targets using only a single dye and a single laser source. We experimentally demonstrate ten-color super-resolution imaging in vitro on synthetic DNA structures as well as four-color two-dimensional (2D) imaging and three-color 3D imaging of proteins in fixed cells.

| S-EPMC4153392 | biostudies-literature

Designing Higher Resolution Self-Assembled 3D DNA Crystals via Strand Terminus Modifications.

Project description:DNA tensegrity triangles self-assemble into rhombohedral three-dimensional crystals via sticky ended cohesion. Crystals containing two-nucleotide (nt) sticky ends (GA:TC) have been reported previously, and those crystals diffracted to 4.9 Å at beamline NSLS-I-X25. Here, we analyze the effect of varying sticky end lengths and sequences as well as the impact of 5'- and 3'-phosphates on crystal formation and resolution. Tensegrity triangle motifs having 1-, 2-, 3-, and 4-nt sticky ends all form crystals. X-ray diffraction data from the same beamline reveal that the crystal resolution for a 1-nt sticky end (G:C) and a 3-nt sticky end (GAT:ATC) were 3.4 and 4.2 Å, respectively. Resolutions were determined from complete data sets in each case. We also conducted trials that examined every possible combination of 1-nucleotide and 2-nucleotide sticky-ended phosphorylated strands and successfully crystallized all 16 possible combinations of strands. We observed the position of the 5'-phosphate on either the crossover (1), helical (2), or central strand (3) affected the resolution of the self-assembled crystals for the 2-turn monomer (3.0 Å for 1-2P-3P) and 2-turn dimer sticky ended (4.1 Å for 1-2-3P) systems. We have also examined the impact of the identity of the base flanking the sticky ends as well as the use of 3'-phosphate. We conclude that crystal resolution is not a simple consequence of the thermodynamics of the direct nucleotide pairing interactions involved in molecular cohesion in this system.

| S-EPMC6660133 | biostudies-literature

Triptycene Tripods for the Formation of Highly Uniform and Densely Packed Self-Assembled Monolayers with Controlled Molecular Orientation.

Project description:When employing self-assembled monolayers (SAMs) for tuning surface and interface properties, organic molecules that enable strong binding to the substrate, large-area structural uniformity, precise alignment of functional groups, and control of their density are highly desirable. To achieve these goals, tripod systems bearing multiple bonding sites have been developed as an alternative to conventional monodentate systems. Bonding of all three sites has, however, hardly been achieved, with the consequence that structural uniformity and orientational order in tripodal SAMs are usually quite poor. To overcome that problem, we designed 1,8,13-trimercaptomethyltriptycene (T1) and 1,8,13-trimercaptotriptycene (T2) as potential tripodal SAM precursors and investigated their adsorption behavior on Au(111) combining several advanced experimental techniques and state-of-the-art theoretical simulations. Both SAMs adopt dense, nested hexagonal structures but differ in their adsorption configurations and structural uniformity. While the T2-based SAM exhibits a low degree of order and noticeable deviation from the desired tripodal anchoring, all three anchoring groups of T1 are equally bonded to the surface as thiolates, resulting in an almost upright orientation of the benzene rings and large-area structural uniformity. These superior properties are attributed to the effect of conformationally flexible methylene linkers at the anchoring groups, absent in the case of T2. Both SAMs display interesting electronic properties, and, bearing in mind that the triptycene framework can be functionalized by tail groups in various positions and with high degree of alignment, especially T1 appears as an ideal docking platform for complex and highly functional molecular films.

| S-EPMC6483319 | biostudies-literature

DNA-assembled superconducting 3D nanoscale architectures.

Project description:Studies of nanoscale superconducting structures have revealed various physical phenomena and led to the development of a wide range of applications. Most of these studies concentrated on one- and two-dimensional structures due to the lack of approaches for creation of fully engineered three-dimensional (3D) nanostructures. Here, we present a 'bottom-up' method to create 3D superconducting nanostructures with prescribed multiscale organization using DNA-based self-assembly methods. We assemble 3D DNA superlattices from octahedral DNA frames with incorporated nanoparticles, through connecting frames at their vertices, which result in cubic superlattices with a 48 nm unit cell. The superconductive superlattice is formed by converting a DNA superlattice first into highly-structured 3D silica scaffold, to turn it from a soft and liquid-environment dependent macromolecular construction into a solid structure, following by its coating with superconducting niobium (Nb). Through low-temperature electrical characterization we demonstrate that this process creates 3D arrays of Josephson junctions. This approach may be utilized in development of a variety of applications such as 3D Superconducting Quantum interference Devices (SQUIDs) for measurement of the magnetic field vector, highly sensitive Superconducting Quantum Interference Filters (SQIFs), and parametric amplifiers for quantum information systems.

| S-EPMC7656258 | biostudies-literature

From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal.

Project description:We live in a macroscopic three-dimensional (3D) world, but our best description of the structure of matter is at the atomic and molecular scale. Understanding the relationship between the two scales requires a bridge from the molecular world to the macroscopic world. Connecting these two domains with atomic precision is a central goal of the natural sciences, but it requires high spatial control of the 3D structure of matter. The simplest practical route to producing precisely designed 3D macroscopic objects is to form a crystalline arrangement by self-assembly, because such a periodic array has only conceptually simple requirements: a motif that has a robust 3D structure, dominant affinity interactions between parts of the motif when it self-associates, and predictable structures for these affinity interactions. Fulfilling these three criteria to produce a 3D periodic system is not easy, but should readily be achieved with well-structured branched DNA motifs tailed by sticky ends. Complementary sticky ends associate with each other preferentially and assume the well-known B-DNA structure when they do so; the helically repeating nature of DNA facilitates the construction of a periodic array. It is essential that the directions of propagation associated with the sticky ends do not share the same plane, but extend to form a 3D arrangement of matter. Here we report the crystal structure at 4 A resolution of a designed, self-assembled, 3D crystal based on the DNA tensegrity triangle. The data demonstrate clearly that it is possible to design and self-assemble a well-ordered macromolecular 3D crystalline lattice with precise control.

| S-EPMC2764300 | biostudies-literature

3D Cell Culture in a Self-Assembled Nanofiber Environment.

Project description:The development and utilization of three-dimensional cell culture platforms has been gaining more traction. Three-dimensional culture platforms are capable of mimicking in vivo microenvironments, which provide greater physiological relevance in comparison to conventional two-dimensional cultures. The majority of three-dimensional culture platforms are challenged by the lack of cell attachment, long polymerization times, and inclusion of undefined xenobiotics, and cytotoxic cross-linkers. In this study, we review the use of a highly defined material composed of naturally occurring compounds, hyaluronic acid and chitosan, known as Cell-Mate3DTM. Moreover, we provide an original measurement of Young's modulus using a uniaxial unconfined compression method to elucidate the difference in microenvironment rigidity for acellular and cellular conditions. When hydrated into a tissue-like hybrid hydrocolloid/hydrogel, Cell-Mate3DTM is a highly versatile three-dimensional culture platform that enables downstream applications such as flow cytometry, immunostaining, histological staining, and functional studies to be applied with relative ease.

| S-EPMC5025053 | biostudies-literature

Self-Assembled Flexible and Integratable 3D Microtubular Asymmetric Supercapacitors.

Project description:The rapid development of microelectronics has equally rapidly increased the demand for miniaturized energy storage devices. On-chip microsupercapacitors (MSCs), as promising power candidates, possess great potential to complement or replace electrolytic capacitors and microbatteries in various applications. However, the areal capacities and energy densities of the planar MSCs are commonly limited by the low voltage window, the thin layer of the electrode materials and complex fabrication processes. Here, a new-type three-dimensional (3D) tubular asymmetric MSC with small footprint area, high potential window, ultrahigh areal energy density, and long-term cycling stability is fabricated with shapeable materials and photolithographic technologies, which are compatible with modern microelectronic fabrication procedures widely used in industry. Benefiting from the novel architecture, the 3D asymmetric MSC displays an ultrahigh areal capacitance of 88.6 mF cm-2 and areal energy density of 28.69 mW h cm-2, superior to most reported interdigitated MSCs. Furthermore, the 3D tubular MSCs demonstrate remarkable cycling stability and the capacitance retention is up to 91.8% over 12 000 cycles. It is believed that the efficient fabrication methodology can be used to construct various integratable microscale tubular energy storage devices with small footprint area and high performance for miniaturized electronics.

| S-EPMC6794616 | biostudies-literature

Self-Assembled Epitaxial Cathode-Electrolyte Nanocomposites for 3D Microbatteries.

Project description:The downscaling of electronic devices requires rechargeable microbatteries with enhanced energy and power densities. Here, we evaluate self-assembled vertically aligned nanocomposite (VAN) thin films as a platform to create high-performance three-dimensional (3D) microelectrodes. This study focuses on controlling the VAN formation to enable interface engineering between the LiMn2O4 cathode and the (Li,La)TiO3 solid electrolyte. Electrochemical analysis in a half cell against lithium metal showed the absence of sharp redox peaks due to the confinement in the electrode pillars at the nanoscale. The (100)-oriented VAN thin films showed better rate capability and stability during extensive cycling due to the better alignment to the Li-diffusion channels. However, an enhanced pseudocapacitive contribution was observed for the increased total surface area within the (110)-oriented VAN thin films. These results demonstrate for the first time the electrochemical behavior of cathode-electrolyte VANs for lithium-ion 3D microbatteries while pointing out the importance of control over the vertical interfaces.

| S-EPMC9501919 | biostudies-literature

Aligning 3D nanofibrous networks from self-assembled phenylalanine nanofibers.

Project description:Self-assembled synthetic materials are typically disordered, and controlling the alignment of such materials at the nanometer scale may be important for a variety of biological applications. In this study, we have applied directional freeze-drying, for the first time, to develop well aligned three dimensional (3D) nanofibrous materials using amino acid like L-phenylalanine (Phe). 3D free-standing Phe nanofibrous monoliths have been successfully prepared using directional freeze-drying, and have presented a unique hierarchical structure with well-aligned nanofibers at the nanometer scale and an ordered compartmental architecture at the micrometer scale. We have found that the physical properties (e.g. nanofiber density and alignment) of the nanofibrous materials could be tuned by controlling the concentration and pH of the Phe solution and the freezing temperature. Moreover, the same strategy (i.e. directional freeze-drying) has been successfully applied to assemble peptide nanofibrous materials using a dipeptide (i.e. diphenylalanine), and to assemble Phe-based nanofibrous composites using polyethylenimine and poly(vinyl alcohol). The tunability of the nanofibrous structures together with the biocompatibility of Phe may make these 3D nanofibrous materials suitable for a variety of applications, including biosensor templates, tissue scaffolds, filtration membranes, and absorbents. The strategy reported here is likely applicable to create aligned nanofibrous structures using other amino acids, peptides, and polymers.

| S-EPMC4303580 | biostudies-literature

Self-assembled micro-organogels for 3D printing silicone structures.

Project description:The widespread prevalence of commercial products made from microgels illustrates the immense practical value of harnessing the jamming transition; there are countless ways to use soft, solid materials that fluidize and become solid again with small variations in applied stress. The traditional routes of microgel synthesis produce materials that predominantly swell in aqueous solvents or, less often, in aggressive organic solvents, constraining ways that these exceptionally useful materials can be used. For example, aqueous microgels have been used as the foundation of three-dimensional (3D) bioprinting applications, yet the incompatibility of available microgels with nonpolar liquids, such as oils, limits their use in 3D printing with oil-based materials, such as silicone. We present a method to make micro-organogels swollen in mineral oil, using block copolymer self-assembly. The rheological properties of this micro-organogel material can be tuned, leveraging the jamming transition to facilitate its use in 3D printing of silicone structures. We find that the minimum printed feature size can be controlled by the yield stress of the micro-organogel medium, enabling the fabrication of numerous complex silicone structures, including branched perfusable networks and functional fluid pumps.

| S-EPMC5425239 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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