Self-assembled DNA nanostructures enable nanometre-precise patterning that can be used to create programmable molecular machines and arrays of functional materials. DNA origami is particularly ...versatile in this context because each DNA strand in the origami nanostructure occupies a unique position and can serve as a uniquely addressable pixel. However, the scale of such structures has been limited to about 0.05 square micrometres, hindering applications that demand a larger layout and integration with more conventional patterning methods. Hierarchical multistage assembly of simple sets of tiles can in principle overcome this limitation, but so far has not been sufficiently robust to enable successful implementation of larger structures using DNA origami tiles. Here we show that by using simple local assembly rules that are modified and applied recursively throughout a hierarchical, multistage assembly process, a small and constant set of unique DNA strands can be used to create DNA origami arrays of increasing size and with arbitrary patterns. We illustrate this method, which we term 'fractal assembly', by producing DNA origami arrays with sizes of up to 0.5 square micrometres and with up to 8,704 pixels, allowing us to render images such as the Mona Lisa and a rooster. We find that self-assembly of the tiles into arrays is unaffected by changes in surface patterns on the tiles, and that the yield of the fractal assembly process corresponds to about 0.95
for arrays containing m tiles. When used in conjunction with a software tool that we developed that converts an arbitrary pattern into DNA sequences and experimental protocols, our assembly method is readily accessible and will facilitate the construction of sophisticated materials and devices with sizes similar to that of a bacterium using DNA nanostructures.
To determine whether intravenous ferumoxytol can be used to effectively label mesenchymal stem cells (MSCs) in vivo and can be used for tracking of stem cell transplants.
This study was approved by ...the institutional animal care and use committee. Sprague-Dawley rats (6-8 weeks old) were injected with ferumoxytol 48 hours prior to extraction of MSCs from bone marrow. Ferumoxytol uptake by these MSCs was evaluated with fluorescence, confocal, and electron microscopy and compared with results of traditional ex vivo-labeling procedures. The in vivo-labeled cells were subsequently transplanted in osteochondral defects of 14 knees of seven athymic rats and were evaluated with magnetic resonance (MR) imaging up to 4 weeks after transplantation. T2 relaxation times of in vivo-labeled MSC transplants and unlabeled control transplants were compared by using t tests. MR data were correlated with histopathologic results.
In vivo-labeled MSCs demonstrated significantly higher ferumoxytol uptake compared with ex vivo-labeled cells. With electron microscopy, iron oxide nanoparticles were localized in secondary lysosomes. In vivo-labeled cells demonstrated significant T2 shortening effects in vitro and in vivo when they were compared with unlabeled control cells (T2 in vivo, 15.4 vs 24.4 msec; P < .05) and could be tracked in osteochondral defects for 4 weeks. Histologic examination confirmed the presence of iron in labeled transplants and defect remodeling.
Intravenous ferumoxytol can be used to effectively label MSCs in vivo and can be used for tracking of stem cell transplants with MR imaging. This method eliminates risks of contamination and biologic alteration of MSCs associated with ex vivo-labeling procedures.
(15)N-labeled rosette nanotubes were synthesized and investigated using high-field solid-state NMR spectroscopy, X-ray diffraction, atomic force microscopy, and electron microscopy. The results ...established the H-bond network involved in the self-assembly of the nanostructure as well as bound water molecules in the nanotube's channel.
Molecular computing programmed with complementary nucleic acid strands allows the construction of sophisticated biomolecular circuits. Now, systems with partially complementary strands have been ...shown to enable more compact and faster molecular circuits, and may illuminate biological processes.
Scaling up the complexity and diversity of synthetic molecular structures will require strategies that exploit the inherent stochasticity of molecular systems in a controlled fashion. Here we ...demonstrate a framework for programming random DNA tilings and show how to control the properties of global patterns through simple, local rules. We constructed three general forms of planar network-random loops, mazes and trees-on the surface of self-assembled DNA origami arrays on the micrometre scale with nanometre resolution. Using simple molecular building blocks and robust experimental conditions, we demonstrate control of a wide range of properties of the random networks, including the branching rules, the growth directions, the proximity between adjacent networks and the size distribution. Much as combinatorial approaches for generating random one-dimensional chains of polymers have been used to revolutionize chemical synthesis and the selection of functional nucleic acids, our strategy extends these principles to random two-dimensional networks of molecules and creates new opportunities for fabricating more complex molecular devices that are organized by DNA nanostructures.
Supramolecular synthesis emerged recently as a new formalism to devise complex architectures held through noncovalent forces. Much of the research endeavor has been devoted to the use of H-bonds as ...the alphabet for chemical information encoding, and the structures expressed have spanned the range of dimensions and shapes, from discrete to infinite networks. Here we describe the synthesis and characterization of a G∧C base bearing two C12 alkyl chains, which undergoes a solvent-controlled multistep hierarchical self-assembly process into lamellar prolate nanospheroids. These assemblies were characterized by AFM, SEM, TEM, XRD, and SAXS, and a mechanism for their formation is proposed.
Triangular DNA Origami Tilings Tikhomirov, Grigory; Petersen, Philip; Qian, Lulu
Journal of the American Chemical Society,
12/2018, Letnik:
140, Številka:
50
Journal Article
Recenzirano
Odprti dostop
DNA origami tilings provide methods for creating complex molecular patterns and shapes using flat DNA origami structures as building blocks. Square tiles have been developed to construct ...micrometer-scale arrays and to generate patterns using stochastic or deterministic strategies. Here we show triangular tiles as a complementary approach for enriching the design space of DNA tilings and for extending the shape of the self-assembled arrays from 2D to 3D. We introduce a computational approach for maximizing binding specificity in a fully symmetric tile design, with which we construct a 20-tile structure resembling a rhombic triacontahedron. We demonstrate controlled transition between 3D and 2D structures using simple methods including tile concentration, magnesium, and fold symmetry in tile edge design. Using these approaches, we construct 2D arrays with unbounded and designed sizes. The programmability of the edge design and the flexibility of the structure make the triangular DNA origami tile an ideal building block for complex self-assembly and reconfiguration in artificial molecular machines and fabricated nanodevices.
Cancer cells overexpress matrix‐type metalloproteinases (MMPs, shown as pacmen). MMPs cleave the peptide linker connecting anticancer prodrug to the dextran coated magnetic nanoparticle. After the ...cleavage, the drug becomes toxic (active drug shown in purple). As J. Rao, H. E. Daldrup‐Link, and co‐workers describe on page 566, this tumor specific drug release reduces the side‐effects of cancer therapy. The magnetic core of the nanoparticles allows for MRI monitoring of their distribution in the body.
The ability to control and manipulate semiconductor/bio interfaces is essential to enable biological nanofabrication pathways and bioelectronic devices. Traditional surface functionalization methods, ...such as self-assembled monolayers (SAMs), provide limited customization for these interfaces. Polymer brushes offer a wider range of chemistries, but choices that maintain compatibility with both lithographic patterning and biological systems are scarce. Here, we developed a class of bioinspired, sequence-defined polymers, i.e., polypeptoids, as tailored polymer brushes for surface modification of semiconductor substrates. Polypeptoids featuring a terminal hydroxyl (−OH) group are designed and synthesized for efficient melt grafting onto the native oxide layer of Si substrates, forming ultrathin (∼1 nm) monolayers. By programming monomer chemistry, our polypeptoid brush platform offers versatile surface modification, including adjustments to surface energy, passivation, preferential biomolecule attachment, and specific biomolecule binding. Importantly, the polypeptoid brush monolayers remain compatible with electron-beam lithographic patterning and retain their chemical characteristics even under harsh lithographic conditions. Electron-beam lithography is used over polypeptoid brushes to generate highly precise, binary nanoscale patterns with localized functionality for the selective immobilization (or passivation) of biomacromolecules, such as DNA origami or streptavidin, onto addressable arrays. This surface modification strategy with bioinspired, sequence-defined polypeptoid brushes enables monomer-level control over surface properties with a large parameter space of monomer chemistry and sequence and therefore is a highly versatile platform to precisely engineer semiconductor/bio interfaces for bioelectronics applications.
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