Dynamic self-assembly of compartmentalized DNA nanotubes.
Ontology highlight
ABSTRACT:
SUBMITTER: Agarwal S
PROVIDER: S-EPMC8196065 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:We describe a novel self-assembling supramolecular nanotube system formed by a heterocyclic cationic molecule which was originally designed for its potential as an antiparasitic and DNA sequence recognition agent. Our structural characterisation work indicates that the nanotubes form via a hierarchical assembly mechanism that can be triggered and tuned by well-defined concentrations of simple alkali halide salts in water. The nanotubes assembled in NaCl have inner and outer diameters of ca. 22 nm and 26 nm respectively, with lengths that reach into several microns. Our results suggest the tubes consist of DB921 molecules stacked along the direction of the nanotube long axis. The tubes are stabilised by face-to-face π-π stacking and ionic interactions between the charged amidinium groups of the ligand and the negative halide ions. The assembly process of the nanotubes was followed using small-angle X-ray and neutron scattering, transmission electron microscopy and ultraviolet/visible spectroscopy. Our data demonstrate that assembly occurs through the formation of intermediate ribbon-like structures that in turn form helices that tighten and compact to form the final stable filament. This assembly process was tested using different alkali-metal salts, showing a strong preference for chloride or bromide anions and with little dependency on the type of cation. Our data further demonstrates the existence of a critical anion concentration above which the rate of self-assembly is greatly enhanced.
| S-EPMC5885265 | biostudies-literature
Project description:Utilization of a self-assembled two-dimensional DNA nanostructure to arrange single-walled carbon nanotubes (SWNTs) into predetermined structures at controllable angles is presented. A specially designed DNA three-way junction (3WJ) composed of three double-stranded DNA arms containing single-stranded overhang sequences was prepared by annealing of partially complementary ssDNA sequences and ultrasonicated with SWNTs, resulting in DNA-3WJ/SWNT hybrid nanostructures. Utilization of DNA-3WJ not only allowed the precise dispersion of SWNTs but also acted as a rigid template for the self-assembly of SWNTs into three-armed junctions at an angle of approximately 120° to each other as visualized by scanning electron microscopy and atomic force microscopy. Prepared DNA-3WJ/SWNT nanostructures were also demonstrated to have the appropriate binding sites for fluorophores, providing a simple method for the fluorescent labeling of SWNTs. When ssDNA sequences forming the DNA-3WJ are ultrasonicated with SWNTs, followed by annealing of resulting ssDNA wrapped SWNTs, instead of hybrid junctions composed of three SWNT molecules, a web-like structure composed of interconnected SWNT junctions was obtained. The design approaches demonstrated here provide simple methods for the arrangement of SWNTs into desired nanostructures utilizing pre-assembled DNA nanostructures as linkers in aqueous solution through noncovalent interactions which can greatly contribute to efforts along the controlled assembly of SWNTs.
| S-EPMC6044768 | biostudies-literature
Project description:Rosette nanotubes are a new class of organic nanotubes obtained through the hierarchical self-assembly of low molecular weight synthetic modules in water. Here we demonstrate that these materials can serve as scaffolds for the supramolecular synthesis of multichannel nanotubular architectures and report on the discovery of their entropy-driven self-assembly process.
| S-EPMC128555 | biostudies-literature
Project description:The discovery of coronands and cryptands, organic compounds that can accommodate metal ions in a preorganized two- or three-dimensional environment, was a milestone in supramolecular chemistry, leading to countless applications from organic synthesis to metallurgy and medicine. These compounds are typically prepared via multistep organic synthesis and one of their characteristic features is the high stability of their covalent framework. Here we report the use of a dynamic covalent exchange reaction for the one-pot template synthesis of a new class of coronates and cryptates, in which acid-labile O,O,O-orthoesters serve as bridgeheads. In contrast to their classic analogues, the compounds described herein are constitutionally dynamic in the presence of acid and can be induced to release their guest via irreversible deconstruction of the cage. These properties open up a wide range of application opportunities, from systems chemistry to molecular sensing and drug delivery.
| S-EPMC4455094 | biostudies-literature
Project description:The ability to influence the direction of polymerization of a self-assembling biomolecular system has the potential to generate materials with extremely high anisotropy. In biological systems where highly-oriented cellular populations give rise to aligned and often load-bearing tissue such organized molecular scaffolds could aid in the contact guidance of cells for engineered tissue constructs (e.g. cornea and tendon). In this investigation we examine the detailed dynamics of pepsin-extracted type I bovine collagen assembly on a glass surface under the influence of flow between two plates. Differential Interference Contrast (DIC) imaging (60x-1.4NA) with focal plane stabilization was used to resolve and track the growth of collagen aggregates on borosilicate glass for 4 different shear rates (500, 80, 20, and 9s(-1)). The detailed morphology of the collagen fibrils/aggregates was examined using Quick Freeze Deep Etch (QFDE) electron microscopy. Nucleation of fibrils on the glass was observed to occur rapidly (approximately 2 min) followed by continued growth of the fibrils. The growth rates were dependent on flow in a complex manner with the highest rate of axial growth (0.1 micro/s) occurring at a shear rate of 9s(-1). The lowest growth rate occurred at the highest shear. Fibrils were observed to both branch and join during the experiments. The best alignment of fibrils was observed at intermediate shear rates of 20 and 80s(-1). However, the investigation revealed that fibril directional growth was not stable. At high shear rates, fibrils would often turn downstream forming what we term "hooks" which are likely the combined result of monomer interaction with the initial collagen layer or "mat" and the high shear rate. Further, QFDE examination of fibril morphology demonstrated that the assembled fibrillar structure did not possess native D-periodicity. Instead, fibrils comprised a collection of generally aligned, monomers which were self-assembled to form a fibril-like aggregate. In conclusion, though constant shear-rate clearly influences collagen fibrillar alignment, the formation of highly-organized collagenous arrays of native-like D-banded fibrils remains a challenge. Modulation of shear in combination with surface energy patterning to produce a highly-aligned initial mat may provide significant improvement of both the fibril morphology and alignment.
| S-EPMC3299540 | biostudies-literature
Project description:Various biomaterial scaffolds have been developed for improving stem cell anchorage and function in tissue constructs for in vitro and in vivo uses. Growth factors are typically applied to scaffolds to mediate cell differentiation. Conventionally, growth factors are not strictly localized in the scaffolds; thus, they may leak into the surrounding environment, causing undesired side effects on tissues or cells. Hence, there is a need for improved tissue construct strategies based on highly localized drug delivery and a homeostatic microenvironment. This study developed an injectable nanomatrix (NM) scaffold with a layer-by-layer structure inside each nanosized fiber of the scaffold based on controlled self-assembly at the molecular level. The NM was hierarchically assembled from Janus base nanotubes (JBNTs), matrilin-3, and transforming growth factor β-1 (TGF-β1) via bioaffinity. JBNTs, which form the NM backbone, are novel DNA-inspired nanomaterials that mimic the natural helical nanostructures of collagens. The chondrogenic factor, TGF-β1, was enveloped in the inner layer inside the NM fibers to prevent its release. Matrilin-3 was incorporated into the outer layer to create a cartilage-mimicking microenvironment and to maintain tissue homeostasis. Interestingly, human mesenchymal stem cells (hMSCs) had a strong preference to anchor along the NM fibers and formed a localized homeostatic microenvironment. Therefore, this NM has successfully generated highly organized structures via molecular self-assembly and achieved localized drug delivery and stem cell anchorage for homeostatic tissue constructs.
| S-EPMC8982526 | biostudies-literature
Project description:The folding and assembly of sequence-defined polymers into precisely ordered nanostructures promises a class of well-defined biomimetic architectures with specific function. Amphiphilic diblock copolymers are known to self-assemble in water to form a variety of nanostructured morphologies including spheres, disks, cylinders, and vesicles. In all of these cases, the predominant driving force for assembly is the formation of a hydrophobic core that excludes water, whereas the hydrophilic blocks are solvated and extend into the aqueous phase. However, such polymer systems typically have broad molar mass distributions and lack the purity and sequence-defined structure often associated with biologically derived polymers. Here, we demonstrate that purified, monodisperse amphiphilic diblock copolypeptoids, with chemically distinct domains that are congruent in size and shape, can behave like molecular tile units that spontaneously assemble into hollow, crystalline nanotubes in water. The nanotubes consist of stacked, porous crystalline rings, and are held together primarily by side-chain van der Waals interactions. The peptoid nanotubes form without a central hydrophobic core, chirality, a hydrogen bond network, and electrostatic or ?-? interactions. These results demonstrate the remarkable structure-directing influence of n-alkane and ethyleneoxy side chains in polymer self-assembly. More broadly, this work suggests that flexible, low-molecular-weight sequence-defined polymers can serve as molecular tile units that can assemble into precision supramolecular architectures.
| S-EPMC4839393 | biostudies-literature
Project description:Tandem repeat proteins exhibit native designability and represent potentially useful scaffolds for the construction of synthetic biomimetic assemblies. We have designed 2 synthetic peptides, HEAT_R1 and LRV_M3Δ1, based on the consensus sequences of single repeats of thermophilic HEAT (PBS_HEAT) and Leucine-Rich Variant (LRV) structural motifs, respectively. Self-assembly of the peptides afforded high-aspect ratio helical nanotubes. Cryo-electron microscopy with direct electron detection was employed to analyze the structures of the solvated filaments. The 3D reconstructions from the cryo-EM maps led to atomic models for the HEAT_R1 and LRV_M3Δ1 filaments at resolutions of 6.0 and 4.4 Å, respectively. Surprisingly, despite sequence similarity at the lateral packing interface, HEAT_R1 and LRV_M3Δ1 filaments adopt the opposite helical hand and differ significantly in helical geometry, while retaining a local conformation similar to previously characterized repeat proteins of the same class. The differences in the 2 filaments could be rationalized on the basis of differences in cohesive interactions at the lateral and axial interfaces. These structural data reinforce previous observations regarding the structural plasticity of helical protein assemblies and the need for high-resolution structural analysis. Despite these observations, the native designability of tandem repeat proteins offers the opportunity to engineer novel helical nanotubes. Moreover, the resultant nanotubes have independently addressable and chemically distinguishable interior and exterior surfaces that would facilitate applications in selective recognition, transport, and release.
| S-EPMC6642399 | biostudies-literature
Project description:We demonstrate experimentally and in computer simulations that magnetic microfloaters can self-organize into various functional structures while energized by an external alternating (ac) magnetic field. The structures exhibit self-propelled motion and an ability to carry a cargo along a pre-defined path. The morphology of the self-assembled swimmers is controlled by the frequency and amplitude of the magnetic field.
| S-EPMC5677019 | biostudies-literature
Project description:Two experimental studies relating to electrostatic self-assembly have been the subject of dynamic computer simulations, where the consequences of changing the charge and the dielectric constant of the materials concerned have been explored. One series of calculations relates to experiments on the assembly of polymer particles that have been subjected to tribocharging and the simulations successfully reproduce many of the observed patterns of behaviour. A second study explores events observed following collisions between single particles and small clusters composed of charged particles derived from a metal oxide composite. As before, observations recorded during the course of the experiments are reproduced by the calculations. One study in particular reveals how particle polarizability can influence the assembly process.This article is part of the theme issue 'Modern theoretical chemistry'.
| S-EPMC5805913 | biostudies-literature