Biological Nanostructures Research Articles

Self-folding RCA product into a parallel monolayer DNA nanoribbon and woven into a nano-fence structure by a short bridge strand

The universal programmed construction of patterned periodic self-assembled nanostructures is a technical challenge in DNA origami nanotechnology but has numerous potential applications in biotechnology and biomedicine. In order to circumvent the dilemma that traditional DNA origami requires a long unusual single-stranded virus DNA as the scaffold and hundreds or even thousands of short strands as staples, we report a method for constructing periodically-self-folded rolling circle amplification products (RPs). The repeating unit is designed to have 3 intra-unit duplexes (inDP1,2,3) and 2 between-unit duplexes (buDP1,2). Based on the complementary pairing of bases, RPs each can self-fold into a periodic grid-patterned ribbon (GR) without the help of any auxiliary oligonucleotide staple. Moreover, by using only an oligonucleotide bridge strand, the GRs are connected together into the larger and denser planar nano-fence-shaped product (FP), which substantially reduces the number of DNA components compared with DNA origami and eliminates the obstacles in the practical application of DNA nanostructures. More interestingly, the FP-based DNA framework can be easily functionalized to offer spatial addressability for the precise positioning of nanoparticles and guest proteins with high spatial resolution, providing a new avenue for the future application of DNA assembled framework nanostructures in biology, material science, nanomedicine and computer science that often requires the ordered organization of functional moieties with nanometer-level and even molecular-level precision.

Using Phase Contrast 4D-STEM to solve 3D Inorganic and Biological Nanostructures

Using Phase Contrast 4D-STEM to solve 3D Inorganic and Biological Nanostructures

Proteomic, Metabolomic, and Fatty Acid Profiling of Small Extracellular Vesicles from Glioblastoma Stem-Like Cells and Their Role in Tumor Heterogeneity.

Glioblastoma is a deadly brain tumor for which there is no cure. The presence of glioblastoma stem-like cells (GSCs) contributes to the heterogeneous nature of the disease and makes developing effective therapies challenging. Glioblastoma cells have been shown to influence their environment by releasing biological nanostructures known as extracellular vesicles (EVs). Here, we investigated the role of GSC-derived nanosized EVs (<200 nm) in glioblastoma heterogeneity, plasticity, and aggressiveness, with a particular focus on their protein, metabolite, and fatty acid content. We showed that conditioned medium and small extracellular vesicles (sEVs) derived from cells of one glioblastoma subtype induced transcriptomic and proteomic changes in cells of another subtype. We found that GSC-derived sEVs are enriched in proteins playing a role in the transmembrane transport of amino acids, carboxylic acids, and organic acids, growth factor binding, and metabolites associated with amino acid, carboxylic acid, and sugar metabolism. This suggests a dual role of GSC-derived sEVs in supplying neighboring GSCs with valuable metabolites and proteins responsible for their transport. Moreover, GSC-derived sEVs were enriched in saturated fatty acids, while their respective cells were high in unsaturated fatty acids, supporting that the loading of biological cargos into sEVs is a highly regulated process and that GSC-derived sEVs could be sources of saturated fatty acids for the maintenance of glioblastoma cell metabolism. Interestingly, sEVs isolated from GSCs of the proneural and mesenchymal subtypes are enriched in specific sets of proteins, metabolites, and fatty acids, suggesting a molecular collaboration between transcriptionally different glioblastoma cells. In summary, this study revealed the complexity of GSC-derived sEVs and unveiled their potential contribution to tumor heterogeneity and critical cellular processes commonly deregulated in glioblastoma.

Elastocapillarity-driven 2D nano-switches enable zeptoliter-scale liquid encapsulation

Biological nanostructures change their shape and function in response to external stimuli, and significant efforts have been made to design artificial biomimicking devices operating on similar principles. In this work we demonstrate a programmable nanofluidic switch, driven by elastocapillarity, and based on nanochannels built from layered two-dimensional nanomaterials possessing atomically smooth surfaces and exceptional mechanical properties. We explore operational modes of the nanoswitch and develop a theoretical framework to explain the phenomenon. By predicting the switching-reversibility phase diagram—based on material, interfacial and wetting properties, as well as the geometry of the nanofluidic circuit—we rationally design switchable nano-capsules capable of enclosing zeptoliter volumes of liquid, as small as the volumes enclosed in viruses. The nanoswitch will find useful application as an active element in integrated nanofluidic circuitry and could be used to explore nanoconfined chemistry and biochemistry, or be incorporated into shape-programmable materials.

Protonation-mediated DNA tile self-assembly with nuclease resistance characteristic for signal-amplified detection of microRNAs

DNA nanotechnology, developing rapidly in recent years, has unprecedented superiorities in biological application-oriented research including high programmability, convenient functionalization, reconfigurable structure, and intrinsic biocompatibility. However, the susceptibility to nucleases in the physiological environment has been an obstacle to applying DNA nanostructures in biological science research. In this study, a new DNA self-assembly strategy, mediated by double-protonated small molecules instead of classical metal ions, is developed to enhance the nuclease resistance of DNA nanostructures while retaining their integrality and functionality, and the relative application has been launched in the detection of microRNAs (miRNAs). Faced with low-abundance miRNAs, we integrate hybrid chain reaction (HCR) with DNA self-assembly in the presence of double-protonated small molecules to construct a chemiluminescence detection platform with nuclease resistance, which utilizes the significant difference of molecular weight between DNA arrays and false-positive products to effectively separate of reaction products and remove the detection background. This strategy attaches importance to the nucleic acid stability during the assay process via improving nuclease resistance while rendering the detection results for miRNAs more authentic and reliable, opening our eyes to more possibilities for the multiple applications of customized DNA nanostructures in biology, including bioassay, bioimaging, drug delivery, and cell modulation.

Pharmacokinetic and Pharmacodynamic Obstacles for Phage Therapy From the Perspective of Clinical Practice.

Bacteriophages present unique features that enable targeted killing of bacteria, including strains resistant to many antibiotics. However, phage pharmacokinetics and pharmacodynamics constitute much more complex and challenging aspects for researchers than those attributable to antibiotics. This is because phages are not just chemical substances, but also biological nanostructures built of different proteins and genetic material that replicate within their bacterial hosts and may induce immune responses acting as simple antigens. Here, we present a few examples of how primary general assumptions on phage pharmacokinetics and pharmacodynamics are verified by current preclinical and clinical observations, leading to conclusions that may not be obvious at first but are of significant value for the final success of phage therapy in humans.

A new electric-blue tarantula species of the genus Chilobrachys Karsh, 1892 from Thailand (Araneae, Mygalomorphae, Theraphosidae).

The enchanting phenomenon of blue coloration in animals arises from the fact that blue is one of the rarest colors found in nature, and it is a structural color that is produced by the arrangement of biological photonic nanostructures, rather than pigments. This unique coloration has evolved independently in many different species, adding to the fascination and diversity of coloration patterns in the animal kingdom. This study describes a new species of Chilobrachys Karsch, 1892 from southern Thailand that exhibits a blue-violet hue resembling the color of electrical sparks. Photographic illustrations, a morphological description, and the natural habitat of the new species are given. The diagnosis, palpal-bulb structures, spermathecae, and stridulatory organ morphology of related species are discussed.

Multiplexed digital holography for fluid surface profilometry.

Digital holography (DH) has been widely used for imaging and characterization of microstructures and nanostructures in materials science and biology and also has the potential to provide high-resolution, nondestructive measurement of fluid surfaces. DH setups capture the complex wavefronts of light scattered by an object or reflected from a surface, allowing the quantitative measurements of their shape and deformation. However, their use in fluid profilometry is scarce and has not been explored in much depth to the best of our knowledge. We present an alternative use for a DH setup that can measure and monitor the surface of fluid samples. Based on DH reflectometry, our modeling shows that multiple reflections from the sample and the reference interfere and generate multiple holograms of the sample, resulting in a multiplexed image of the wavefront. The individual interferograms can be isolated in the spatial frequency domain, and the fluid surface can be digitally reconstructed from them. We further show that this setup can be used to track changes in the surface of a fluid over time, such as during the formation and propagation of waves or the evaporation of surface layers.

Resolution enhancement with a task-assisted GAN to guide optical nanoscopy image analysis and acquisition

Super-resolution fluorescence microscopy methods enable the characterization of nanostructures in living and fixed biological tissues. However, they require the adjustment of multiple imaging parameters while attempting to satisfy conflicting objectives, such as maximizing spatial and temporal resolution while minimizing light exposure. To overcome the limitations imposed by these trade-offs, post-acquisition algorithmic approaches have been proposed for resolution enhancement and image-quality improvement. Here we introduce the task-assisted generative adversarial network (TA-GAN), which incorporates an auxiliary task (for example, segmentation, localization) closely related to the observed biological nanostructure characterization. We evaluate how the TA-GAN improves generative accuracy over unassisted methods, using images acquired with different modalities such as confocal, bright-field, stimulated emission depletion and structured illumination microscopy. The TA-GAN is incorporated directly into the acquisition pipeline of the microscope to predict the nanometric content of the field of view without requiring the acquisition of a super-resolved image. This information is used to automatically select the imaging modality and regions of interest, optimizing the acquisition sequence by reducing light exposure. Data-driven microscopy methods like the TA-GAN will enable the observation of dynamic molecular processes with spatial and temporal resolutions that surpass the limits currently imposed by the trade-offs constraining super-resolution microscopy.

Nanostructure‐Derived Antireflectivity in Leafhopper Brochosomes

Understanding how insect‐derived biomaterials interact with light has led to new advances and interdisciplinary insights in entomology and physics. Leafhoppers are insects that coat themselves with highly ordered biological nanostructures known as brochosomes. Brochosomes are thought to provide a range of protective properties to leafhoppers, such as hydrophobicity and antireflectivity, which has inspired the development of synthetic brochosomes that mimic their structures. Despite recent progress, the high antireflective properties of brochosome structures are not fully understood. Herein, a combination of experiments and computational modeling is used to understand the structure‐, material‐, and polarization‐dependent optical properties of brochosomes modeled on the geometries found in three leafhopper species. The results qualitatively represent that light interference interaction with nanostructures naturally occurring in brochosomes is responsible for the spectral tuning and the asymmetric line shape of the reflectance spectra. Whereas prior work has focused on the computational modeling of idealized pitted particles, this work shows that light–matter interactions with brochosome structures can be tuned by varying the geometry of their cage‐like nanoscale features and by changing the arrangement of multiparticle assemblies. Broadly, this work establishes principles for the guided design of new optically active materials inspired by these unique insect nanostructures.

Advanced Biomimetic Nanostructured Microelectrode Arrays for Enhanced Extracellular Recordings of Enteric Neurons

AbstractMicroelectrode surfaces covered with nanostructures derived from components of extracellular matrix, such as collagen fibers, have shown immense beneficial effects in promoting neuronal growth and cellular signaling. Synthetic nanostructures mimicking the features of biological nanostructures with durable conductive materials could promote the cell adhesion on microelectrode surfaces by providing topographical cues and simultaneously improve the charge transfer properties by reducing its global impedance. Therefore, an advanced nanostructuring method mimicking the structural and organizational features of natural collagen fibers onto metallic microelectrode surfaces has been presented here, which is adapted from previous technological achievements of the group and is based on nanoimprint lithography and gold electroplating. Surface characterization methods reveal an increase in surface area between 20% and 68% on the microelectrodes fabricated with two different nanostructure heights. Impedance spectroscopy measurements reveal reduction in impedance magnitude (at 1 kHz) between 22% and 41%, depending upon the nanostructure height and density on the microelectrode, which should subsequently modulate its charge transfer properties for biosensing application. Cell adhesion analysis performed with seal impedance measurements reveals a tighter coupling of enteric neurons on the nanostructured microelectrodes. Finally, extracellular recordings from enteric neurons exhibit a significant improvement in spike detection properties of the nanostructured microelectrodes.

Bioinspired Hierarchical Self-Assembled Nanozyme for Efficient Antibacterial Treatment.

Along with the rapid development and ever-deepening understanding of nanoscience and nanotechnology, nanomaterials hold promise to mimic the highly evolved biological exquisite nanostructures and sophisticated functions. Here, inspired by the ubiquitous antibacterial nanostructures on the wingsurfacesofsome insects, a NiCo2 O4 nanozyme with self-adaptive hierarchical nanostructure is developed that can capture bacteria of various morphotypes via the physico-mechanical interaction between the nanostructure and bacteria. Moreover, the developed biomimetic nanostructure further exhibits superior peroxidase-like catalytic activity, which can catalytically generate highly toxic reactive oxygen species that disrupt bacterial membranes and induce bacterial apoptosis. Therefore, the mechano-catalytic coupling property of this NiCo2 O4 nanozyme allows for an extensive and efficient antibacterial application, with no concerns of antimicrobial resistance. This work suggests a promising strategy for the rational design of advanced antibacterial materials by mimicking biological antibiosis.

Protocells and Prebiotic Systems

The de novo synthesis and self-assembly of molecules to establish the framework of living systems is a key target in the field of systems chemistry. The construction of synthetic cellular systems from scratch is one important such route to achieve this goal. This Special Collection on Protocells and Prebiotic Systems, guest edited by Dora Tang and Avinash J. Patil, showcases some of the most exciting work done in this field today. (D.Tang photograph copyright MPI-CBG). The de novo synthesis of molecules and their self-assembly to establish the framework of living systems is a key goal of systems chemistry. One route to achieving this is by building synthetic cellular systems from scratch which provides a gateway to understand and control emergence that arises from an integration of functional molecules and biological nanostructures at various length scales. Progress in this area can have significant impact for unravelling the origins of life, synthetic biology and future biomedical applications whilst providing fundamental insights into the mechanisms of biological systems. This Special Collection on Protocells and Prebiotic Systems brings together new and exciting work that is taking place in this field and demonstrates the extraordinary breadth of contributions required to make progress in this area: From prebiotic chemistry, to a survey of the molecular parts which can be used to design and build programmable cell-like compartments, engineer catalytic microreactors or create higher ordered architectures, to the emergence of adaptable systems where chemical environments can tune the physicochemical properties of soft materials. Furthermore, the capability to assimilate these properties to mimic fundamental biological processes such as chemical signaling; motility; energy transduction or cell growth and division are ever increasing. Whilst these examples are crucial for establishing minimal living systems, there are exciting prospects to exploit synthetic-cell-like compartments in wide-ranging applications including biomimetic materials; novel stimuli-responsive delivery platforms; biocatalysis; environmental remediation; tissue engineering; regenerative medicine; living materials and in adaptive integration to biological cells. The opinions expressed in this publication are the view of the author(s) and do not necessarily reflect the opinions or views of ChemSystemsChem, the Publisher, Chemistry Europe, or the affiliated editors. Dora Tang is currently a research group leader at the MPI-CBG, Dresden (Germany). Her multidisciplinary lab reimagines and translates the physical phenemona which drive out of equilibrium processes in cells to novel, robust and dynamic synthetic cellular systems. The minimal systems address questions in origin of life and modern biology. (Photograph copyright MPI-CBG). Avinash J. Patil is a faculty and group leader at the Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol (UK). His research interests cover the design and construction of artificial cells, smart microreactors, and functional hybrid nanomaterials by combining various aspects of biology, materials chemistry, and micro/nanofabrication techniques.

Error-Correction Method for High-Throughput Sizing of Nanoscale Vesicles with Single-Molecule Localization Microscopy.

Single-molecule localization microscopy (SMLM) allows super-resolution imaging, mapping, counting, and sizing of biological nanostructures such as cell organelles and extracellular vesicles (EVs), but sizing structures smaller than ∼100 nm can be inaccurate due to single-molecule localization error caused by distortion of the point spread function and limited photon number. Here we demonstrate a method to correct localization error when sizing vesicles and other spherical nanoparticles with SMLM and compare sizing results using two vesicle labeling schemes. We use mean approximation theory to derive a simple equation using full width at half-maximum (FWHM) for correcting particle sizes measured by two-dimensional SMLM, validate the method by sizing streptavidin-coated polystyrene nanobeads with the SMLM technique dSTORM with and without error correction, using transmission electron microscopy (TEM) for comparison, and then apply the method to sizing small seminal EVs. Nanobead sizes measured by dSTORM became increasingly less accurate (larger than TEM values) for beads smaller than 50 nm. The error-correction method reduced the size difference versus TEM from 15% without error correction to 7% with error correction for 40 nm beads, from 44% to 9% for 30 nm beads, and from 66% to 15% for 20 nm beads. Seminal EVs were labeled with a lipophilic membrane dye (MemBright 700) and with an Alexa Fluor 488-anti-CD63 antibody conjugate, and were sized separately using both dyes by dSTORM. Error-corrected exosome diameters were smaller than uncorrected values: 72 nm vs 79 nm mean diameter with membrane dyes; 84 nm vs 97 nm with the antibody-conjugated dyes. The mean error-corrected diameter was 12 nm smaller when using the membrane dye than when using the antibody-conjugated dye likely due to the large size of the antibody. Thus, both the error-correction method and the compact membrane labeling scheme reduce overestimation of vesicle size by SMLM. This error-correction method has a low computational cost as it does not require correction of individual blinking events, and it is compatible with all SMLM techniques (e.g., PALM, STORM, and DNA-PAINT).

Large-scale expanded sample imaging with tiling lattice lightsheet microscopy.

The ability to observe biological nanostructures forms a vital step in understanding their functions. Thanks to the invention of expansion microscopy (ExM) technology, super-resolution features of biological samples can now be easily visualized with conventional light microscopies. However, when the sample is physically expanded, the demand for deep and precise 3D imaging increases. Lattice lightsheet microscopy (LLSM), which utilizes a planar illumination that is confined within the imaging depth of high numerical aperture (NA=1.1) detection objective, fulfils such requirements. In addition, optical tiling could be implemented to increase the field of view (FoV) by moving the lightsheet without mechanically moving the samples or the objective for high-precision 3D imaging. In this review article, we will explain the principle of the tiling lattice lightsheet microscopy (tLLSM), which combines optical tiling and lattice lightsheet, and discuss the applications of tLLSM in ExM.

Sizing up DNA nanostructure assembly with native mass spectrometry and ion mobility

Recent interest in biological and synthetic DNA nanostructures has highlighted the need for methods to comprehensively characterize intermediates and end products of multimeric DNA assembly. Here we use native mass spectrometry in combination with ion mobility to determine the mass, charge state and collision cross section of noncovalent DNA assemblies, and thereby elucidate their structural composition, oligomeric state, overall size and shape. We showcase the approach with a prototypical six-subunit DNA nanostructure to reveal how its assembly is governed by the ionic strength of the buffer, as well as how the mass and mobility of heterogeneous species can be well resolved by careful tuning of instrumental parameters. We find that the assembly of the hexameric, barrel-shaped complex is guided by positive cooperativity, while previously undetected higher-order 12- and 18-mer assemblies are assigned to defined larger-diameter geometric structures. Guided by our insight, ion mobility-mass spectrometry is poised to make significant contributions to understanding the formation and structural diversity of natural and synthetic oligonucleotide assemblies relevant in science and technology.

Enamel-like Layer of Nanohydroxyapatite Stabilizes Zn Metal Anodes by Ion Exchange Adsorption and Electrolyte pH Regulation.

The instability of Zn anode caused by severe dendrite growth and side reactions has restricted the practical applications of aqueous zinc-ion batteries (AZIBs). Herein, an enamel-like layer of nanohydroxyapatite (Ca5(PO4)3(OH), nano-HAP) is constructed on Zn anode to enhance its stability. Benefiting from the ion exchange between Zn2+ and Ca2+, the adsorption for Zn2+ in enamel-like nano-HAP (E-nHAP) layer can effectively guide Zn deposition, ensuring homogeneous Zn2+ flux and even nucleation sites to suppress Zn dendrites. Meanwhile, the low pH of acidic electrolyte can be regulated by slightly soluble nano-HAP, restraining electrolyte corrosion and hydrogen evolution. Moreover, the E-nHAP layer features high mechanical flexibility due to its enamel-like organic-inorganic composite nanostructure. Hence, symmetric cells assembled by E-nHAP@Zn show superior stability of long-term cycling at different current densities (0.1, 0.5, 1, 5, and 10 mA cm-2). The E-nHAP@Zn∥E-nHAP@Cu cell exhibits an outstanding cycling life with high Coulombic efficiency of 99.8% over 1000 cycles. Notably, the reversibility of full cell based on CNT/MnO2 cathode can be effectively enhanced. This work shows the potential of drawing inspiration from biological nanostructure in nature to develop stable metal electrodes.

Unifying structural descriptors for biological and bioinspired nanoscale complexes.

Biomimetic nanoparticles are known to serve as nanoscale adjuvants, enzyme mimics and amyloid fibrillation inhibitors. Their further development requires better understanding of their interactions with proteins. The abundant knowledge about protein-protein interactions can serve as a guide for designing protein-nanoparticle assemblies, but the chemical and biological inputs used in computational packages for protein-protein interactions are not applicable to inorganic nanoparticles. Analysing chemical, geometrical and graph-theoretical descriptors for protein complexes, we found that geometrical and graph-theoretical descriptors are uniformly applicable to biological and inorganic nanostructures and can predict interaction sites in protein pairs with accuracy >80% and classification probability ~90%. We extended the machine-learning algorithms trained on protein-protein interactions to inorganic nanoparticles and found a nearly exact match between experimental and predicted interaction sites with proteins. These findings can be extended to other organic and inorganic nanoparticles to predict their assemblies with biomolecules and other chemical structures forming lock-and-key complexes.

Brochosome-Inspired Metal-Containing Particles as Biomimetic Building Blocks for Nanoplasmonics: Conceptual Generalizations.

Recently, biological nanostructures became an important source of inspiration for plasmonics, with many described implementations and proposed applications. Among them are brochosome-inspired plasmonic microstructures—roughly spherical core-shell particles with submicrometer diameters and with indented surfaces. Our intention was to start from the nanoplasmonic point of view and to systematically classify possible alternative forms of brochosome-inspired metal-containing particles producible by the state-of-the-art nanofabrication. A wealth of novel structures arises from this systematization of bioinspired metal-containing nanocomposites. Besides various surface nanoapertures, we consider structures closely related to them in electromagnetic sense like surface nano-protrusions, shell reliefs obtained by nano-sculpting, and various combinations of these. This approach helped us build a new design toolbox for brochosome-inspired structures. Additionally, we used the finite elements method to simulate the optical properties of simple brochosome-inspired structures. We encountered a plethora of advantageous optical traits, including enhanced absorption, antireflective properties, and metamaterial behavior (effective refractive index close to zero or negative). We conclude that the presented approach offers a wealth of traits useful for practical applications. The described research represents our attempt to outline a possible roadmap for further development of bioinspired nanoplasmonic particles and to offer a source of ideas and directions for future research.

Scissor-Shaped Photochromic Dyads: Hierarchical Self-Assembly and Photoresponsive Property.

Unique relationships between hierarchically organized biological nanostructures and functions have motivated chemists to construct sophisticated artificial nanostructured systems from small and simple synthetic molecules through self-assembly. As one of such sophisticated systems, we have investigated scissor-shaped photochromic dyads that can hierarchically self-assemble into discrete nanostructures showing photoresponsive properties. We synthesized various azobenzene dyads and found that these dyads adopt intramolecularly folded conformation like a closed scissor, and then self-assemble into toroidal nanostructures by generating curvature. The toroids further organize into nanotubes and further into helical supramolecular fibers depending on the nature of alkyl substituents. All of these nanostructures can be dissociated and reorganized through the photoisomerization of azobenzene units. On the other hand, the introduction of stilbene chromophores instead of azobenzenes leads to one-dimensional supramolecular polymerization, which upon the intramolecular photocyclization of stilbene chromophores shifts to curved self-assembly leading to helicoidal fibers with distinct supramolecular chirality.