Rapid Discrimination of Extracellular Vesicles by Shape Distribution Analysis.

A rapid and simple cancer detection method independent of cancer type is an important technology for cancer diagnosis. Although the expression profiles of biological molecules contained in cancer cell-derived extracellular vesicles (EVs) are considered candidates for discrimination indexes to identify any cancerous cells in the body, it takes a certain amount of time to examine these expression profiles. Here, we report the shape distributions of EVs suspended in a solution and the potential of these distributions as a discrimination index to discriminate cancer cells. Distribution analysis is achieved by low-aspect-ratio nanopore devices that enable us to rapidly analyze EV shapes individually in solution, and the present results reveal a dependence of EV shape distribution on the type of cells (cultured liver, breast, and colorectal cancer cells and cultured normal breast cells) secreting EVs. The findings in this study provide realizability and experimental basis for a simple method to discriminate several types of cancerous cells based on rapid analyses of EV shape distributions.

Atomic force microscopy analysis of SasA-KaiC complex formation involved in information transfer from the KaiABC clock machinery to the output pathway in cyanobacteria.

The cyanobacterial clock oscillator is composed of three clock proteins: KaiA, KaiB and KaiC. SasA, a KaiC-binding EnvZ-like orthodox histidine kinase involved in the main clock output pathway, exists mainly as a trimer (SasA3mer ) and occasionally as a hexamer (SasA6mer ) in vitro. Previously, the molecular mass of the SasA-KaiCDD complex, where KaiCDD is a mutant KaiC with two Asp substitutions at the two phosphorylation sites, has been estimated by gel-filtration chromatography to be larger than 670 kDa. This value disagrees with the theoretical estimation of 480 kDa for a SasA3mer -KaiC hexamer (KaiC6mer ) complex with a 1:1 molecular ratio. To clarify the structure of the SasA-KaiC complex, we analyzed KaiCDD with 0.1 mmol/L ATP and 5 mmol/L MgCl2 (Mg-ATP), SasA and a mixture containing SasA and KaiCDD6mer with Mg-ATP by atomic force microscopy (AFM). KaiCDD images were classified into two types with height distribution corresponding to KaiCDD monomer (KaiCDD1mer ) and KaiCDD6mer , respectively. SasA images were classified into two types with height corresponding to SasA3mer and SasA6mer , respectively. The AFM images of the SasA-KaiCDD mixture indicated not only KaiCDD1mer , KaiCDD6mer , SasA3mer and SasA6mer , but also wider area "islands," suggesting the presence of a polymerized form of the SasA-KaiCDD complex.

Identifying Single Viruses Using Biorecognition Solid-State Nanopores.

Immunosensing is a bioanalytical technique capable of selective detections of pathogens by utilizing highly specific and strong intermolecular interactions between recognition probes and antigens. Here, we exploited the molecular mechanism in artificial nanopores for selective single-virus identifications. We designed hemagglutinin antibody mimicking oligopeptides with a weak affinity to influenza A virus. By functionalizing the pore wall surface with the synthetic peptides, we rendered specificity to virion-nanopore interactions. The ligand binding thereof was found to perturb translocation dynamics of specific viruses in the nanochannel, which facilitated digital typing of influenza by the resistive pulse bluntness. As amino acid sequence degrees of freedom can potentially offer variety of recognition ability to the molecular probes, this peptide nanopore approach can be used as a versatile immunosensor with single-particle sensitivity that promises wide applications in bioanalysis including bacterial and viral screening to infectious disease diagnosis.

Identification of Individual Bacterial Cells through the Intermolecular Interactions with Peptide-Functionalized Solid-State Pores.

Bioinspired pore sensing for selective detection of flagellated bacteria was investigated. The Au micropore wall surface was modified with a synthetic peptide designed from toll-like receptor 5 (TLR5) to mimic the pathogen-recognition capability. We found that intermolecular interactions between the TLR5-derived recognition peptides and flagella induce ligand-specific perturbations in the translocation dynamics of Escherichia coli, which facilitated the discrimination between the wild-type and flagellin-deletion mutant (ΔfliC) by the resistive pulse patterns thereby demonstrating the sensing of bacteria at a single-cell level. These results provide a novel concept of utilizing weak intermolecular interactions as a recognition probes for single-cell microbial identification.

Stretching-Induced Conductance Variations as Fingerprints of Contact Configurations in Single-Molecule Junctions.

Molecule-electrode contact atomic structures are a critical factor that characterizes molecular devices, but their precise understanding and control still remain elusive. Based on combined first-principles calculations and single-molecule break junction experiments, we herein establish that the conductance of alkanedithiolate junctions can both increase and decrease with mechanical stretching, and the specific trend is determined by the S-Au linkage coordination number (CN) or the molecule-electrode contact atomic structure. Specifically, we find that the mechanical pulling results in the conductance increase for the junctions based on S-Au CN two and CN three contacts, while the conductance is minimally affected by stretching for junctions with the CN one contact and decreases upon the formation of Au monatomic chains. Detailed analysis unravels the mechanisms involving the competition between the stretching-induced upshift of the highest occupied molecular orbital-related states toward the Fermi level of electrodes and the deterioration of molecule-electrode electronic couplings in different contact CN cases. Moreover, we experimentally find a higher chance to observe the conductance enhancement mode under a faster elongation speed, which is explained by ab initio molecular dynamics simulations that reveal an important role of thermal fluctuations in aiding deformations of contacts into low-coordination configurations that include monatomic Au chains. Pointing out the insufficiency in previous notions of associating peak values in conductance histograms with specific contact atomic structures, this work resolves the controversy on the origins of ubiquitous multiple conductance peaks in S-Au-based single-molecule junctions.

Substantial Expansion of Detectable Size Range in Ionic Current Sensing through Pores by Using a Microfluidic Bridge Circuit.

Measuring ionic currents passing through nano- or micropores has shown great promise for the electrical discrimination of various biomolecules, cells, bacteria, and viruses. However, conventional measurements have shown there is an inherent limitation to the detectable particle volume (1% of the pore volume), which critically hinders applications to real mixtures of biomolecule samples with a wide size range of suspended particles. Here we propose a rational methodology that can detect samples with the detectable particle volume of 0.01% of the pore volume by measuring a transient current generated from the potential differences in a microfluidic bridge circuit. Our method substantially suppresses the background ionic current from the µA level to the pA level, which essentially lowers the detectable particle volume limit even for relatively large pore structures. Indeed, utilizing a microscale long pore structure (volume of 5.6 × 104 aL; height and width of 2.0 × 2.0 µm; length of 14 µm), we successfully detected various samples including polystyrene nanoparticles (volume: 4 aL), bacteria, cancer cells, and DNA molecules. Our method will expand the applicability of ionic current sensing systems for various mixed biomolecule samples with a wide size range, which have been difficult to measure by previously existing pore technologies.

Rapid structural analysis of nanomaterials in aqueous solutions.

Rapid structural analysis of nanoscale matter in a liquid environment represents innovative technologies that reveal the identities and functions of biologically important molecules. However, there is currently no method with high spatio-temporal resolution that can scan individual particles in solutions to gain structural information. Here we report the development of a nanopore platform realizing quantitative structural analysis for suspended nanomaterials in solutions with a high z-axis and xy-plane spatial resolution of 35.8 ± 1.1 and 12 nm, respectively. We used a low thickness-to-diameter aspect ratio pore architecture for achieving cross sectional areas of analyte (i.e. tomograms). Combining this with multiphysics simulation methods to translate ionic current data into tomograms, we demonstrated rapid structural analysis of single polystyrene (Pst) beads and single dumbbell-like Pst beads in aqueous solutions.

Identifying DNA methylation in a nanochannel.

DNA methylation is a stable epigenetic modification, which is well known to be involved in gene expression regulation. In general, however, analyzing DNA methylation requires rather time consuming processes (24-96 h) via DNA replication and protein modification. Here we demonstrate a methodology to analyze DNA methylation at a single DNA molecule level without any protein modifications by measuring the contracted length and relaxation time of DNA within a nanochannel. Our methodology is based on the fact that methylation makes DNA molecules stiffer, resulting in a longer contracted length and a longer relaxation time (a slower contraction rate). The present methodology offers a promising way to identify DNA methylation without any protein modification at a single DNA molecule level within 2 h.

Rational Concept for Designing Vapor-Liquid-Solid Growth of Single Crystalline Metal Oxide Nanowires.

Metal oxide nanowires hold great promise for various device applications due to their unique and robust physical properties in air and/or water and also due to their abundance on Earth. Vapor-liquid-solid (VLS) growth of metal oxide nanowires offers the high controllability of their diameters and spatial positions. In addition, VLS growth has applicability to axial and/or radial heterostructures, which are not attainable by other nanowire growth methods. However, material species available for the VLS growth of metal oxide nanowires are substantially limited even though the variety of material species, which has fascinating physical properties, is the most interesting feature of metal oxides. Here we demonstrate a rational design for the VLS growth of various metal oxide nanowires, based on the "material flux window". This material flux window describes the concept of VLS nanowire growth within a limited material flux range, where nucleation preferentially occurs only at a liquid-solid interface. Although the material flux was previously thought to affect primarily the growth rate, we experimentally and theoretically demonstrate that the material flux is the important experimental variable for the VLS growth of metal oxide nanowires. On the basis of the material flux window concept, we discover novel metal oxide nanowires, composed of MnO, CaO, Sm2O3, NiO, and Eu2O3, which were previously impossible to form via the VLS route. The newly grown NiO nanowires exhibited stable memristive properties superior to conventional polycrystalline devices due to the single crystallinity. Thus, this VLS design route offers a useful guideline for the discovery of single crystalline nanowires that are composed of functional metal oxide materials.

Modulation of thermoelectric power factor via radial dopant inhomogeneity in B-doped Si nanowires.

We demonstrate a modulation of thermoelectric power factor via a radial dopant inhomogeneity in B-doped Si nanowires. These nanowires grown via vapor-liquid-solid (VLS) method were naturally composed of a heavily doped outer shell layer and a lightly doped inner core. The thermopower measurements for a single nanowire demonstrated that the power factor values were higher than those of homogeneously B-doped Si nanowires. The field effect measurements revealed the enhancement of hole mobility for these VLS grown B-doped Si nanowires due to the modulation doping effect. This mobility enhancement increases overall electrical conductivity of nanowires without decreasing the Seebeck coefficient value, resulting in the increase of thermoelectric power factor. In addition, we found that tailoring the surface dopant distribution by introducing surface δ-doping can further increase the power factor value. Thus, intentionally tailoring radial dopant inhomogeneity promises a way to modulate the thermoelectric power factor of semiconductor nanowires.

Gate-All-Around Nanopore Osmotic Power Generators.

Nanofluidic channels in a membrane represent a promising avenue for harnessing blue energy from salinity gradients, relying on permselectivity as a pivotal characteristic crucial for inducing electricity through diffusive ion transport. Surface charge emerges as a central player in the osmotic energy conversion process, emphasizing the critical significance of a judicious selection of membrane materials to achieve optimal ion permeability and selectivity within specific channel dimensions. Alternatively, here we report a field-effect approach for in situ manipulation of the ion selectivity in a nanopore. Application of voltage to a surround-gate electrode allows precise adjustment of the surface charge density at the pore wall. Leveraging the gating control, we demonstrate permselectivity turnover to enhanced cation selective transport in multipore membranes, resulting in a 6-fold increase in the energy conversion efficiency with a power density of 15 W/m2 under a salinity gradient. These findings not only advance our fundamental understanding of ion transport in nanochannels but also provide a scalable and efficient strategy for nanoporous membrane osmotic power generation.

Scalability of nanopore osmotic energy conversion.

Artificial nanofluidic networks are emerging systems for blue energy conversion that leverages surface charge-derived permselectivity to induce voltage from diffusive ion transport under salinity difference. Here the pivotal significance of electrostatic inter-channel couplings in multi-nanopore membranes, which impose constraints on porosity and subsequently influence the generation of large osmotic power outputs, is illustrated. Constructive interference is observed between two 20 nm nanopores of 30 nm spacing that renders enhanced permselectivity to osmotic power output via the recovered electroneutrality. On contrary, the interference is revealed as destructive in two-dimensional arrays causing significant deteriorations of the ion selectivity even for the nanopores sparsely distributed at an order of magnitude larger spacing than the Dukhin length. Most importantly, a scaling law is provided for deducing the maximal membrane area and porosity to avoid the selectivity loss via the inter-pore electrostatic coupling. As the electric crosstalk is inevitable in any fluidic network, the present findings can be a useful guide to design nanoporous membranes for scalable osmotic power generations.

Identifying Viral Vector Characteristics by Nanopore Sensing.

Using viral vectors as gene delivery vehicles for gene therapy necessitates their quality control. Here, we report on nanopore sensing for nondestructively inspecting genomes inside the nanoscale cargoes at the single-molecule level. Using ionic current measurements, we motion-tracked the adeno-associated virus (AAV) vectors as they translocated through a solid-state nanopore. Considering the varying contributions of the electrophoretic forces from the negatively charged internal polynucleotides of different lengths, the nanocargoes carrying longer DNA moved more slowly in the nanochannel. Moreover, ion blockage characteristics revealed their larger volume by up to approximately 3600 nm3 in proportion to the length of single-stranded DNA packaged inside, thereby allowing electrical discriminations of AAV vectors by the gene-derived physical features. The present findings can be a promising tool for the enhanced quality control of AAV products by enabling the screening of empty and intermediate vectors at the single-particle level.

Mechanism of how salt-gradient-induced charges affect the translocation of DNA molecules through a nanopore.

Experiments using nanopores demonstrated that a salt gradient enhances the capture rate of DNA and reduces its translocation speed. These two effects can help to enable electrical DNA sequencing with nanopores. Here, we provide a quantitative theoretical evaluation that shows the positive net charges, which accumulate around the pore entrance due to the salt gradient, are responsible for the two observed effects: they reinforce the electric capture field, resulting in promoted molecule capture rate; and they induce cationic electroosmotic flow through the nanopore, thus significantly retarding the motion of the anionic DNA through the nanopore. Our multiphysical simulation results show that, during the polymer trapping stage, the former effect plays the major role, thus resulting in promoted DNA capture rate, while during the nanopore-penetrating stage the latter effect dominates and consequently reduces the DNA translocation speed significantly. Quantitative agreement with experimental results has been reached by further taking nanopore wall surface charges into account.

Impact of preferential indium nucleation on electrical conductivity of vapor-liquid-solid grown indium-tin oxide nanowires.

Highly conductive and transparent indium-tin oxide (ITO) single-crystalline nanowires, formed by the vapor-liquid-solid (VLS) method, hold great promise for various nanoscale device applications. However, increasing an electrical conductivity of VLS grown ITO nanowires is still a challenging issue due to the intrinsic difficulty in controlling complex material transports of the VLS process. Here, we demonstrate a crucial role of preferential indium nucleation on the electrical conductivity of VLS grown ITO nanowires using gold catalysts. In spite of the fact that the vapor pressure of tin is lower than that of indium, we found that the indium concentration within the nanowires was always higher than the nominal composition. The VLS growth of ITO through gold catalysts significantly differs from ITO film formations due to the emergence of preferential indium nucleation only at a liquid-solid interface. Furthermore, we demonstrate that the averaged resistivity of ITO nanowires can be decreased down to 2.1 × 10(-4) Ω cm, which is the lowest compared with values previously reported, via intentionally increasing the tin concentration within the nanowires.

Ion-selective detection by plasticized poly(vinyl chloride) membrane in glass nanopipette with alternating voltage modulation.

An alternating current (AC) voltage modulation was applied to ion-selective observations with plasticized poly(vinyl chloride) membranes in glass nanopipettes. The liquid confronting the membranes in the nanopipettes, the conditioning process, and AC voltage modulation play important roles in the ion-selective detection. In the AC detection system developed by us, where distilled water was used as the liquid within the nanopipettes, potassium ions were selectively detected in the sample solution of sodium and potassium ions because sodium ions were captured at the membrane containing bis(12-crown-4) ionophores, before the saturation of the ionophores. The membrane lost the selectivity after the saturation. On using sodium chloride as the liquid within the nanopipette, the membrane selectively detected potassium and sodium ions before and after the saturation of ionophores, respectively. The ion-selective detection of our system can be explained by the ion extraction-diffusion-dissolution mechanism through the bis(12-crown-4) ionophores with AC voltage modulation.

Prominent thermodynamical interaction with surroundings on nanoscale memristive switching of metal oxides.

This study demonstrates the effect of surroundings on a memristive switching at nanoscale by utilizing an open top planar-type device. NiO(x) and CoO(x) planar-type devices have exhibited a memristive behavior under atmospheric pressure, whereas TiO(2-x) planar-type devices did not show a memristive switching even under the same surroundings. A memristive behavior of TiO(2-x) planar-type devices has emerged when reducing an ambient pressure and/or employing a SiO(2) passivation layer. These results reveal that a thermodynamical interaction with surroundings critically determines the occurrence of memristive switching via varying a stability of nonstoichiometry. Since this effect tends to be more significant for smaller devices with larger specific surface area, tailoring the surrounding effect by an appropriate passivation will be essential for high density devices.

Protocol for preparation of solid-state multipore osmotic power generators.

Nanopore is an emerging energy-harvesting device that can create electricity directly from salt solutions. Here, we present a protocol for the preparation and structure optimization of solid-state multipore osmotic power generators. We describe steps for sculpting multiple pores at well-defined positions in a thin SiNx membrane using electron-beam lithography. We also detail an imprinting technique to form polydimethylsiloxane blocks with fluidic channels bonded to the multipore membrane. This approach facilitates repeated liquid-exchange processes involved in ionic current measurements. For complete details on the use and execution of this protocol, please refer to Tsutsui et al.1.

Dual defects of cation and anion in memristive nonvolatile memory of metal oxides.

The electrically driven resistance change of metal oxides, called bipolar memristive switching, is a fascinating phenomenon in the development of next-generation nonvolatile memory alternatives to flash technology. However, our understanding of the nature of bipolar memristive switching is unfortunately far from comprehensive, especially the relationship between the electrical transport and the local nonstoichiometry. Here we demonstrate that the coexistence of anion and cation defects is critical to the transport properties of NiO, one of the most promising memristive oxides, by utilizing first-principles calculations. We find that, in the presence of both nickel and oxygen defects, which must exist in any real experimental systems, carrier concentrations of holes generated by nickel defects can be modulated by the presence or absence of oxygen defects around the nickel defect. Such alternation of local nonstoichiometry can be understood in terms of an oxygen ion drift induced by an external electric field. This implication provides a foundation for understanding universally the nature of bipolar memristive switching in various p-type metal oxides.