Three-dimensional Nanowire Structures for Ultra-Fast Separation of DNA, Protein and RNA Molecules

Integrated In-Plane Nanofluidic Devices for Resistive-Pulse Sensing

Single-particle (or digital) measurements enhance sensitivity (10- to 100-fold improvement) and uncover heterogeneity within a population (one event in 100 to 10,000). Many biological systems are significantly influenced by rare or infrequent events, and determining what species is present, in what quantity, and the role of that species is critically important to unraveling many questions. To develop these measurement systems, resistive-pulse sensing is used as a label-free, single-particle detection technique and can be combined with a range of functional elements, e.g., mixers, reactors, filters, separators, and pores. Virtually, any two-dimensional layout of the micro- and nanofluidic conduits can be envisioned, designed, and fabricated in the plane of the device. Multiple nanopores in series lead to higher-precision measurements of particle size, shape, and charge, and reactions coupled directly with the particle-size measurements improve temporal response. Moreover, other detection techniques, e.g., fluorescence, are highly compatible with the in-plane format. These integrated in-plane nanofluidic devices expand the toolbox of what is possible with single-particle measurements.

Rational Strategy for Space-Confined Atomic Layer Deposition

Atomic layer deposition (ALD) offers excellent controllability of spatial uniformity, film thickness at the Angstrom level, and film composition even for high-aspect-ratio nanostructured surfaces, which are rarely attainable by other conventional deposition methodologies. Although ALD has been successfully applied to various substrates under open-top circumstances, the applicability of ALD to confined spaces has been limited because of the inherent difficulty of supplying precursors into confined spaces. Here, we propose a rational methodology to apply ALD growths to confined spaces (meter-long microtubes with an aspect ratio of up to 10 000). The ALD system, which can generate differential pressures to confined spaces, was newly developed. By using this ALD system, it is possible to deposit TiO_x layers onto the inner surface of capillary tubes with a length of 1000 mm and an inner diameter of 100 μm with spatial deposition uniformity. Furthermore, we show the superior thermal and chemical robustness of TiO_x-coated capillary microtubes for molecular separations when compared to conventional molecule-coated capillary microtubes. Thus, the present rational strategy of space-confined ALD offers a useful approach to design the chemical and physical properties of the inner surfaces of various confined spaces.

Oligonucleotide separation techniques for purification and analysis: What can we learn for today's tasks?

Nucleic acids are the blueprint of life. They are not only the construction plan of the single cell or higher associations of them, but also necessary for function, communication and regulation. Due to the pandemic, the attention shifted in particular to their therapeutic potential as a vaccine. As pharmaceutical oligonucleotides are unique in terms of their stability and application, special delivery systems were also considered. Oligonucleotide production systems can vary and depend on the feasibility, availability, price and intended application. To achieve good purity, reliable results and match the strict specifications in the pharmaceutical industry, the separation of oligonucleotides is always essential. Besides the separation required for production, additional and specifically different separation techniques are needed for analysis to determine if the product complies with the designated specifications. After a short introduction to ribonucleic acids (RNAs), messenger RNA vaccines, and their production and delivery systems, an overview regarding separation techniques will be provided. This not only emphasises electrophoretic separations but also includes spin columns, extractions, precipitations, magnetic nanoparticles and several chromatographic separation principles, such as ion exchange chromatography, ion-pair reversed-phase, size exclusion and affinity.

Oxide nanowire microfluidics addressing previously-unattainable analytical methods for biomolecules towards liquid biopsy

Nanowire microfluidics using a combination of self-assembly and nanofabrication technologies is expected to be applied to various fields due to its unique properties. We have been working on the fabrication of nanowire microfluidic devices and the development of analytical methods for biomolecules using the unique phenomena generated by the devices. The results of our research are not just limited to the development of nanospace control with "targeted dimensions" in "targeted arrangements" with "targeted materials/surfaces" in "targeted spatial locations/structures" in microfluidic channels, but also cover a wide range of analytical methods for biomolecules (extraction, separation/isolation, and detection) that are impossible to achieve with conventional technologies. Specifically, we are working on the extraction technology "the cancer-related microRNA extraction method in urine," the separation technology "the ultrafast and non-equilibrium separation method for biomolecules," and the detection technology "the highly sensitive electrical measurement method." These research studies are not just limited to the development of biomolecule analysis technology using nanotechnology, but are also opening up a new academic field in analytical chemistry that may lead to the discovery of new pretreatment, separation, and detection principles.

Label-Free Isolation of Exosomes Using Microfluidic Technologies

Exosomes are cell-derived structures packaged with lipids, proteins, and nucleic acids. They exist in diverse bodily fluids and are involved in physiological and pathological processes. Although their potential for clinical application as diagnostic and therapeutic tools has been revealed, a huge bottleneck impeding the development of applications in the rapidly burgeoning field of exosome research is an inability to efficiently isolate pure exosomes from other unwanted components present in bodily fluids. To date, several approaches have been proposed and investigated for exosome separation, with the leading candidate being microfluidic technology due to its relative simplicity, cost-effectiveness, precise and fast processing at the microscale, and amenability to automation. Notably, avoiding the need for exosome labeling represents a significant advance in terms of process simplicity, time, and cost as well as protecting the biological activities of exosomes. Despite the exciting progress in microfluidic strategies for exosome isolation and the countless benefits of label-free approaches for clinical applications, current microfluidic platforms for isolation of exosomes are still facing a series of problems and challenges that prevent their use for clinical sample processing. This review focuses on the recent microfluidic platforms developed for label-free isolation of exosomes including those based on sieving, deterministic lateral displacement, field flow, and pinched flow fractionation as well as viscoelastic, acoustic, inertial, electrical, and centrifugal forces. Further, we discuss advantages and disadvantages of these strategies with highlights of current challenges and outlook of label-free microfluidics toward the clinical utility of exosomes.

Giant Magnetoresistance and Magneto-Thermopower in 3D Interconnected NixFe1-x/Cu Multilayered Nanowire Networks

The versatility of the template-assisted electrodeposition technique to fabricate complex three-dimensional networks made of interconnected nanowires allows one to easily stack ferromagnetic and non-magnetic metallic layers along the nanowire axis. This leads to the fabrication of unique multilayered nanowire network films showing giant magnetoresistance effect in the current-perpendicular-to-plane configuration that can be reliably measured along the macroscopic in-plane direction of the films. Moreover, the system also enables reliable measurements of the analogous magneto-thermoelectric properties of the multilayered nanowire networks. Here, three-dimensional interconnected NixFe1−x/Cu multilayered nanowire networks (with 0.60≤x≤0.97) are fabricated and characterized, leading to large magnetoresistance and magneto-thermopower ratios up to 17% and −25% in Ni80Fe20/Cu, respectively. A strong contrast is observed between the amplitudes of magnetoresistance and magneto-thermoelectric effects depending on the Ni content of the NiFe alloys. In particular, for the highest Ni concentrations, a strong increase in the magneto-thermoelectric effect is observed, more than a factor of 7 larger than the magnetoresistive effect for Ni97Fe3/Cu multilayers. This sharp increase is mainly due to an increase in the spin-dependent Seebeck coefficient from −7 µV/K for the Ni60Fe40/Cu and Ni70Fe30/Cu nanowire arrays to −21 µV/K for the Ni97Fe3/Cu nanowire array. The enhancement of the magneto-thermoelectric effect for multilayered nanowire networks based on dilute Ni alloys is promising for obtaining a flexible magnetic switch for thermoelectric generation for potential applications in heat management or logic devices using thermal energy.

Rational Strategy for Space-Confined Seeded Growth of ZnO Nanowires in Meter-Long Microtubes

Seeded crystal growths of nanostructures within confined spaces offer an interesting approach to design chemical reaction spaces with tailored inner surface properties. However, such crystal growth within confined spaces tends to be inherently difficult as the length increases as a result of confinement effects. Here, we demonstrate a space-confined seeded growth of ZnO nanowires within meter-long microtubes of 100 μm inner diameter with the aspect ratio of up to 10 000, which had been unattainable to previous methods of seeded crystal growths. ZnO nanowires could be grown via seeded hydrothermal crystal growth for relatively short microtubes below the length of 40 mm, while any ZnO nanostructures were not observable at all for longer microtubes above 60 mm with the aspect ratio of 600. Microstructural and mass spectrometric analysis revealed that a conventional seed layer formation using zinc acetate is unfeasible within the confined space of long microtubes as a result of the formation of detrimental residual Zn complex compounds. To overcome this space-confined issue, a flow-assisted seed layer formation is proposed. This flow-assisted method enables growth of spatially uniform ZnO nanowires via removing residual compounds even for 1 m long microtubes with the aspect ratio of up to 10 000. Finally, the applicably of ZnO-nanowire-decorated long microtubes for liquid-phase separations was demonstrated.

High-Fidelity Capture, Threading, and Infinite-Depth Sequencing of Single DNA Molecules with a Double-Nanopore System

Nanopore sequencing of nucleic acids has an illustrious history of innovations that eventually made commercial nanopore sequencing possible. Nevertheless, the present nanopore sequencing technology leaves much room for improvement, especially with respect to accuracy of raw reads and detection of nucleotide modifications. Double-nanopore sequencing-an approach where a DNA molecule is pulled back and forth by a tug-of-war of two nanopores-could potentially improve single-molecule read accuracy and modification detection by offering multiple reads of the same DNA fragment. One principle difficulty in realizing such a technology is threading single-stranded DNA through both nanopores. Here, we describe and demonstrate through simulations a nanofluidic system for loading and threading DNA strands through a double-nanopore setup with nearly 100% fidelity. The high-efficiency loading is realized by using hourglass-shaped side channels that not only deliver the molecules to the nanopore but also retain molecules that missed the nanopore at the first passage to attempt the nanopore capture again. The second nanopore capture is facilitated by an orthogonal microfluidic flow that unravels the molecule captured by the first nanopore and delivers it to the capture volume of the second nanopore. We demonstrate the potential utility of our double-nanopore system for DNA sequencing by simulating repeat back-and-forth motion-flossing-of a DNA strand through the double-nanopore system. We show that repeat exposure of the same DNA fragments to the nanopore sensing volume considerably increases accuracy of the nucleotide sequence determination and that correlated displacement of ssDNA through the two nanopores may facilitate recognition of homopolymer fragments.

Vertical nanowire array-based biosensors: device design strategies and biomedical applications

Biosensors have been extensively studied in the areas of biology, electronics, chemistry, biotechnology, medicine, and various engineering fields. The interdisciplinarity creates an ideal platform for scientists to analyze biological species and chemical materials in a direct, efficient, and sensitive manner; this is expected to revolutionize the life sciences, basic medicine, and the healthcare industry. To carry out high-performance biosensing, nanoprobes - with specific nanoscale properties - have been proposed for ultrasensitive and in situ monitoring/detection of tracer biomolecules, cellular behavior, cellular microenvironments, and electrophysiological activity. Here, we review the development of vertical nanowire (VNW) array-based devices for the effective collection of biomedical information at the molecular level, extracellular level, and intracellular level. In particular, we summarize VNW-based technologies in the aspects of detecting biochemical information, cellular information, and bioelectrical information, all of which facilitate the understanding of fundamental biology and development of therapeutic techniques. Finally, we present a conclusion and prospects for the development of VNW platforms in practical biomedical applications, and we identify the challenges and opportunities for VNW-based biosensor systems in future biological research.

Separation Phenomena in Tailored Micro- and Nanofluidic Environments

Separations of bioanalytes require robust, effective, and selective migration phenomena. However, due to the complexity of biological matrices such as body fluids or tissue, these requirements are difficult to achieve. The separations field is thus constantly evolving to develop suitable methods to separate biomarkers and fractionate biospecimens for further interrogation of biomolecular content. Advances in the field of microfabrication allow the tailored generation of micro- and nanofluidic environments. These can be exploited to induce interactions and dynamics of biological species with the corresponding geometrical features, which in turn can be capitalized for novel separation approaches. This review provides an overview of several unique separation applications demonstrated in recent years in tailored micro- and nanofluidic environments. These include electrokinetic methods such as dielectrophoresis and electrophoresis, but also rather nonintuitive ratchet separation mechanisms, continuous flow separations, and fractionations such as deterministic lateral displacement, as well as methods employing entropic forces for separation.

Engineering Nanowire-Mediated Cell Lysis for Microbial Cell Identification

Researchers have demonstrated great promise for inorganic nanowire use in analyzing cells or intracellular components. Although a stealth effect of nanowires toward cell surfaces allows preservation of the living intact cells when analyzing cells, as a completely opposite approach, the applicability to analyze intracellular components through disrupting cells is also central to understanding cellular information. However, the reported lysis strategy is insufficient for microbial cell lysis due to the cell robustness and wrong approach taken so far ( i. e., nanowire penetration into a cell membrane). Here we propose a nanowire-mediated lysis method for microbial cells by introducing the rupture approach initiated by cell membrane stretching; in other words, the nanowires do not penetrate the membrane, but rather they break the membrane between the nanowires. Entangling cells with the bacteria-compatible and flexible nanowires and membrane stretching of the entangled cells, induced by the shear force, play important roles for the nanowire-mediated lysis to Gram-positive and Gram-negative bacteria and yeast cells. Additionally, the nanowire-mediated lysis is readily compatible with the loop-mediated isothermal amplification (LAMP) method because the lysis is triggered by simply introducing the microbial cells. We show that an integration of the nanowire-mediated lysis with LAMP provides a means for a simple, rapid, one-step identification assay (just introducing a premixed solution into a device), resulting in visual chromatic identification of microbial cells. This approach allows researchers to develop a microfluidic analytical platform not only for microbial cell identification including drug- and heat-resistance cells but also for on-site detection without any contamination.

One-Dimensional Nanostructures: Microfluidic-Based Synthesis, Alignment and Integration towards Functional Sensing Devices

Microfluidic-based synthesis of one-dimensional (1D) nanostructures offers tremendous advantages over bulk approaches e.g., the laminar flow, reduced sample consumption and control of self-assembly of nanostructures. In addition to the synthesis, the integration of 1D nanomaterials into microfluidic chips can enable the development of diverse functional microdevices. 1D nanomaterials have been used in applications such as catalysts, electronic instrumentation and sensors for physical parameters or chemical compounds and biomolecules and hence, can be considered as building blocks. Here, we outline and critically discuss promising strategies for microfluidic-assisted synthesis, alignment and various chemical and biochemical applications of 1D nanostructures. In particular, the use of 1D nanostructures for sensing chemical/biological compounds are reviewed.

Screening of bacteria-binding peptides and one-pot ZnO surface modification for bacterial cell entrapment

Short functional peptides are promising materials for use as targeting recognition probes. Toll-like receptor 4 (TLR4) plays an essential role in pathogen recognition and in activation of innate immunity. Here, the TLR4 amino acid sequence was used to screen for bacterial cell binding peptides using a peptide array. Several octamer peptides, including GRHIFWRR, demonstrated binding to Escherichia coli as well as lipopolysaccharides. Linking this peptide with the ZnO-binding peptide HKVAPR, creates a bi-functional peptide capable of one-step ZnO surface modification for bacterial cell entrapment. Ten-fold increase in entrapment of E. coli was observed using the bi-functional peptide. The screened peptides and the simple strategy for nanomaterial surface functionalization can be employed for various biotechnological applications including bacterial cell entrapment onto ZnO surfaces.

Linking the screened bacteria-binding peptide with the ZnO-binding peptide HKVAPR, created a bifunctional peptide capable of one-step simple ZnO surface modification and of bacterial cell entrapment.

Selective hierarchical patterning of silicon nanostructures via soft nanostencil lithography

It is challenging to hierarchically pattern high-aspect-ratio nanostructures on microstructures using conventional lithographic techniques, where photoresist (PR) film is not able to uniformly cover on the microstructures as the aspect ratio increases. Such non-uniformity causes poor definition of nanopatterns over the microstructures. Nanostencil lithography can provide an alternative means to hierarchically construct nanostructures on microstructures via direct deposition or plasma etching through a free-standing nanoporous membrane. In this work, we demonstrate the multiscale hierarchical fabrication of high-aspect-ratio nanostructures on microstructures of silicon using a free-standing nanostencil, which is a nanoporous membrane consisting of metal (Cr), PR, and anti-reflective coating. The nanostencil membrane is used as a deposition mask to define Cr nanodot patterns on the predefined silicon microstructures. Then, deep reactive ion etching is used to hierarchically create nanostructures on the microstructures using the Cr nanodots as an etch mask. With simple modification of the main fabrication processes, high-aspect-ratio nanopillars are selectively defined only on top of the microstructures, on bottom, or on both top and bottom.

On-chip hydrodynamic chromatography of DNA through centimeters-long glass nanocapillaries

This study demonstrates hydrodynamic chromatography of DNA fragments in a microchip. The microchip contains a highly regular array of nanofluidic channels (nanocapillaries) that are essential for resolving DNA in this chromatography mode. The nanocapillaries are self-enclosed robust structures built inside a doped glass layer on silicon using low-resolution photolithography and standard semiconductor processing techniques. Additionally, the unique nanocapillaries feature a cylindrical inner radius of 600 nm maintained over a length scale of 5 cm. The microchip with bare open nanocapillaries is shown to rapidly separate a digest of lambda DNA in free solution (<5 min under the elution pressure of 60 to 120 psi), relying entirely on pressure-driven flows and, in doing so, avoiding the field-induced DNA aggregations encountered in gel-free electrophoresis. The nanocapillaries, despite their relatively short length, are observed to fractionate DNA fragments reasonably well with a minimum resolvable size difference below 5 kbp. In the chromatograms obtained, the number of theoretical plates exceeds 10⁵ plates per m for 3.5 and 21 kbp long DNA fragments. The relative mobility of fragments in relation to their size is found to be in excellent agreement with the simple quadratic model of hydrodynamic chromatography. The model is shown to estimate greater effective hydrodynamic radii than those of respective fragments being unconfined in bulk solution, implying increased drag forces and reduced diffusion coefficients, which is also a noticeable trend among diffusion coefficient estimates derived from the experimentally obtained plate heights. This robust mass-producible microchip can be further developed into a fully integrated bioanalytic microsystem.

Magnetic and Magnetoresistive Properties of 3D Interconnected NiCo Nanowire Networks

Track-etched polymer membranes with crossed nanochannels have been revealed to be most suitable as templates to produce large surface area and mechanically stable 3D interconnected nanowire (NW) networks by electrodeposition. Geometrically controlled NW superstructures made of NiCo ferromagnetic alloys exhibit appealing magnetoresistive properties. The combination of exact alloy compositions with the spatial arrangement of NWs in the 3D network is decisive to obtain specific magnetic and magneto-transport behavior. A proposed simple model based on topological aspects of the 3D NW networks is used to accurately determine the anisotropic magnetoresistance ratios. Despite of their complex topology, the microstructure of Co-rich NiCo NW networks display mixed fcc-hcp phases with the c-axis of the hcp phase oriented perpendicular to their axis. These interconnected NW networks have high potential as reliable and stable magnetic field sensors.

DNA separation and enrichment using electro-hydrodynamic bidirectional flows in viscoelastic liquids

DNA size separation followed by purification and enrichment constitute essential operations for genetic engineering. These processes are mostly carried out using DNA electrophoresis in gels or in polymer solutions, a well-established yet lengthy technique which has been notably improved using Lab-on-Chip technologies. So far, innovations for DNA separation or enrichment have been mostly undertaken separately, and we present an approach that allows us to perform these two processes simultaneously for DNA fragments spanning 0.2-50 kilo base pairs (kbp) in length. Our technology involves an electric field and a counter hydrodynamic flow in viscoelastic liquids, in which we show the occurrence of transverse forces oriented toward the walls. These forces increase with DNA molecular weight (MW) and hence induce a progressive reduction in DNA migration speed that triggers size separation in microfluidic channels as well as in capillaries. The separation of MW markers in the range 1-50 kbp is achieved in 15 minutes, thus outperforming gel electrophoresis that takes ∼3 hours for this sample. Furthermore, the use of a funnel, where electric and flow fields are modulated spatially, enables us to adjust the transverse forces so as to stall the motion of DNA molecules at a position where they accumulate at factors of up to 1000 per minute. In this configuration, we establish that the operations of DNA enrichment and separation can be carried out simultaneously for the bands of a DNA MW marker between 0.2-1.5 kbp diluted at 0.02 ng μL(-1) in 30 s. Altogether, our technology, which can readily be integrated as an in-line module in Lab-on-Chips, offers unique opportunities for sample preparation and analysis of minute genomic samples.

Recent developments in nanowires for bio-applications from molecular to cellular levels

This review highlights the most promising applications of nanowires for bioanalytical chemistry and medical diagnostics. The materials discussed here are metal oxide and Si semiconductors, which are integrated with various microfluidic systems. Nanowire structures offer desirable advantages such as a very small diameter size with a high aspect ratio and a high surface-to-volume ratio without grain boundaries; consequently, nanowires are promising tools to study biological systems. This review starts with the integration of nanowire structures into microfluidic systems, followed by the discussion of the advantages of nanowire structures in the separation, manipulation and purification of biomolecules (DNA, RNA and proteins). Next, some representative nanowire devices are introduced for biosensors from molecular to cellular levels based on electrical and optical approaches. Finally, we conclude the review by highlighting some bio-applications for nanowires and presenting the next challenges that must be overcome to improve the capabilities of nanowire structures for biological and medical systems.