Biorecognition layer engineering: overcoming screening limitations of nanowire-based FET devices

Detection of biological species is of great importance to numerous areas of medical and life sciences from the diagnosis of diseases to the discovery of new drugs. Essential to the detection mechanism is the transduction of a signal associated with the specific recognition of biomolecules of interest. Nanowire-based electrical devices have been demonstrated as a powerful sensing platform for the highly sensitive detection of a wide-range of biological and chemical species. Yet, detecting biomolecules in complex biosamples of high ionic strength (>100 mM) is severely hampered by ionic screening effects. As a consequence, most of existing nanowire sensors operate under low ionic strength conditions, requiring ex situ biosample manipulation steps, that is, desalting processes. Here, we demonstrate an effective approach for the direct detection of biomolecules in untreated serum, based on the fragmentation of antibody-capturing units. Size-reduced antibody fragments permit the biorecognition event to occur in closer proximity to the nanowire surface, falling within the charge-sensitive Debye screening length. Furthermore, we explored the effect of antibody surface coverage on the resulting detection sensitivity limit under the high ionic strength conditions tested and found that lower antibody surface densities, in contrary to high antibody surface coverage, leads to devices of greater sensitivities. Thus, the direct and sensitive detection of proteins in untreated serum and blood samples was effectively performed down to the sub-pM concentration range without the requirement of biosamples manipulation.

Following aptamer-thrombin binding by force measurements

The rupture forces between an aptamer (1)-functionalized AFM tip and a thrombin-modified Au surface are analyzed. The rupture force for a single aptamer/thrombin complex is determined as approximately 4.45 pN. The analysis of the system reveals that the rupture forces correspond to the melting of the G-quadruplex structure of the aptamer bound to the thrombin. This melting of the G-quadruplex leads to the dissociation of the aptamer/thrombin complex.

Compression and deposition of microgel monolayers from fluid interfaces: particle size effects on interface microstructure and nanolithography

Controlling the microstructure of monolayers of microgels confined at a water/oil interface is the key to their successful application as nanolithography masks after deposition on a solid substrate.

Endonuclease-Based Logic Gates and Sensors Using Magnetic Force-Amplified Readout of DNA Scission on Cantilevers

The endonuclease scission of magnetic particles functionalized with sequence-specific DNAs, which are associated on cantilevers, is followed by the magnetic force-amplified readout of the reactions by the nano-mechanical deflection/retraction of the cantilevers. The systems are employed to develop AND or OR logic gates and to detect single base mismatch specificity of the endonucleases. The two endonucleases EcoRI (E(A)) and AscI (E(B)) are used as inputs. The removal of magnetic particles linked to the cantilever by the duplexes 1/1a and 2/2a via the simultaneous cleavage of the DNAs by E(A) and E(B) leads to the retraction of the magnetically deflected cantilever and to the establishment of the "AND" gate. The removal of the magnetic particles linked to the cantilevers by the duplex 3/3a by either E(A) or E(B) leads to the retraction of the magnetically deflected cantilever and to the establishment of the "OR" gate. The magnetic force-amplified readout of endonuclease activities is also employed to reveal single base mismatch specificity of the biocatalysts.

Cellular Deformations Induced by Conical Silicon Nanowire Arrays Facilitate Gene Delivery

Engineered cell-nanostructured interfaces generated by vertically aligned silicon nanowire (SiNW) arrays have become a promising platform for orchestrating cell behavior, function, and fate. However, the underlying mechanism in SiNW-mediated intracellular access and delivery is still poorly understood. This study demonstrates the development of a gene delivery platform based on conical SiNW arrays for mechanical cell transfection, assisted by centrifugal force, for both adherent and nonadherent cells in vitro. Cells form focal adhesions on SiNWs within 6 h, and maintain high viability and motility. Such a functional and dynamic cell-SiNW interface features conformational changes in the plasma membrane and in some cases the nucleus, promoting both direct penetration and endocytosis; this synergistically facilitates SiNW-mediated delivery of nucleic acids into immortalized cell lines, and into difficult-to-transfect primary immune T cells without pre-activation. Moreover, transfected cells retrieved from SiNWs retain the capacity to proliferate-crucial to future biomedical applications. The results indicate that SiNW-mediated intracellular delivery holds great promise for developing increasingly sophisticated investigative and therapeutic tools.

Tutorial: using nanoneedles for intracellular delivery

Intracellular delivery of advanced therapeutics, including biologicals and supramolecular agents, is complex because of the natural biological barriers that have evolved to protect the cell. Efficient delivery of therapeutic nucleic acids, proteins, peptides and nanoparticles is crucial for clinical adoption of emerging technologies that can benefit disease treatment through gene and cell therapy. Nanoneedles are arrays of vertical high-aspect-ratio nanostructures that can precisely manipulate complex processes at the cell interface, enabling effective intracellular delivery. This emerging technology has already enabled the development of efficient and non-destructive routes for direct access to intracellular environments and delivery of cell-impermeant payloads. However, successful implementation of this technology requires knowledge of several scientific fields, making it complex to access and adopt by researchers who are not directly involved in developing nanoneedle platforms. This presents an obstacle to the widespread adoption of nanoneedle technologies for drug delivery. This tutorial aims to equip researchers with the knowledge required to develop a nanoinjection workflow. It discusses the selection of nanoneedle devices, approaches for cargo loading and strategies for interfacing to biological systems and summarises an array of bioassays that can be used to evaluate the efficacy of intracellular delivery.

Non-covalent monolayer-piercing anchoring of lipophilic nucleic acids: preparation, characterization, and sensing applications

Functional interfaces of biomolecules and inorganic substrates like semiconductor materials are of utmost importance for the development of highly sensitive biosensors and microarray technology. However, there is still a lot of room for improving the techniques for immobilization of biomolecules, in particular nucleic acids and proteins. Conventional anchoring strategies rely on attaching biomacromolecules via complementary functional groups, appropriate bifunctional linker molecules, or non-covalent immobilization via electrostatic interactions. In this work, we demonstrate a facile, new, and general method for the reversible non-covalent attachment of amphiphilic DNA probes containing hydrophobic units attached to the nucleobases (lipid-DNA) onto SAM-modified gold electrodes, silicon semiconductor surfaces, and glass substrates. We show the anchoring of well-defined amounts of lipid-DNA onto the surface by insertion of their lipid tails into the hydrophobic monolayer structure. The surface coverage of DNA molecules can be conveniently controlled by modulating the initial concentration and incubation time. Further control over the DNA layer is afforded by the additional external stimulus of temperature. Heating the DNA-modified surfaces at temperatures >80 °C leads to the release of the lipid-DNA structures from the surface without harming the integrity of the hydrophobic SAMs. These supramolecular DNA layers can be further tuned by anchoring onto a mixed SAM containing hydrophobic molecules of different lengths, rather than a homogeneous SAM. Immobilization of lipid-DNA on such SAMs has revealed that the surface density of DNA probes is highly dependent on the composition of the surface layer and the structure of the lipid-DNA. The formation of the lipid-DNA sensing layers was monitored and characterized by numerous techniques including X-ray photoelectron spectroscopy, quartz crystal microbalance, ellipsometry, contact angle measurements, atomic force microscopy, and confocal fluorescence imaging. Finally, this new DNA modification strategy was applied for the sensing of target DNAs using silicon-nanowire field-effect transistor device arrays, showing a high degree of specificity toward the complementary DNA target, as well as single-base mismatch selectivity.

Si nanowires forest-based on-chip biomolecular filtering, separation and preconcentration devices: nanowires do it all

The development of efficient biomolecular separation and purification techniques is of critical importance in modern genomics, proteomics, and biosensing areas, primarily due to the fact that most biosamples are mixtures of high diversity and complexity. Most of existent techniques lack the capability to rapidly and selectively separate and concentrate specific target proteins from a complex biosample, and are difficult to integrate with lab-on-a-chip sensing devices. Here, we demonstrate the development of an on-chip all-SiNW filtering, selective separation, desalting, and preconcentration platform for the direct analysis of whole blood and other complex biosamples. The separation of required protein analytes from raw biosamples is first performed using a antibody-modified roughness-controlled SiNWs (silicon nanowires) forest of ultralarge binding surface area, followed by the release of target proteins in a controlled liquid media, and their subsequent detection by supersensitive SiNW-based FETs arrays fabricated on the same chip platform. Importantly, this is the first demonstration of an all-NWs device for the whole direct analysis of blood samples on a single chip, able to selectively collect and separate specific low abundant proteins, while easily removing unwanted blood components (proteins, cells) and achieving desalting effects, without the requirement of time-consuming centrifugation steps, the use of desalting or affinity columns. Futhermore, we have demonstrated the use of our nanowire forest-based separation device, integrated in a single platform with downstream SiNW-based sensors arrays, for the real-time ultrasensitive detection of protein biomarkers directly from blood samples. The whole ultrasensitive protein label-free analysis process can be practically performed in less than 10 min.

Fully Tunable Silicon Nanowire Arrays Fabricated by Soft Nanoparticle Templating

We demonstrate a fabrication breakthrough to produce large-area arrays of vertically aligned silicon nanowires (VA-SiNWs) with full tunability of the geometry of the single nanowires and of the whole array, paving the way toward advanced programmable designs of nanowire platforms. At the core of our fabrication route, termed "Soft Nanoparticle Templating", is the conversion of gradually compressed self-assembled monolayers of soft nanoparticles (microgels) at a water-oil interface into customized lithographical masks to create VA-SiNW arrays by means of metal-assisted chemical etching (MACE). This combination of bottom-up and top-down techniques affords excellent control of nanowire etching site locations, enabling independent control of nanowire spacing, diameter and height in a single fabrication route. We demonstrate the fabrication of centimeter-scale two-dimensional gradient photonic crystals exhibiting continuously varying structural colors across the entire visible spectrum on a single silicon substrate, and the formation of tunable optical cavities supported by the VA-SiNWs, as unambiguously demonstrated through numerical simulations. Finally, Soft Nanoparticle Templating is combined with optical lithography to create hierarchical and programmable VA-SiNW patterns.

Precision Surface Microtopography Regulates Cell Fate via Changes to Actomyosin Contractility and Nuclear Architecture

Cells are able to perceive complex mechanical cues from their microenvironment, which in turn influences their development. Although the understanding of these intricate mechanotransductive signals is evolving, the precise roles of substrate microtopography in directing cell fate is still poorly understood. Here, UV nanoimprint lithography is used to generate micropillar arrays ranging from 1 to 10 µm in height, width, and spacing to investigate the impact of microtopography on mechanotransduction. Using mesenchymal stem cells (MSCs) as a model, stark pattern-specific changes in nuclear architecture, lamin A/C accumulation, chromatin positioning, and DNA methyltransferase expression, are demonstrated. MSC osteogenesis is also enhanced specifically on micropillars with 5 µm width/spacing and 5 µm height. Intriguingly, the highest degree of osteogenesis correlates with patterns that stimulated maximal nuclear deformation which is shown to be dependent on myosin-II-generated tension. The outcomes determine new insights into nuclear mechanotransduction by demonstrating that force transmission across the nuclear envelope can be modulated by substrate topography, and that this can alter chromatin organisation and impact upon cell fate. These findings have potential to inform the development of microstructured cell culture substrates that can direct cell mechanotransduction and fate for therapeutic applications in both research and clinical sectors.

Antibacterial properties of silver dendrite decorated silicon nanowires

Silicon nanowires fabricated through Ag-assisted chemical etching were found to be effective bacterial-traps with strong antibacterial properties resulting from Ag-nanoclusters.

Knocking down highly-ordered large-scale nanowire arrays

The large-scale assembly of nanowire elements with controlled and uniform orientation and density at spatially well-defined locations on solid substrates presents one of the most significant challenges facing their integration in real-world electronic applications. Here, we present the universal "knocking-down" approach, based on the controlled in-place planarization of nanowire elements, for the formation of large-scale ordered nanowire arrays. The controlled planarization of the nanowires is achieved by the use of an appropriate elastomer-covered rigid-roller device. After being knocked down, each nanowire in the array can be easily addressed electrically, by a simple single photolithographic step, to yield a large number of nanoelectrical devices with an unprecedented high-fidelity rate. The approach allows controlling, in only two simple steps, all possible array parameters, that is, nanowire dimensions, chemical composition, orientation, and density. The resulting knocked-down arrays can be further used for the creation of massive nanoelectronic-device arrays. More than million devices were already fabricated with yields over 98% on substrate areas of up, but not limited to, to 10 cm(2).

Silicon-Nanotube-Mediated Intracellular Delivery Enables Ex Vivo Gene Editing

Engineered nano-bio cellular interfaces driven by vertical nanostructured materials are set to spur transformative progress in modulating cellular processes and interrogations. In particular, the intracellular delivery-a core concept in fundamental and translational biomedical research-holds great promise for developing novel cell therapies based on gene modification. This study demonstrates the development of a mechanotransfection platform comprising vertically aligned silicon nanotube (VA-SiNT) arrays for ex vivo gene editing. The internal hollow structure of SiNTs allows effective loading of various biomolecule cargoes; and SiNTs mediate delivery of those cargoes into GPE86 mouse embryonic fibroblasts without compromising their viability. Focused ion beam scanning electron microscopy (FIB-SEM) and confocal microscopy results demonstrate localized membrane invaginations and accumulation of caveolin-1 at the cell-NT interface, suggesting the presence of endocytic pits. Small-molecule inhibition of endocytosis suggests that active endocytic process plays a role in the intracellular delivery of cargo from SiNTs. SiNT-mediated siRNA intracellular delivery shows the capacity to reduce expression levels of F-actin binding protein (Triobp) and alter the cellular morphology of GPE86. Finally, the successful delivery of Cas9 ribonucleoprotein (RNP) to specifically target mouse Hprt gene is achieved. This NT-enhanced molecular delivery platform has strong potential to support gene editing technologies.

Versatile Particle-Based Route to Engineer Vertically Aligned Silicon Nanowire Arrays and Nanoscale Pores

Control over particle self-assembly is a prerequisite for the colloidal templating of lithographical etching masks to define nanostructures. This work integrates and combines for the first time bottom-up and top-down approaches, namely, particle self-assembly at liquid-liquid interfaces and metal-assisted chemical etching, to generate vertically aligned silicon nanowire (VA-SiNW) arrays and, alternatively, arrays of nanoscale pores in a silicon wafer. Of particular importance, and in contrast to current techniques, including conventional colloidal lithography, this approach provides excellent control over the nanowire or pore etching site locations and decouples nanowire or pore diameter and spacing. The spacing between pores or nanowires is tuned by adjusting the specific area of the particles at the liquid-liquid interface before deposition. Hence, the process enables fast and low-cost fabrication of ordered nanostructures in silicon and can be easily scaled up. We demonstrate that the fabricated VA-SiNW arrays can be used as in vitro transfection platforms for transfecting human primary cells.

Dense arrays of uniform submicron pores in silicon and their applications

We report a versatile particle-based route to dense arrays of parallel submicron pores with high aspect ratio in silicon and explore the application of these arrays in sensors, optics, and polymer micropatterning. Polystyrene (PS) spheres are convectively assembled on gold-coated silicon wafers and sputter-etched, resulting in well-defined gold disc arrays with excellent long-range order. The gold discs act as catalysts in metal-assisted chemical etching, yielding uniform pores with straight walls, flat bottoms, and high aspect ratio. The resulting pore arrays can be used as robust antireflective surfaces, in biosensing applications, and as templates for polymer replica molding.

Ordered Silicon Pillar Arrays Prepared by Electrochemical Micromachining: Substrates for High-Efficiency Cell Transfection

Ordered arrays of silicon nano- to microscale pillars are used to enable biomolecular trafficking into primary human cells, consistently demonstrating high transfection efficiency can be achieved with broader and taller pillars than reported to date. Cell morphology on the pillar arrays is often strikingly elongated. Investigation of the cellular interaction with the pillar reveals that cells are suspended on pillar tips and do not interact with the substrate between the pillars. Although cells remain suspended on pillar tips, acute local deformation of the cell membrane was noted, allowing pillar tips to penetrate the cell interior, while retaining cell viability.

Tunable 2D binary colloidal alloys for soft nanotemplating

The realization of non-close-packed nanoscale patterns with multiple feature sizes and length scales via colloidal self-assembly is a highly challenging task. We demonstrate here the creation of a variety of tunable particle arrays by harnessing the sequential self-assembly and deposition of two differently sized microgel particles at the fluid-fluid interface. The two-step process is essential to achieve a library of 2D binary colloidal alloys, which are kinetically inaccessible by direct co-assembly. These versatile binary patterns can be exploited for a range of end-uses. Here we show that they can for instance be transferred to silicon substrates, where they act as masks for the metal-assisted chemical etching of binary arrays of vertically aligned silicon nanowires (VA-SiNWs) with fine geometrical control. In particular, continuous binary gradients in both NW spacing and height can be achieved. Notably, these binary VA-SiNW platforms exhibit interesting anti-reflective properties in the visible range, in agreement with simulations. The proposed strategy can also be used for the precise placement of metallic nanoparticles in non-close-packed arrays. Sequential depositions of soft particles enable therefore the exploration of complex binary patterns, e.g. for the future development of substrates for biointerfaces, catalysis and controlled wetting.

Highly ordered large-scale neuronal networks of individual cells - toward single cell to 3D nanowire intracellular interfaces

The use of artificial, prepatterned neuronal networks in vitro is a promising approach for studying the development and dynamics of small neural systems in order to understand the basic functionality of neurons and later on of the brain. The present work presents a high fidelity and robust procedure for controlling neuronal growth on substrates such as silicon wafers and glass, enabling us to obtain mature and durable neural networks of individual cells at designed geometries. It offers several advantages compared to other related techniques that have been reported in recent years mainly because of its high yield and reproducibility. The procedure is based on surface chemistry that allows the formation of functional, tailormade neural architectures with a micrometer high-resolution partition, that has the ability to promote or repel cells attachment. The main achievements of this work are deemed to be the creation of a large scale neuronal network at low density down to individual cells, that develop intact typical neurites and synapses without any glia-supportive cells straight from the plating stage and with a relatively long term survival rate, up to 4 weeks. An important application of this method is its use on 3D nanopillars and 3D nanowire-device arrays, enabling not only the cell bodies, but also their neurites to be positioned directly on electrical devices and grow with registration to the recording elements underneath.

Confinement-guided shaping of semiconductor nanowires and nanoribbons: "writing with nanowires"

To fully exploit their full potential, new semiconductor nanowire building blocks with ab initio controlled shapes are desired. However, and despite the great synthetic advances achieved, the ability to control nanowire's geometry has been significantly limited. Here, we demonstrate a simple confinement-guided nanowire growth method that enables to predesign not only the chemical and physical attributes of the synthesized nanowires but also allows a perfect and unlimited control over their geometry. Our method allows the synthesis of semiconductor nanowires in a wide variety of two-dimensional shapes such as any kinked (different turning angles), sinusoidal, linear, and spiral shapes, so that practically any desired geometry can be defined. The shape-controlled nanowires can be grown on almost any substrate such as silicon wafer, quartz and glass slides, and even on plastic substrates (e.g., Kapton HN).

Emerging Roles of 1D Vertical Nanostructures in Orchestrating Immune Cell Functions

Engineered nano-bio cellular interfaces driven by 1D vertical nanostructures (1D-VNS) are set to prompt radical progress in modulating cellular processes at the nanoscale. Here, tuneable cell-VNS interfacial interactions are probed and assessed, highlighting the use of 1D-VNS in immunomodulation, and intracellular delivery into immune cells-both crucial in fundamental and translational biomedical research. With programmable topography and adaptable surface functionalization, 1D-VNS provide unique biophysical and biochemical cues to orchestrate innate and adaptive immunity, both ex vivo and in vivo. The intimate nanoscale cell-VNS interface leads to membrane penetration and cellular deformation, facilitating efficient intracellular delivery of diverse bioactive cargoes into hard-to-transfect immune cells. The unsettled interfacial mechanisms reported to be involved in VNS-mediated intracellular delivery are discussed. By identifying up-to-date progress and fundamental challenges of current 1D-VNS technology in immune-cell manipulation, it is hoped that this report gives timely insights for further advances in developing 1D-VNS as a safe, universal, and highly scalable platform for cell engineering and enrichment in advanced cancer immunotherapy such as chimeric antigen receptor-T therapy.

Synthesis of hybrid multicomponent disklike nanoparticles

This manuscript describes the synthesis of a new generation of multicomponent disklike nanoparticles. In this work, we present for the first time, through the template-based sequential electrochemical deposition of metal/semiconductor/polymer segments, an innovative and effective method for preparing a wide range of metallic, semiconductor, and polymeric hybrid multicomponent disklike nanoparticles covering a wide and controlled dimension range from a few nanometers to hundreds of nanometers. Moreover, we can readily tailor the desired final size, aspect ratio, and composition of the disklike nanoparticles by varying the precursor material used and the electrochemical deposition approach. Furthermore, this simple route leads to a highly reproducible and high-throughput synthetic platform of new multicomponent and multifunctional nanoscale building blocks.

Fabrication of silicon nanowire arrays by near-field laser ablation and metal-assisted chemical etching

We present an elegant route for the fabrication of ordered arrays of vertically-aligned silicon nanowires with tunable geometry at controlled locations on a silicon wafer. A monolayer of transparent microspheres convectively assembled onto a gold-coated silicon wafer acts as a microlens array. Irradiation with a single nanosecond laser pulse removes the gold beneath each focusing microsphere, leaving behind a hexagonal pattern of holes in the gold layer. Owing to the near-field effects, the diameter of the holes can be at least five times smaller than the laser wavelength. The patterned gold layer is used as catalyst in a metal-assisted chemical etching to produce an array of vertically-aligned silicon nanowires. This approach combines the advantages of direct laser writing with the benefits of parallel laser processing, yielding nanowire arrays with controlled geometry at predefined locations on the silicon surface. The fabricated VA-SiNW arrays can effectively transfect human cells with a plasmid encoding for green fluorescent protein.