Photolithographic generation of protein micropatterns for neuron culture applications

DNA-POINT: DNA Patterning of Optical Imprint for Nanomaterials Topography

Engineering well-defined scale-spanning structures through transfer of diverse biomolecules and materials to a surface is of tremendous interest in life sciences research yet remains profoundly challenging. Here, we report a novel method, termed as DNA patterning of optical imprint for nanomaterials topography (DNA-POINT), for rapid photopatterning of large area, geometrically complex surfaces via light-responsive DNA. Our method employs top-down multiphoton-driven patterning of azobenzene-modified DNA strands, offering precise position control of molecules and nanoparticles along the axial plane and a template for bottom-up self-assembly of multiple layers of different chemical composition along the vertical plane. We demonstrate the surface patterning of plasmonic gold nanoparticles, fluorophore-labeled oligonucleotides, and multiple layers consisting of molecule-nanoparticle hybrid patterns into preconceived shapes without compromising on the functionality of the biomolecules. Furthermore, we exhibit scanning mode operation of DNA-POINT, thereby paving the way for maskless and cleanroom-free fast fabrication of biochips for high-throughput diagnostics and biosensing applications.

Photopolymerized Features via Beam Pen Lithography as a Novel Tool for the Generation of Large Area Protein Micropatterns

A cantilever-free scanning probe lithography (CF-SPL)-based method for the rapid polymerization of nanoscale features on a surface via crosslinking and thiol-acrylate photoreactions is described, wherein the nanoscale position, height, and diameter of each feature can be finely and independently tuned. With precise spatiotemporal control over the illumination pattern, beam pen lithography (BPL) allows for the photo-crosslinking of polymers into ultrahigh resolution features over centimeter-scale areas using massively parallel >160 000 pen arrays of individually addressable pens that guide and focus light onto the surface with sub-diffraction resolution. The photoinduced crosslinking reaction of the ink material, which is composed of photoinitiator, diphenyl(2,4,6-trimethylbenzoyl) phosphine oxide, poly(ethylene glycol) diacrylate, and thiol-modified functional binding molecules (i.e., thiol-PEG-biotin or 16-mercaptohexanoic acid), proceeds to ≈80% conversion with UV exposure (72 mW cm^-2 ) for short time periods (0.5 s). Such polymer patterns are further reacted with proteins (streptavidin and fibronectin) to yield protein arrays with feature arrangements at high resolution and densities controlled by local UV exposure. This platform, which combines polymer photochemistry and massive arrays of scanning probes, constitutes a new approach to making biomolecular microarrays in a high-throughput and high-yielding manner, opening new routes for biochip synthesis, bioscreening, and cell biology research.

Surface patterning techniques for proteins on nano- and micro-systems: a modulated aspect in hierarchical structures

The surface patterning of protein using fabrication or the external functionalization of structures demonstrates various applications in the biomedical field for bioengineering, biosensing and antifouling. This review article offers an outline of the existing advances in protein patterning technology with a special emphasis on the current physical and physicochemical methods, including stencil patterning, trap- and droplet-based microfluidics, and chemical modification of surfaces via photolithography, microcontact printing and scanning probe nanolithography. Different approaches are applied for the biological studies of recent trends for single-protein patterning technology, such as robotic printing, stencil printing and colloidal lithography, wherein the concepts of physical confinement, electrostatic and capillary forces, as well as dielectrophoretics, are summarised to understand the design approaches. Photochemical alterations with diazirine, nitrobenzyl and aryl azide functional groups for the implication of modified substrates, such as self-assembled monolayers functionalized with amino silanes, organosilanes and alkanethiols on gold surfaces, as well as topographical effects of patterning techniques for protein functionalization and orientation, are discussed. Analytical methods for the evaluation of protein functionality are also mentioned. Regarding their selectivity, protein pattering methods will be readily used to fabricate modified surfaces and target-specific delivery systems for the transportation of macromolecules such as streptavidin, and albumin. Future applications of patterning techniques include high-throughput screening, the evaluation of intracellular interactions, accurate screening and personalized treatments.

Dynamic Creation of 3D Hydrogel Architectures via Selective Swelling Programmed by Interfacial Bonding

The topological features of material surfaces are crucial to the emergence of functions based on characteristic architectures. Among them, the combination of surface architectures and soft materials, which are highly deformable and flexible, has great potential as regards developing functional materials toward providing/enhancing advanced functions such as switchability and variability. Therefore, a simple yet versatile method for creating three-dimensional (3D) architectures based on soft materials is strongly required. In this study, hydrogels are selected as the soft materials and hydrogel film/rigid substrate layer composites are fabricated to obtain a 3D hydrogel architecture based on swelling instability. When a hydrogel film weakly attached to a rigid substrate is exposed to water, swelling-driven compressive stress induces buckle-delamination of the film from the substrate. Utilizing the chemical modification of a rigid substrate and a conventional photolithography technique, the delamination location is successfully controlled, resulting in a high-aspect-ratio folding architecture at an arbitrary position. In addition, we systematically designed the delamination geometry and chemically tuned the swelling ratio of the hydrogel, leading to the discovery of several new morphology transitions and relationships between the morphologies and the controllable parameters. This work provides a new approach to fabricating highly programmable 3D architectures of soft materials.

Engineering the cellular mechanical microenvironment - from bulk mechanics to the nanoscale

The field of mechanobiology studies how mechanical properties of the extracellular matrix (ECM), such as stiffness, and other mechanical stimuli regulate cell behaviour. Recent advancements in the field and the development of novel biomaterials and nanofabrication techniques have enabled researchers to recapitulate the mechanical properties of the microenvironment with an increasing degree of complexity on more biologically relevant dimensions and time scales. In this Review, we discuss different strategies to engineer substrates that mimic the mechanical properties of the ECM and outline how these substrates have been applied to gain further insight into the biomechanical interaction between the cell and its microenvironment.

Germanium as a scalable sacrificial layer for nanoscale protein patterning

We demonstrate the use of germanium (Ge) films as water-soluble features that allow the patterning of proteins onto surfaces with commonly used organic solvents. This technique is scalable for manufacturing and is compatible with nano- and microfabrication processes, including standard lithography. We use Ge as a sacrificial layer to mask and protect areas of the substrate during surface functionalization. Since Ge dissolves in 0.35% hydrogen peroxide (H2O2) in water but not in organic solvents, Ge can be removed after patterning without significantly affecting protein activities. In this paper, we present examples of protein patterning with two different techniques. We show that 50 nm thick Ge layers can be completely removed in 10 min without residues and, importantly, nanoscale resolution and misalignment can be achieved with conventional photolithography equipment. Both biotin and streptavidin maintain ~80% and >50% activity after 10 min and 360 min incubation in 0.35% H2O2, respectively. Lastly, the process can be used to functionalize sidewalls with proteins, a capability of recent interest for cell-cell adhesion studies.

Protein patterning using germanium as a sacrificial layer

With the rise of microfluidic diagnostics, there is a need for more efficient methods of patterning surface-attached moieties, including proteins like antibodies, onto microchannel surfaces. This arises because almost all of the solvents and processes used for surface-attachment chemistries (or their payloads) are incompatible with sacrificial layers usually photoresist during microfabrication, rendering it difficult to easily pattern active chemistry onto a surface in manufacture scale. We present a simple method, based on thin film germanium dissolution, which is compatible with both modern nanolithographic techniques and surface chemistries. Simply, because germanium thin films dissolve readily, controllably and rapidly in water (but not organic solvents), these films can be used to mask and protect areas of the substrate during the attachment of surface chemistries. We demonstrate the process and results using microscale patterns. The resolution and alignment of this method depends on the photolithography tool used; nanoscale patterning is not difficult to achieve. In addition, we show that with non-conformal germanium deposition (e.g. e-beam evaporation), the conjugation of surface chemistry on vertical side walls can be manipulated by controlling the thickness of the deposited germanium layer, opening another dimension for microfluidic devices and cell manipulation research.

Interactions of Neurons with Physical Environments

Nerve growth strongly relies on multiple chemical and physical signals throughout development and regeneration. Currently, a cure for injured neuronal tissue is an unmet need. Recent advances in fabrication technologies and materials led to the development of synthetic interfaces for neurons. Such engineered platforms that come in 2D and 3D forms can mimic the native extracellular environment and create a deeper understanding of neuronal growth mechanisms, and ultimately advance the development of potential therapies for neuronal regeneration. This progress report aims to present a comprehensive discussion of this field, focusing on physical feature design and fabrication with additional information about considerations of chemical modifications. We review studies of platforms generated with a range of topographies, from micro-scale features down to topographical elements at the nanoscale that demonstrate effective interactions with neuronal cells. Fabrication methods are discussed as well as their biological outcomes. This report highlights the interplay between neuronal systems and the important roles played by topography on neuronal differentiation, outgrowth, and development. The influence of substrate structures on different neuronal cells and parameters including cell fate, outgrowth, intracellular remodeling, gene expression and activity is discussed. Matching these effects to specific needs may lead to the emergence of clinical solutions for patients suffering from neuronal injuries or brain-machine interface (BMI) applications.

Transient microfluidic compartmentalization using actionable microfilaments for biochemical assays, cell culture and organs-on-chip

We report here a simple yet robust transient compartmentalization system for microfluidic platforms. Cylindrical microfilaments made of commercially available fishing lines are embedded in a microfluidic chamber and employed as removable walls, dividing the chamber into several compartments. These partitions allow tight sealing for hours, and can be removed at any time by longitudinal sliding with minimal hydrodynamic perturbation. This allows the easy implementation of various functions, previously impossible or requiring more complex instrumentation. In this study, we demonstrate the applications of our strategy, firstly to trigger chemical diffusion, then to make surface co-coating or cell co-culture on a two-dimensional substrate, and finally to form multiple cell-laden hydrogel compartments for three-dimensional cell co-culture in a microfluidic device. This technology provides easy and low-cost solutions, without the use of pneumatic valves or external equipment, for constructing well-controlled microenvironments for biochemical and cellular assays.

Compartmentalized Platforms for Neuro-Pharmacological Research

Dissociated primary neuronal cell culture remains an indispensable approach for neurobiology research in order to investigate basic mechanisms underlying diverse neuronal functions, drug screening and pharmacological investigation. Compartmentalization, a widely adopted technique since its emergence in 1970s enables spatial segregation of neuronal segments and detailed investigation that is otherwise limited with traditional culture methods. Although these compartmental chambers (e.g. Campenot chamber) have been proven valuable for the investigation of Peripheral Nervous System (PNS) neurons and to some extent within Central Nervous System (CNS) neurons, their utility has remained limited given the arduous manufacturing process, incompatibility with high-resolution optical imaging and limited throughput. The development in the area of microfabrication and microfluidics has enabled creation of next generation compartmentalized devices that are cheap, easy to manufacture, require reduced sample volumes, enable precise control over the cellular microenvironment both spatially as well as temporally, and permit highthroughput testing. In this review we briefly evaluate the various compartmentalization tools used for neurobiological research, and highlight application of the emerging microfluidic platforms towards in vitro single cell neurobiology.

Thermochemical scanning probe lithography of protein gradients at the nanoscale

Patterning nanoscale protein gradients is crucial for studying a variety of cellular processes in vitro. Despite the recent development in nano-fabrication technology, combining nanometric resolution and fine control of protein concentrations is still an open challenge. Here, we demonstrate the use of thermochemical scanning probe lithography (tc-SPL) for defining micro- and nano-sized patterns with precisely controlled protein concentration. First, tc-SPL is performed by scanning a heatable atomic force microscopy tip on a polymeric substrate, for locally exposing reactive amino groups on the surface, then the substrate is functionalized with streptavidin and laminin proteins. We show, by fluorescence microscopy on the patterned gradients, that it is possible to precisely tune the concentration of the immobilized proteins by varying the patterning parameters during tc-SPL. This paves the way to the use of tc-SPL for defining protein gradients at the nanoscale, to be used as chemical cues e.g. for studying and regulating cellular processes in vitro.

Direct photo-patterning on anthracene containing polymer for guiding stem cell adhesion

Background

Various micropatterned surfaces capable of guiding the selective adhesion of biomolecules such as proteins and cells are of great interests in biosensor, diagnostics, drug screening, and tissue engineering. In this study, we described a simple photo-patterning method to prepare micro-patterned films for stem cell patterning using anthracene containing polymers (PMAn). This micro patterned polymer film was prepared by the facile photo-reaction of anthracene units in polymer backbone structure.

Results

The UV irradiation of PMAn through a photomask resulted in the quenching of fluorescent intensity as well as the changes in surface wettability from hydrophobic to hydrophilic surface. As a result, UV exposed regions of PMAn film show lower fluorescent intensity as well as higher proliferation rate of mesenchymal stem cells (MSCs) than unexposed region of PMAn film. Furthermore, the selective MSC attachment was clearly observed in the UV exposed regions of PMAn film.

Conclusion

We developed a simple cell patterning method with a fluorescent, biocompatible, and patternable polymer film containing anthracene units. This method provides a facile stem cell patterning method and could be extended to various patterning of biomaterials without labor-intensive preparation and no pre-treatment for complex interactions of cell-microenvironment.

Rebuilding Brain Circuitry with Living Micro-Tissue Engineered Neural Networks

Prominent neuropathology following trauma, stroke, and various neurodegenerative diseases includes neuronal degeneration as well as loss of long-distance axonal connections. While cell replacement and axonal pathfinding strategies are often explored independently, there is no strategy capable of simultaneously replacing lost neurons and re-establishing long-distance axonal connections in the central nervous system. Accordingly, we have created micro-tissue engineered neural networks (micro-TENNs), which are preformed constructs consisting of long integrated axonal tracts spanning discrete neuronal populations. These living micro-TENNs reconstitute the architecture of long-distance axonal tracts, and thus may serve as an effective substrate for targeted neurosurgical reconstruction of damaged pathways in the brain. Cerebral cortical neurons or dorsal root ganglia neurons were precisely delivered into the tubular constructs, and properties of the hydrogel exterior and extracellular matrix internal column (180-500 μm diameter) were optimized for robust neuronal survival and to promote axonal extensions across the 2.0 cm tube length. The very small diameter permits minimally invasive delivery into the brain. In this study, preformed micro-TENNs were stereotaxically injected into naive rats to bridge deep thalamic structures with the cerebral cortex to assess construct survival and integration. We found that micro-TENN neurons survived at least 1 month and maintained their long axonal architecture along the cortical-thalamic axis. Notably, we also found neurite penetration from micro-TENN neurons into the host cortex, with evidence of synapse formation. These micro-TENNs represent a new strategy to facilitate nervous system repair by recapitulating features of neural pathways to restore or modulate damaged brain circuitry.

"Click" Patterning of Self-Assembled Monolayers on Hydrogen-Terminated Silicon Surfaces and Their Characterization Using Light-Addressable Potentiometric Sensors

Two potential strategies for chemically patterning alkyne-terminated self-assembled monolayers (SAMs) on oxide-free silicon or silicon-on-sapphire (SOS) substrates were investigated and compared. The patterned surfaces were validated using a light-addressable potentiometric sensor (LAPS) for the first time. The first strategy involved an integration of photolithography with "click" chemistry. Detailed surface characterization (i.e. water contact angle, ellipsometry, AFM, and XPS) and LAPS measurements showed that photoresist processing not only decreases the coverage of organic monolayers but also introduces chemically bonded contaminants on the surfaces, thus significantly reducing the quality of the SAMs and the utility of "click" surface modification. The formation of chemical contaminants in photolithography was also observed on carboxylic acid- and alkyl-terminated monolayers using LAPS. In contrast, a second approach combined microcontact printing (μCP) with "click" chemistry; that is azide (azido-oligo(ethylene glycol) (OEG)-NH2) inks were printed on alkyne-terminated SAMs on silicon or SOS through PDMS stamps. The surface characterization results for the sample printed with a flat featureless PDMS stamp demonstrated a nondestructive and efficient method of μCP to perform "click" reactions on alkyne-terminated, oxide-free silicon surfaces for the first time. For the sample printed with a featured PDMS stamp, LAPS imaging showed a good agreement with the pattern of the PDMS stamp, indicating the successful chemical patterning on non-oxidized silicon and SOS substrates and the capability of LAPS to image the molecular patterns with high sensitivity.

Preparation of hydroxy-PAAm hydrogels for decoupling the effects of mechanotransduction cues

It is now well established that many cellular functions are regulated by interactions of cells with physicochemical and mechanical cues of their extracellular matrix (ECM) environment. Eukaryotic cells constantly sense their local microenvironment through surface mechanosensors to transduce physical changes of ECM into biochemical signals, and integrate these signals to achieve specific changes in gene expression. Interestingly, physicochemical and mechanical parameters of the ECM can couple with each other to regulate cell fate. Therefore, a key to understanding mechanotransduction is to decouple the relative contribution of ECM cues on cellular functions. Here we present a detailed experimental protocol to rapidly and easily generate biologically relevant hydrogels for the independent tuning of mechanotransduction cues in vitro. We chemically modified polyacrylamide hydrogels (PAAm) to surmount their intrinsically non-adhesive properties by incorporating hydroxyl-functionalized acrylamide monomers during the polymerization. We obtained a novel PAAm hydrogel, called hydroxy-PAAm, which permits immobilization of any desired nature of ECM proteins. The combination of hydroxy-PAAm hydrogels with microcontact printing allows to independently control the morphology of single-cells, the matrix stiffness, the nature and the density of ECM proteins. We provide a simple and rapid method that can be set up in every biology lab to study in vitro cell mechanotransduction processes. We validate this novel two-dimensional platform by conducting experiments on endothelial cells that demonstrate a mechanical coupling between ECM stiffness and the nucleus.

Micropatterning neuronal networks

A simple and effective method for patterning primary neuronal networks and circuits.

Biorecognition by DNA oligonucleotides after exposure to photoresists and resist removers

Combining biological molecules with integrated circuit technology is of considerable interest for next generation sensors and biomedical devices. Current lithographic microfabrication methods, however, were developed for compatibility with silicon technology rather than bioorganic molecules, and consequently it cannot be assumed that biomolecules will remain attached and intact during on-chip processing. Here, we evaluate the effects of three common photoresists (Microposit S1800 series, PMGI SF6, and Megaposit SPR 3012) and two photoresist removers (acetone and 1165 remover) on the ability of surface-immobilized DNA oligonucleotides to selectively recognize their reverse-complementary sequence. Two common DNA immobilization methods were compared: adsorption of 5'-thiolated sequences directly to gold nanowires and covalent attachment of 5'-thiolated sequences to surface amines on silica coated nanowires. We found that acetone had deleterious effects on selective hybridization as compared to 1165 remover, presumably due to incomplete resist removal. Use of the PMGI photoresist, which involves a high temperature bake step, was detrimental to the later performance of nanowire-bound DNA in hybridization assays, especially for DNA attached via thiol adsorption. The other three photoresists did not substantially degrade DNA binding capacity or selectivity for complementary DNA sequences. To determine whether the lithographic steps caused more subtle damage, we also tested oligonucleotides containing a single base mismatch. Finally, a two-step photolithographic process was developed and used in combination with dielectrophoretic nanowire assembly to produce an array of doubly contacted, electrically isolated individual nanowire components on a chip. Postfabrication fluorescence imaging indicated that nanowire-bound DNA was present and able to selectively bind complementary strands.

Specific immobilization of biotinylated fusion proteins NGF and Sema3A utilizing a photo-cross-linkable diazirine compound for controlling neurite extension

In this study we report the successful synthesis of N-(2-mercaptoethyl)-3-(3-methyl-3H-diazirine-3-yl) propanamide (N-MCEP-diazirine), with sulfhydryl and amine photoreactive ends to allow recombinant protein tethering to chitosan films. This regimen allows mimicry of the physiological endeavor of axon pathfinding in the nervous system where neurons rely on cues for guidance during development and regeneration. Our strategy incorporates strong covalent and noncovalent interactions, utilizing N-MCEP-diazirine, maleimide-streptavidin complex, and two custom biotinylated-fusion proteins, nerve growth factor (bNGF), and semaphorin3A (bSema3A). Synthetic yield of N-MCEP-diazirine was 87.3 ± 1.9%. Characteristic absorbance decrease at 348 nm after N-MCEP-diazirine exposure to UV validated the photochemical properties of the diazirine moiety, and the attachment of cross-linker to chitosan films was verified with Fourier transform infrared spectroscopy (FTIR). Fluorescence techniques showed no significant difference in the detection of immobilized proteins compared to absorbing the proteins to films (p < 0.05); however, in vitro outgrowth of dorsal root ganglia (DRG) was more responsive to immobilized bNGF and bSema3A compared to adsorbed bNGF and bSema3A over a 5 day period. Immobilized bNGF significantly increased DRG length over time (p < 0.0001), but adsorbed bNGF did not increase in axon extension from day 1 to day 5 (p = 0.4476). Immobilized bSema3A showed a significant decrease in neurite length (524.42 ± 57.31 μm) at day 5 compared to adsorbed bSema3A (969.13 ± 57.31 μm). These results demonstrate the superiority of our immobilization approach to protein adsorption because biotinylated-fusion proteins maintain their active confirmation and their tethering can be spatially controlled via a UV activated N-MCEP-diazirine cross-linker.

Mobile and three-dimensional presentation of adhesion proteins within microwells

On traditional cell culture substrates cells adhere to a planar 2D surface where ligands are presented immobile. A more realistic presentation of cell adhesion ligands which can account for lateral mobility and a more tissue-like 3D presentation would allow studies addressing fundamental questions of significant importance for applications such as tissue engineering and implant intregration. To study the effect of lateral mobility of cell membrane interaction cues in three dimensions, we have developed and characterized a platform which generically enables patterning of single cells into microwells presenting a cell membrane mimetic interface pre-patterned to its walls. Here, we describe its application in presenting a soluble cell adhesive ligand coupled through streptavidin-antibody linkage to lipids in a supported lipid bilayer (SLB) coated microwell. The lateral mobility of the presented ligands was controlled through a small change in temperature. The SLB phospholipid composition was choosen such that below its melting transition at 30 °C the ligands are immobile, while above 30 °C they are laterally mobile. The platform thus enables the investigation of cell adhesion to either laterally immobile or mobile E-cadherin ligand presented on the same cell membrane mimetic surface.

Microfluidic impact printer with interchangeable cartridges for versatile non-contact multiplexed micropatterning

Biopatterning has been increasingly used for well-defined cellular microenvironment, patterned surface topology, and guided biological cues; however, it meets challenges on biocompatibility, thermal and chemical sensitivity, as well as limited availability of reagents. In this paper, we aim at combining the desired features from non-contact inkjet printing and dot-matrix impact printing to establish a versatile multiplexed micropatterning platform, referred to as Microfluidic Impact Printer (MI-Printer), for emerging biomedical applications. Using this platform, we can achieve the distinct features of no cross-contamination, sub-microliter ink loading with a minimal dead volume, high-throughput printing, biocompatible non-contact processing, sequential patterning with self-alignment, wide adaptability for complex media (e.g., cell suspension or colloidal solutions), interchangeable/disposable cartridge design, and simple assembly and configuration, all highly desirable towards laboratory-based research and development. Specifically, the printing resolution of the MI-printer platform has been experimentally characterized and theoretically analysed. Optimal printing resolution of 80 μm has been repeatedly obtained. Furthermore, two useful functions of the MI-printer, multiplexed printing and combinatorial printing, have been experimentally demonstrated with less than 10 μm misalignment. Moreover, molecular and biological patterning, utilizing the multiplexed and combinatorial printing, has been implemented to illustrate the utility of this versatile printing technique for emerging biomedical applications.

Self-sorting click reactions that generate spatially controlled chemical functionality on surfaces

This Article describes the generation of a patterned surface that can be postpolymerization modified to incorporate fragile macromolecules or delicate biomolecules without the need for special equipment. Two monomers that undergo different click reactions, pentafluorophenyl acrylate (PFPA) and 4-(trimethylsilyl) ethynylstyrene (TMSES), were sequentially polymerized from a silicon surface in the presence of a shadowmask with UV light, generating 12.5 and 62 μm pitch patterns. Two different dyes, 1-aminomethylpyrene (AMP) and 5-azidofluorescein (AF), were covalently attached to the polymer brushes through aminolysis and dual desilylation/copper(I)-catalyzed alkyne/azide cycloaddition (CuAAC) in one pot. Unlike most CuAAC reactions, the terminal alkyne of TMSES was not deprotected prior to functionalization. Although a 2 nm thickness increase was observed for poly(PFPA) brushes after polymerization of TMSES, cross-contamination was not visible through fluorescence microscopy after functionalization.

A simple route to functionalize polyacrylamide hydrogels for the independent tuning of mechanotransduction cues

Physico-chemical and biochemical factors in the local cellular microenvironment are known to impact on multiple aspects of cell behaviour through specific signal pathways. These mechanotransduction cues can couple each other to regulate cell fate, and it remains unclear whether mechanotransduction in different contexts shares common mechanisms. Undoubtedly, a challenge will involve the further characterization of such cooperative mechanisms, as well as clearly defining the individual role of each mechanical and biochemical parameter. To control these mechanotransduction cues in an independent manner, we developed a simple and efficient strategy to immobilize any desired nature of proteins on polyacrylamide hydrogels and independently control various parameters of the cell microenvironment, such as matrix stiffness, cell-binding ligand density and confined adhesiveness. This novel platform is validated by conducting single-cell experiments and opens a broad avenue for studying complex interplays involved in mechanotransduction with a facile and versatile approach.

Characterization of freestanding photoresist films for biological and MEMS applications

Photoresists are light-sensitive resins used in a variety of technological applications. In most applications, however, photoresists are generally used as sacrificial layers or a structural layer that remains on the fabrication substrate. Thin layers of patterned 1002F photoresist were fabricated and released to form a freestanding film. Films of thickness in the range of 4.5-250 μm were patterned with through-holes to a resolution of 5 μm and an aspect ratio of up to 6:1. Photoresist films could be reliably released from the substrate after a 12-hour immersion in water. The Young's modulus of a 50 μm-thick film was 1.43 ± 0.20 GPa. Use of the films as stencils for patterning sputtered metal onto a surface was demonstrated. These 1002F stencils were used multiple times without deterioration in feature quality. Furthermore, the films provided biocompatible, transparent surfaces of low autofluorescence on which cells could be grown. Culture of cells on a film with an isolated small pore enabled a single cell to be accessed through the underlying channel and loaded with exogenous molecules independently of nearby cells. Thus 1002F photoresist was patterned into thin, flexible, free-standing films that will have numerous applications in the biological and MEMS fields.

Effects of molecular size and surface hydrophobicity on oligonucleotide interfacial dynamics

Single-molecule total internal reflection fluorescence microscopy was used to observe the dynamic behavior of polycytosine single-stranded DNA (ssDNA) (1-50 nucleotides long) at the interface between aqueous solution and hydrophilic (oligoethylene glycol-modified fused silica, OEG) and hydrophobic (octadecyltriethoxysilane-modified fused silica, OTES) solid surfaces. High throughput molecular tracking was used to determine >75,000 molecular trajectories for each molecular length, which were then used to calculate surface residence time and squared displacement (i.e., "step-size") distributions. On hydrophilic OEG surfaces, the surface residence time increased systematically with ssDNA chain length, as expected due to increasing molecule-surface interactions. Interestingly, the residence time decreased with increasing ssDNA length on the hydrophobic OTES surface, particularly for longer chains. Similarly, the interfacial mobility of polynucleotides slowed with increasing chain length on OEG, but became faster on OTES. On OTES surfaces, the rates associated with desorption and surface diffusion exhibited the distinctive anomalous temperature dependence that is characteristic of hydrophobic interactions for short-chain species but not for longer chains. These combined observations suggest that long oligonucleotides adopt conformations minimizing hydrophobic interactions, e.g., by internal sequestration of hydrophobic nucleobases.

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.

Maskless projection lithography for the fast and flexible generation of grayscale protein patterns

Protein patterns of different shapes and densities are useful tools for studies of cell behavior and to create biomaterials that induce specific cellular responses. Up to now the dominant techniques for creating protein patterns are mostly based on serial writing processes or require templates such as photomasks or elastomer stamps. Only a few of these techniques permit the creation of grayscale patterns. Herein, the development of a lithography system using a digital mirror device which allows fast patterning of proteins by immobilizing fluorescently labeled molecules via photobleaching is reported. Grayscale patterns of biotin with pixel sizes in the range of 2.5 μm are generated within 10 s of exposure on an area of about 5 mm(2) . This maskless projection lithography method permits the rapid and inexpensive generation of protein patterns definable by any user-defined grayscale digital image on substrate areas in the mm(2) to cm(2) range.

Neural regenerative strategies incorporating biomolecular axon guidance signals

There are currently no acceptable cures for central nervous system injuries, and damage induced large gaps in the peripheral nervous system have been challenging to bridge to restore neural functionality. Innervation by neurons is made possible by the growth cone. This dynamic structure is unique to neurons, and can directly sense physical and chemical activity in its environment, utilizing these cues to propel axons to precisely reach their targets. Guidance can occur through chemoattractive factors such as neurotrophins and netrins, chemorepulsive agents like semaphorins and slits, or contact-mediated molecules such as ephrins and those located in the extracellular matrix. The understanding of biomolecular activity during nervous system development and injury has generated new techniques and tactics for improving and restoring function to the nervous system after injury. This review will focus on the major neuronal guidance molecules and their utility in current tissue engineering and neural regenerative strategies.

Combination of integrin-binding peptide and growth factor promotes cell adhesion on electron-beam-fabricated patterns

Understanding and controlling cell adhesion on engineered scaffolds is important in biomaterials and tissue engineering. In this report we used an electron-beam (e-beam) lithography technique to fabricate patterns of a cell adhesive integrin ligand combined with a growth factor. Specifically, micron-sized poly(ethylene glycol) (PEG) hydrogels with aminooxy- and styrene sulfonate-functional groups were fabricated. Cell adhesion moieties were introduced using a ketone-functionalized arginine-glycine-aspartic acid (RGD) peptide to modify the O-hydroxylamines by oxime bond formation. Basic fibroblast growth factor (bFGF) was immobilized by electrostatic interaction with the sulfonate groups. Human umbilical vein endothelial cells (HUVECs) formed focal adhesion complexes on RGD- and RGD and bFGF-immobilized patterns as shown by immunostaining of vinculin and actin. In the presence of both bFGF and RGD, cell areas were larger. The data demonstrate confinement of cellular focal adhesions to chemically and physically well-controlled microenvironments created by a combination of e-beam lithography and "click" chemistry techniques. The results also suggest positive implications for addition of growth factors into adhesive patterns for cell-material interactions.

High fidelity neuronal networks formed by plasma masking with a bilayer membrane: analysis of neurodegenerative and neuroprotective processes

Spatially defined neuronal networks have great potential to be used in a wide spectrum of neurobiology assays. We present an original technique for the precise and reproducible formation of neuronal networks. A PDMS membrane comprising through-holes aligned with interconnecting microchannels was used during oxygen plasma etching to dry mask a protein rejecting poly(ethylene glycol) (PEG) adlayer. Patterns were faithfully replicated to produce an oxidized interconnected array pattern which supported protein adsorption. Differentiated human SH-SY5Y neuron-like cells adhered to the array nodes with the micron-scale interconnecting tracks guiding neurite outgrowth to produce neuronal connections and establish a network. A 2.0 μm track width was optimal for high-level network formation and node compliance. These spatially standardized neuronal networks were used to analyse the dynamics of acrylamide-induced neurite degeneration and the protective effects of co-treatment with calpeptin or brain derived neurotrophic factor (BDNF).

Large-area protein patterns generated by ordered binary colloidal assemblies as templates

We demonstrate the use of binary colloidal assemblies as lithographic masks to generate tunable Au patterns on SiO(2) substrates with dimensions ranging from micrometers to nanometers. Such patterns can be modified with different chemistries to create patterns with well-defined sites for selective adsorption of proteins, where the pattern size and spacing is adjustable depending on particle choice. In our system, the binary colloidal assemblies contain large and small particles of similar or different material and are self-assembled from dilute dispersions with particle size ratios ranging from 0.10 to 0.50. This allows masks with variable morphology and thus production of chemical patterns of tunable geometry. Finally, the Au or SiO(2) regions of the pattern are surface modified with protein resistant oligoethyleneglycol self-assembled molecules, which facilitates site selective adsorption of proteins into the unmodified regions of the pattern. This we show with fluorescently labeled bovine serum albumin.

Single-molecule resolution of interfacial fibrinogen behavior: effects of oligomer populations and surface chemistry

Through the use of single-molecule total internal reflection fluorescence microscopy, the dynamic behavior of fibrinogen was observed at the interface between aqueous solution and various solid surfaces. Multiple populations of objects were observed, as characterized by surface residence times, interfacial diffusion, and fluorescence intensity. On all surfaces, populations exhibited direct links between surface residence time, rate of diffusion, and fluorescence intensity. In particular, longer-lived populations diffused more slowly and exhibited greater fluorescence intensity, leading to the conclusion that the objects represented fibrinogen monomers and discrete oligomer populations (dimers, trimers, etc.), and that these oligomer populations play an important role in the protein-surface interaction because of their long surface residence times. Two or three diffusive modes were observed for most populations, indicating that protein aggregates have multiple mechanisms for interaction with solid substrates. In addition, the fastest diffusive mode is believed to represent a hopping mode that often precedes desorption events. Surprisingly, a monolayer of 5000 Da poly(ethylene glycol) (PEG5000) increased surface residence time and slowed diffusion of fibrinogen relative to bare fused silica or hydrophobically modified fused silica, suggesting that the mechanism of PEG resistance to protein adhesion is more sophisticated than the simple repulsion of individual proteins.

Photopatterning of cell-adhesive-modified poly(ethyleneimine) for guided neuronal growth

We describe photopatterning technique that employs the photodegradation of cell-adhesive-modified poly(ethyleneimine) (m-PEI) to fabricate precise micropatterns on the indium tin oxide (ITO) substrate for guided neuronal growth. The photodegradation of m-PEI coated on hydroxyl group-terminated ITO substrate created micropatterns over a large area through deep UV irradiation. The photopatterned m-PEI layer can effectively guide neurite outgrowth and control neurite extensions from individual neurons.

Microwell device for targeting single cells to electrochemical microelectrodes for high-throughput amperometric detection of quantal exocytosis

Electrochemical microelectrodes are commonly used to detect spikes of amperometric current that correspond to exocytosis of oxidizable transmitter from individual vesicles, i.e., quantal exocytosis. We are developing transparent multielectrochemical electrode arrays on microchips in order to automate measurement of quantal exocytosis. Here, we report development of an improved device to target individual cells to each microelectrode in an array. Efficient targeting (~75%) is achieved using cell-sized microwell traps fabricated in SU-8 photoresist together with patterning of poly(l-lysine) in register with electrodes to promote cell adhesion. The surface between electrodes is made resistant to cell adhesion using poly(ethylene glycol) in order to facilitate movement of cells to electrode "docking sites". We demonstrate the activity of the electrodes using the test analyte ferricyanide and perform recordings of quantal exocytosis from bovine adrenal chromaffin cells on the device. Multiple cell recordings on a single device demonstrate the consistency of spike measurements, and multiple recordings from the same electrodes demonstrate that the device can be cleaned and reused without degradation of performance. The new device will enable high-throughput studies of quantal exocytosis and may also find application in rapidly screening drugs or toxins for effects on exocytosis.

UV-induced grafting processes with in situ formed photomask for micropatterning of two-component biomolecules

We report a photolithographic process for micropatterning of two-component biomolecules on a transparent organic film via lateral functional polymer brushes of poly(sodium acrylate) (P(AA)) and poly(glycidyl methacrylate) (P(GMA)). The pattern of binary polymer brushes were prepared via consecutive UV-initiated grafting processes, under the assistance of the in situ formed poly (4,4'-bi[N-(4-vinylbenzyl) pyridinium]) (P(BVV)) photomask. The epoxy groups of the P(GMA) microdomains can be aminated for covalently coupling biotin, while the P(AA) microdomains were used for immobilizing immunoglobulin (IgG). The resulting biotin- and IgG-coupled microdomains interact specifically with their corresponding target proteins, avidin and anti-IgG, respectively.

Biomolecule patterning on analytical devices: a microfabrication-compatible approach

The present work describes a methodology for patterning biomolecules on silicon-based analytical devices that reconciles 3-D biological functionalization with standard resist lift-off techniques. Unlike classic sol-gel approaches in which the biomolecule of interest is introduced within the sol mixture, a two-stage scenario has been developed. It consists first of patterning micrometer/submicrometer polycondensate scaffold structures, using classic microfabrication tools, that are then loaded with native biomolecules via a second simple incubation step under biologically friendly environmental conditions. The common compatibility issue between the biological and microfabrication worlds has been circumvented because native recognition biomolecules can be introduced into the host scaffold downstream from all compatibility issues. The scaffold can be generated on any silicon substrate via the polycondensation of aminosilane, namely, aminopropyltriethoxy silane (APTES), under conditions that are fully compatible with resist mask lithography. The scaffold porosity and high primary amine content allow proteins and nucleic acid sequences to penetrate the polycondensate and to interact strongly, thus giving rise to micrometer/submicrometer 3-D structures exhibiting high biological activity. The integration of such a biopatterning approach in the microfabrication process of silicon analytical devices has been demonstrated via the successful completion of immunoassays and nucleic acid assays.