Bio-Microarray Fabrication Techniques—A Review

(Micro)managing the mechanical microenvironment

Mechanical forces are critical components of the cellular microenvironment and play a pivotal role in driving cellular processes in vivo. Dissecting cellular responses to mechanical forces is challenging, as even "simple" mechanical stimulation in vitro can cause multiple interdependent changes in the cellular microenvironment. These stimuli include solid deformation, fluid flows, altered physical and chemical surface features, and a complex transfer of loads between the various interacting components of a biological culture system. The active mechanical and biochemical responses of cells to these stimuli in generating internal forces, reorganizing cellular structures, and initiating intracellular signals that specify cell fate and remodel the surrounding environment further complicates cellular response to mechanical forces. Moreover, cells present a non-linear response to combinations of mechanical forces, materials, chemicals, surface features, matrix properties and other effectors. Microtechnology-based approaches to these challenges can yield key insights into the mechanical nature of cellular behaviour, by decoupling stimulation parameters; enabling multimodal control over combinations of stimuli; and increasing experimental throughput to systematically probe cellular response. In this critical review, we briefly discuss the complexities inherent in the mechanical stimulation of cells; survey and critically assess the applications of present microtechnologies in the field of experimental mechanobiology; and explore opportunities and possibilities to use these tools to obtain a deeper understanding of mechanical interactions between cells and their environment.

Micropatterns of double-layered nanofiber scaffolds with dual functions of cell patterning and metabolite detection

This paper describes the development of multi-functional nanofiber scaffolds consisting of multiple layers of nanofiber scaffolds and nanofiber-incorporated poly(ethylene glycol) (PEG) hydrogels. As a proof-of-concept demonstration, we fabricated micropatterned polymeric nanofiber scaffolds that were capable of simultaneously generating cellular micropatterns within a biomimetic environment and detecting cellular metabolic products within well-defined microdomains. To achieve this goal, we designed nanofiber scaffolds with both vertical and lateral microdomains. Vertically heterogeneous structures that were responsible for multi-functionality were realized by preparing double-layered nanofiber scaffolds consisting of an antibody-immobilized bottom layer of nanofibers and an upper layer of bare polystyrene (PS) nanofibers by a two-step sequential electrospinning process. Photopatterning of poly(ethylene glycol) (PEG) hydrogel on the electrospun nanofibers produced laterally heterogeneous micropatterned nanofiber scaffolds made of hydrogel microwells filled with a nanofibrous region, which is capable of generating cell and protein micropatterns due to the different interactions that cells and proteins have with PEG hydrogels and nanofibers. When HepG2 cells were seeded into resultant nanofiber scaffolds, cells selectively adhered within the 200 μm × 200 μm PS fiber microdomain and formed 180.2 ± 6.7 μm spheroids after 5 days of culture in the upper layer. Furthermore, immobilized anti-albumin in the bottom layer detected albumin secreted by micropatterned HepG2 cells with higher sensitivity than flat PS substrates, demonstrating successful accomplishment of dual functions using micropatterned double-layered nanofiber scaffolds.

A robotics platform for automated batch fabrication of high density, microfluidics-based DNA microarrays, with applications to single cell, multiplex assays of secreted proteins

Microfluidics flow-patterning has been utilized for the construction of chip-scale miniaturized DNA and protein barcode arrays. Such arrays have been used for specific clinical and fundamental investigations in which many proteins are assayed from single cells or other small sample sizes. However, flow-patterned arrays are hand-prepared, and so are impractical for broad applications. We describe an integrated robotics/microfluidics platform for the automated preparation of such arrays, and we apply it to the batch fabrication of up to eighteen chips of flow-patterned DNA barcodes. The resulting substrates are comparable in quality with hand-made arrays and exhibit excellent substrate-to-substrate consistency. We demonstrate the utility and reproducibility of robotics-patterned barcodes by utilizing two flow-patterned chips for highly parallel assays of a panel of secreted proteins from single macrophage cells.

Controlled density patterning of tolylterpyridine-tagged oligonucleotides

An efficient surface anchoring strategy of tolylterpyridine-tagged DNA single strands (ssDNA-ttpy) synthesized on gold electrodes is reported. The method is based on exchange reactions between Fe(II)bis-terpyridine complexed SAMs and ssDNA-ttpy, and allows efficient hybrydization of the cDNA strands. Moreover, by using low-current focused ion beam lithography, micropatterned arrays are obtained, homogeneously covered with ssDNA-ttpy. The surface adsorption kinetics of ssDNA-ttpy, as well as its hybridization efficiency, was monitored by in situ quartz crystal microbalance with dissipation monitoring (QCM-D) technique. The effective confinement of the ssDNA-ttpy at the micrometer level has been monitored by time of flight secondary ion mass spectrometry (ToF-SIMS) and ellipsometric surface imaging experiments, providing laterally resolved chemical and topographic mapping.

Review of transducer principles for label-free biomolecular interaction analysis

Label-free biomolecular interaction analysis is an important technique to study the chemical binding between e.g., protein and protein or protein and small molecule in real-time. The parameters obtained with this technique, such as the affinity, are important for drug development. While the surface plasmon resonance (SPR) instruments are most widely used, new types of sensors are emerging. These developments are generally driven by the need for higher throughput, lower sample consumption or by the need of complimentary information to the SPR data. This review aims to give an overview about a wide range of sensor transducers, the working principles and the peculiarities of each technology, e.g., concerning the set-up, sensitivity, sensor size or required sample volume. Starting from optical technologies like the SPR and waveguide based sensors, acoustic sensors like the quartz crystal microbalance (QCM) and the film bulk acoustic resonator (FBAR), calorimetric and electrochemical sensors are covered. Technologies long established in the market are presented together with those newly commercially available and with technologies in the early development stage. Finally, the commercially available instruments are summarized together with their sensitivity and the number of sensors usable in parallel and an outlook for potential future developments is given.

Graft copolymer-templated mesoporous TiO(2) films micropatterned with poly(ethylene glycol) hydrogel: novel platform for highly sensitive protein microarrays

In this study, we describe the use of organized mesoporous titanium oxide (TiO(2)) films as three-dimensional templates for protein microarrays with enhanced protein loading capacity and detection sensitivity. Multilayered mesoporous TiO(2) films with high porosity and good connectivity were synthesized using a graft copolymer consisting of a poly(vinyl chloride) (PVC) backbone and poly(oxyethylene methacrylate) (POEM) side chains as a structure-directing template. The average pore size and thickness of the TiO(2) films were 50-70 nm and 1.5 μm, respectively. Proteins were covalently immobilized onto mesoporous TiO(2) film via 3-aminopropyltriethoxysilane (APTES), and protein loading onto TiO(2) films was about four times greater than on planar glass substrates, which consequently improved the protein activity. Micropatterned mesoporous TiO(2) substrates were prepared by fabricating poly(ethylene glycol) (PEG) hydrogel microstructures on TiO(2) films using photolithography. Because of non-adhesiveness of PEG hydrogel towards proteins, proteins were selectively immobilized onto surface-modified mesoporous TiO(2) region, creating protein microarray. Specific binding assay between streptavidin/biotin and between PSA/anti-PSA demonstrated that the mesoporous TiO(2)-based protein microarrays yielded higher fluorescence signals and were more sensitive with lower detection limits than microarrays based on planar glass slides.

Microfluidic devices for bioapplications

Harnessing the ability to precisely and reproducibly actuate fluids and manipulate bioparticles such as DNA, cells, and molecules at the microscale, microfluidics is a powerful tool that is currently revolutionizing chemical and biological analysis by replicating laboratory bench-top technology on a miniature chip-scale device, thus allowing assays to be carried out at a fraction of the time and cost while affording portability and field-use capability. Emerging from a decade of research and development in microfluidic technology are a wide range of promising laboratory and consumer biotechnological applications from microscale genetic and proteomic analysis kits, cell culture and manipulation platforms, biosensors, and pathogen detection systems to point-of-care diagnostic devices, high-throughput combinatorial drug screening platforms, schemes for targeted drug delivery and advanced therapeutics, and novel biomaterials synthesis for tissue engineering. The developments associated with these technological advances along with their respective applications to date are reviewed from a broad perspective and possible future directions that could arise from the current state of the art are discussed.

Quantitative analysis of phosphoproteins using microspot immunoassays

Protein microarrays are an ideal technology platform which allow for a robust and standardized profiling of the cellular proteome. Many cellular functions are not simply controlled by the presence of certain proteins, especially the propagation of external stimuli, which depend on transient post-translational modifications that determine whether a protein is in its active or inactive state. Thus, complex biological processes require the availability of a sound set of quantitative and time-resolved measurements to be understood. For this reason, new assay platforms which allow for the investigation of several proteins in parallel are necessary. The current best understood mode of cellular regulation occurs via phosphorylation and dephosphorylation processes, which are mediated via a large panel of kinases and phosphatases. The microspot immunoassay technique described here allows for an exact determination of several different phosphorylated proteins in parallel, as well as from small sample amounts, and is therefore an appropriate system to deepen the understanding of the complex regulatory networks implicated in health and disease.

Generation of protein and cell microarrays on functionalized surfaces

The technique of selective immobilization of biomolecules in defined positions or areas using a simple procedure is essential for various applications such as biosensors, biochips, biomedical microdevices, and tissue engineering. For the generation of biomolecule microarrays, it is necessary to develop a functional surface retaining protein functionality and cell viability, and an efficient patterning tool having flexibility of size and shape. In this chapter, we have presented the simple tools of protein and cell microarray based on functionalized surface such as a spotting method with improvement of protein functionality, a functionalized silicon-based surface using photolithography, and an orthogonally polyelectrolyte-coated surface based on soft-lithography.

Whole-cell biochips for bio-sensing: integration of live cells and inanimate surfaces

Recent advances in the convergence of the biological, chemical, physical, and engineering sciences have opened new avenues of research into the interfacing of diverse biological moieties with inanimate platforms. A main aspect of this field, the integration of live cells with micro-machined platforms for high throughput and bio-sensing applications, is the subject of the present review. These unique hybrid systems are configured in a manner that ensures positioning of the cells in designated patterns, and enables cellular viability maintenance, and monitoring of cellular functionality. Here we review both animate and inanimate surface properties and how they affect cellular attachment, describe relevant modifications of both types of surfaces, list technologies for platform engineering and for cell deposition in the desired configurations, and discuss the influence of various deposition and immobilization methods on the viability and performance of the immobilized cells.

Microfluidic DNA microarray analysis: a review

Microarray DNA hybridization techniques have been used widely from basic to applied molecular biology research. Generally, in a DNA microarray, different probe DNA molecules are immobilized on a solid support in groups and form an array of microspots. Then, hybridization to the microarray can be performed by applying sample DNA solutions in either the bulk or the microfluidic manner. Because the immobilized probe DNA binds and retains its complementary target DNA, detection is achieved through the read-out of the tagged markers on the sample target molecules. The recent microfluidic hybridization method shows the advantages of less sample usage and reduced incubation time. Here, sample solutions are confined in microfabricated channels and flow through the probe microarray area. The high surface-to-volume ratio in microchannels of nanolitre volume greatly enhanced the sensitivity as obtained with the bulk solution method. To generate nanolitre flows, different techniques have been developed, and this including electrokinetic control, vacuum suction and syringe pumping. The latter two are pressure-driven methods which are more flexible without the need of considering the physicochemical properties of solutions. Recently, centrifugal force is employed to drive liquid movement in microchannels. This method utilizes the body force from the liquid itself and there are no additional solution interface contacts such as from electrodes or syringes and tubing. Centrifugal force driven flow also features the ease of parallel hybridizations. In this review, we will summarize the recent advances in microfluidic microarray hybridization and compare the applications of various flow methods.

Unconventional low-cost fabrication and patterning techniques for point of care diagnostics

The potential of rapid, quantitative, and sensitive diagnosis has led to many innovative ‘lab on chip’ technologies for point of care diagnostic applications. Because these chips must be designed within strict cost constraints to be widely deployable, recent research in this area has produced extremely novel non-conventional micro- and nano-fabrication innovations. These advances can be leveraged for other biological assays as well, including for custom assay development and academic prototyping. The technologies reviewed here leverage extremely low-cost substrates and easily adoptable ways to pattern both structural and biological materials at high resolution in unprecedented ways. These new approaches offer the promise of more rapid prototyping with less investment in capital equipment as well as greater flexibility in design. Though still in their infancy, these technologies hold potential to improve upon the resolution, sensitivity, flexibility, and cost-savings over more traditional approaches.

Recent advances in DNA-based directed assembly on surfaces

In the last decade, "small" and "integrated" have been keywords in the field of device fabrication as the desire to exploit nanoscale phenomena and make electronic, photonic and magnetic arrays has grown. In an effort to improve resolution and control costs, much work has been dedicated to developing alternatives to conventional microfabrication technology. For this purpose, biomolecular assembly and DNA nanotechnology in particular are appealing owing to their inherent size and capacity for molecular recognition. Herein, we review recent achievements in DNA-based directed assembly on substrates. These include novel methods for patterning and depositing nanomaterials on DNA-modified surfaces as well as using synthetic DNA nanostructures such as DNA tiles and origami as templates to direct the assembly of nanoscale components. Particular attention is paid to integrating self-assembly with top-down lithography, and some possible directions for future work are discussed.

Substrate independent assembly of optical structures guided by biomolecular interactions

The chip-scale integration of optical components is crucial for technologies as diverse as optical communications, optoelectronics displays, and photovoltaics. However, the realization of integrated optical devices from discrete components is often hampered by the lack of a universal substrate for achieving monolithic integration and by incompatibilities between materials. Emergent technologies such as chip-scale biophotonics, organic optoelectronics, and optofluidics present a host of new challenges for optical device integration, which cannot be solved with existing bonding techniques. Here, we report a new method for substrate independent integration of dissimilar optical components by way of biological recognition-directed assembly. Bonding in this scheme is achieved by locally modifying the substrate with a protein receptor and the optical component with a biomolecular ligand or vice versa. The key features of this new technology include substrate independent assembly, cross-platform vertical scale integration, and selective registration of components based on complementary biomolecular interactions.

Interface design and multiplexed analysis with surface plasmon resonance (SPR) spectroscopy and SPR imaging

Ever since the advent of surface plasmon resonance (SPR) and SPR imaging (SPRi) in the early 1990s, their use in biomolecular interaction analysis (BIA) has expanded phenomenally. An important research area in SPR sensor development is the design of novel and effective interfaces that allow for the probing of a variety of chemical and biological interactions in a highly selective and sensitive manner. A well-designed and robust interface is a necessity to obtain both accurate and pertinent biological information. This review covers the recent research efforts in this area with a specific focus towards biointerfaces, new materials for SPR biosensing, and novel array designs for SPR imaging. Perspectives on the challenges ahead and next steps for SPR technology are discussed.

High throughput surface characterization: A review of a new tool for screening prospective biomedical material arrays

The application of high throughput surface characterization (HTSC) to the analysis of polymeric biomaterial libraries is an important advancement for the discovery and development of new biomedical materials and is the focus of this review. The potential for HTSC to identify structure/activity relationships for large libraries of materials can be utilized to accelerate materials discovery as well as providing insight into the underlying biological-material interactions. Furthermore, the correlations identified between surface chemical structure and cellular behavior could not have been predicted by a rational design approach based simply on review of bulk structure, which demonstrates the importance of HTSC in the assessment of cell-material and cell-biomolecular interactions that are dependent on surface properties.

NanoProbeArrays for the analysis of ultra-low-volume protein samples using piezoelectric liquid dispensing technology

Antibody microarrays are gaining popularity as a high-throughput technology to investigate the proteome. However, protein extracts from most body fluid or biopsy samples are available in very small volumes and are often unsuitable for large-scale antibody microarray studies. To demonstrate the potential for protein analysis with as little as a few nanoliters of sample, we have developed a new technology called NanoProbeArrays based on piezoelectric liquid dispensing for non-contact printing and probing of antibody arrays. Instead of flooding the protein sample on the antibody microarray surface, as in conventional microarray screening, a piezoelectric inkjet printer is used to dispense nanoliters of fluorescently labeled proteins over the antibody spots on the array. The ability of NanoProbeArrays to precisely identify and reliably distinguish between test proteins from different sources, without any loss of sensitivity and specificity as compared with conventional antibody microarrays, is illustrated here. The utility of NanoProbeArrays for biomarker identification in a complex biological sample was tested by detecting the cytokine interleukin-4 in serum. The significant reduction in volume of sample during NanoProbeArray analysis, as compared with conventional antibody microarrays, offers new opportunities for basic and applied proteomic research.

Novel concept microarray enabling PCR and multistep reactions through pipette-free aperture-to-aperture parallel transfer

Background

The microarray has contributed to developing the omic analysis. However, as it depends basically on the surface reaction, it is hard to perform bulk reactions and sequential multistep reactions. On the other hand, the popular microplate technology, which has a great merit of being able to perform parallel multistep reactions, has come to its limit in increasing the number of wells (currently, up to 9600) and reducing the volume to deal with due to the difficulty in operations.

Results

Here, we report a novel microarray technology which enables us to explore advanced applications, termed microarray-with-manageable volumes (MMV). The technical essence is in the pipette-free direct parallel transfer from well to well performed by centrifugation, evading the evaporation and adsorption-losses during handling. By developing the MMV plate, accompanying devices and techniques, generation of multiple conditions (256 kinds) and performance of parallel multistep reactions, including PCR and in vitro translation reactions, have been made possible. These were demonstrated by applying the MMV technology to searching lysozyme-crystallizing conditions and selecting peptides aimed for Aβ-binding or cathepsin E-inhibition.

Conclusions

With the introduction of a novel concept microarray (MMV) technology, parallel and multistep reactions in sub-μL scale have become possible.

On-chip immunoassay using electrostatic assembly of streptavidin-coated bead micropatterns

We propose an original concept for a sandwich immunoassay that is completely performed on-chip using streptavidin-coated beads as substrate. The latter are electrostatically self-assembled on aminosilane micropatterns at the bottom of a microfluidic channel. We use mouse IgG diluted in phosphate buffered saline (PBS) with 1% bovine serum albumin (BSA) solution as target antigen. The fluorescent sandwich immunocomplex is formed on the beads during the operation of the chip both in stop-flow and continuous-flow modes. Target mouse IgG antigen is detected down to a concentration of 15 ng/mL in stop-flow mode and 250 pg/mL in continuous-flow mode, using only 1300 nL of sample volume. We also demonstrate the possibility of simultaneous detection of two different antigens in a PBS-BSA solution using a dual microfluidic channel structure.

Improved biomolecule microarrays by printing on nanoporous aluminum oxide using a continuous-flow microspotter

Biomolecules, including protein A, albumin, and immunoglobulin G, are spotted on top of a nanoporous substrate by using a continuous-flow microspotter (CFM) system, which normally produces spots 3 to 4 orders of magnitude more sensitive than conventional biomolecule printing methods. The spots are observed with a fluorescence scanner. By using the CFM to print spots on nanoporous substrates, an additional order of magnitude increase in signal is observed, which leads to high signal-to-background ratios, highly saturated spots, and a measurable signal at printing concentrations as low as 1.6 ng mL(-1). This technique produces highly concentrated biomolecular spots from dilute samples and significantly increases the sensitivity of sensing platforms.

Comparison of label-free biosensing in microplate, microfluidic, and spot-based affinity capture assays

Using both experimental assays and fluid-dynamic finite element simulation models, we directly compared the achievable performance limits of four distinct assay configurations for label-free detection of an analyte from a test sample on a biosensor surface. The assay configurations studied in this work included a biosensor incorporated into the bottom surface of a microplate well and a microfluidic channel. For each configuration, we compared assay performance for the scenario in which the entire bottom surface of the fluid-handling vessel is coated with capture ligands with assay performance for the scenario in which the capture ligands are applied in the form of localized spots. As a model system, we used detection of the protein biomarker tumor necrosis factor-alpha (TNF-alpha) using immobilized TNF-alpha capture antibody. Results show that the microfluidic assay format dramatically reduces the time required to establish a stable equilibrium. Spot-based assays are advantageous for microplate-based detection for reducing the time required for equilibrium sensor response. The results derived are generally applicable to any label-free biosensor technology and any ligand-analyte system with adjustable variables that include sensor mass density sensitivity, analyte-ligand adsorption/desorption rate constants, immobilized ligand density, flow channel geometry, flow rate, and spot size.

Use of IgY antibodies and semiconductor nanocrystal detection in cancer biomarker quantitation

Biomarkers play a pivotal role in the early detection and diagnosis of cancer. Accurate quantitation of certain biomarkers is crucial to reach correct treatment decisions. In practice, immunohistochemistry (IHC) remains the most important diagnostic technique to evaluate protein biomarker expression in tissue biopsies. However, IHC has largely been qualitative. Low specificity of the mammalian IgG antibodies used to capture the analytes and instability of fluorescence from the organic dyes used as the detecting agents are among the major factors that have impeded the development of quantitative IHC. Avian IgY antibodies have many attractive biochemical, immunological and production advantages over IgGs and are, therefore, better substitutes in diagnostic applications. Using IgY in immunoassays can potentially eliminate false positives and often results in low background and interference. Quantum dots (QDs) have recently emerged as a novel class of fluorophores, promising for many biomedical imaging applications. Fluorescence from QDs is significantly brighter and more photostable than organic dyes. In addition, QDs offer the capacity of multiplexed detection of several biomarkers simultaneously. Combining the high sensitivity and specificity of IgY antibodies and the high brightness and photostability of QDs in IHC has been demonstrated to improve biomarker detection and quantitation.

Self-assembly of colloidal particles from evaporating droplets: role of DLVO interactions and proposition of a phase diagram

The shape of deposits obtained from drying drops containing colloidal particles matters for technologies such as inkjet printing, microelectronics, and bioassay manufacturing. In this work, the formation of deposits during the drying of nanoliter drops containing colloidal particles is investigated experimentally with microscopy and profilometry, and theoretically with an in-house finite-element code. The system studied involves aqueous drops containing titania nanoparticles evaporating on a glass substrate. Deposit shapes from spotted drops at different pH values are measured using a laser profilometer. Our results show that the pH of the solution influences the dried deposit pattern, which can be ring-like or more uniform. The transition between these patterns is explained by considering how DLVO interactions such as the electrostatic and van der Waals forces modify the particle deposition process. Also, a phase diagram is proposed to describe how the shape of a colloidal deposit results from the competition among three flow patterns: a radial flow driven by evaporation at the wetting line, a Marangoni recirculating flow driven by surface tension gradients, and the transport of particles toward the substrate driven by DLVO interactions. This phase diagram explains three types of deposits commonly observed experimentally, such as a peripheral ring, a small central bump, or a uniform layer. Simulations and experiments are found in very good agreement.

Selective breast cancer cell capture, culture, and immunocytochemical analysis using self-assembled magnetic bead patterns in a microfluidic chip

Separation and subsequent culturing of MCF-7 breast cancer cells on self-assembled protein-coated magnetic beads in a microfluidic chip is demonstrated. The beads were patterned in situ inside a sealed microfluidic channel using magnetic-field-assisted electrostatic self-assembly. Hereafter, they were grafted by exposure to a solution of 5D10 monoclonal antibodies (mAb) and fibronectin (FN), with the first being used for immunospecific cell capture and the latter being used for cell adhesion and growth. A solution of target MCF-7 cells mixed with Jurkat cells was brought inside the microchannel, leading to specific MCF-7 cell capture; the latter were then cultured and evidenced by cell immuno-luminescence.

Building off-the-shelf tissue-engineered composites

Rapid advances in technology have created the realistic possibility of personalized medicine. In 2000, Time magazine listed tissue engineering as one of the 'hottest 10 career choices'. However, in the past decade, only a handful of tissue-engineered products were translated to the clinical market and none were financially viable. The reality of complex business planning and the high-investment, high-technology environment was not apparent, and the promise of tissue engineering was overstated. In the meantime, biologists were steadily applying three-dimensional benchtop tissue-culture systems for cellular research, but the systems were gelatinous and thus limited in their ability to facilitate the development of complex tissues. Now, the bioengineering literature has seen an emergence of literature describing biofabrication of tissues and organs. However, if one looks closely, again, the viable products appear distant. 'Rapid' prototyping to reproduce the intricate patterns of whole organs using large volumes of cellular components faces daunting challenges. Homogenous forms are being labelled 'tissues', but, in fact, do not represent the heterogeneous structure of the native biological system. In 2003, we disclosed the concept of combining rapid prototyping techniques with tissue engineering technologies to facilitate precision development of heterogeneous complex tissue-test systems, i.e. systems to be used for drug discovery and the study of cellular behaviour, biomedical devices and progression of disease. The focus of this paper is on the challenges we have faced since that time, moving this concept towards reality, using the case of breast tissue as an example.

Quantifying protein-protein interactions in high throughput using protein domain microarrays

Protein microarrays provide an efficient way to identify and quantify protein-protein interactions in high throughput. One drawback of this technique is that proteins show a broad range of physicochemical properties and are often difficult to produce recombinantly. To circumvent these problems, we have focused on families of protein interaction domains. Here we provide protocols for constructing microarrays of protein interaction domains in individual wells of 96-well microtiter plates, and for quantifying domain-peptide interactions in high throughput using fluorescently labeled synthetic peptides. As specific examples, we will describe the construction of microarrays of virtually every human Src homology 2 (SH2) and phosphotyrosine binding (PTB) domain, as well as microarrays of mouse PDZ domains, all produced recombinantly in Escherichia coli. For domains that mediate high-affinity interactions, such as SH2 and PTB domains, equilibrium dissociation constants (K(D)s) for their peptide ligands can be measured directly on arrays by obtaining saturation binding curves. For weaker binding domains, such as PDZ domains, arrays are best used to identify candidate interactions, which are then retested and quantified by fluorescence polarization. Overall, protein domain microarrays provide the ability to rapidly identify and quantify protein-ligand interactions with minimal sample consumption. Because entire domain families can be interrogated simultaneously, they provide a powerful way to assess binding selectivity on a proteome-wide scale and provide an unbiased perspective on the connectivity of protein-protein interaction networks.

Gene expression analysis with an integrated CMOS microarray by time-resolved fluorescence detection

DNA microarrays have proven extraordinarily powerful for differential expression studies across thousands of genes in a single experiment. Microarrays also have the potential for clinical applications, including the detection of infectious and immunological diseases and cancer, if they can be rendered both reliable and cost-effective. Here we report the first practical application of an active microarray based on integrated circuit technology, completely obviating the need for external measurement instrumentation while employing protocols compatible with traditional fluorescence-based surface bioassays. In a gene expression biodosimetry study, we determine the differential activity of genes from leucocytes in irradiated human blood. Quantum dots are used as fluorescence labels to realize filterless, time-gated fluorescence detection on an active complementary metal-oxide-semiconductor (CMOS) microarray with 100-pM sensitivity. Improvements in surface chemistry should allow sensitivities that approach the microarray hardware limit of less than 10 pM. Techniques for covalent attachment of DNA capture strands to the CMOS active microarrays allow integrated sensors to be placed in immediate proximity to hybridized analyte strands, maximizing photon collection efficiencies.

Cell micropatterning on an albumin-based substrate using an inkjet printing technique

Positioning of cells in a desired pattern on a substrate is an important technique for cell-based technologies, including the fundamental investigation of cell functions, tissue-engineering applications, and the fabrication of cell-based biosensors and cell arrays. Recently, the inkjet printing technique was recognized as a promising approach to the creation of cellular patterns on substrates, and it has been achieved by the printing of living cells or cell adhesive proteins. In this article, we created complex cellular patterns by using an albumin-based substrate and inkjet printing technique. Albumin was cross-linked using ethylene glycol diglycidyl ether. Subsequent casting of the cross-linked albumin solution onto glass plates prevented cells from adhering to their surfaces. Through screening various chemical reagents, we found that these cross-linked albumin surfaces dramatically changed into cell adhesive surfaces after immersion in cationic polymer solutions. Based on this finding, cell adhesive regions were prepared with a desired pattern by printing the polyethyleneimine (PEI) solution onto a cross-linked albumin substrate using a modified commercial inkjet printer. Various cellular patterns including figures, letters, and gradients could be fabricated by seeding mouse L929 fibroblast cells or mouse Neuro-2a neuroblastoma cells onto the printed PEI-patterned substrate. Compared with the printing of fragile living cells or proteins, printing of stable PEI circumvents clogging of printer head nozzles and enables reproducible printing. Therefore, the present method will allow the creation of complex cell patterns.

Microcantilever sensors for monitoring the evaporation of microdrops of pure liquids and mixtures

We describe in detail a nonimaging technique that allows the measurement of the mass, the radius, and the contact angle of evaporating sessile microdrops of pure liquids and binary mixtures. The microdrops were deposited onto hydrophobized silicon microcantilevers whose bending and resonance frequency were monitored during drop evaporation. We verify the laws of evaporation kinetics for microdrops with diameters from 80 down to 10 microm. The evaporation of mixtures of water/ethanol drops confirmed previous results with millimeter sized drops. N,N-dimethylformamide drops undergo a transformation from an initial spherical shape to a thin film. Flattening of the drop causes a slowdown of the evaporation kinetics at the end. Two concurring factors are at its origin: the rising disjoining pressure stabilizes the thin liquid film and the increasing radius of curvature of the drop reduces the vapor pressure.

Biopatterning for label-free detection

We present a biopatterning technique suitable for applications which demand a high degree of surface cleanliness, such as immobilization of biological recognition elements onto label-free biosensors. In the case of label-free biosensing, the mechanism of signal transduction is based on surface bound matter, making them highly sensitive to surface contamination including residues left during the biopatterning process. In this communication we introduce a simple, rapid processing step that removes 98% of the residues that often remain after standard parylene lift-off patterning. Residue-free parylene biopatterning is combined with microfluidics to localize biomolecule immobilization onto the sensing region and to enable multiplexed biopatterning. We demonstrate the applicability of this method to multiplexed label-free detection platforms by patterning nucleic acid capture probes corresponding to the four different serotypes of Dengue virus onto parallel 1D photonic crystal resonator sensors. Scanning electron microscopy (SEM) and atomic force microscopy (AFM) are used to quantify surface cleanliness and uniformity. In addition to label-free biosensors, this technique is well suited to other nanobiotechnology patterning applications which demand a pristine, residue-free surface, such as immobilization of enzymes, antibodies, growth factors, or cell cultures.

Affinity-based Protein Surface Pattern Formation by Ligand Self-Selection from Mixed Protein Solutions

Photolithographically prepared surface patterns of two affinity ligands (biotin and chloroalkane) specific for two proteins (streptavidin and HaloTag®, respectively) are used to spontaneously form high-fidelity surface patterns of the two proteins from their mixed solution. High affinity protein-surface self-selection onto patterned ligands on surfaces exhibiting low non-specific adsorption rapidly yields the patterned protein surfaces. Fluorescence images after protein immobilization show high specificity of the target proteins to their respective surface patterned ligands. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) imaging further supports the chemical specificity of streptavidin and HaloTag® for their surface patterned ligands from mixed protein solutions. However, ToF-SIMS did detect some non-specific adsorption of bovine serum albumin, a masking protein present in excess in the adsorbing solutions, on the patterned surfaces. Protein amino acid composition, surface coverage, density and orientation are important parameters that determine the relative ToF-SIMS fragmentation pattern yields. ToF-SIMS amino acid-derived ion fragment yields summed to produce surface images can reliably determine which patterned surface regions contain bound proteins, but do not readily discriminate between different co-planar protein regions. Principal component analysis (PCA) of these ToF-SIMS data, however, improves discrimination of ions specific to each protein, facilitating surface pattern discrimination and contrast.

Patterned and switchable surfaces for biomolecular manipulation

The interactions of biomolecules and cells with solid interfaces play a pivotal role in a range of biomedical applications and have therefore been studied in great detail. An improved understanding of these interactions results in the ability to manipulate DNA, proteins and other biomolecules, as well as cells, spatially and temporally at surfaces with high precision. This in turn engenders the development of advanced devices, such as biosensors, bioelectronic components, smart biomaterials and microarrays. Spatial control can be achieved by the production of patterned surface chemistries using modern high-resolution patterning technologies based on lithography, microprinting or microfluidics, whilst temporal control is accessible through the application of switchable surface architectures. The combination of these two surface properties offers unprecedented control over the behaviour of biomolecules and cells at the solid-liquid interface. This review discusses the behaviour of biomolecules and cells at solid interfaces and highlights fundamental and applied research exploring patterned and switchable surfaces.

Fabrication and characterization of a sialoside-based carbohydrate microarray biointerface for protein binding analysis with surface plasmon resonance imaging

Monitoring multiple biological interactions in a multiplexed array format has numerous advantages. However, converting well-developed surface chemistry for spectroscopic measurements to array-based high-throughput screening is not a trivial process and often proves to be the bottleneck in method development. This paper reports the fabrication and characterization of a new carbohydrate microarray with synthetic sialosides for surface plasmon resonance imaging (SPRi) analysis of lectin-carbohydrate interactions. Contact printing of functional sialosides on neutravidin-coated surfaces was carried out and the properties of the resulting elements were characterized by fluorescence microscopy and atomic force microscopy (AFM). Sambucus nigra agglutinin (SNA) was deposited on four different carbohydrate functionalized surfaces and differential binding was analyzed to reveal affinity variation as a function of headgroup sialic acid structures and linking bonds. SPRi studies indicated that this immobilization method could result in high quality arrays with RSD < 5% from array element to array element, superior to the conventional covalent linkage used for protein cholera toxin (CT) in a comparison experiment, which yields nonuniform array elements with RSD > 15%. Multiplexed detection of SNA/biotinylated sialoside interactions on arrays up to 400 elements has been performed with good data correlation, demonstrating the effectiveness of the biotin-neutravidin-based biointerface to control probe orientation for reproducible and efficient protein binding to take place. Additionally, the regeneration of the array surface was demonstrated with a glycine stripping buffer, rendering this interface reusable. This in-depth study of array surface chemistry offers useful insight into experimental conditions that can be optimized for better performance, allowing many different protein-based biointeractions to be monitored in a similar manner.

Fluorescence lifetime imaging microscopy and fluorescence resonance energy transfer from cyan to yellow fluorescent protein validates a novel method to cluster proteins on solid surfaces

A novel method to distribute proteins on solid surfaces is proposed. Proteins microencapsulated in the water pool of reverse micelles were used to coat a solid surface with well-individualized round spots of 1 to 3 microm in diameter. The number of spots per unit area can be increased through the concentration of reverse micelles, and networks of spots were obtained at high concentrations of large reverse micelles. Moreover, depending on the pool size of the water reverse micelles, proteins can be deposited far from each other or in close proximity within the range of 50 to 70 A. This proximity obtained with small reverse micelles was proved through fluorescence lifetime imaging microscopy and fluorescence resonance energy transfer (FLIM-FRET) measurements for the most relevant FRET pair in cell biology studies, the cyan and yellow fluorescent proteins. This novel procedure has several advantages and reveals the potential for study of protein-protein interactions on solid surfaces and for developing novel biomaterials and molecular devices based on biorecognition elements.

On the relationship between jetted inks and printed biopatterns: molecular-thin functional microarrays of glucose oxidase

Arrays of circular spots of glucose oxidase have been obtained on functionalized silicon oxide by piezoelectric inkjet printing and the enzymatic activity toward glucose recognition has been monitored. The addition of glycerol to the molecular ink allows to obtain high spot definition and resolution (tens of micrometers wide; one molecule tall), but in spite of its well-known structural stabilizing properties, in dynamic conditions it may lead to increased protein stresses. The jetting voltage and pulse length have been found to be critical factors for both activity retention and pattern definition. High voltages and pulse lengths results in stress effects along with the loss of activity, which, at least in our experimental conditions, has been found to be recovered in time.