Applications of protein microarray technology

Protein microarrays, an emerging class of proteomic technologies, are quickly becoming essential tools for large-scale and high throughput biochemistry and molecular biology. Recent progress has been made in all the key steps of protein microarray fabrication and application, such as the large-scale cloning of expression-ready prokaryotic and eukaryotic ORFs, high throughput protein purification, surface chemistry, protein delivery systems, and detection methods. Two classes of protein microarrays are currently available: analytical and functional protein microarrays. In the case of analytical protein microarrays, well-characterized molecules with specific activity, such as antibodies, peptide-MHC complexes, or lectins, are used as immobilized probes. These arrays have become one of the most powerful multiplexed detection platforms. Functional protein microarrays are being increasingly applied to many areas of biological discovery, including drug target identification/validation and studies of protein interaction, biochemical activity, and immune responses. Great progress has been achieved in both classes of protein microarrays in terms of sensitivity and specificity, and new protein microarray technologies are continuing to emerge. Finally, protein microarrays have found novel applications in both scientific research and clinical diagnostics.     

Protein microarrays for diagnostic assays

Protein microarray technology has enormous potential for in vitro diagnostics (IVD). Miniaturized parallelized immunoassays are perfectly suited to generating a maximum of diagnostically relevant information from minute amounts of sample whilst only requiring small amounts of reagent. Protein microarrays have become well-established research tools in basic and applied research and the first products are already on the market. This article reviews the current state of protein microarrays and discusses developments and future demands relating to protein arrays in their role as multiplexed immunoassays in the field of diagnostics.

Microarray technology as a universal tool for high-throughput analysis of biological systems

Over the last years microarray technology has become one of the principal platform technologies for the high-throughput analysis of biological systems. Starting with the construction of first DNA microarrays in the 1990s, microarray technology has flourished in the last years and many different new formats have been developed. Peptide and protein microarrays are now applied for the elucidation of interaction partners, modification sites and enzyme substrates. Antibody microarrays are envisaged to be of high importance for the high-throughput determination of protein abundances in translational profiling approaches. First cell microarrays have been constructed to transform microarray technology from an in vitro technology to an in vivo functional analysis tool. All of these approaches share a common prerequisite: the solid support on which they are generated. The demands on this solid support are thereby as manifold as the applications themselves. This review is aimed to display the recent developments in surface chemistry and derivatization, and to summarize the latest developments in the different application areas of microarray technology.     

糖芯片的检测及应用

糖芯片技术具有样品少、通量高和特异性强等优点,是一种糖组学研究的新的技术平台和强大的分析工具,已经广泛用于糖和蛋白质的特异性作用、酶活性和抑制剂、病毒入侵机理、细菌检测和免疫反应等方面的研究.本文简要介绍了糖芯片的原理、制备和信号的检测技术(荧光标记法、质谱法、SPR法等),分析了糖芯片在各个领域的应用及其发展前景.     

A chip-based miniaturized format for protein-expression profiling: the exploitation of comprehensively produced antibodies

Numerous antibodies have been developed and validated in recent years, and show promise for use in novel functional protein assays. Such assays would be an alternative to pre-existing comprehensive assays, such as DNA microarrays. Antibody microarrays are thought to represent those functional protein assays. While a variety of attempts have been made to apply DNA microarray technology to antibody microarrays, a fully optimized protocol has not been established. We have been conducting a project to comprehensively produce antibodies against mouse KIAA ("KI" stands for "Kazusa DNA Research Institute" and "AA" are reference characters) proteins. Using our library of antibodies, we established a novel antibody microarray format that utilizes surface plasmon resonance (SPR) technology. A label-free real-time measurement of protein expression in crude cell lysates was achieved by direct readout of the bindings using SPR. Further refinement of the antibody microarray format enabled us to detect a smaller quantity of target proteins in the lysate without the bulk effect. In this review, we first summarize available antibody array formats and then describe the above-mentioned format utilizing updated SPR technology.     

Application of Lectin Microarrays for Biomarker Discovery

Many proteins in living organisms are glycosylated. As their glycan patterns exhibit protein-, cell-, and tissue-specific heterogeneity, changes in the glycosylation levels could serve as useful indicators of various pathological and physiological states. Thus, the identification of glycoprotein biomarkers from specific changes in the glycan profiles of glycoproteins is a trending field. Lectin microarrays provide a new glycan analysis platform, which enables rapid and sensitive analysis of complex glycans without requiring the release of glycans from the protein. Recent developments in lectin microarray technology enable high-throughput analysis of glycans in complex biological samples. In this review, we will discuss the basic concepts and recent progress in lectin microarray technology, the application of lectin microarrays in biomarker discovery, and the challenges and future development of this technology. Given the tremendous technical advancements that have been made, lectin microarrays will become an indispensable tool for the discovery of glycoprotein biomarkers.     

Active bead-linked immunoassay on protein microarrays

Protein microarrays are becoming a powerful tool in proteome, biochemical, and clinical studies. In addition to the quality of arrayed immobilized probe molecules, sensitivity of the microarray-based assay is highly dependent on the detection technique. Here we suggest four simple techniques for rapid detection of analytes bound to protein microarrays. The techniques employ functionalized magnetic and non-magnetic beads moved to, from, or along the array surface by external forces. In contrast to other labeling techniques actively controlled physical labels: (i) make detection extremely fast to allow microarray reading in seconds; (ii) provide a low background due to active removal of weakly bound beads; and (iii) provide a highly sensitive detection, since one antigen-antibody bond is capable of holding bead immobilized on the array surface. In combination with the electrophoretically assisted active immunoassay we described recently such active reading allows to reduce total indirect immunoassay time to 7-10 min while having sensitivity in the femtomolar concentration range. High speed, sensitivity, and specificity make active bead-linked detection an ideal choice in rapid high-throughput screening and in emergency diagnostics.     

Sacrificial layer microfluidic device fabrication methods

Over the past 15 years, research in the field of microfluidics has experienced rapid growth due to significant potential advantages such as low cost, short analysis times, and elimination of sources of contamination. Although etched and thermally bonded glass substrates have seen widespread use and offer solid performance, device fabrication still remains cumbersome. Recent advances in sacrificial layer microfabrication methods for microfluidics have overcome many disadvantages of conventional fabrication approaches. Phase-changing sacrificial layers have been implemented in making inexpensive and high-performance polymer microchips for electrophoretic analysis, protein focusing, and sample preconcentration. In addition, novel channel fabrication methods based on standard thin-film processes, which are readily integratable with microfabrication techniques used for electrical components, are being applied increasingly for the creation of microfluidic devices. These new sacrificial layer fabrication approaches will be instrumental in making low-cost and high-quality polymer microchips, and in interfacing electrical and fluidic systems on glass or semiconductor substrates.     

Carboxyl-terminated dendrimer-coated bioactive interface for protein microarray: high-sensitivity detection of antigen in complex biological samples

Protein microarrays are promising tools that can potentially enable high throughput proteomic screening in areas such as disease diagnosis and drug discovery. A critical aspect in the development of protein microarrays is the optimization of the array's surface chemistry to achieve the high sensitivity required for detection of proteins in cell lysate and other complex biological mixtures. In the present study, a high-density antibody array with minimal nonspecific cellular protein adsorption was prepared using a glass surface coated with a poly(propyleneimine) dendrimer terminated with carboxyl group (PAMAM-COOH). The carboxyl-terminated dendrimer-modified surface has almost similar nonspecific cellular protein adsorption when compared to an inert PEG-modified surface. In addition, the multiple functional sites available for reaction on the dendrimer surface facilitated high-density immobilization of antibodies and efficient capture of bioanalytes. Various molecules were tested for their ability to block or deactivate the reactive carboxyl surface after antibody immobilization to further reduce the nonspecific binding. A short oligoethylene glycol (NH2-d4-PEG-COOH), was found to significantly improve the signal-to-noise ratio of the assay, resulting in higher sensitivity. The properties and functional qualities of the various surfaces were characterized by contact angle and AFM measurements. Nonspecific protein adsorption and protein immobilization as a function of dendrimer generations and sensitivity of antigen capturing from a buffer (1 pM) as well as from the complex cell lysate (10 pM) system were examined. Our detailed experimental studies demonstrated a facile method of preparing surfaces with high protein loading and low nonspecific protein binding for the development of high sensitivity protein microarrays.     

化学生物学中光敏分子微阵列的表面构建与应用

分子微阵列是有机合成（特别是组合化学合成）方法应用于生物和医学研究而发展起来的高科技集成技术,通过把微电子、微加工技术和有机化学合成反应相结合,在固体基质（如硅片、玻片、瓷片等）表面构建微型的生物有机化学分子系统,以实现对细胞、蛋白质、核酸及其他生物组分进行快速、敏感、高效地处理．近年来,随着表面化学构建策略研究的不断深入和迅猛发展,分子微阵列技术的应用领域不断拓展,已从最初用于核酸分子的杂交测序延伸到基因组功能研究的各个方面．本文着重综述了光敏分子微阵列的表面化学构建策略研究及其在化学生物学分析中应用的最新进展,并展望了其发展的未来趋势．内容主要包括：小分子与多肽分子微阵列、蛋白质分子微阵列、核酸分子微阵列和糖分子微阵列等．     

蛋白质DNA混合微点阵和微流控芯片的整合

在活化的石英片上制作蛋白质和DNA微点阵, 并可逆地将其与含有通道的多聚二甲基硅氧烷弹性橡胶封接在一起, 使蛋白质和DNA微点阵组装在微通道列阵内; 实现在微通道列阵内同时检测和分析蛋白质与DNA的功能. 为了降低多聚二甲基硅氧烷弹性橡胶的疏水性, 增强其生物相容性, 实验通过多聚赖氨酸对多聚二甲基硅氧烷弹性橡胶的修饰, 提高了它的亲水性, 使溶液能够在微通道内顺畅地流通. 实验表明, 这种混合芯片能够提高检测速度和增加检测的信息量.     

DNA microarrays: tools for the 21st Century

Profiling of gene expression patterns with microarray technology is widely used in both basic and applied research. DNA microarrays have also shown great promise in clinical medicine and are paving the way toward effective pharmaceutical drug discovery and individualized drug regimens. With growing utilization of this high-throughput technology, new applications are making headlines on a regular basis. This review aims to outline the pros and cons of this methodology and direct the reader towards available useful resources. Various major array formats such as high-density oligonucleotide arrays and spotted cDNA arrays are examined, and advantages and options for using each format are presented. Factors important for the design and analysis of microarray experiments are also discussed.     

Bioaffinity chromatography on monolithic supports

Affinity chromatography on monolithic supports is a powerful analytical chemical platform because it allows for fast analyses, small sample volumes, strong enrichment of trace biomarkers and applications in microchips. In this review, the recent research using monolithic materials in the field of bioaffinity chromatography (including immunochromatography) is summarized and discussed. After giving an introduction into affinity chromatography, information on different biomolecules (antibodies, enzymes, lectins, aptamers) that can act as ligands in bioaffinity chromatography is presented. Subsequently, the history of monoliths, their advantages, preparation and formats (disks, capillaries and microchips) as well as ligand immobilization techniques are mentioned. Finally, analytical and preparative applications of bioaffinity chromatography on monoliths are presented. During the last four years 37 papers appeared. Protein A and G are still most often used as ligands for the enrichment of immunoglobulins. Antibodies and lectins remain popular for the analysis of mainly smaller molecules and saccharides, respectively. The highly porous cryogels modified with ligands are applied for the sorting of different cells or bacteria. New is the application of aptamers and phages as ligands on monoliths. Convective interaction media (epoxy CIM disks) are currently the most used format in monolithic bioaffinity chromatography.     

Construction of CdSe/ZnS quantum dot microarray in a microfluidic chip

Microarray technology has been proved to be greatly helpful for biomedical and biological diagnosis. And the evaluation of its biological applications lies in the detection sensitivity, which requires high intensity and stability of the signal. Recently, several nanomaterials, especially semiconductor nanomaterials, due to their excellent fluorescence properties, have been widely used to construct microarrays for biosensors. Here, we presented an approach for constructing CdSe/ZnS quantum dot (QD) microarray in microfluidic channels on a glass slide by photolithography. The conditions for immobilizing stable and uniform QD microarray on the glass slide were optimized. Several types of QD microarrays with different emission wavelengths and modified groups were constructed using silanization and lithography technology. Based on the fluorescence quenching effect of Cu2+ on QDs, the microfluidic chip with QD microarray was applied for the determination of Cu2+. 1 nmol/L Cu2+ could be detected by this method.     

A rejuvenation method for poly(N,N-dimethylacrylamide)-coated glass microfluidic chips

As microfluidic chips come to integrate the higher levels of functionality required for the implementation of advanced bioanalytical protocols, a crucial factor is that of cost. Although glass chips provide advantages in multilayer integrations, their cost is far higher than that of polymer chips. However, a simple and effective rejuvenation protocol for glass microchips may enable higher levels of integration and functionality on glass microchips. Here we present a method to rejuvenate glass microchips that had been used for capillary electrophoresis to the extent that their performance was degraded. This degradation was due to one of the two mechanisms: (i) a deterioration of the polymer coating on the inner surface of the microchannel or (ii) an aging of the glass substrate. Using the method presented here, we have rejuvenated more than 50 such "aged" microchips. The performance of these microchips was fully restored after the rejuvenation and lasted for hundreds of DNA separation runs. Our experiments indicate that the loss of resolution in microchip separations was not associated with glass aging, but was due to the degradation of the polymer coating on the inner surface of microchannels. This suggests that it is possible to extend the microchip lifetime "forever" using the rejuvenation protocol and that the exploration of higher levels of integration and functionality on glass microchips (or of hybrid structures involving materials capable of withstanding the reagents and elevated temperatures used) is feasible.     

Use of photolithography to encode cell adhesive domains into protein microarrays

Protein microarrays are rapidly emerging as valuable tools in creating combinatorial cell culture systems where inducers of cellular differentiation can be identified in a rapid and multiplexed fashion. In the present study, protein microarraying was combined with photoresist lithography to enable printing of extracellular matrix (ECM) protein arrays while precisely controlling "on-the-spot" cell-cell interactions. In this surface engineering approach, the micropatterned photoresist layer formed on a glass substrate served as a temporary stencil during the microarray printing, defining the micrometer-scale dimensions and the geometry of the cell-adhesion domains within the printed protein spots. After removal of the photoresist, the glass substrates contained micrometer-scale cell-adhesive regions that were encoded within 300 or 500 microm diameter protein domains. Fluorescence microscopy and atomic force microscopy (AFM) were employed to characterize protein micropatterns. When incubated with micropatterned surfaces, hepatic (HepG2) cells attached on 300 or 500 mum diameter protein spots; however, the extent of cell-cell contacts within each spot varied in accordance with dimensions of the photoresist stencil, from single cells attaching on 30 microm diameter features to multicell clusters residing on 100 or 200 microm diameter regions. Importantly, the photoresist removal process was shown to have no detrimental effects on the ability of several ECM proteins (collagens I, II, and IV and laminin) to support functional hepatic cultures. The micropatterning approach described here allows for a small cell population seeded onto a single cell culture substrate to be exposed to multiple scenarios of cell-cell and cell-surface interactions in parallel. This technology will be particularly useful for high-throughput screening of biological stimuli required for tissue specification of stem cells or for maintenance of differentiated phenotype in scarce primary cells.     

Microcontact Printing Techniques in Bioscience

The microcontact printing (μCP) technology available for patterning protein, DNA hybridization, immunoassay and cellular cocultures onto solid surface are reviewed. This review describes some of the techniques currently employed for creating two-dimensional biomolecular microarray, and the research results regarding their effectiveness. In addition, the applications of the impact of/-,CP technology in the field of biosciences are also presented.     

Colorimetric detection of immobilized horseradish peroxidase based on the co-oxidation of benzidine derivatives and 4-chloro-1-naphthol

Enzymatic co-oxidation of benzidine derivatives and 4-chloro-1-naphthol with hydrogen peroxide was studied for the colorimetric detection of horseradish peroxidase using the DNA microarray on glass surface technology. The co-oxidation of o-dianisidine and 4-chloro-1-naphthol affords a new product with the intense violet color characterized by a high rate of accumulation, good adsorbability on the glass surface, and stability. This reaction can be used as a detection system for the identification of β-lactamase genes on DNA microarrays. The DNA microarray technique using horseradish peroxidase and colorimetric detection is characterized by high sensitivity and reproducibility comparable to the characteristics of the microarrays with fluorescence detection.