Peptide and small molecule microarray for high throughput cell adhesion and functional assays

Quality considerations and selection of surface chemistry for glass-based DNA, peptide, antibody, carbohydrate, and small molecule microarrays

The complexity of workflows for the production of high quality microarrays asks for the careful evaluation and implementation of materials and methods. As a cornerstone of the whole microarray process, the microarray substrate has to be chosen appropriately and a number of crucial considerations in respect to matching the research question with the technical requirements and possibilities have to be taken into account. In the following, how to lay the fundamental for high performance microarray experiments by evaluating basic quality requirements and the selection of suitable slide surface architectures for a variety of applications was concentrated.

A Peptide Microarray for the Detection of Protein Kinase Activity in Cell Lysate

DNA microarray enables the analysis of DNA or mRNA expression levels, but it has not been possible to completely understand life using obtained information. Consequently, protein or peptide arrays have attracted much interest. Since the development of a practical protein microarray is still far away in light of handling difficulties, the peptide microarray is a promising tool for analyzing protein functions. We have developed a peptide microarray to detect protein kinase activity in cell lysate. All substrate peptides for kinases were immobilized chemoselectively on amino-coated glass slides. After phosphorylation of the immobilized peptides, phosphorylation was detected by fluorescence imaging. We detected the protein kinase activities, including that in cell lysate, in response to drug stimulation. Therefore, this peptide microarray would be useful for a high-throughput kinase assay of intracellular signals and would be applicable to drug screening.

Thiol-mediated anchoring of ligands to self-assembled monolayers for studies of biospecific interactions

We report a method to immobilize thiol-containing ligands onto self-assembled monolayers (SAMs) of alkanethiolates presenting chloracetylated hexa(ethylene glycol) groups. The chloroacetyl groups react with thiols under mild basic conditions, enabling the stable immobilization of biologically active ligands in a well-defined orientation. These SAMs on gold are well suited for studies of biospecific interactions of immobilized ligands with proteins and cells. As a demonstration, we functionalized these SAMs with thiol-containing derivatives of biotin and benzene sulfonamide and observed the specific binding of neutravidin and carbonic anhydrase, respectively. We also used this method to generate mixed SAMs presenting the Arg-Gly-Asp (RGD) peptide sequence and demonstrated the integrin-mediated adhesion of fibroblast cells to these SAMs. This approach would allow the immobilization of proteins and other sensitive biomolecules and ligands for a wide variety of applications in biotechnology.

Reactivity of intein thioesters: appending a functional group to a protein

The success of genome sequencing has heightened the demand for new means to manipulate proteins. An especially desirable goal is the ability to modify a target protein at a specific site with a functional group of orthogonal reactivity. Here, we achieve that goal by exploiting the intrinsic electrophilicity of the thioester intermediate formed during intein-mediated protein splicing. Detailed kinetic analyses of the reaction of nitrogen nucleophiles with a chromogenic small-molecule thioester revealed that the alpha-hydrazino acetyl group was the optimal nucleophile for attacking a thioester at neutral pH to form a stable linkage. A bifunctional reagent bearing an alpha-hydrazino acetamido and azido group was synthesized in high overall yield. This reagent was used to attack the thioester linkage between a target protein and intein, and thereby append an azido group to the target protein in a single step. The azido protein retained full biological activity. Furthermore, its azido group was available for chemical modification by Huisgen 1,3-dipolar azide-alkyne cycloaddition. Thus, the mechanism of intein-mediated protein splicing provides the means to install a useful functional group at a specific site-the C terminus-of virtually any protein.

Specific capture of mammalian cells by cell surface receptor binding to ligand immobilized on gold thin films

Aldehyde-terminated self-assembled monolayers (SAMs) on gold surfaces were modified with proteins and employed to capture intact living cells through specific ligand-cell surface receptor interactions. In our model system, the basic fibroblast growth factor (bFGF) binding receptor was targeted on baby hamster kidney (BHK-21) cells. Negative control and target proteins were immobilized on a gold surface by coupling protein primary amines to surface aldehyde groups. Cell-binding was monitored by phase contrast microscopy or surface plasmon resonance (SPR) imaging. The specificity of the receptor-ligand interaction was confirmed by the lack of cell binding to the negative control proteins, cytochrome c and insulin, and by the disruption of cell binding by treatment with heparitinase to destroy heparan sulfate which plays an essential role in the binding of bFGF to FGF receptors. This approach can simultaneously probe a large number of receptor-ligand interactions in cell populations and has potential for targeting and isolating cells from mixtures according to the receptors expressed on their surface.

Recent developments in microarray-based enzyme assays: from functional annotation to substrate/inhibitor fingerprinting

Recent advances in proteomics have provided impetus towards the development of robust technologies for high-throughput studies of enzymes. The term "catalomics" defines an emerging '-omics' field in which high-throughput studies of enzymes are carried out by using advanced chemical proteomics approaches. Of the various available methods, microarrays have emerged as a powerful and versatile platform to accelerate not only the functional annotation but also the substrate and inhibitor specificity (e.g. substrate and inhibitor fingerprinting, respectively) of enzymes. Herein, we review recent developments in the fabrication of various types of microarray technologies (protein-, peptide- and small-molecule-based microarrays) and their applications in high-throughput characterizations of enzymes.

Cell adhesion profiling using extracellular matrix protein microarrays

We have developed a microarray-based system for cell adhesion profiling of large panels of cell-adhesive proteins to increase the throughput of in vitro cell adhesion assays, which are currently primarily performed in multiwell plates. Miniaturizing cell adhesion assays to an array format required the development of protocols for the reproducible microspotting of extracellular matrix (ECM) protein solutions and for the handling of cell suspensions during the assay. We generated ECM protein microarrays with high re-producibility in microspot protein content using nitrocellulose-coated glass microslides, combined with piezoelectric microspotting of protein solutions. Protocols were developed that allowed us to use 5000 cells or fewer on an array of 4 × 4 mm consisting of 64 microspots. Using this microarray system, we identified differences of adhesive properties of three cell lines to 14 different ECM proteins. Furthermore, the sensitivity and accuracy of the assays were increased using microarrays with ranges of ECM protein amounts. This microarray system will be particularly useful for extensive comparative cell adhesion profiling studies when only low amounts of adhesive substrate and cells, such as stem cells or cells from biopsies, are available.

Photoimmobilized array of panel cells for assay of antibodies

Antibodies in blood are checked with panel blood cells before blood transfusion. In this investigation, for the first time, a panel cell-microarray was prepared by using a photoimmobilization method. Different types of red blood cells were microarrayed on a plate. A water-soluble photoreactive polymer as a matrix was synthesized by the coupling reaction of azidoaniline with poly(2-methacryloyloxyethylphosphorylcholine-co-methacrylic acid). The polymer was mixed with cells and the mixtures were microspotted on substrate and photoirradiated after drying in air. For the antibody assay, monoclonal antibodies or human serum was added to the cell-arrayed plate and adsorbed antibodies were detected by horseradish peroxidase-labeled secondary antibody, which recognized the adsorbed antibodies. Antibodies specifically adsorbed on the immobilized cells as expected. The aggregation method has been available for this type of assay, but extensive experience was needed to apply it correctly. The method using a cell array will be useful for antibody detection.

Protein and peptide arrays: recent trends and new directions

Microarrays of proteins and peptides make it possible the screening of thousands of binding events in a parallel and high throughput fashion; therefore they are emerging as a powerful tool for proteomics and clinical assays. The complex nature of Proteome, the wide dynamic range of protein concentration in real samples and the critical role of immobilized protein orientation must be taken into account to maximize the utility of protein microarrays. Immobilization strategy and designing of an ideal local chemical environment on the solid surface are both essential for the success of a protein microarray experiment. This review article will focus on protein and peptide arrays highlighting their technical challenges and presenting new directions by means of a set of selected recent applications.

Clinically Related Protein–Peptide Interactions Monitored in Real Time on Novel Peptide Chips by Surface Plasmon Resonance Imaging

Background: Developing rapid, high-throughput assays for detecting and characterizing protein–protein interactions is a great challenge in the postgenomic era. We have developed a new method that allows parallel analysis of multiple analytes in biological fluids and is suitable for biological and medical studies.

Methods: This technology for studying peptide–antibody interactions is based on polypyrrole-peptide chips and surface plasmon resonance imaging (SPRi). We generated a chip bearing a large panel of peptide probes by successive electro-directed copolymerizations of pyrrole–peptide conjugates on a gold surface.

Results: We provide evidence that (a) the signal produced by antibody binding is highly specific; (b) the detected signal specifically reflects the antibody concentration of the tested solution in a dose-dependent manner; (c) this technique is appropriate for analyzing complex media such as undiluted sera, a novelty with respect to previous techniques; and (d) correlation between classic ELISA results and the SPRi signal is good (P = 0.008). We also validated this system in a medical model by detecting anti-hepatitis C antibodies in patient-derived sera.

Conclusion: Because of its characteristics (easy preparation of the peptide chip; high-throughput, label-free, real-time detection; high specificity; and low background), this technology is suitable for screening biological samples and for large-scale studies.

Protein-detecting microarrays: current accomplishments and requirements

The sequencing of the human genome has been successfully completed and offers the chance of obtaining a large amount of valuable information for understanding complex cellular events simply and rapidly in a single experiment. Interestingly, in addressing these proteomic studies, the importance of protein-detecting microarray technology is increasing. In the coming few years, microarray technology will become a significantly promising and indispensable research/diagnostic tool from just a speculative technology. It is clear that the protein-detecting microarray is supported by three independent but strongly related technologies (surface chemistry, detection methods, and capture agents). Firstly, a variety of surface-modification methodologies are now widely available and offer site-specific immobilization of capture agents onto surfaces in such a way as to keep the native conformation and activity. Secondly, sensitive and parallel detection apparatuses are being developed to provide highly engineered microarray platforms for simultaneous data acquisition. Lastly, in the development of capture agents, antibodies are now probably the most prominent capture agents for analyzing protein abundances. Alternative scaffolds, such as phage-displayed antibody and protein fragments, which provide the advantage of increasing diversity of proteinic capture agents, however, are under development. An approach involving recombinant proteins fused with affinity tag(s) and coupled with a highly engineered surface chemistry will provide simple production protocols and specific orientations of capture agents on the microarray formats. Peptides and other small molecules can be employed in screening highly potent ligands as well as in measuring enzymatic activities. Protein-detecting microarrays supported by the three key technologies should contribute in accelerating diagnostic/biological research and drug discovery.

Advanced analytical tools in proteomics

Proteomics deals with the study of proteins, their structures, localizations, posttranslational modifications, functions and interactions with other proteins. The mapping of protein structure-function holds the key to a better understanding of cellular functions under both normal and disease states, which is critical for modern drug discovery. However, the study of human proteome presents scientists with a task much more daunting than the human genome project. In fact, the estimated >100,000 different proteins expressed from 30,000 to 40,000 human genes make it extremely challenging, if not impossible with existing protein analysis techniques, to map the entire cellular functions at the translational level. Consequently, there have been rapid advances in the techniques and methods capable of large-scale proteomic studies. Among them, the recently developed high-throughput screening methods have enabled scientists to analyze proteins quickly and efficiently at an organism-wide scale. Herein, we overview some of these emerging tools for high-throughput protein analysis. In particular, we focus on recent advances in the bioassay development, which has provided sensitive and selective tools for high-throughput identification and characterizations of enzymes. Finally, the recently developed bioimaging techniques to visualize and quantify proteins in living cells are also discussed.

Probing lipid-protein interactions using lipid microarrays

Lipids are central to the regulation and control of several cellular functions. They form many of the important structural features of cells, and are critical members of cellular signal transduction pathways. Cellular dysfunction is often caused by errors in lipid signaling; therefore, the proteins that interact with, synthesize or metabolize the lipids are potential therapeutic targets. Characterizing the contingent of cellular lipids and their abundance and how this is associated with disease will facilitate understanding how to intervene to correct diseases caused by dysfunctional lipid signaling. Since lipid-signaling networks involve several classes of proteins it is essential to determine the identity and role of these proteins in order to understand the networks. These proteins may be receptors, effectors, transporters or enzymes. We present tools, specifically, a lipid microarray platform, to uncover lipid-binding effector proteins that function in lipid signaling pathways. Lipid microarrays will allow researchers to obtain a comparable fingerprint of the proteins from a cell or tissue that bind to lipids, and also enable the identification of functionally important lipid-binding proteins. By applying a systematic approach to the quantification of lipid-protein interactions, lipid microarrays will provide an integrated knowledge base for the human lipidome. These tools have the potential to identify and validate targets to improve personalized medicine and health.

Combinatorial solid phase peptide synthesis and bioassays

Solid phase peptide synthesis method, which was introduced by Merrifield in 1963, has spawned the concept of combinatorial chemistry. In this review, we summarize the present technologies of solid phase peptide synthesis (SPPS) that are related to combinatorial chemistry. The conventional methods of peptide library synthesis on polymer support are parallel synthesis, split and mix synthesis and reagent mixture synthesis. Combining surface chemistry with the recent technology of microelectronic semiconductor fabrication system, the peptide microarray synthesis methods on a planar solid support are developed, which leads to spatially addressable peptide library. There are two kinds of peptide microarray synthesis methodologies: pre-synthesized peptide immobilization onto a glass or membrane substrate and in situ peptide synthesis by a photolithography or the SPOT method. This review also discusses the application of peptide libraries for high-throughput bioassays, for example, peptide ligand screening for antibody or cell signaling, enzyme substrate and inhibitor screening as well as other applications.

Protein "fingerprinting" in complex mixtures with peptoid microarrays

We report here that microarrays comprised of several thousand peptoids (oligo-N-substituted glycines) are useful tools for the identification of proteins via a "fingerprinting" approach. By using maltose-binding protein, glutathione S-transferase, and ubiquitin, a specific and highly reproducible pattern of binding was observed when fluorescently labeled protein was hybridized to the array. A similar pattern was obtained when binding of an unlabeled protein to the array was visualized by secondary hybridization of a labeled antibody against that protein, showing that native proteins can be identified without the requirement for prior chemical labeling. This work suggests that small-molecule microarrays might be used for more complex fingerprinting assays of potential diagnostic value.

Microarray-Based Detection of Protein Binding and Functionality by Gold Nanoparticle Probes

We report a microarray format for the detection of proteins and protein functionality (kinase activity) based on marking either specific antibody-protein binding or peptide phosphorylation events by attachment of gold nanoparticles followed by silver deposition for signal enhancement. The attachment of the gold nanoparticles is achieved by standard avidin-biotin chemistry. The detection principle is resonance light scattering. Highly selective recognition of standard proteins (proteins A and G) down to 1 pg/mL for proteins in solution and 10 fg for proteins on the microarray spots is demonstrated. Enzyme activity of the kinase (PKA) is detected with high specificity down to a limit of 1 fg for an established peptide substrate (kemptide) on the microarray spots. Kinase inhibition by the inhibitor (H89) is shown, demonstrating the potential for high-throughput screening for inhibitors.

Peptide microarrays for the characterization of antigenic regions of human chromogranin A

Microarraying peptides is a powerful proteomics technique for studying molecular recognition events. Since peptides have small molecular mass, they are not easily accessible when adsorbed onto solid supports. Moreover, peptides can lack a well-defined three-dimensional structure, and therefore a correct orientation is essential to promote the interaction with their target. In this work, we investigated the suitability as a peptide array substrate of a glass slide coated with a copolymer of N,N-dimethylacrylamide, N,N-acryloyloxysuccinimide, and [3-(methacryloyl-oxy)propyl]trimethoxysilyl. This polymeric surface was used as substrate for peptides in the characterization of linear antigenic sites of human chromogranin A, a useful tissue and serum marker for neuroendocrine tumors and a precursor of many biologically active peptides. The microarray support provided sufficient accessibility of the ligand, with no need for a spacer, as the polymer chains prevent interaction of immobilized peptides with substrate. In addition, the polymeric surface constitutes an aqueous micro-environment in which linear epitopes are freely exposed despite peptide random orientation. The results reported in this article are in accordance with those obtained in conventional ELISA assays using biotinylated and non-biotinylated peptides.

Protein micropatterns using a pH-responsive polymer and light

Protein and peptide microarrays are popular candidates for medical diagnostics because of the possibility for high sensitivity and simultaneous marker screening. To realize the potential of these arrays, new strategies for ligand patterning are needed. We report a method for patterning proteins that utilizes a pH-responsive polymer, deep ultraviolet (DUV) light, and a photoacid generator (PAG). Poly(3,3'-diethoxypropyl methacrylate) (PDEPMA) contains reactive acetal side chains which are converted to aldehydes following treatment with acid. PDEPMA was spin-coated onto Si-SiO(2) substrates and was either chemically deprotected with 1 M HCl or photochemically deprotected by exposure to DUV in the presence of triphenylsulfonium triflate. Conversion to aldehyde groups was confirmed with Purpald and by reaction with a green fluorescent hydroxylamine. Protein microarrays were demonstrated by incubating photochemically patterned surfaces with an aldehyde-reactive biotin followed by red fluorescent streptavidin. This methodology provides a new substrate for the precise patterning of both peptides and proteins for various biological applications including medical sensors.

Development of a novel protein microarray method for serotyping Salmonella enterica strains

An antibody microarray assay was developed for Salmonella serotyping based on the Kauffmann-White scheme. A model (8 by 15) array was constructed using 35 antibodies for identification of 20 common Salmonella serovars and evaluated using 117 target and 73 nontarget Salmonella strains. The assay allowed complete serovar identification of 86 target strains and partial identification of 30 target strains and allowed exclusion of the 73 nontarget strains from the target serovars.

Photothermal Readout of Surface-Arrayed Proteins: Attomole Detection Levels with Gold Nanoparticle Visualization

Transverse photothermal beam deflection (tPBD) is used to detect and quantify proteins arrayed on slides. The slides are "read" using an argon-ion excitation source. Optical absorption cross-sections of most proteins are too small for submonolayer coverages to produce thermal gradients of sufficient magnitude for detection using tPBD. Thus, surface-arrayed proteins are stained using mercaptoalkanoic acid coated gold nanoparticles (maa-AuNP). The large optical cross-sections of AuNP combined with electrolyte-induced AuNP aggregation afford a highly sensitive method for protein detection. Following maa-AuNP staining, the tPBD signal varies linearly with the amount of protein (Neutravidin) spotted on the slide surface: from 0.001 to 1.0 monolayer of protein. In a single 0.7 mm diameter array spot, the tPBD detection limit is 33 amol of Neutravidin or fewer than 55 protein molecules per microm2. Despite the nonspecific nature of interactions between maa-AuNP and proteins, significant variations in protein staining efficacy are observed. The factors controlling staining are not elucidated in detail, but there is a correlation between protein pI and protein staining. Proteins with pI approximately 6 are more effectively visualized by maa-AuNp than are more acidic or more basic proteins. The influence of AuNP diameter and mercaptoalkanoic acid chain length on protein staining and selectivity is investigated. The results demonstrate that AuNP staining coupled with tPBD detection constitutes a sensitive and practical method for probing protein arrays.

Orientations of nematic liquid crystals on surfaces presenting controlled densities of peptides: amplification of protein-peptide binding events

We report a study of the orientations of nematic liquid crystals (LCs) in contact with peptide-modified, oligoethylene glycol-containing, self-assembled monolayers (SAMs). The SAMs were formed on gold films that were prepared by physical vapor deposition at an oblique angle of incidence. Two peptides were investigated: the optimized substrate for the Src protein kinase (IYGEFKKKC) and the synthetic equivalent of that peptide after kinase modification (IpYGEFKKKC). Polarization modulation-infrared reflectance absorbance spectroscopy (PM-IRRAS) was used to characterize the relative areal densities and orientations of these peptides at the interface. We conclude that the presence/absence of a phosphate group can influence the maximum packing density of immobilized peptide. We evaluated the orientations of the nematic liquid crystal 5CB in contact with these peptide-modified surfaces by using polarized microscopy. The time required for the nematic phase of 5CB to exhibit long-range orientational ordering (uniform alignment) was found to increase with increasing areal densities of immobilized peptide. We also found that the specific binding event between anti-phosphotyrosine IgG and the surface-immobilized phosphopeptide leads to an increase in the time required for the liquid crystal to achieve uniform anchoring (exceeding the experimentally accessible time scales). These results, when combined, suggest that the areal density and size of biomolecules at an interface can influence the time required for liquid crystals in contact with nanostructured surfaces to exhibit long-range orientational order. Finally, we illustrate the potential utility of this system by demonstrating that liquid crystals can be used to amplify and report protein binding events occurring on a spatially resolved peptide array.

Detection and Quantification of On-Chip Phosphorylated Peptides by Surface Plasmon Resonance Imaging Techniques Using a Phosphate Capture Molecule

We describe herein a detection and quantification system for on-chip phosphorylation of peptides by surface plasmon resonance (SPR) imaging techniques using a newly synthesized phosphate capture molecule (i.e., biotinylated zinc(II) complex). The biotinylated compound is a dinuclear zinc(II) complex that is suitable for accessing phosphate anions as a bridging ligand on the two zinc(II) ions. The compound was exposed on the peptide array and detected with streptavidin (SA) via a biotin-SA interaction by SPR imaging. In the conventional method using antibody, both anti-phosphoserine and anti-phosphotyrosine antibodies were required for phosphoserine and phosphotyrosine detection, respectively. Detection of the phosphate group by the zinc(II) complex, however, was independent of the phosphorylated amino acid residues. The calibration curve for the phosphorylation ratios was established with a calibration chip, on which phosphoserine-containing peptide probes were immobilized. The peptide probes, which were phosphorylated on the surface by protein kinase A, were detected and quantified by SPR imaging using the zinc(II) complex, SA, and anti-SA antibody. The reaction rate and the kinetics of on-chip phosphorylation were also evaluated with the peptide array. The phosphorylation ratio was saturated at approximately 20% in 2 h in this study.

Producing peptide arrays for epitope mapping by intein-mediated protein ligation

Peptide arrays are increasingly used to define antibody epitopes and substrate specificities of protein kinases. Their use is hampered, however, by ineffective and variable binding efficiency of peptides, which often results in low sensitivity and inconsistent results. To overcome these limitations, we have developed a novel method for making arrays of synthetic peptides on various membranes after ligating the peptide substrates to an intein-generated carrier protein. We have conducted screening for optimal carrier proteins by immunoreactivity and direct assessment of binding using a peptide derivatized at a lysine sidechain with fluorescein, CDPEK(fluorescein)DS. Ligation of a synthetic peptide antigen to a carrier protein, HhaI methylase, resulted in an improved retention of peptides and an increased sensitivity of up to 10(4)-fold in immunoassay- and epitope-scanning experiments. Denaturing the ligation products with 2% sodium dodecyl sulfate (SDS) or an organic solvent (20% methanol) prior to arraying did not significantly affect the immunoreactivity of the HhaI methylase-peptide product. Because the carrier protein dominates the binding of ligation products and contains one peptide reactive site, the amount of peptide arrayed onto the membranes can be effectively normalized. This technique was utilized in the alanine scanning of hemagglutinin (HA) antigen using two monoclonal antibodies, resulting in distinguishing the different antigen epitope profiles. Furthermore, we show that this method can be used to characterize the antibodies that recognize phosphorylated peptides. This novel approach allows for synthetic peptides to be uniformly arrayed onto membranes, compatible with a variety of applications.

Ligand discovery using small molecule microarrays

Small molecule microarrays have recently been used to identify ligands for several proteins, and several themes regarding screening strategies and limitations have emerged. In this review, some of the technical issues related to the manufacture and screening of small molecule microarrays, as well as prospects for small molecule microarrays in several areas of drug discovery and chemistry, are discussed.

Gene expression profiling of cerebellar development with high-throughput functional analysis

We measured the expression levels of 450 genes during mouse postnatal cerebellar development by quantitative PCR using RNA purified from layers of the cerebellar cortex. Principal component analysis of the data matrix demonstrated that the first and second components corresponded to general levels of gene expression and gene expression patterns, respectively. We introduced 288 of the 450 genes into PC12 cells using a high-throughput transfection assay based on atelocollagen and determined the ability of each gene to promote neurite outgrowth or cell proliferation. Five genes induced neurite outgrowth, and seven genes enhanced proliferation. Evaluation of the functional data and gene expression patterns showed that none of these genes exhibited elevated expression at maturation, suggesting that genes characteristic of mature neurons are not likely to participate in neuronal development. These results demonstrate that functional data can facilitate interpretation of expression profiles and identification of new molecules that participate in biological processes.

Semicarbazide-functionalized Si(111) surfaces for the site-specific immobilization of peptides

The covalent attachment of semicarbazide-functionalized layers to hydrogen-terminated Si(111) surfaces is reported. The surface modification, based on the photoinduced hydrosilylation of a Si(111) surface with protected semicarbazide-functionalized alkenes, was investigated by means of X-ray photoelectron spectroscopy (XPS), contact angle measurements, and atomic force microscopy (AFM). The removal of the protecting group yielded a semicarbazide-terminated monolayer which was reacted with peptides bearing a glyoxylyl group for site-specific alpha-oxo semicarbazone ligation.

A new compact disc format of high density array synthesis applied to peptide nucleic acids and in situ MALDI analysis

A fully automated synthesizer was constructed and designed to perform high speed miniaturized syntheses of compound libraries using the SPOT technique. Utilizing magnetically controlled drop-on-demand ink jet nozzles, an r/phi array format of 2500 spots can be simultaneously dispensed from up to 24 separate reagent valves onto a rotating disc as the solid phase in less than three minutes. In addition, a complete wash station is on board allowing for fully programmable combinatorial syntheses without manual attention. A new carbon black/polypropylene composite solid phase disc was developed and tested for its functionalisation/loading, spot detection, durability and MALDI-TOF target capabilities. The carbon black/polypropylene composite was then successfully employed jointly as the solid phase in the syntheses of short peptide and PNA oligomers and as the target probe holder for MALDI-TOF measurement without transfer of the material. Several protocols for PNA syntheses were also investigated and an optimised PNA methodology for the carbon black/polypropylene composite is reported.

An extracellular matrix microarray for probing cellular differentiation

We present an extracellular matrix (ECM) microarray platform for the culture of patterned cells atop combinatorial matrix mixtures. This platform enables the study of differentiation in response to a multitude of microenvironments in parallel. The fabrication process required only access to a standard robotic DNA spotter, off-the-shelf materials and 1,000 times less protein than conventional means of investigating cell-ECM interactions. To demonstrate its utility, we applied this platform to study the effects of 32 different combinations of five extracellular matrix molecules (collagen I, collagen III, collagen IV, laminin and fibronectin) on cellular differentiation in two contexts: maintenance of primary rat hepatocyte phenotype indicated by intracellular albumin staining and differentiation of mouse embryonic stem (ES) cells toward an early hepatic fate, indicated by expression of a beta-galactosidase reporter fused to the fetal liver-specific gene, Ankrd17 (also known as gtar). Using this technique, we identified combinations of ECM that synergistically impacted both hepatocyte function and ES cell differentiation. This versatile technique can be easily adapted to other applications, as it is amenable to studying almost any insoluble microenvironmental cue in a combinatorial fashion and is compatible with several cell types.

Fully automated synthesis of (phospho)peptide arrays in microtiter plate wells provides efficient access to protein tyrosine kinase characterization

Background

Synthetic peptides have played a useful role in studies of protein kinase substrates and interaction domains. Synthetic peptide arrays and libraries, in particular, have accelerated the process. Several factors have hindered or limited the applicability of various techniques, such as the need for deconvolution of combinatorial libraries, the inability or impracticality of achieving full automation using two-dimensional or pin solid phases, the lack of convenient interfacing with standard analytical platforms, or the difficulty of compartmentalization of a planar surface when contact between assay components needs to be avoided. This paper describes a process for synthesis of peptides and phosphopeptides on microtiter plate wells that overcomes previous limitations and demonstrates utility in determination of the epitope of an autophosphorylation site phospho-motif antibody and utility in substrate utilization assays of the protein tyrosine kinase, p60^c-src.

Results

The overall reproducibility of phospho-peptide synthesis and multiplexed EGF receptor (EGFR) autophosphorylation site (pY1173) antibody ELISA (9H2) was within 5.5 to 8.0%. Mass spectrometric analyses of the released (phospho)peptides showed homogeneous peaks of the expected molecular weights. An overlapping peptide array of the complete EGFR cytoplasmic sequence revealed a high redundancy of 9H2 reactive sites. The eight reactive phospopeptides were structurally related and interestingly, the most conserved antibody reactive peptide motif coincided with a subset of other known EGFR autophosphorylation and SH2 binding motifs and an EGFR optimal substrate motif. Finally, peptides based on known substrate specificities of c-src and related enzymes were synthesized in microtiter plate array format and were phosphorylated by c-Src with the predicted specificities. The level of phosphorylation was proportional to c-Src concentration with sensitivities below 0.1 Units of enzyme.

Conclusions

The ability of this method to interface with various robotics and instrumentation is highly flexible since the microtiter plate is an industry standard. It is highly scalable by increasing the surface area within the well or the number of wells and does not require specialized robotics. The microtiter plate array system is well suited to the study of protein kinase substrates, antigens, binding molecules, and inhibitors since these all can be quantitatively studied at a single uniform, reproducible interface.

Use of protein-acrylamide copolymer hydrogels for measuring protein concentration and activity

We report the development and characterization of a polyacrylamide-based protein immobilization strategy for surface-bound protein assays, including concentration detection, binding affinity, and enzyme kinetics. Glutathione S-transferase (GST) fusion proteins have been labeled with an acrylic moiety and attached to acrylic-functionalized glass surfaces through copolymerization with acrylic monomer. The specific attachment of GST-green fluorescent protein (GFP) fusion protein was more than sevenfold greater than the nonspecific attachment of nonacrylic-labeled GST-GFP; 0.32 ng/mm(2) of surface-attached GST-GFP was detectable by direct measurement of GFP fluorescence and this lower detection limit was reduced to 0.080 ng/mm(2) using indirect antibody-based detection. The polyacrylamide-based surface attachment strategy was also used to measure the kinetics of substrate phosphorylation by the kinase c-Src. Michaelis-Menten kinetic constants for the reaction occurring in solution were K(m) = 2.7 +/- 1.0 microM and V(max) = 8.1 +/- 3.1 (arbitrary units). Kinetic values for the reaction utilizing surface-immobilized substrate were K(m) = 0.36 +/- 0.033 microM and V(max) = 9.7 +/- 0.63 and were found to be independent of the acrylamide concentration within the copolymer. Such a surface attachment strategy should be applicable to the proteomics field and addresses denaturation and dehydration problems associated with protein microarray development.

Immobilization of amine-modified oligonucleotides on aldehyde-terminated alkanethiol monolayers on gold

Chemistry is described for the fabrication of DNA arrays on gold surfaces. Alkanethiols modified with terminal aldehyde groups are used to prepare a self-assembled monolayer (SAM). The aldehyde groups of the monolayer may be reacted with amine-modified oligonucleotides or other amine-bearing biomolecules to form a Schiff base, which may then be reduced to a stable secondary amine by treatment with sodium cyanoborohydride. The surface modifications and reactions are characterized by polarization modulation Fourier transform infrared reflection absorption spectroscopy (PM-FTIRRAS), and the accessibility, binding specificity, and stability of the DNA-modified surfaces are demonstrated in hybridization experiments.

Exploring biology with small organic molecules

Small organic molecules have proven to be invaluable tools for investigating biological systems, but there is still much to learn from their use. To discover and to use more effectively new chemical tools to understand biology, strategies are needed that allow us to systematically explore 'biological-activity space'. Such strategies involve analysing both protein binding of, and phenotypic responses to, small organic molecules. The mapping of biological-activity space using small molecules is akin to mapping the stars--uncharted territory is explored using a system of coordinates that describes where each new feature lies.

Peptide and small-molecule microarrays

Two methods that use chemoselective ligation chemistry to prepare peptide and small-molecule microarrays are described here. The first method involves the functionalization of a glass slide with a glyoxylyl group, followed by chemoselective ligation of small molecules or peptides to the functionalized surface via a covalent bond. In the second method, peptides or small molecules are first conjugated to a macromolecular scaffold. The final ligand-scaffold conjugates are then spotted and adsorbed onto the solid surface. Three different assay methods to screen such chemical microarrays are described.

Photo-reactive polyvinylalcohol for photo-immobilized microarray

A new photo-reactive polymer, polyvinylalcohol modified with phenylazido groups, was synthesized as a microarray matrix. The polymer is soluble in water and spin-coated onto glass plate. Aqueous solutions of proteins were micro-spotted onto the coated glass and were fixed by ultraviolet light irradiation. Subsequently, cell adhesion on the photo-immobilized protein microarray was investigated. Non-specific adhesion of cells onto non-protein-spotted regions was reduced in comparison with the previously prepared microarray chip (Biomaterials 24 (2003) 3021). The adhesion behavior of cells depended on the kind of immobilized proteins and the type of cells. The microarray will be useful for cell diagnosis and for the selection of biomaterials to regulate cell behavior.

Arrays for the combinatorial exploration of cell adhesion

A new method for the fabrication of arrays of self-assembled monolayers (SAMs) of alkane thiols (ATs) on gold to combinatorially assay surfaces for cell adhesion is reported. A fluorous SAM, which is both cytophobic and solvophobic, was used as the background between the array features. The resulting solvophobic background permits the application of an assembly after conjugation strategy for fabrication. SAMs containing mixtures of ATs and peptide-terminated ATs were generated. Multiple cell types demonstrated differential and specific binding to these surfaces. Additionally, pluripotent human embryonic stem cells proliferated on surfaces generated by this method.

Microarrays of small molecules embedded in biodegradable polymers for use in mammalian cell-based screens

We developed a microarray-based system for screening small molecules in mammalian cells. This system is compatible with image-based screens and requires fewer than 100 cells per compound. Each compound is impregnated in a 200-microm-diameter disc composed of biodegradable poly-(D),(L)-lactide/glycolide copolymer. Cells are seeded on top of these discs, and compounds slowly diffuse out, affecting proximal cells. In contrast with microtiter-based screening, this system does not involve the use of wells or walls between each compound-treated group of cells. We demonstrate detection of the effects of a single compound in a large microarray, that diverse compounds can be released in this format, and that extended release over several days is feasible. We performed a small synthetic lethal screen and identified a compound (macbecin II) that has reduced activity in cells with RNA interference-mediated decrease in the expression of tuberous sclerosis 2. Thus, we have developed a microarray-based screening system for testing the effects of small molecules on mammalian cells by using an imaging-based readout. This method will be useful to those performing small-molecule screens to discover new chemical tools and potential therapeutic agents.

New approaches in identifying drugs to inactivate oncogene products

With an information explosion on the molecular mechanism of oncogenesis, the completion of the human genome sequence project, and the advances in genomic and proteomic methods, many therapeutic targets for various cancers have been identified. It is timely that a number of new drug development techniques have been developed in this last decade. Candidate drug targets can now be efficiently validated with RNA interference and transgenic animals studies. Combinatorial chemistry provides large numbers of chemical compounds for drug lead discovery and optimization. High throughput assays and high content cell-based assays, in conjunction with sophisticated robotics, are now available for screening large numbers of compounds. Based on X-ray crystallographic structure data, drug leads can be discovered through in silico screening of virtual libraries. By applying these various drug discovery techniques, it is anticipated that more potent and specific anti-cancer agents will be discovered within the next decade.

Kinome profiling for studying lipopolysaccharide signal transduction in human peripheral blood mononuclear cells

The DNA array technique allows comprehensive analysis of the genome and transcriptome, but the high throughput array-based assessment of intracellular signal transduction remains troublesome. The goal of this study was to test a new peptide array technology for studying the activity of all kinases of whole cell lysates, the kinome. Cell lysates from human peripheral blood mononuclear cells before and after stimulation with lipopolysaccharide were used for in vitro phosphorylation with [gamma-33P]ATP arrays consisting of 192 peptides (substrates for kinases) spotted on glass. The usefulness of peptide arrays for studying signal transduction was demonstrated by the generation of the first comprehensive description of the temporal kinetics of phosphorylation events induced by lipopolysaccharide stimulation. Furthermore analysis of the signals obtained suggested activation of p21Ras by lipopolysaccharide, and this was confirmed by direct measurement of p21Ras GTP levels in lipopolysaccharide-stimulated human peripheral blood mononuclear cells, which represents the first direct demonstration of p21Ras activation by stimulation of a Toll receptor family member. Further confidence in the usefulness of peptide array technology for studying signal transduction came from Western blot analysis of lipopolysaccharide-stimulated cells, which corroborated the signals obtained using peptide arrays as well as from the demonstration that kinase inhibitors effected peptide array phosphorylation patterns consistent with the expected action of these inhibitors. We conclude that this first metabolic array is a useful method to determine the enzymatic activities of a large group of kinases, offering high throughput analysis of cellular metabolism and signal transduction.

Microarrays of Tagged Combinatorial Triazine Libraries in the Discovery of Small-Molecule Ligands of Human IgG

A novel and highly diverse tagged triazine library incorporating a triethylene glycol-based linker was synthesized using an orthogonal combinatorial approach on the solid phase and covalently immobilized on a glass substrate as a small molecule microarray (SMM). The SMM was screened with a fluorophore-conjugated human IgG, and 4 novel binders from a library of 2688 compounds were identified from the fully spatially addressable array without the need for compound decoding. Using surface plasmon resonance (SPR) analysis, binding seen on the array was confirmed, and a binding constant as low as Kd = 2.02 x10(-6) M was measured.