Manual manufacturing of oligonucleotide, DNA, and protein microchips

Shrinkable Hydrogel-Enhanced Biomarker Detection with X-ray Fluorescent Nanoparticles

This paper reports a new method to enhance the sensitivity of nanoparticle-based protein detection with X-ray fluorescence by exploiting the large volume reduction of hydrogel upon dehydration. A carboxylated agarose hydrogel with uniaxial microchannels is used to allow rapid diffusion of nanoparticles and biomolecules into the hydrogel and water molecules out of the hydrogel. Carboxylated hydrogels are modified to capture protein biomarkers and X-ray fluorescence nanoparticles (iron oxide nanoparticles) are modified with antibodies that are specific to protein biomarkers. The presence of protein biomarkers in solution binds the nanoparticles on the hydrogel channels. The dehydration of hydrogels leads to a size reduction of over 80 times, which increases the number of nanoparticles in the interaction volume of the primary X-ray beam and the intensity of characteristic X-ray fluorescence signal. A detection limit of 2 μg/mL for protein detection has been established by determining the number of nanoparticles using X-ray fluorescence.

The Role of Surface Chemistry in the Efficacy of Protein and DNA Microarrays for Label-Free Detection: An Overview

The importance of microarrays in diagnostics and medicine has drastically increased in the last few years. Nevertheless, the efficiency of a microarray-based assay intrinsically depends on the density and functionality of the biorecognition elements immobilized onto each sensor spot. Recently, researchers have put effort into developing new functionalization strategies and technologies which provide efficient immobilization and stability of any sort of molecule. Here, we present an overview of the most widely used methods of surface functionalization of microarray substrates, as well as the most recent advances in the field, and compare their performance in terms of optimal immobilization of the bioreceptor molecules. We focus on label-free microarrays and, in particular, we aim to describe the impact of surface chemistry on two types of microarray-based sensors: microarrays for single particle imaging and for label-free measurements of binding kinetics. Both protein and DNA microarrays are taken into consideration, and the effect of different polymeric coatings on the molecules' functionalities is critically analyzed.

Sandwich-Based Antibody Arrays for Protein Detection

Sandwich-based antibody arrays enable the detection of multiple proteins simultaneously, thus offering a time- and cost-effective alternative to single-plex platforms. The protein of interest is "sandwiched" between an antibody that captures it to the array and a second antibody that is used for detection. Here we describe a 1-day procedure to process samples, such as serum or cell lysates, with a quantitative sandwich-based antibody array on a glass substrate using fluorescence.

The Surface Science of Microarray Generation-A Critical Inventory

Microarrays are powerful tools in biomedical research and have become indispensable for high-throughput multiplex analysis, especially for DNA and protein analysis. The basis for all microarray processing and fabrication is surface modification of a chip substrate and many different strategies to couple probe molecules to such substrates have been developed. We present here a critical assessment of typical biochip generation processes from a surface science point of view. While great progress has been made from a molecular biology point of view on the development of qualitative assays and impressive results have been obtained on the detection of rather low concentrations of DNA or proteins, quantitative chip-based assays are still comparably rare. We argue that lack of stable and reliable deposition chemistries has led in many cases to suboptimal quantitative reproducibility, impeded further progress in microarray development and prevented a more significant penetration of microarray technology into the diagnostic market. We suggest that surface-attached hydrogel networks might be a promising strategy to achieve highly sensitive and quantitatively reproducible microarrays.

A Quasi-direct LC-MS/MS-based Targeted Proteomics Approach for miRNA Quantification via a Covalently Immobilized DNA-peptide Probe

MicroRNAs (miRNAs) play a vital role in regulating gene expression and are associated with a variety of cancers, including breast cancer. Their distorted and unique expression is a potential marker in clinical diagnoses and prognoses. Thus, accurate determination of miRNA expression levels is a prerequisite for their applications. However, the assays currently available for miRNA detection typically require pre-enrichment, amplification and labeling steps, and most of the assays are only semi-quantitative. Therefore, we developed a quasi-direct liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based targeted proteomics approach to quantify target miRNA by innovatively converting the miRNA signal into the mass response of a reporter peptide via a covalently immobilized DNA-peptide probe. Specifically, the probe containing the targeted proteomics-selected substrate/reporter peptide, GDRAVQLGVDPFR/AVQLGVDPFR, and the DNA sequence complementary to the target miRNA (i.e., miR-21) was first immobilized on APMTS modified silica nanoparticles using PDITC. After the immobilized probe was recognized and hybridized with the target miRNA, the excess probe was degraded using MBN and followed by a trypsin digestion of the hybrids. The reporter peptide was released and quantified using LC-MS/MS. The obtained LOQ was 5 pM. Finally, the developed assay was used for the quantitative analysis of miR-21 in breast cells and tissue samples.

Analytical Protein Microarrays: Advancements Towards Clinical Applications

Protein microarrays represent a powerful technology with the potential to serve as tools for the detection of a broad range of analytes in numerous applications such as diagnostics, drug development, food safety, and environmental monitoring. Key features of analytical protein microarrays include high throughput and relatively low costs due to minimal reagent consumption, multiplexing, fast kinetics and hence measurements, and the possibility of functional integration. So far, especially fundamental studies in molecular and cell biology have been conducted using protein microarrays, while the potential for clinical, notably point-of-care applications is not yet fully utilized. The question arises what features have to be implemented and what improvements have to be made in order to fully exploit the technology. In the past we have identified various obstacles that have to be overcome in order to promote protein microarray technology in the diagnostic field. Issues that need significant improvement to make the technology more attractive for the diagnostic market are for instance: too low sensitivity and deficiency in reproducibility, inadequate analysis time, lack of high-quality antibodies and validated reagents, lack of automation and portable instruments, and cost of instruments necessary for chip production and read-out. The scope of the paper at hand is to review approaches to solve these problems.

Targeting of Pu.Py Duplexes by GA and GT Rich Oligonucleotides on Microchip and in Solution

Abstract Formation of triple helices with GA and GT third strands has been studied. Besides the usual investigation techniques common for characterizing triple helical formation (CD spectroscopy, gel shift mobility assay, chemical probing and S1 nuclease footprinting) we have used a new technique in which targeting of polypurine sequences in duplexes was demonstrated on oligonucleotide microchips. This technique is very successful to quickly test a large number of potential triple helix formation. In this work we used oligonucleotide microairay to study the specificity of DNA duplex recognition by GA and GT strands. Generic 6-mer microchip containing all possible 4(6) = 4,096 single-stranded hexadeoxyribonucleotides immobilized within individual gel pads was applied. To study formation of intermolecular triple helices on the generic microchip, a number of Pu.Py duplexes were formed by hybridization of the mixture of purine octadeoxyribonucleotides on the microchip followed by targeting of the duplexes by GA or GT third strands. Melting behavior of the formed structures was investigated using fluorescence measurements under microscope. In solution we present the results obtained for GT triplexes and discuss the characteristics of the CD spectra. Results obtained by S1 nuclease footprinting, KMnO(4) and DMS chemical probing are consistent with the spectroscopic data reflecting triplex structure formation.

Temperature-Invariant Aqueous Microgels as Hosts for Biomacromolecules

Immobilization of enzymes on solid supports has been widely used to improve enzyme recycling, enzyme stability, and performance. We are interested in using aqueous microgels (colloidal hydrogels) as carriers for enzymes used in high-temperature reactions. These microgels should maintain their volume and colloidal stability in aqueous media up to 100 °C to serve as thermo-stable supports for enzymes. For this purpose, we prepared poly(N-hydroxyethyl acrylamide) (PHEAA) microgels via a two-step synthesis. First, we used precipitation polymerization in water to synthesize colloidal poly(diethylene glycol-ethyl ether acrylate) (PDEGAC) particles as a precursor. PDEGAC forms solvent swollen microgels in organic solvents such as methanol and dioxane and in water at temperatures below 15 °C. In the second step, these PDEGAC particles were transformed to PHEAA microgels through aminolysis in dioxane with ethanolamine and a small amount of ethylenediamine. Dynamic laser scattering studies confirmed that the colloidal stability of microgels was maintained during the aminolysis in dioxane and subsequent transfer to water. Characterization of the PHEAA microgels indicated about 9 mol % of primary amino groups. These provide functionality for bioconjugation. As proof-of-concept experiments, we attached the enzyme horseradish peroxidase (HRP) to these aqueous microgels through (i) N-(3-(dimethylamino)propyl)-N'-ethylcarbodiimide hydrochloride (EDC) coupling to the carboxylated microgels or (ii) bis-aryl hydrazone (BAH) coupling to microgels functionalized with 6-hydrazinonicotinate acetone (PHEAA-HyNic). Our results showed that HRP maintained its catalytic activity after covalent attachment (87% for EDC coupling, 96% for BAH coupling). The microgel enhanced the stability of the enzyme to thermal denaturation. For example, the residual activity of the microgel-supported enzyme was 76% after 330 min of annealing at 50 °C, compared to only 20% for the free enzyme under these conditions. PHEAA microgels in water show great promise as hosts for enzymatic reaction, especially at elevated temperatures.

Parylene C surface functionalization and patterning with pH-responsive microgels

Parylene C is a polymer well-known for its inertness and chemical resistance, thus ideal for covering and sealing 3D substrates and structures by conformal coating. In the present study, the Parylene C surface is modified by functionalization with pH-responsive poly(methacrylic acid) microgels either over the whole surface, or in a pattern through a poly(dimethylsiloxane) stamp. The surface functionalization consists of two phases: first, an oxygen plasma treatment is used to make the surface superhydrophilic, inducing the formation of polar functional groups and surface topography modifications; then, the plasma-treated samples are functionalized by drop casting a solution of pH-responsive microgels, or in a pattern via microcontact printing of the same solution. While both techniques, namely, drop casting and microcontact printing, are easy to use, fast, and cheap, the microcontact printing was found to provide a more homogeneous functionalization and to be applicable to any shape of substrate. The functionalization effectiveness was tested by the repeated uptake and release of a fluorescent labeled monoclonal CD4 antibody at different pH values, thus suggesting a new sensing approach.

A novel cassette method for probe evaluation in the designed biochips

A critical step in biochip design is the selection of probes with identical hybridisation characteristics. In this article we describe a novel method for evaluating DNA hybridisation probes, allowing the fine-tuning of biochips, that uses cassettes with multiple probes. Each cassette contains probes in equimolar proportions so that their hybridisation performance can be assessed in a single reaction. The model used to demonstrate this method was a series of probes developed to detect TORCH pathogens. DNA probes were designed for Toxoplasma gondii, Chlamidia trachomatis, Rubella, Cytomegalovirus, and Herpes virus and these were used to construct the DNA cassettes. Five cassettes were constructed to detect TORCH pathogens using a variety of genes coding for membrane proteins, viral matrix protein, an early expressed viral protein, viral DNA polymerase and the repetitive gene B1 of Toxoplasma gondii. All of these probes, except that for the B1 gene, exhibited similar profiles under the same hybridisation conditions. The failure of the B1 gene probe to hybridise was not due to a position effect, and this indicated that the probe was unsuitable for inclusion in the biochip. The redesigned probe for the B1 gene exhibited identical hybridisation properties to the other probes, suitable for inclusion in a biochip.

Array-based immunoassays with rolling-circle amplification detection

This chapter describes methods for the use of antibody microarrays with rolling-circle amplification (RCA). The methods are divided into three sections. The first section covers antibody preparation and microarray production, the second describes the method for using biological samples on antibody microarrays, and the third describes the method for RCA use on antibody microarrays. RCA can be used on antibody microarrays to increase the signal from each antibody spot and lower the detection limits of the assays. We also describe a practical method for running multiple, low-volume microarrays on a single microscope slide. These methods should be useful for researchers interested in rapidly developing and optimizing custom immunoassays for the analysis of low-abundance analytes using low sample volumes.

Integrated amplification microarray system in a lateral flow cell for warfarin genotyping from saliva

BACKGROUND

Genetic polymorphisms in the CYP2C9 and VKORC1 genes have been linked to sensitivity of the anticoagulant drug warfarin. The aim of this study is to demonstrate a method for warfarin sensitivity genotyping using gel element microarray technology in a simplified workflow from sample collection to analysis and detection.

METHODS

We developed an integrated amplification microarray system combining PCR amplification, target labeling, and microarray hybridization within a single, closed-amplicon "lateral flow cell" for genotyping three single nucleotide polymorphisms (SNPs) that influence warfarin response. We combined nucleic acid extraction of saliva using the TruTip technology together with the lateral flow cell assay and with fully automated array detection and analysis.

RESULTS

The analytical performance of the assay was tested using 20 genotyped human genomic DNA samples and found to be sensitive down to 330 input genomic copies (1 ng). A follow-up pre-clinical evaluation was performed with 65 blinded saliva samples and the genotyping results were in agreement with those determined by bidirectional sequencing.

CONCLUSIONS

Combined with the use of non-invasive saliva samples, rapid DNA extraction, the lateral flow cell, automatic imaging and data analysis provides a simple and fast sample-to-answer microarray test for warfarin sensitivity genotyping.

Solid-phase supports for oligonucleotide synthesis

This unit attempts to provide a reasonably complete inventory of over 280 solid supports available to oligonucleotide chemists for preparation of natural and 3'-modified oligonucleotides. Emphasis is placed on non-nucleosidic solid supports. The relationship between the structural features of linkers and their behavior in oligonucleotide synthesis and deprotection is discussed wherever the relevant observations are available.

Patterned polymer nanowire arrays as an effective protein immobilizer for biosensing and HIV detection

We report an array of polymeric nanowires for effectively immobilizing biomolecules on biochips owing to the large surface area. The nanowires were fabricated in predesigned patterns using an inductively coupled plasma (ICP) etching process. Microfluidic biochips integrated using the substrates with arrays of nanowires and polydimethylsiloxane channels have been demonstrated to be effective for detecting antigens, and a detection limit of antigens at 0.2 μg mL(-1) has been achieved, which is improved by a factor of 50 compared to that based on flat substrates without the nanowires. In addition, the high sensitivity for clinical detection of human immunodeficiency virus (HIV) antibody has also been demonstrated, showing a 20 times enhancement in fluorescent signal intensity between the samples with positive and negative HIV.

pH controlled staining of CD4(+) and CD19(+) cells within functionalized microfluidic channel

Herein proposed is a simple system to realize hands-free labeling and simultaneous detection of two human cell lines within a microfluidic device. This system was realized by novel covalent immobilization of pH-responsive poly(methacrylic acid) microgels onto the inner glass surface of an assembled polydimethylsiloxane/glass microfluidic channel. Afterwards, selected thiophene labeled monoclonal antibodies, specific for recognition of CD4 antigens on T helper/inducer cells and CD19 antigens on B lymphocytes cell lines, were encapsulated in their active state by the immobilized microgels. When the lymphocytes suspension, containing the two target subpopulations, was flowed through the microchannel, the physiological pH of the cellular suspension induced the release of the labeled antibodies from the microgels and thus the selective cellular staining. The selective pH-triggered staining of the CD4- and CD19-positive cells was investigated in this preliminary experimental study by laser scanning confocal microscopy. This approach represents an interesting and versatile tool to realize cellular staining in a defined module of lab-on-a-chip devices for subsequent detection and counting.

Multiplex detection platform for tumor markers and glucose in serum based on a microfluidic microparticle array

We present a multiplex detection platform based on a microfluidic microparticle array to detect proteins and glucose in serum simultaneously. Multiplex detection of proteins and glucose was performed using biofunctionalized microparticles arrayed on gel-based microstructures integrated in microfluidics. The microparticles immobilized on these microstructures showed high stability under microfluidic flow conditions. With arrays of antibody-coated microbeads, microfluidic quantitative immunoassays for two protein tumor markers, human chorionic gonadotropin (hCG) and prostate specific antigen (PSA) were performed in serum samples with detection limits bellow the cut-off values for cancer diagnosis. Parallel to the immunoassays, quantitative enzymatic assays for glucose in the physiological concentration range were performed. Multiplex detection was achieved by using a spatially encoded microarray. By patterning antibody-coated microbeads and enzyme-containing microparticles on a novel mixed structure array, we successfully demonstrated simultaneous immunoassays (binding based assay) for proteins and an enzymatic assay (reaction kinetic based assay) for glucose. Our microparticle arrays could be potentially used for the detection of multiple categories of biomolecules (proteins, small metabolites and DNA) for clinical diagnostics and other biological applications.

Applications of functional protein microarrays in basic and clinical research

The protein microarray technology provides a versatile platform for characterization of hundreds of thousands of proteins in a highly parallel and high-throughput manner. It is viewed as a new tool that overcomes the limitation of DNA microarrays. On the basis of its application, protein microarrays fall into two major classes: analytical and functional protein microarrays. In addition, tissue or cell lysates can also be directly spotted on a slide to form the so-called "reverse-phase" protein microarray. In the last decade, applications of functional protein microarrays in particular have flourished in studying protein function and construction of networks and pathways. In this chapter, we will review the recent advancements in the protein microarray technology, followed by presenting a series of examples to illustrate the power and versatility of protein microarrays in both basic and clinical research. As a powerful technology platform, it would not be surprising if protein microarrays will become one of the leading technologies in proteomic and diagnostic fields in the next decade.

Three-dimensional hydrogel structures as optical sensor arrays, for the detection of specific DNA sequences

The fabrication and characterization of surface-attached PEG-diacrylate hydrogel structures and their application as sensing platforms for the detection of specific target sequences are reported. Hydrogel structures were formed by a photopolymerization process, using substrate-bound Eosin Y molecules for the production of free radicals. We have demonstrated that this fabrication process allows for control over hydrogel growth down to the micrometer scale. Confocal imaging revealed relatively large pore structures for 25% (v/v) PEG-diacrylate hydrogels, which appear to lie in tightly packed layers. Our data suggest that these pore structures decrease in size for hydrogels with increasing levels of PEG-diacrylate. Surface coverage values calculated for hydrogels immobilized with 21-mer DNA probe sequences were significantly higher compared to those previously reported for 2- and 3-dimensional sensing platforms, on the order of 10(16)molecules cm(-2). Used as sensing platforms in DNA hybridization assays, a detection limit of 3.9 nM was achieved for hybridization reactions between 21-mer probe and target sequences. The ability of these hydrogel sensing platforms to discriminate between wild-type and mutant allele sequences was also demonstrated, down to target concentrations of 1-2 nM. A reduction in the hybridization time down to a period of 15 min was also achieved, while still maintaining confident results, demonstrating the potential for future integration of these sensing platforms within Lab-on-Chip or diagnostic devices.

Nonvolatile copolymer compositions for fabricating gel element microarrays

By modifying polymer compositions and cross-linking reagents, we have developed a simple yet effective manufacturing strategy for copolymerized three-dimensional gel element arrays. A new gel-forming monomer, 2-(hydroxyethyl) methacrylamide (HEMAA), was used. HEMAA possesses low volatility and improves the stability of copolymerized gel element arrays to on-chip thermal cycling procedures relative to previously used monomers. Probe immobilization efficiency within the new polymer was 55%, equivalent to that obtained with acrylamide (AA) and methacrylamide (MA) monomers. Nonspecific binding of single-stranded targets was equivalent for all monomers. Increasing cross-linker chain length improved hybridization kinetics and end-point signal intensities relative to N,N-methylenebisacrylamide (Bis). The new copolymer formulation was successfully applied to a model orthopox array. Because HEMAA greatly simplifies gel element array manufacture, we expect it (in combination with new cross-linkers described here) to find widespread application in microarray science.

Functional protein microarray technology

Functional protein microarrays are emerging as a promising new tool for large-scale and high-throughput studies. In this article, we review their applications in basic proteomics research, where various types of assays have been developed to probe binding activities to other biomolecules, such as proteins, DNA, RNA, small molecules, and glycans. We also report recent progress of using functional protein microarrays in profiling protein post-translational modifications, including phosphorylation, ubiquitylation, acetylation, and nitrosylation. Finally, we discuss potential of functional protein microarrays in biomarker identification and clinical diagnostics. We strongly believe that functional protein microarrays will soon become an indispensible and invaluable tool in proteomics research and systems biology.

A polyacrylamide microbead-integrated chip for the large-scale manufacture of ready-to-use esiRNA

Endoribonuclease-prepared siRNAs (esiRNAs) have the advantages of cost effectiveness and lower off-target effects than chemically synthesized siRNA. However, the current manufacture of esiRNA is a complex process, requiring an expensive instrument and demanding skills to accomplish the transfer, purification, quantification and normalization of liquid samples. These performances significantly hamper the application of esiRNAs on a large-scale level. In this study, we present a polymer microbead-integrated chip capable of the large-scale manufacture of esiRNA in a convenient and robust manner. This chip is able to perform the amplification, transcription and enzymatic digestion of targets on polymer scaffold, thus simplifying the transfer and purification manipulation process. What is also noted, this chip can readily tailor and normalize the amount of esiRNA product by controlling the number of DNA probes and the cycle of the amplification reaction. Thus the esiRNA, also referred to as gel-esiRNA, can be immediately applied to loss-of-function study without any further treatment. The silencing specificity and efficiency of gel-esiRNAs were assessed on transcriptional, translational or cell functional levels. All data of real-time PCR, Western blot assay, or FACS clearly supported that the gel-esiRNA produced specific gene silencing as effectively as the one generated following the conventional approach. We believe that this approach would provide a more robust and cost-effective choice to manufacture esiRNAs, thus promising both more intensive and extensive applications of these heterogeneous RNA strands.

Microarrays made easy: biofunctionalized hydrogel channels for rapid protein microarray production

We present a simple, inexpensive, and sensitive technique for producing multiple copies of a hydrogel-based protein microarray. An agarose block containing 25 biofunctionalized channels is sliced perpendicularly to produce many identical biochips. Each microarray consists of 500 μm spots, which contain protein-coated microparticles physically trapped in porous SeaPrep agarose. Proteins diffuse readily through SeaPrep agarose, while the larger microparticles are immobilized in the hydrogel matrix. Without major assay optimization, the limit of detection is 12 pM for a sandwich assay detecting human IgG. These highly flexible, multiplexed arrays can be produced rapidly without any special instrumentation and are compatible with standard fluorescence-based read-out.

Microvalve and micropump controlled shuttle flow microfluidic device for rapid DNA hybridization

We present a novel microfluidic device integrated with microvalves and micropumps for rapid DNA hybridization using shuttle flow. The device is composed of 48 hybridization units containing 48 microvalves and 96 micropumps for the automation of shuttle flow. We used four serotypes of Dengue Virus genes (18mer) to demonstrate that the automatic shuttle flow shortened the hybridization time to 90 s, reduced sample consumption to 1 μL and lowered detection limit to 100 pM (100 amol in a 1 μL sample). Moreover, we applied this device to realize single base discrimination and analyze 48 samples containing different DNA targets, simultaneously. For kinetic measurements of nucleotide hybridization, on-line monitoring of the processes was carried out. This rapid hybridization device has the ability for accommodating the entire hybridization process (i.e., injection, hybridization, washing, detection, signal acquisition) in an automated and high-throughput fashion.

Search for genetic markers and functional variants involved in the development of opiate and cocaine addiction and treatment

Addiction to opiates and illicit use of psychostimulants is a chronic, relapsing brain disease that, if left untreated, can cause major medical, social, and economic problems. This article reviews recent progress in studies of association of gene variants with vulnerability to develop opiate and cocaine addictions, focusing primarily on genes of the opioid and monoaminergic systems. In addition, we provide the first evidence of a cis-acting polymorphism and a functional haplotype in the PDYN gene, of significantly higher DNA methylation rate of the OPRM1 gene in the lymphocytes of heroin addicts, and significant differences in genotype frequencies of three single-nucleotide polymorphisms of the P-glycoprotein gene (ABCB1) between "higher" and "lower" methadone doses in methadone-maintained patients. In genomewide and multigene association studies, we found association of several new genes and new variants of known genes with heroin addiction. Finally, we describe the development and application of a novel technique: molecular haplotyping for studies in genetics of drug addiction.

Affinity peptidomics: Peptide selection and affinity capture on hydrogels and microarrays

Affinity peptidomics relies on the successfully proven approach used widely in mass-spectrometry-based protein analysis, where protein samples are proteolytically digested prior to the analysis. Unlike traditional proteomic analyses, affinity peptidomics employs affinity detection instead of, or in addition to, the mass-spectrometry detection. Affinity peptidomics, therefore, bridges the gap between protein microarrays and mass spectrometry and can be used for the detection, identification and quantification of endogenous or proteolytic peptides on microarrays and by MALDI-MS. Phage display technology is a widely applicable generic molecular display method suitable for studying protein-protein or protein-peptide interactions and the development of recombinant affinity reagents. Phage display complements the affinity peptidomics approach when the latter is used, e.g. to characterise a repertoire of antigenic determinants of polyclonal, monoclonal antibodies or other recombinantly obtained affinity reagents or in studying protein-protein interactions. 3D materials such as membrane-based porous substrates and acrylamide hydrogels provide convenient alternatives and are superior to many 2D surfaces in maintaining protein conformation and minimising non-specific interactions. Hydrogels have been found to be advantageous in performing antibody affinity assays and peptide-binding assays. Here we report a range of peptide selection and peptide-binding assays used for the detection, quantification or validation of peptide targets using array-based techniques and fluorescent or MS detection.

Construction of oligonucleotide microarrays (biochips) via thioether linkage for the detection of bacterial meningitis

Oligonucleotide-based arrays are increasingly becoming useful tools for the analysis of gene expression and single-nucleotide polymorphism. Here, we report a method that allows the direct immobilization of thiolated oligonucleotides onto an epoxy-activated glass surface via a stable thioether linkage under microwaves. The described chemistry efficiently immobilizes the probes via terminal thiol groups with uniform spot morphology. The thioether linkage could endure repeated PCR-like heat cycling with only 2.5% loss after 20 cycles, indicating that the chemistry can be used in integrated PCR/microarray devices. The highlighting feature of the proposed method is that the detection limit for the probe concentration can be reduced to 0.25 microM with 20-mer oligonucleotides. The efficiency of the projected method (approximately 33%) indicates its advantage over the existing standard methods, viz., NTMTA (approximately 9.8%), epoxide-amine (approximately 9.8%) and disulfide (approximately 1.7%). The constructed microarrays were validated through the detection of base mismatches and bacterial meningitis. These features make the projected strategy ideal for manufacturing oligonucleotide arrays and detection of mismatches and bacterial diseases.

Use of intein-mediated protein ligation strategies for the fabrication of functional protein arrays

This section introduces a simple, rapid, high-throughput methodology for the site-specific biotinylation of proteins for the purpose of fabricating functional protein arrays. Step-by-step protocols are provided to generate biotinylated proteins using in vitro, in vivo, or cell-free systems, together with useful hints for troubleshooting. In vitro and in vivo biotinylation rely on the chemoselective native chemical ligation (NCL) reaction between the reactive alpha-thioester group at the C-terminus of target proteins, generated via intein-mediated cleavage, and the added cysteine biotin. The cell-free system uses a low concentration of biotin-conjugated puromycin. The biotinylated proteins can be either purified or directly captured from crude cellular lysates onto an avidin-functionalized slide to afford the corresponding protein array. The methods were designed to preserve the activity of the immobilized protein such that the arrays provide a highly miniaturized platform to simultaneously interrogate the functional activities of thousands of proteins. This is of paramount significance, as new applications of microarray technologies continue to emerge, fueling their growth as an essential tool for high-throughput proteomic studies.

Gel-pad microarrays templated by patterned porous silicon for dual-mode detection of proteins

A proof-of-concept study demonstrated the feasibility of a novel gel-pad microarray on porous silicon chips, by initiation of an atom transfer radical propagation (ATRP) polymerisation of (polyethylene glycol) methacrylate (PEGMA) with surface Si-H species, stepwise chemical conversions of the gel membrane to an NTA-Ni2+/histidine-tagged protein system, and matrix-assisted laser desorption/ionisation mass spectroscopy (MALDI MS) and fluorescence detections.

Immobilization chemistries

Among the parameters which influence the success of a microarray experiment, the attachment of the nucleic acid captures to the support surface plays a decisive role.This article attempts to review the main concepts and ideas of the multiple variants which exist in terms of the immobilization chemistries used in nucleic acid microarray technology. Starting from the attachment of unmodified nucleic acids to modified glass slides by adsorption, further strategies for the coupling of nucleic acid capture molecules to a variety of support materials are surveyed with a focus on the reactive groups involved in the respective process.After a brief introduction, an overview is given about microarray substrates with special emphasis on the approaches used for the activation of these - usually chemically inert - materials. In the next sections strategies for the "undefined" and "defined" immobilization of captures on the substrates are described. While the latter approach tries to accomplish the coupling via a defined reactive moiety of the molecule to be immobilized, the former mentioned techniques involve multiply occurring reactive groups in the capture.The article finishes with an example for microarray manufacture, the production of aminopropyltriethoxysilane (APTES) functionalized glass substrates to which PDITC homobifunctional linker molecules are coupled; on their part providing reactive functional groups for the covalent immobilization of pre-synthesized, amino-modified oligonucleotides.This survey does not seek to be comprehensive rather it tries to present and provide key examples for the basic techniques, and to enable orientation if more detailed studies are needed. This review should not be considered as a guide to how to use the different chemistries described, but instead as a presentation of various principles and approaches applied in the still evolving field of nucleic acid microarray technology.

Protein Microarrays for the Detection of Biothreats

Although protein microarrays have proven to be an important tool in proteomics research, the technology is emerging as useful for public health and defense applications. Recent progress in the measurement and characterization of biothreat agents is reviewed in this chapter. Details concerning validation of various protein microarray formats, from contact-printed sandwich assays to supported lipid bilayers, are presented. The reviewed technologies have important implications for in vitro characterization of toxin–ligand interactions, serotyping of bacteria, screening of potential biothreat inhibitors, and as core components of biosensors, among others, research and engineering applications.

Chemical strategies for generating protein biochips

Protein biochips are at the heart of many medical and bioanalytical applications. Increasing interest has been focused on surface activation and subsequent functionalization strategies for immobilizing these biomolecules. Different approaches using covalent and noncovalent chemistry are reviewed; particular emphasis is placed on the chemical specificity of protein attachment and on retention of protein function. Strategies for creating protein patterns (as opposed to protein arrays) are also outlined. An outlook on promising and challenging future directions for protein biochip research and applications is also offered.