Microminiaturized immunoassays using atomic force microscopy and compositionally patterned antigen arrays

Label-Free Protein and Pathogen Detection Using the Atomic Force Microscope

The atomic force microscope (AFM) uses a sharp micron-scale tip to scan and amplify surface features, providing exceptionally detailed topographical information with magnification on the order of ×106. This instrument is used extensively for quality control in the computer and semiconductor industries and is becoming a progressively more important tool in the biological sciences. Advantages of the AFM for biological application include the ability to obtain information in a direct, label-free manner and the ability to image in solution, providing real-time data acquisition under physiologically relevant conditions. A novel application of the AFM currently under development combines its surface profiling capabilities with fixed immuno-capture using antibodies immobilized in a nanoarray format. This provides a distinctive platform for direct, label-free detection and characterization of viral particles and other pathogens.

Effect of hydration on plasmonic coupling of bioconjugated gold nanoparticles immobilized on a gold film probed by surface-enhanced Raman spectroscopy

Gold nanoparticle (AuNP)-Au film constructs were prepared using antibody-antigen interactions or a small organic cross-linker to systematically control the gap between the AuNP and Au film. Surface-enhanced Raman spectroscopy (SERS), scanning electron micrsocopy (SEM), and atomic force microscopy (AFM) were used to characterize each construct and elucidate structure-activity relationships. Interestingly, plasmonic coupling and SERS intensity were reversibly modulated with wetting/drying cycles for the protein immobilized AuNP, and this effect was attributed to changes in protein size with hydration state. This work provides insight into fundamental limitations of AuNP-enabled SERS bioassays and will facilitate rational design of novel biospecific ligands that maximize SERS sensitivity.

Quinone-based polymers for label-free and reagentless electrochemical immunosensors: application to proteins, antibodies and pesticides detection

Polyquinone derivatives are widely recognized in the literature for their remarkable properties, their biocompatibility, simple synthesis, and easy bio-functionalization. We have shown that polyquinones present very stable electroactivity in neutral aqueous medium within the cathodic potential domain avoiding side oxidation of interfering species. Besides, they can act as immobilized redox transducers for probing biomolecular interactions in sensors. Our group has been working on devices based on such modified electrodes with a view to applications for proteins, antibodies and organic pollutants using a reagentless label-free electrochemical immunosensor format. Herein, these developments are briefly reviewed and put into perspective.

Gold nanorods as plasmonic nanotransducers: distance-dependent refractive index sensitivity

Owing to the facile tunability of the localized surface plasmon resonance wavelength (LSPR) and large refractive index sensitivity, gold nanorods (AuNR) are of high interest as plasmonic nanotransducers for label-free biological sensing. We investigate the influence of gold nanorod dimensions on distance-dependent LSPR sensitivity and electromagnetic (EM) decay length using electrostatic layer-by-layer (LbL) assembly of polyelectrolytes. The electromagnetic decay length was found to increase linearly with both nanorod length and diameter, although to variable degrees. The rate of EM decay length increase with nanorod diameter is significantly higher compared to that of the length, indicating that diameter is a convenient handle to tune the EM decay length of gold nanorods. The ability to precisely measure the EM decay length of nanostructures enables the rational selection of plasmonic nanotransducer dimensions for the particular biosensing application.

Bioplasmonic paper as a platform for detection of kidney cancer biomarkers

We demonstrate that a common laboratory filter paper uniformly adsorbed with biofunctionalized plasmonic nanostructures can serve as a highly sensitive transduction platform for rapid detection of trace bioanalytes in physiological fluids. In particular, we demonstrate that bioplasmonic paper enables rapid urinalysis for the detection of kidney cancer biomarkers in artificial urine down to a concentration of 10 ng/mL. Compared to conventional rigid substrates, bioplasmonic paper offers numerous advantages such as high specific surface area (resulting in large dynamic range), excellent wicking properties (naturally microfluidic), mechanical flexibility, compatibility with conventional printing approaches (enabling multiplexed detection and multimarker biochips), and significant cost reduction.

Protein microarrays for systems biology

Systems biology holds the key for understanding biological systems on a system level. It eventually holds the key for the treatment and cure of complex diseases such as cancer, diabetes, obesity, mental disorders, and many others. The '-omics' technologies, such as genomics, transcriptomics, proteomics, and metabonomics, are among the major driving forces of systems biology. Featured as high-throughput, miniaturized, and capable of parallel analysis, protein microarrays have already become an important technology platform for systems biology. In this review, we will focus on the system level or global analysis of biological systems using protein microarrays. Four major types of protein microarrays will be discussed: proteome microarrays, antibody microarrays, reverse-phase protein arrays, and lectin microarrays. We will also discuss the challenges and future directions of protein microarray technologies and their applications for systems biology. We strongly believe that protein microarrays will soon become an indispensable and invaluable tool for systems biology.

Rotationally induced hydrodynamics: fundamentals and applications to high-speed bioassays

Bioassays are indispensable tools in areas ranging from fundamental life science research to clinical practice. Improving assay speed and levels of detection will have a profound impact in all of these areas. We recently developed a rapid, sensitive format for immunosorbent assays that expedites antigen mass transport by rotating the capture substrate. This review outlines the theoretical foundation of rotationally induced hydrodynamics and its application in heterogeneous assays. We describe a general solution that solves the rates of immunoreactions on rotating capture substrates, taking into account both diffusion and the rate of reaction between antibody and antigen. The general solution applies to a wide range of rotation rates, including mass transport-limited to reaction rate-limited assays, and is validated experimentally. We discuss several applications that demonstrate how immunoassays can be tailored to increase speed as well as lower the limit of detection of viral particles, pathogens, toxins, and proteins.

Surface-enhanced Raman scattering biosensor for DNA detection on nanoparticle island substrates

We present a study on the surface-enhanced Raman scattering (SERS) properties of Ag nanoparticle island substrates (NIS) and their applications for target oligonucleotide (OND) detection. It has been found that the surface nanostructure of NIS samples can be controlled with a good degree of reproducibility, and a high SERS enhancement can be achieved when the peak extinction wavelength of NIS is tuned to a spectral window (approximately 60 nm) between the excitation wavelength and the scattered Raman wavelength. The highest SERS enhancement was obtained from the NIS substrates with a nominal thickness of 50 A. Detection of target OND was performed with a sandwich format in which the target OND was hybridized both to a capture OND immobilized on the NIS substrate, and a detection OND conjugated with a Raman-active dye for SERS signal generation. We compare the detection performance of two strategies based on the use of the detection OND with or without the gold nanoparticle (Au-NP). Our results confirm that, when the detection OND is coupled to the Au-NP, a better sensitivity for the target OND detection, in terms of a wider dynamic range and a lower detection limit (0.4 fM versus 1 nM without Au-NP), would be achieved.

Nanotube-antibody biosensor arrays for the detection of circulating breast cancer cells

Recent reports have shown that nanoscale electronic devices can be used to detect a change in electrical properties when receptor proteins bind to their corresponding antibodies functionalized on the surface of the device, in extracts from as few as ten lysed tumor cells. We hypothesized that nanotube-antibody devices could sensitively and specifically detect entire live cancer cells. We report for the first time a single nanotube field effect transistor array, functionalized with IGF1R-specific and Her2-specific antibodies, which exhibits highly sensitive and selective sensing of live, intact MCF7 and BT474 human breast cancer cells in human blood. Those two cell lines both overexpress IGF1R and Her2, at different levels. Single or small bundle of nanotube devices that were functionalized with IGF1R-specific or Her2-specific antibodies showed 60% decreases in conductivity upon interaction with BT474 or MCF7 breast cancer cells in two µl drops of blood. Control experiments with non-specific antibodies or with MCF10A control breast cells produced a less than 5% decrease in electrical conductivity, illustrating the high sensitivity for whole cell binding by these single nanotube-antibody devices. We postulate that the free energy change due to multiple simultaneous cell-antibody binding events exerted stress along the nanotube surface, decreasing its electrical conductivity due to an increase in band gap. Because the free energy change upon cell-antibody binding, the stress exerted on the nanotube, and the change in conductivity are specific to a specific antigen-antibody interaction; these properties might be used as a fingerprint for the molecular sensing of circulating cancer cells. From optical microscopy observations during sensing, it appears that the binding of a single cell to a single nanotube field effect transistor produced the change in electrical conductivity. Thus we report a nanoscale oncometer with single cell sensitivity with a diameter 1000 times smaller than a cancer cell that functions in a drop of fresh blood.

Electrical protein detection in cell lysates using high-density peptide-aptamer microarrays

BACKGROUND

The dissection of biological pathways and of the molecular basis of disease requires devices to analyze simultaneously a staggering number of protein isoforms in a given cell under given conditions. Such devices face significant challenges, including the identification of probe molecules specific for each protein isoform, protein immobilization techniques with micrometer or submicrometer resolution, and the development of a sensing mechanism capable of very high-density, highly multiplexed detection.

RESULTS

We present a novel strategy that offers practical solutions to these challenges, featuring peptide aptamers as artificial protein detectors arrayed on gold electrodes with feature sizes one order of magnitude smaller than existing formats. We describe a method to immobilize specific peptide aptamers on individual electrodes at the micrometer scale, together with a robust and label-free electronic sensing system. As a proving proof of principle experiment, we demonstrate the specific recognition of cyclin-dependent protein kinases in whole-cell lysates using arrays of ten electrodes functionalized with individual peptide aptamers, with no measurable cross-talk between electrodes. The sensitivity is within the clinically relevant range and can detect proteins against the high, whole-cell lysate background.

CONCLUSION

The use of peptide aptamers selected in vivo to recognize specific protein isoforms, the ability to functionalize each microelectrode individually, the electronic nature and scalability of the label-free detection and the scalability of the array fabrication combine to yield the potential for highly multiplexed devices with increasingly small detection areas and higher sensitivities that may ultimately allow the simultaneous monitoring of tens or hundreds of thousands of protein isoforms.

Impact of protein shedding on detection of Mycobacterium avium subsp. paratuberculosis by a whole-cell immunoassay incorporating surface-enhanced Raman scattering

The etiological agent of Johne's disease is Mycobacterium avium subsp. paratuberculosis. Controlling the spread of this disease is hindered by the lack of sensitive, selective, and rapid detection methods for M. avium subsp. paratuberculosis. By using a recently optimized sandwich immunoassay (B. J. Yakes, R. J. Lipert, J. P. Bannantine, and M. D. Porter, Clin. Vaccine Immunol. 15:227-234, 2008), which incorporates a new monoclonal antibody for the selective capture and labeling of M. avium subsp. paratuberculosis and surface-enhanced Raman scattering for sensitive readout, detection limits of approximately 630 and approximately 740 M. avium subsp. paratuberculosis cells/ml are achieved in phosphate-buffered saline and whole milk samples, respectively, after spiking with heat-treated M. avium subsp. paratuberculosis. Surprisingly, these detection limits are 3 orders of magnitude lower than expected based on theoretical predictions. Experiments designed to determine the origin of the improvement revealed that the major membrane protein targeted by the monoclonal antibody was present in the sample suspensions as shed protein. This finding indicates that the capture and labeling of shed protein function as a facile amplification strategy for lowering the limit of detection for M. avium subsp. paratuberculosis that may also be applicable to the design of a wide range of highly sensitive assays for other cells and viruses.

Peptide-based Biopolymers in Biomedicine and Biotechnology

Peptides are emerging as a new class of biomaterials due to their unique chemical, physical, and biological properties. The development of peptide-based biomaterials is driven by the convergence of protein engineering and macromolecular self-assembly. This review covers the basic principles, applications, and prospects of peptide-based biomaterials. We focus on both chemically synthesized and genetically encoded peptides, including poly-amino acids, elastin-like polypeptides, silk-like polymers and other biopolymers based on repetitive peptide motifs. Applications of these engineered biomolecules in protein purification, controlled drug delivery, tissue engineering, and biosurface engineering are discussed.

Direct Transfer of Preformed Patterned Bio-Nanocomposite Films on Polyelectrolyte Multilayer Templates

Microarrays containing multiple, nanostructured layers of biological materials would enable high-throughput screening of drug candidates, investigation of protein-mediated cell adhesion, and fabrication of novel biosensors. In this paper, we have examined in detail an approach that allows high-quality microarrays of layered, bionanocomposite films to be deposited on virtually any substrate. The approach uses LBL self-assembly to pre-establish a multilayered structure on an elastomeric stamp, and then uses microCP to transfer the 3-D structure intact to the target surface. For examples, different 3-D patterns containing dendrimers, polyelectrolyte multilayers and two proteins, sADH and sDH, have been fabricated. For the first time, the approach was also extended to create overlaid bionanocomposite patterns and multiple proteins containing patterns. The approach overcomes a problem encountered when using microCP to establish a pattern on the target surface and then building sequential layers on the pattern via LBL self-assembly. Amphiphilic molecules such as proteins and dendrimers tend to adsorb both to the patterned features as well as the underlying substrate, resulting in low-quality patterns. By circumventing this problem, this research significantly extends the range of surfaces and layering constituents that can be used to fabricate 3-D, patterned, bionanocomposite structures. [image in text]

Control of antigen mass transfer via capture substrate rotation: An absolute method for the determination of viral pathogen concentration and reduction of heterogeneous immunoassay incubation times

Immunosorbent assays are commonly employed as diagnostic tests in human healthcare, veterinary medicine and bioterrorism prevention. These assays, however, often require long incubation times, limiting sample throughput. As an approach to overcome this weakness, this paper examines the use of rotating capture substrates to increase the flux of antigen to the surface, thereby reducing the incubation time. To assess the capability of this approach, porcine parvovirus (PPV) was selectively extracted from solution by systematically varying the rotation rate of a gold substrate modified with a layer of anti-PPV monoclonal antibodies. The captured PPV were then directly imaged and quantified by atomic force microscopy. The benefits of substrate rotation are demonstrated by comparing an assay performed under stagnant conditions to one carried out with substrate rotation at 800 rpm, both for 10 min incubations at 25 degrees C. The use of rotation lowered the limit of detection to 3.4x10(4)TCID50/mL (approximately 80 fM) from 3.2x10(5)TCID50/mL (approximately 800 fM) under stagnant conditions. Results are also presented that show this strategy can be used: (1) to determine antigen concentrations without standards and (2) to establish the numerical relationship between quantal concentration units (e.g., 50% tissue culture infective dose (TCID50)) and quantitative concentration units (e.g., viruses/mL) The potential to broadly apply this technique to heterogeneous immunoassays is also briefly discussed.

Nanowell-array surfaces prepared by argon plasma etching through a nanopore alumina mask

A method for preparing a glass surface containing an ordered array of nanowells is described. These nanowell arrays are prepared via a plasma-etch method using a nanopore alumina film as the etch mask. A replica of the pore structure of the alumina mask is etched into the glass. We demonstrate that chemical information in the form of negatively charged latex nanoparticles can be selectively stored within these nanowells and not indiscriminately deposited on the surface surrounding the nanowells. To accomplish this, the chemistry of the glass surfaces within these nanowells (walls and bottoms) must be different from the chemistry of the surface surrounding the nanowells. Two different procedures were developed to make the inside vs. surrounding surface chemistries different. Atomic force microscopy (AFM) was used to image the nanowells and, via friction-force measurements, to prove that the inner nanowell surfaces can be made chemically different from the surface surrounding the nanowells.

Surface-enhanced Raman scattering studies on immunoassay

Surface-enhanced Raman scattering (SERS) has recently been a matter of keen interest from the points of both basic science and applications because by using the SERS effect one can obtain Raman signals even from a single molecule. Immunoassay is one of the most promising fields in the applications of SERS, and the purpose of this review paper is to discuss the potential of SERS in immunoassay. This paper consists of four parts work on the indirect and direct methods of immunoassay via SERS. These methods provide the laboratorial attempts on biomedical diagnostic applications of SERS.

Competitive adsorption of model charged proteins: the effect of total charge and charge distribution

The adsorption of mixtures of charged proteins on charged surfaces is studied using a molecular theory. The theory explicitly treats each of the molecular species in the system. The mixtures treated in this work are composed by two types of proteins, dissociated monovalent salt and solvent. The intermolecular and surface interactions include electrostatic, van der Waals and excluded volume. The theory is more general than the Poisson-Boltzmann approach since the size and shape of all the molecular components are explicitly treated. The studies presented in this work concentrate on the differences in competitive adsorption when the proteins in the mixtures differ in their total charge or in the spatial distribution of the charges within the proteins. In the cases of mixtures that differ in the number of charges it is found, as expected, that the particles with the larger charge adsorb in excess. The ratio of adsorbed proteins can vary by 3-5 orders of magnitude by varying the bulk salt concentration from 1 to 100 mM. This is the result of an increase on the adsorption of the proteins with larger charge and an even stronger decrease on the adsorption of the less charged particles. The simple model systems studied provide guidelines on how to separate charge ladder proteins and proteins with different charge distributions. In the case of proteins with the same total charge but different charge distribution, it is found that the partition of the proteins depends upon the bulk composition. However, in general the particles with the highest localized charge tend to adsorb more on the surfaces. The proteins are adsorbed in one or more layers. The structure of the second adsorbed layer is determined mostly by the bulk properties of the solution. In all cases it is found that in the range of salt concentrations studied the number of adsorbed ions from the salt is very large. This is due to competitive adsorption with the proteins and their very low bulk concentration compared to the salt. The limitations of the theory and directions for improvement of the approach as well as the model for the proteins are discussed.

Protein microarray detection strategies: focus on direct detection technologies

Protein microarrays are being utilized for functional proteomic analysis, providing information not obtainable by gene arrays. Microarray technology is applicable for studying protein-protein, protein-ligand, kinase activity and posttranslational modifications of proteins. A precise and sensitive protein microarray, the direct detection or reverse-phase microarray, has been applied to ongoing clinical trials at the National Cancer Institute for studying phosphorylation events in EGF-receptor-mediated cell signaling pathways. The variety of microarray applications allows for multiple, creative microarray designs and detection strategies. Herein, we discuss detection strategies and challenges for protein microarray technology, focusing on direct detection of protein microarrays.

Botulinum toxin type B micromechanosensor

Botulinum neurotoxin (BoNT) types A, B, E, and F are toxic to humans; early and rapid detection is essential for adequate medical treatment. Presently available tests for detection of BoNTs, although sensitive, require hours to days. We report a BoNT-B sensor whose properties allow detection of BoNT-B within minutes. The technique relies on the detection of an agarose bead detachment from the tip of a micromachined cantilever resulting from BoNT-B action on its substratum, the synaptic protein synaptobrevin 2, attached to the beads. The mechanical resonance frequency of the cantilever is monitored for the detection. To suspend the bead off the cantilever we use synaptobrevin's molecular interaction with another synaptic protein, syntaxin 1A, that was deposited onto the cantilever tip. Additionally, this bead detachment technique is general and can be used in any displacement reaction, such as in receptor-ligand pairs, where the introduction of one chemical leads to the displacement of another. The technique is of broad interest and will find uses outside toxicology.

A nonredundant human protein chip for antibody screening and serum profiling

There is burgeoning interest in protein microarrays, but a source of thousands of nonredundant, purified proteins was not previously available. Here we show a glass chip containing 2413 nonredundant purified human fusion proteins on a polymer surface, where densities up to 1600 proteins/cm(2) on a microscope slide can be realized. In addition, the polymer coating of the glass slide enables screening of protein interactions under nondenaturing conditions. Such screenings require only 200-microl sample volumes, illustrating their potential for high-throughput applications. Here we demonstrate two applications: the characterization of antibody binding, specificity, and cross-reactivity; and profiling the antibody repertoire in body fluids, such as serum from patients with autoimmune diseases. For the first application, we have incubated these protein chips with anti-RGSHis(6), anti-GAPDH, and anti-HSP90beta antibodies. In an initial proof of principle study for the second application, we have screened serum from alopecia and arthritis patients. With analysis of large sample numbers, identification of disease-associated proteins to generate novel diagnostic markers may be possible.

Protein arrays and their role in proteomics

Arraying technologies have shown the way to smaller sample volumes, more efficient analyses and higher throughput. Proteomics is a field, which has grown in significance in the last five years. This review outlines recent developments in protein arrays and their applications in proteomics, and discusses the requirements, current limitations and the potential and future perspectives of the technology.

Preparing protein microarrays by soft-landing of mass-selected ions

Intact, multiply protonated proteins of particular mass and charge were selected from ionized protein mixtures and gently landed at different positions on a surface to form a microarray. An array of cytochrome c, lysozyme, insulin, and apomyoglobin was generated, and the deposited proteins showed electrospray ionization mass spectra that matched those of the authentic compounds. Deposited lysozyme and trypsin retained their biological activity. Multiply charged ions of protein kinase A catalytic subunit and hexokinase were also soft-landed into glycerol-based liquid surfaces. These soft-landed kinases phosphorylated LRRASLG oligopeptide and D-fructose, respectively.

Gas-phase detection of trinitrotoluene utilizing a solid-phase antibody immobilized on a gold film by means of surface plasmon resonance spectroscopy

A multilayered biosensor was constructed and found to detect trinitrotoluene (TNT) in ppb concentrations in air both prior to and after detonation of TNT without use of a liquid phosphate buffered saline (PBS) superstrate. The biosensor surface was fabricated from a monoclonal antibody for TNT covalently bound to an 11,11'-dithio-bis(succinimidoylundecanoate) (DSU) self-assembled monolayer immobilized on a thin gold film bonded to a BK7 glass slide. The binding between the immobilized antibody and TNT antigen was detected using surface plasmon resonance spectroscopy (SPRS). Biosensor specificity for TNT was demonstrated with chemical homologues as well as against an unrelated explosive, RDX.

Solid supports for microarray immunoassays

Stimulated by the achievements of the first phase in genomics and the resulting need of assigning functions to the acquired sequence information, novel formats of immunoassays are being developed for high-throughput multi-analyte studies. In principle, they are similar in nature to the microarray assays already established at the level of nucleic acids. However, the biochemical diversity and the sheer number of proteins are such that an equivalent analysis is much more complex and thus difficult to accomplish. The wide range of protein concentration complicates matters further. Performing microarray immunoassays already represents a challenge at the level of preparing a working chip surface. Arrays have been produced on filter supports, in microtiter plate wells and on glass slides, the last two usually coated with one-, two- or three-dimensionally structured surface modifications. The usefulness and suitability of all these support media for the construction and application of antibody microarrays are reviewed in this manuscript in terms of the different kinds of immunoassay and the various detection procedures. Additionally, the employment of microarrays containing alternative sensor molecules is discussed in this context. The sensitivity of microspot immunoassays predicted by the current analyte theory is not yet a reality, indicating the extent of both the technology's potential and the size of the task still ahead.

Protein chip technology

Microarray technology has become a crucial tool for large-scale and high-throughput biology. It allows fast, easy and parallel detection of thousands of addressable elements in a single experiment. In the past few years, protein microarray technology has shown its great potential in basic research, diagnostics and drug discovery. It has been applied to analyse antibody-antigen, protein-protein, protein-nucleic-acid, protein-lipid and protein-small-molecule interactions, as well as enzyme-substrate interactions. Recent progress in the field of protein chips includes surface chemistry, capture molecule attachment, protein labeling and detection methods, high-throughput protein/antibody production, and applications to analyse entire proteomes.

Biochips beyond DNA: technologies and applications

Technological advances in miniaturization have found a niche in biology and signal the beginning of a new revolution. Most of the attention and advances have been made with DNA chips yet a lot of progress is being made in the use of other biomolecules and cells. A variety of reviews have covered only different aspects and technologies but leading to the shared terminology of "biochips." This review provides a basic introduction and an in-depth survey of the different technologies and applications involving the use of non-DNA molecules such as proteins and cells. The review focuses on microarrays and microfluidics, but also describes some cellular systems (studies involving patterning and sensor chips) and nanotechnology. The principles of each technology including parameters involved in biochip design and operation are outlined. A discussion of the different biological and biomedical applications illustrates the significance of biochips in biotechnology.

Physics and applications of microfluidics in biology

Fluid flow at the microscale exhibits unique phenomena that can be leveraged to fabricate devices and components capable of performing functions useful for biological studies. The physics of importance to microfluidics are reviewed. Common methods of fabricating microfluidic devices and systems are described. Components, including valves, mixers, and pumps, capable of controlling fluid flow by utilizing the physics of the microscale are presented. Techniques for sensing flow characteristics are described and examples of devices and systems that perform bioanalysis are presented. The focus of this review is microscale phenomena and the use of the physics of the scale to create devices and systems that provide functionality useful to the life sciences.

Protein array technology. Potential use in medical diagnostics

The human genome is sequenced, but only a minority of genes have been assigned a function. Whole-genome expression profiling is an important tool for functional genomic studies. Automated technology allows high-throughput gene activity monitoring by analysis of complex expression patterns, resulting in fingerprints of diseased versus normal or developmentally distinct tissues. Differential gene expression can be most efficiently monitored by DNA hybridization on arrays of oligonucleotides or cDNA clones. Starting from high-density filter membranes, cDNA microarrays have recently been devised in chip format. We have shown that the same cDNA libraries can be used for high-throughput protein expression and antibody screening on high-density filters and microarrays. These libraries connect recombinant proteins to clones identified by DNA hybridization or sequencing, hence creating a direct link between gene catalogs and functional catalogs. Microarrays can now be used to go from an individual clone to a specific gene and its protein product. Clone libraries become amenable to database integration including all steps from DNA sequencing to functional assays of gene products.

The impact of protein biochips and microarrays on the drug development process

With the genome sequences of several organisms now in public databases, the scientific community has realized that it is time to prepare for the next step: the understanding of biological systems or systems biology. Whereas genes contain the information for life, the encoded proteins and RNAs fulfill nearly all the functions, from replication to regulation. At present, there is a perceived demand for high-throughput and parallel analytical devices as research tools in systems biology, and, in addition, for new concepts to extract knowledge and value from these data. Protein biochips will play a decisive role in meeting this need in the future.

Immobilization of Antibodies on Glass Surfaces through Sugar Residues

This work characterizes substrates for immunoassays obtained through the immobilization of vectorially oriented antibodies on glass. The method of preparation is based on the condensation reaction between an aldehyde group on the F(c) portion of antibodies and the hydrazide group on the modified glass surface. Light microscopy and AFM imaging in height and phase modes were used to assess the properties of the modified surface. Both techniques are consistent with a fairly uniform antibody coverage on the micrometer and submicrometer scales. ELISA tests were used to evaluate the activity and surface distribution of immobilized antibodies as well as nonspecific binding to surfaces after various modification steps. It was shown that exposure of the surfaces to a BSA solution minimized nonspecific binding to undetectable levels.

Biomedical applications of protein chips

The development of microchips involving proteins has accelerated within the past few years. Although DNA chip technologies formed the precedent, many different strategies and technologies have been used because proteins are inherently a more complex type of molecule. This review covers the various biomedical applications of protein chips in diagnostics, drug screening and testing, disease monitoring, drug discovery (proteomics), and medical research. The proteomics and drug discovery section is further subdivided to cover drug discovery tools (on-chip separations, expression profiling, and antibody arrays), molecular interactions and signaling pathways, the identification of protein function, and the identification of novel therapeutic compounds. Although largely focused on protein chips, this review includes chips involving cells and tissues as a logical extension of the type of data that can be generated from these microchips.

High throughput peptide mass fingerprinting and protein macroarray analysis using chemical printing strategies

We describe a chemical printer that uses piezoelectric pulsing for rapid, accurate, and non-contact microdispensing of fluid for proteomic analysis of immobilized protein macroarrays. We demonstrate protein digestion and peptide mass fingerprinting analysis of human plasma and platelet proteins direct from a membrane surface subsequent to defined microdispensing of trypsin and matrix solutions, hence bypassing multiple liquid-handling steps. Detection of low abundance, alkaline proteins from whole human platelet extracts has been highlighted. Membrane immobilization of protein permits archiving of samples pre-/post-analysis and provides a means for subanalysis using multiple chemistries. This study highlights the ability to increase sequence coverage for protein identification using multiple enzymes and to characterize N-glycosylation modifications using a combination of PNGase F and trypsin. We also demonstrate microdispensing of multiple serum samples in a quantitative microenzyme-linked immunosorbent assay format to rapidly screen protein macroarrays for pathogen-derived antigens. We anticipate the chemical printer will be a major component of proteomic platforms for high throughput protein identification and characterization with widespread applications in biomedical and diagnostic discovery.

Scanning force microscopy in the applied biological sciences

Fifteen years after its invention, the scanning force microscope (SFM) is rooted deep in the biological sciences. Here we discuss the use of SFM in biotechnology and biomedical research. The spectrum of applications reviewed includes imaging, force spectroscopy and mapping, as well as sensor applications. It is our hope that this review will be useful for researchers considering the use of SFM in their studies but are uncertain about its scope of capabilities. For the benefit of readers unfamiliar with SFM technology, the fundamentals of SFM imaging and force measurement are also briefly introduced.

Bioassay of prostate-specific antigen (PSA) using microcantilevers

Diagnosis and monitoring of complex diseases such as cancer require quantitative detection of multiple proteins. Recent work has shown that when specific biomolecular binding occurs on one surface of a microcantilever beam, intermolecular nanomechanics bend the cantilever, which can be optically detected. Although this label-free technique readily lends itself to formation of microcantilever arrays, what has remained unclear is the technologically critical issue of whether it is sufficiently specific and sensitive to detect disease-related proteins at clinically relevant conditions and concentrations. As an example, we report here that microcantilevers of different geometries have been used to detect two forms of prostate-specific antigen (PSA) over a wide range of concentrations from 0.2 ng/ml to 60 microg/ml in a background of human serum albumin (HSA) and human plasminogen (HP) at 1 mg/ml, making this a clinically relevant diagnostic technique for prostate cancer. Because cantilever motion originates from the free-energy change induced by specific biomolecular binding, this technique may offer a common platform for high-throughput label-free analysis of protein-protein binding, DNA hybridization, and DNA-protein interactions, as well as drug discovery.

Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front

Protein arrays are described for screening of molecular markers and pathway targets in patient matched human tissue during disease progression. In contrast to previous protein arrays that immobilize the probe, our reverse phase protein array immobilizes the whole repertoire of patient proteins that represent the state of individual tissue cell populations undergoing disease transitions. A high degree of sensitivity, precision and linearity was achieved, making it possible to quantify the phosphorylated status of signal proteins in human tissue cell subpopulations. Using this novel protein microarray we have longitudinally analysed the state of pro-survival checkpoint proteins at the microscopic transition stage from patient matched histologically normal prostate epithelium to prostate intraepithelial neoplasia (PIN) and then to invasive prostate cancer. Cancer progression was associated with increased phosphorylation of Akt (P<0.04), suppression of apoptosis pathways (P<0.03), as well as decreased phosphorylation of ERK (P<0.01). At the transition from histologically normal epithelium to PIN we observed a statistically significant surge in phosphorylated Akt (P<0.03) and a concomitant suppression of downstream apoptosis pathways which proceeds the transition into invasive carcinoma.

Protein and antibody arrays and their medical applications

Many new gene products are being discovered by large-scale genomics and proteomics strategies, the challenge is now to develop high throughput approaches to systematically analyse these proteins and to assign a biological function to them. Having access to these gene products as recombinantly expressed proteins, would allow them to be robotically arrayed to generate protein chips. Other applications include using these proteins for the generation of specific antibodies, which can also be arrayed to produce antibody chips. The availability of such protein and antibody arrays would facilitate the simultaneous analysis of thousands of interactions within a single experiment. This chapter will focus on current strategies used to generate protein and antibody arrays and their current applications in biological research, medicine and diagnostics. The shortcomings of these approaches, the developments required, as well as the potential applications of protein and antibody arrays will be discussed.

Fabrication of nanometer-sized protein patterns using atomic force microscopy and selective immobilization

A new methodology is introduced to produce nanometer-sized protein patterns. The approach includes two main steps, nanopatterning of self-assembled monolayers using atomic force microscopy (AFM)-based nanolithography and subsequent selective immobilization of proteins on the patterned monolayers. The resulting templates and protein patterns are characterized in situ using AFM. Compared with conventional protein fabrication methods, this approach is able to produce smaller patterns with higher spatial precision. In addition, fabrication and characterization are completed in near physiological conditions. The adsorption configuration and bioreactivity of the proteins within the nanopatterns are also studied in situ.