Readout of protein microarrays using intrinsic time resolved UV fluorescence for label-free detection

Label-Free Fluorescence Quantitative Detection Platform on Plasmonic Silica Photonic Crystal Microsphere Array

We have demonstrated the proof-of-concept of a label-free fluorescence quantitative detection platform based on gold nanoparticle (AuNP) enhancement intrinsic fluorescence of protein on the silica photonic crystal microsphere (SPCM) array. The label-free one-step competitive fluorescence immunoassay protocol has been proposed on the surface of the SPCM. Aflatoxin B₁ (AFB₁) as a model molecule was detected by the newly established method. AFB₁-bovine serum albumin and monoclonal antibodies (Abs) of anti-AFB₁ have been immobilized on the surfaces of SPCMs and AuNPs, respectively. AuNPs remarkably enhanced the intrinsic fluorescence of artificial antigens on the surface of the SPCM at near UV excitation. The simulation of electric field distribution showed that the maximum value of the near-field enhancement |E/E₀| of the SPCM with AuNPs could reach 20. The label-free fluorescence enhancement effect comes from the synergistic effects of photonic crystal effect and AuNP plasmon effect. Such a label-free fluorescence detection method can provide a linear detection range from 0.1 to 10 ng/mL with a limit of detection of 0.025 ng/mL and good specificity for AFB₁. The recovery rates in the spiked cereal samples were measured in the range of 84.07 ± 5.71%-101.02 ± 5.13%, which were consistent with that of the traditional enzyme linked immunosorbent assay method. The label-free detection platform displays great application potential in biology, medicine, agriculture, food industry, chemical industry, energy source, and environmental protection.

Controlling the immobilization process of an optically enhanced protein microarray for highly reproducible immunoassay

By virtue of its high throughput multiplex detection capability, superior read-out sensitivity, and tiny analyte consumption, an optically enhanced protein microarray assay has been developed as a promising diagnostic tool for various applications, ranging from the field of pharmacology to diagnostics. However, so far, the development of an optically enhanced protein microarray (OEPM) toward widespread commercial availability is mainly hampered by insufficient detection reproducibility. Here, we develop an OEPM platform with an order of magnitude optical enhancement induced by the interference effect. High assay reproducibility of the OEPM is achieved by optimizing the protein immobilization schemes, linking to the surface energy of the substrate, surfactant-tuned wetting ability, and the washing and drying dynamics. As a result, smearing-free and uniform spot arrays with a coefficient of variation less than 7% can be achieved. Furthermore, we demonstrate the assay performance of the OEPM by detecting five biomarkers, showing an order of magnitude higher sensitivity, many-fold higher throughput, and 10 times less analyte consumption than those of the commercial enzyme-linked immunosorbent assay kits. Our results provide new insight for improving the reproducibility of OEPMs toward practical and commercial diagnostic assays.

Exploiting fluorescence for multiplex immunoassays on protein microarrays

Protein microarray technology is becoming the method of choice for identifying protein interaction partners, detecting specific proteins, carbohydrates and lipids, or for characterizing protein interactions and serum antibodies in a massively parallel manner. Availability of the well-established instrumentation of DNA arrays and development of new fluorescent detection instruments promoted the spread of this technique. Fluorescent detection has the advantage of high sensitivity, specificity, simplicity and wide dynamic range required by most measurements. Fluorescence through specifically designed probes and an increasing variety of detection modes offers an excellent tool for such microarray platforms. Measuring for example the level of antibodies, their isotypes and/or antigen specificity simultaneously can offer more complex and comprehensive information about the investigated biological phenomenon, especially if we take into consideration that hundreds of samples can be measured in a single assay. Not only body fluids, but also cell lysates, extracted cellular components, and intact living cells can be analyzed on protein arrays for monitoring functional responses to printed samples on the surface. As a rapidly evolving area, protein microarray technology offers a great bulk of information and new depth of knowledge. These are the features that endow protein arrays with wide applicability and robust sample analyzing capability. On the whole, protein arrays are emerging new tools not just in proteomics, but glycomics, lipidomics, and are also important for immunological research. In this review we attempt to summarize the technical aspects of planar fluorescent microarray technology along with the description of its main immunological applications.

Multiplex approaches in protein microarray technology

The success of genome sequencing projects has provided the basis for systematic analysis of protein function and has led to a shift from the description of single molecules to the characterization of complex samples. Such a task would not be possible without the provision of appropriate high-throughput technologies, such as protein microarray technology. In addition, the increasing number of samples necessitates the adaptation of such technologies to a multiplex format. This review will discuss protein microarray technology in the context of multiplex analysis and highlight its current prospects and limitations.

Label-free microcavity biosensors: steps towards personalized medicine

Personalized medicine has the potential to improve our ability to maintain health and treat disease, while ameliorating continuously rising healthcare costs. Translation of basic research findings to clinical applications within regulatory compliance is required for personalized medicine to become the new foundation for practice of medicine. Deploying even a few of the thousands of potential diagnostic biomarkers identified each year as part of personalized treatment workflows requires clinically efficient biosensor technologies to monitor multiple biomarkers in patients in real time. This paper discusses a critical component of a regulatory system, a microcavity optical biosensor for label-free monitoring of biomolecular interactions at physiologically-relevant concentrations. While most current biosensor research focuses on improving sensitivity, this paper emphasizes other characteristics a biosensor technology requires to be practical in a clinical setting, presenting robust microcavity biosensors which are easy to manufacture and integrate with microfluidics into flexible and redesignable platforms making the microcavity biosensors deployable for continuous monitoring of biomarkers in body fluids in the clinic, in dense 2D random arrays for high-throughput applications like drug-library screening in interactomics, and of the secretory behavior of single cells in the laboratory.

Label-free real-time imaging in microchip free-flow electrophoresis applying high speed deep UV fluorescence scanning

We report on label-free monitoring of microfluidic free-flow electrophoresis (μFFE) separations in real-time using a custom built high speed deep UV laser scanner. In combination with a novel layout realized in fused silica (FS) FFE chips the setup was successfully applied for continuous separations and detection of unlabeled analytes including native proteins by space-resolved intrinsic deep UV fluorescence scanning.

Label-free detection techniques for protein microarrays: prospects, merits and challenges

Protein microarrays, on which thousands of discrete proteins are printed, provide a valuable platform for functional analysis of the proteome. They have been widely used for biomarker discovery and to study protein–protein interactions. The accomplishments of DNA microarray technology, which had enabled massive parallel studies of gene expression, sparked great interest for the development of protein microarrays to achieve similar success at the protein level. Protein microarray detection techniques are often classified as being label‐based and label‐free. Most of the microarray applications have employed labelled detection such as fluorescent, chemiluminescent and radioactive labelling. These labelling strategies have synthetic challenges, multiple label issues and may exhibit interference with the binding site. Therefore, development of sensitive, reliable, high‐throughput, label‐free detection techniques are now attracting significant attention. Label‐free detection techniques monitor biomolecular interactions and simplify the bioassays by eliminating the need for secondary reactants. Moreover, they provide quantitative information for the binding kinetics. In this article, we will review several label‐free techniques, which offer promising applications for the protein microarrays, and discuss their prospects, merits and challenges.

Two-color two-photon excitation of intrinsic protein fluorescence: label-free observation of proteolytic digestion of bovine serum albumin

Two-color two-photon (2c2p) excitation fluorescence is used to monitor the enzymatic cleavage of bovine serum albumin (BSA) by subtilisin. Fluorescence is generated by irradiation with spatially and temporally overlapping femtosecond laser beams resulting in simultaneous absorption of an 800 and a 400 nm photon. Thereby, excitation of the fluorescent amino acid tryptophan present in BSA corresponds to an effective one-photon wavelength of 266 nm. The progress of protein cleavage is monitored by time-resolved fluorescence analysis. The fluorescence lifetime of tryptophan decreases during the reaction. This demonstrates a novel label-free multiphoton observation technique for conformational changes of proteins containing tryptophan. Due to the strong 2c2p fluorescence signal it is suitable for fast evaluation and monitoring of protein reactions. The course of the reaction is monitored simultaneously by gel electrophoresis. In contrast to conventional one-photon techniques, 2c2p excitation enables label-free protein fluorescence studies without irradiating the sample with UV light. Due to the dependence of the excitation on the power of both laser beams, excitation is limited to a relatively small focal volume. This results in dramatically reduced overall photodamage compared to direct UV irradiation. This method can be easily extended to microscopy imaging techniques.

Development of a fluorescent and colorimetric detection methods-based protein microarray for serodiagnosis of TORCH infections

We developed a protein microarray methodology that has the ability of serodiagnosis of IgM antibodies directed against TORCH pathogens. Six chemical surface modifications were validated by a dimension atomic force microscope (AFM) and contact angle measurement, agarose modified surface of which offered an appropriate platform for detecting IgM antibody. Further, signal amplification sensitivities on agarose modified microarrays were detected by Cy3-labeled biotin-streptavidin and immunogold-based assays. The detection limits of IgM antibody on the microarrays were 0.48 and 0.24 microg/ml, quantitatively equal to 0.25 and 12.5pg, respectively, on each spot as ascertained by the two assays. Satisfactory linear correlations between the signal intensity and the logarithm of the IgM concentration were obtained. Finally, 60 serum samples characterized by a commercial ELISA were evaluated by the protein microarray. There were good concordances between the results of the protein microarray and ELISA assay for sorting of the TORCH infected sera (95.0% by fluorescence-based assay and 96.7% by immunogold-based assay). Clearly, the potential application of this protein microarray format facilitates clinical detection of not only the antibodies directed against TORCH pathogens but also other autoimmune diseases.

Label-free detection of protein interactions using deep UV fluorescence lifetime microscopy

We present a label-free detection of protein interaction between beta-galactosidase from Escherichia coli (Ecbeta-Gal) and monoclonal anti-Ecbeta-Gal using deep UV laser-based fluorescence lifetime microscopy. The native fluorescence from intrinsic tryptophan emission was observed after one-photon excitation at 266 nm. Applying the time-correlated single-photon counting (TCSPC) method, we investigated the mean fluorescence lifetime and lifetime distributions from tryptophan residues in Ecbeta-Gal protein, monoclonal anti-Ecbeta-Gal, and corresponding complex. The results demonstrate that deep UV laser-based fluorescence lifetime microscopy is useful for sensitive identification of biological macromolecules interaction using intrinsic fluorescence.

Ubiquitous cancer genes: Multipurpose molecules for protein micro-arrays

Multipurpose genes in the human genome which are over-expressed in a large variety of different cancers have been identified. Forty-two of the 19,016 human genes annotated to date (0.2%) are ubiquitously over-expressed in half or more of the 36 investigated human cancers. Of these genes, 15 are involved in protein biosynthesis and folding, six of them in glycolysis. A group of 13 solid tumours over-express almost all (39-42 of 42) ubiquitous cancer genes, suggesting a common mechanism underlying these cancers. Others, such as endocrine cancers, have only a few over-expressed ubiquitous cancer genes. The proteins for which these genes code or the corresponding antibodies are candidates for small protein microarrays aiming at maximum information with only a limited number of proteins. Since the over-expression pattern varies from cancer to cancer, distinction between different cancer classes is possible using one single set of protein or antibody molecules.

UV Fluorescence Lifetime Imaging Microscopy: A Label-Free Method for Detection and Quantification of Protein Interactions

Due to the ability to detect multiple parameters simultaneously, protein microarrays have found widespread applications from basic biological research to diagnosis of diseases. Generally, readout of protein microarrays is performed by fluorescence detection using either dye-labeled detector antibodies or direct labeling of the target proteins. We developed a method for the label-free detection and quantification of proteins based on time-gated, wide-field, camera-based UV fluorescence lifetime imaging microscopy to gain lifetime information from each pixel of a sensitive CCD camera. The method relies on differences in the native fluorescence lifetime of proteins and takes advantage of binding-induced lifetime changes for the unequivocal detection and quantification of target proteins. Since fitting of the fluorescence decay for every pixel in an image using a classical exponential decay model is time-consuming and unstable at very low fluorescence intensities, we used a new, very robust and fast alternative method to generate UV fluorescence lifetime images by calculating the average lifetime of the decay for each pixel in the image stack using a model-free average decay time algorithm.To validate the method, we demonstrate the detection and quantification of p53 antibodies, a tumor marker in cancer diagnosis. Using tryptophan-containing capture peptides, we achieved a detection sensitivity for monoclonal antibodies down to the picomolar concentration range. The obtained affinity constant, Ka, of (1.4 +/- 0.6) x 10(9) M(-1), represents a typical value for antigen/antibody binding and is in agreement with values determined by traditional binding assays.

Antibody microarrays for native toxin detection

We have developed antibody-based microarray techniques for the multiplexed detection of cholera toxin beta-subunit, diphtheria toxin, anthrax lethal factor and protective antigen, Staphylococcus aureus enterotoxin B, and tetanus toxin C fragment in spiked samples. Two detection schemes were investigated: (i) a direct assay in which fluorescently labeled toxins were captured directly by the antibody array and (ii) a competition assay that employed unlabeled toxins as reporters for the quantification of native toxin in solution. In the direct assay, fluorescence measured at each array element is correlated with labeled toxin concentration to yield baseline binding information (Langmuir isotherms and affinity constants). Extending from the direct assay, the competition assay yields information on the presence, identity, and concentration of toxins. A significant advantage of the competition assay over reported profiling assays is the minimal sample preparation required prior to analysis because the competition assay obviates the need to fluorescently label native proteins in the sample of interest. Sigmoidal calibration curves and detection limits were established for both assay formats. Although the sensitivity of the direct assay is superior to that of the competition assay, detection limits for unmodified toxins in the competition assay are comparable to values reported previously for sandwich-format immunoassays of antibodies arrayed on planar substrates. As a demonstration of the potential of the competition assay for unlabeled toxin detection, we conclude with a straightforward multiplexed assay for the differentiation and identification of both native S. aureus enterotoxin B and tetanus toxin C fragment in spiked dilute serum samples.