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

Surface plasmon resonance imaging (SPRi) for analysis of DNA aptamer:β-conglutin interactions

Surface plasmon resonance imaging (SPRi) is a label-free detection method that offers a suitable and reliable platform for the real time monitoring of biomolecular interactions. In the work reported here, SPRi was used to evaluate the affinity and specificity of three different aptamers selected against the Lup an 1 anaphylactic allergen β-conglutin (β-conglutin binding aptamers I and II (β-CBA I and β-CBA II)), as well as an 11-mer truncated version of β-CBA I. Thiol modified aptamers were immobilised on a gold substrate through a self-assembling process and the use of different blocking strategies to prevent non-specific binding were evaluated. Dissociation constants of 20, 13 and 1 nM were determined for β-CBA I, β-CBA II and the 11-mer truncated aptamer, respectively. The three aptamers were then studied in various different sandwich formats and the β-CBA I/11-mer and β-CBA II were observed to bind to different aptatopes on the target protein. Each of the aptamers were then used either as surface immobilised aptamer, or as reporter aptamer, and added with the protein target β-conglutin in either a sequential of simultaneous manner, and the changes in SPR signal monitored. The preferred approach for formation of a sandwich aptacomplex was with immobilised β-CBA II, followed by addition of pre-incubated β-conglutin and 11-mer, whilst addition of the 11-mer following addition of the β-conglutin, resulted in displacement of the bound target. The ability to provide parallel qualitative and quantitative detection establishes SPRi as a powerful tool for the study of immobilised aptamer-target interactions.

Surface conformations of an anti-ricin aptamer and its affinity for ricin determined by atomic force microscopy and surface plasmon resonance

We used atomic force microscopy (AFM) and surface plasmon resonance (SPR) to study the surface conformations of an anti-ricin aptamer and its specific binding affinity for ricin molecules. The effect of surface modification of the Au(111) substrate on the aptamer affinity was also estimated. The AFM topography images had a resolution high enough to distinguish different aptamer conformations. The specific binding site on the aptamer molecule was clearly located by the AFM recognition images. The aptamer on a Au(111) surface modified with carboxymethylated-dextran (CD) showed both similarities to and differences from the one without CD modification. The influence of CD modification was evaluated using AFM images of various aptamer conformations on the Au(111) surface. The affinity between ricin and the anti-ricin aptamer was estimated using the off-rate values measured using AFM and SPR. The SPR measurements of the ricin sample were conducted in the range from 83.3 pM to 8.33 nM, and the limit of detection was estimated as 25 pM (1.5 ng mL(-1)). The off-rate values of the ricin-aptamer interactions were estimated using both single-molecule dynamic force spectroscopy (DFS) and SPR as (7.3 ± 0.4) × 10(-4) s(-1) and (1.82 ± 0.067) × 10(-2) s(-1), respectively. The results show that single-molecule measurements can obtain different reaction parameters from bulk solution measurements. In AFM single-molecule measurements, the various conformations of the aptamer immobilized on the gold surface determined the availability of each specific binding site to the ricin molecules. The SPR bulk solution measurements averaged the signals from specific and non-specific interactions. AFM images and DFS measurements provide more specific information on the interactions of individual aptamer and ricin molecules.

Diazonium Chemistry for the Bio-Functionalization of Glassy Nanostring Resonator Arrays

Resonant glassy nanostrings have been employed for the detection of biomolecules. These devices offer high sensitivity and amenability to large array integration and multiplexed assays. Such a concept has however been impaired by the lack of stable and biocompatible linker chemistries. Diazonium salt reduction-induced aryl grafting is an aqueous-based process providing strong chemical adhesion. In this work, diazonium-based linker chemistry was performed for the first time on glassy nanostrings, which enabled the bio-functionalization of such devices. Large arrays of nanostrings with ultra-narrow widths down to 10 nm were fabricated employing electron beam lithography. Diazonium modification was first developed on SiCN surfaces and validated by X-ray photoelectron spectroscopy. Similarly modified nanostrings were then covalently functionalized with anti-rabbit IgG as a molecular probe. Specific enumeration of rabbit IgG was successfully performed through observation of downshifts of resonant frequencies. The specificity of this enumeration was confirmed through proper negative control experiments. Helium ion microscopy further verified the successful functionalization of nanostrings.

Multi-spot, label-free immunoassay on reflectionless glass

Biosensing platforms that combine high sensitivity, operational simplicity and affordable costs find wide application in many fields, including human diagnostics, food and environmental monitoring. In this work, we introduce a label-free biosensing chip made of glass with a single anti-reflective layer of SiO2. This common and economic material coated by a multi-functional copolymer based on dimethylacrylamide enables the detection even in turbid media. The copolymer coating provides covalent immobilization of antibodies onto the surface and prevents the non-specific adsorption of analytes and matrix constituents. The specific capture of target compounds yields a local increase of surface reflectivity measured by a simple imaging system. Chip design and quantitative interpretation of the data are based on a theoretical optical model. This approach enables the multiplex detection of biomolecular interactions with state-of-the-art sensitivity and minimal instrumental complexity. The detection performance is demonstrated by characterizing the interaction between human growth hormone in solution and the corresponding antibodies immobilized on the sensing surface, both in buffer and human serum, obtaining a clear signal for concentrations as small as 2.8 ng/ml.

Diagnosing dengue virus infection: rapid tests and the role of micro/nanotechnologies

Due to the progressive spread of the dengue virus and a rising incidence of dengue disease, its rapid diagnosis is important for developing countries and of increasing relevance for countries in temperate climates. Recent advances in bioelectronics, micro- and nanofabrication technologies have led to new miniaturized point-of-care devices and analytical platforms suited for rapid detection of infections. Starting from the available tests for dengue diagnosis, this review examines emerging rapid, micro/nanotechnologies-based tools, including label-free biosensor methods, microarray and microfluidic platforms, which hold significant potential, but still need further development and evaluation. The epidemiological and clinical setting as key determinants for selecting the best analytical strategy in patients presenting with fever is then discussed. This review is aimed at the clinicians and microbiologists to deepen understanding and enhance application of dengue diagnostics, and also serves as knowledge base for researchers and test developers to overcome the challenges posed by this disease.

FROM THE CLINICAL EDITOR

Dengue disease remains a significant problem in many developing countries. Unfortunately rapid diagnosis with easy and low cost tests for this disease is currently still not realized. In this comprehensive review, the authors highlighted recent advances in nanotechnology which would enable development in this field, which would result in beneficial outcomes to the population.

Nanotechnologies in protein microarrays

Protein microarray technology became an important research tool for study and detection of proteins, protein-protein interactions and a number of other applications. The utilization of nanoparticle-based materials and nanotechnology-based techniques for immobilization allows us not only to extend the surface for biomolecule immobilization resulting in enhanced substrate binding properties, decreased background signals and enhanced reporter systems for more sensitive assays. Generally in contemporarily developed microarray systems, multiple nanotechnology-based techniques are combined. In this review, applications of nanoparticles and nanotechnologies in creating protein microarrays, proteins immobilization and detection are summarized. We anticipate that advanced nanotechnologies can be exploited to expand promising fields of proteins identification, monitoring of protein-protein or drug-protein interactions, or proteins structures.

Kinetic analysis of the weak affinity interaction between tris and lysozyme

The biosensor based on total internal reflection imaging ellipsometry (TIRIE), regarded as an automotive real-time research approach for biomolecular interaction, is introduced to analyze the kinetic process of the weak interaction between tris and lysozyme. The experiment is performed by delivering lysozyme solution diluted to different concentrations to the biosensor substrate interface immobilized with tris. By applying pseudo-first-order interaction kinetics model, we are able to obtain the kinetic parameters from fitting experimental data. The calculated association rate constant and dissociation rate constant of tris and lysozyme interaction are in 10(-2) mol(-1) s(-1) and 10(3)s(-1) magnitude, respectively. To further improve TIRIE's ability for kinetically characterizing biomolecular interaction, a theoretical method to deduce associate rate constant before experiment is proposed.

Considerations for designing chemical screening strategies in plant biology

Traditionally, biologists regularly used classical genetic approaches to characterize and dissect plant processes. However, this strategy is often impaired by redundancy, lethality or pleiotropy of gene functions, which prevent the isolation of viable mutants. The chemical genetic approach has been recognized as an alternative experimental strategy, which has the potential to circumvent these problems. It relies on the capacity of small molecules to modify biological processes by specific binding to protein target(s), thereby conditionally modifying protein function(s), which phenotypically resemble mutation(s) of the encoding gene(s). A successful chemical screening campaign comprises three equally important elements: (1) a reliable, robust, and quantitative bioassay, which allows to distinguish between potent and less potent compounds, (2) a rigorous validation process for candidate compounds to establish their selectivity, and (3) an experimental strategy for elucidating a compound's mode of action and molecular target. In this review we will discuss details of this general strategy and additional aspects that deserve consideration in order to take full advantage of the power provided by the chemical approach to plant biology. In addition, we will highlight some success stories of recent chemical screenings in plant systems, which may serve as teaching examples for the implementation of future chemical biology projects.

Label free detection of specific protein binding using a microwave sensor

The specific binding of streptavidin to biotinylated protein A was demonstrated using a microwave detection system. In control experiments, the degree of non-specific binding was negligible. The method of detection was used to monitor the adsorption of two other proteins, cytochrome c and glucose oxidase, on to the IDE microwave sensor surface. The response of the sensor was also examined on different substrate materials, with detection of protein binding observed obtained on both smooth, conductive (gold) and on rough, insulating (hydroxyapatite) surfaces.

Array-based proteomic approaches to study signal transduction pathways: prospects, merits and challenges

Very often dysfunctional aspects of various signalling networks are found to be associated with human diseases and disorders. The major characteristics of signal transduction pathways are specificity, amplification of the signal, desensitisation and integration, which is accomplished not solely, but majorly by proteins. Array-based profiling of protein-protein and other biomolecular interactions is a versatile approach, which holds immense potential for multiplex interactome mapping and provides an inclusive representation of the signal transduction pathways and networks. Protein microarrays such as analytical protein microarrays (antigen-antibody interactions, autoantibody screening), RP microarrays (interaction of a particular ligand with all the possible targets in cell), functional protein microarrays (protein-protein or protein-ligand interactions) are implemented for various applications, including analysis of protein interactions and their significance in signalling cascades. Additionally, successful amalgamation of the array-based approaches with different label-free detection techniques allows real-time analysis of interaction kinetics of multiple interaction events simultaneously. This review discusses the prospects, merits and limitations of different variants of array-based techniques and their promising applications for studying the modifications and interactions of biomolecules, and highlights the studies associated with signal transduction pathways and their impact on disease pathobiology.

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.

Label-free, real-time detection of the dynamic processes of protein degradation using oblique-incidence reflectivity difference method

Based on the requirements for studying the dynamic process of proteinase action substrates in life science, we selected six random proteins including 1L-10, SCGB2A2, CENPQ, GST, HK1, KLHL7, as well as five different concentrations of 1L-10 proteins of 1 mg/ml, 0.5 mg/ml, 0.25 mg/ml, 0.125 mg/ml, and 0.0625 mg/ml, and fabricated two types of substrate protein microarrays, respectively. We detected the dynamic processes of proteins degraded by proteinase K using oblique-incidence reflectivity difference (OIRD) method in a label-free and real-time manner. We obtained the relevant degradation velocities and the degradation time. The experimental results demonstrate that OIRD has the ability to study proteinase action substrates which is out of reach of label methods and is expected to offer opportunities to determine protease-substrate relationships on the systems biology level.

A paper-based calorimetric microfluidics platform for bio-chemical sensing

In this report, a paper-based micro-calorimetric biochemical detection method is presented. Calorimetric detection of biochemical reactions is demonstrated as an extension of current colorimetric and electrochemical detection mechanisms of paper-based biochemical analytical systems. Reaction and/or binding temperature of glucose/glucose oxidase, DNA/hydrogen peroxide, and biotin/streptavidin, are measured by the paper-based micro-calorimeter. Commercially available glucose calibration samples of 0.05, 0.15 and 0.3% wt/vol concentration are used for comparing the device performance with a commercially available glucose meter (electrochemical detection). The calorimetric glucose detection demonstrates a measurement error less than 2%. The calorimetric detection results of DNA concentrations from 0.9 to 7.3 mg/mL and temperature changes in biotin and streptavidin reaction are presented to demonstrate the feasibility of integrating the calorimetric detection method with paper based microfluidic devices.

Digital imprinting of RNA recognition and processing on a self-assembled nucleic acid matrix

The accelerating progress of research in nanomedicine and nanobiotechnology has included initiatives to develop highly-sensitive, high-throughput methods to detect biomarkers at the single-cell level. Current sensing approaches, however, typically involve integrative instrumentation that necessarily must balance sensitivity with rapidity in optimizing biomarker detection quality. We show here that laterally-confined, self-assembled monolayers of a short, double-stranded(ds)[RNA-DNA] chimera enable permanent digital detection of dsRNA-specific inputs. The action of ribonuclease III and the binding of an inactive, dsRNA-binding mutant can be permanently recorded by the input-responsive action of a restriction endonuclease that cleaves an ancillary reporter site within the dsDNA segment. The resulting irreversible height change of the arrayed ds[RNA-DNA], as measured by atomic force microscopy, provides a distinct digital output for each dsRNA-specific input. These findings provide the basis for developing imprinting-based bio-nanosensors, and reveal the versatility of AFM as a tool for characterizing the behaviour of highly-crowded biomolecules at the nanoscale.

Label-free detection of native proteins by surface-enhanced Raman spectroscopy using iodide-modified nanoparticles

Proteins perform vital functional and structural duties in living systems, and the in-depth investigation of protein in its native state is one of the most important challenges in the postgenomic era. Surface-enhanced Raman spectroscopy (SERS) can provide the intrinsic fingerprint information of samples with ultrahigh sensitivity but suffers from the reproducibility and reliability issues. In this paper, we proposed an iodide-modified Ag nanoparticles method (Ag IMNPs) for label-free detection of proteins. The silver nanoparticles provide the huge enhancement to boost the Raman signal of proteins, and the coated iodide layer offers a barrier to prevent the direct interaction between the proteins and the metal surface, helping to keep the native structures of proteins. With this method, highly reproducible and high-quality SERS signals of five typical proteins (lysozyme, avidin, bovine serum albumin, cytochrome c, and hemoglobin) have been obtained, and the SERS features of the proteins without chromophore were almost identical to the respective normal Raman spectra. This unique feature allows the qualitative identification of them by simply taking the intensity ratio of the Raman peaks of tryptophan to phenylalanine residues. We further demonstrated that the method can also be used for label-free multiplex analysis of protein mixture as well as to study the dynamic process of protein damage stimulated by hydrogen peroxide. This method proves to be very promising for further applications in proteomics and biomedical research.

Differential expression of serum/plasma proteins in various infectious diseases: specific or nonspecific signatures

Apart from direct detection of the infecting organisms or biomarker of the pathogen itself, surrogate host markers are also useful for sensitive and early diagnosis of pathogenic infections. Early detection of pathogenic infections, discrimination among closely related diseases with overlapping clinical manifestations, and monitoring of disease progression can be achieved by analyzing blood biomarkers. Therefore, over the last decade large numbers of proteomics studies have been conducted to identify differentially expressed human serum/plasma proteins in different infectious diseases with the intent of discovering novel potential diagnostic/prognostic biomarkers. However, in-depth review of the literature indicates that many reported biomarkers are altered in the same way in multiple infectious diseases, regardless of the type of infection. This might be a consequence of generic acute phase reactions, while the uniquely modulated candidates in different pathogenic infections could be indicators of some specific responses. In this review article, we will provide a comprehensive analysis of differentially expressed serum/plasma proteins in various infectious diseases and categorize the protein markers associated with generic or specific responses. The challenges associated with the discovery, validation, and translational phases of serum/plasma biomarker establishment are also discussed.

Ultrasensitive protein detection: a case for microfluidic magnetic bead-based assays

We review the use of magnetic micro- and nanoparticles ('magnetic beads') in microfluidic systems for ultrasensitive protein detection. During recent years magnetic beads have been used frequently in immunoassays, either as mobile substrates on which the target antigen is captured, as detection labels, or simultaneously as substrates and labels. The major part of the reviewed work has as application the detection of antibodies or disease biomarkers in serum or of biotoxins from food samples. Several of the most sensitive assays allow protein detection down to fg mL(-1) concentrations. We benchmark the performance of these microfluidic magnetic bead-based assays with the most promising earlier work and with alternative solutions.

Proteomic studies related to genetic determinants of variability in protein concentrations

Genetic variation has multiple effects on the proteome. It may influence the expression level of proteins, modify their sequences through single nucleotide polymorphisms, the occurrence of allelic variants, or alternative splicing (ASP) events. This perspective paper summarizes the major effects of genetic variability on protein expression and isoforms and provides an overview of proteomics techniques and methods that allow studying the effects of genetic variability at different levels of the proteome. The paper provides an overview of recent quantitative trait loci studies performed to explore the effect of genetic variation on protein expression (pQTL). Finally it gives a perspective view on advances in proteomics technology and the role of the Chromosome-Centric Human Proteome Project (C-HPP) by creating large-scale resources that may facilitate performing more comprehensive pQTL experiments in the future.

Recent advances in nanobiotechnology and high-throughput molecular techniques for systems biomedicine

Nanotechnology-based tools are beginning to emerge as promising platforms for quantitative high-throughput analysis of live cells and tissues. Despite unprecedented progress made over the last decade, a challenge still lies in integrating emerging nanotechnology-based tools into macroscopic biomedical apparatuses for practical purposes in biomedical sciences. In this review, we discuss the recent advances and limitations in the analysis and control of mechanical, biochemical, fluidic, and optical interactions in the interface areas of nanotechnologybased materials and living cells in both in vitro and in vivo settings.

Carbon nanotubes as optical biomedical sensors

Biosensors are important tools in biomedical research. Moreover, they are becoming an essential part of modern healthcare. In the future, biosensor development will become even more crucial due to the demand for personalized-medicine, point-of care devices and cheaper diagnostic tools. Substantial advances in sensor technology are often fueled by the advent of new materials. Therefore, nanomaterials have motivated a large body of research and such materials have been implemented into biosensor devices. Among these new materials carbon nanotubes (CNTs) are especially promising building blocks for biosensors due to their unique electronic and optical properties. Carbon nanotubes are rolled-up cylinders of carbon monolayers (graphene). They can be chemically modified in such a way that biologically relevant molecules can be detected with high sensitivity and selectivity. In this review article we will discuss how carbon nanotubes can be used to create biosensors. We review the latest advancements of optical carbon nanotube based biosensors with a special focus on near-infrared (NIR)-fluorescence, Raman-scattering and fluorescence quenching.

Patterned biochemical functionalization improves aptamer-based detection of unlabeled thrombin in a sandwich assay

Here we propose a platform for the detection of unlabeled human α-thrombin down to the picomolar range in a fluorescence-based aptamer assay. In this concept, thrombin is captured between two different thrombin binding aptamers, TBA1 (15mer) and TBA2 (29mer), each labeled with a specific fluorescent dye. One aptamer is attached to the surface, the second one is in solution and recognizes surface-captured thrombin. To improve the limit of detection and the comparability of measurements, we employed and compared two approaches to pattern the chip substrate-microcontact printing of organosilanes onto bare glass slides, and controlled printing of the capture aptamer TBA1 in arrays onto functionalized glass substrates using a nanoplotter device. The parallel presence of functionalized and control areas acts as an internal reference. We demonstrate that both techniques enable the detection of thrombin concentrations in a wide range from 0.02 to 200 nM with a detection limit at 20 pM. Finally, the developed method could be transferred to any substrate to probe different targets that have two distinct possible receptors without the need for direct target labeling.

Phosphoproteomics in drug discovery

Several important aspects of the drug discovery process, including target identification, mechanism of action determination and biomarker identification as well as drug repositioning, require complete understanding of the effects of drugs on protein phosphorylation in relevant biological systems. Novel high-throughput phosphoproteomic technologies can be employed to measure these phosphorylation events. In this review, we describe the advantages and limitations of state-of-the-art phosphoproteomic approaches such as mass spectrometry and antibody-based technologies in terms of sample and data throughput as well as data quality. We then discuss how datasets from each technology can be analyzed and how the results can be and have been applied to advance different aspects of the drug discovery process.

Quantitative real-time imaging of protein-protein interactions by LSPR detection with micropatterned gold nanoparticles

Localized surface plasmon resonance (LSPR) offers powerful means for sensitive label-free detection of protein-protein interactions in a highly multiplexed format. We have here established self-assembly and surface modification of plasmonic nanostructures on solid support suitable for quantitative protein-protein interaction analysis by spectroscopic and microscopic LSPR detection. These architectures were obtained by layer-by-layer assembly via electrostatic attraction. Gold nanoparticles (AuNP) were adsorbed on a biocompatible amine-terminated poly(ethylene glycol) (PEG) polymer brush and further functionalized by poly-l-lysine graft PEG (PLL-PEG) copolymers. Stable yet reversible protein immobilization was achieved via tris(nitrilotriacetic acid) groups incorporated into the PLL-PEG coating. Thus, site-specific immobilization of His-tagged proteins via complexed Ni(II) ions was achieved. Functional protein immobilization on the surface was confirmed by real-time detection of LSPR scattering by reflectance spectroscopy. Association and dissociation rate constants obtained for a reversible protein-protein interaction were in good agreement with the data obtained by other surface-sensitive detection techniques. For spatially resolved detection, AuNP were assembled into micropatterns by means of photolithographic uncaging of surface amines. LSPR imaging of reversible protein-protein interactions was possible in a conventional wide field microscope, yielding detection limits of ∼30 protein molecules within a diffraction-limited surface area.

Selective functionalization of the protein N terminus with N-myristoyl transferase for bioconjugation in cell lysate

A site to behold: Robust site-specific functionalization of engineered proteins is achieved with N-myristoyl transferase (NMT) in bacterial cells. NMT tolerates non-natural substrate proteins as well as reactive fatty acid tags, rendering it a powerful tool for protein conjugation applications, including the construction of protein microarrays from lysate.

Biosensors in the small scale: methods and technology trends

This study presents a review on biosensors with an emphasis on recent developments in the field. A brief history accompanied by a detailed description of the biosensor concepts is followed by rising trends observed in contemporary micro- and nanoscale biosensors. Performance metrics to quantify and compare different detection mechanisms are presented. A comprehensive analysis on various types and subtypes of biosensors are given. The fields of interest within the scope of this review are label-free electrical, mechanical and optical biosensors as well as other emerging and popular technologies. Especially, the latter half of the last decade is reviewed for the types, methods and results of the most prominently researched detection mechanisms. Tables are provided for comparison of various competing technologies in the literature. The conclusion part summarises the noteworthy advantages and disadvantages of all biosensors reviewed in this study. Furthermore, future directions that the micro- and nanoscale biosensing technologies are expected to take are provided along with the immediate outlook.

Label-free biodetection using a smartphone

Utilizing its integrated camera as a spectrometer, we demonstrate the use of a smartphone as the detection instrument for a label-free photonic crystal biosensor. A custom-designed cradle holds the smartphone in fixed alignment with optical components, allowing for accurate and repeatable measurements of shifts in the resonant wavelength of the sensor. Externally provided broadband light incident upon an entrance pinhole is subsequently collimated and linearly polarized before passing through the biosensor, which resonantly reflects only a narrow band of wavelengths. A diffraction grating spreads the remaining wavelengths over the camera's pixels to display a high resolution transmission spectrum. The photonic crystal biosensor is fabricated on a plastic substrate and attached to a standard glass microscope slide that can easily be removed and replaced within the optical path. A custom software app was developed to convert the camera images into the photonic crystal transmission spectrum in the visible wavelength range, including curve-fitting analysis that computes the photonic crystal resonant wavelength with 0.009 nm accuracy. We demonstrate the functionality of the system through detection of an immobilized protein monolayer, and selective detection of concentration-dependent antibody binding to a functionalized photonic crystal. We envision the capability for an inexpensive, handheld biosensor instrument with web connectivity to enable point-of-care sensing in environments that have not been practical previously.

Latest developments in experimental and computational approaches to characterize protein-lipid interactions

Understanding the functional roles of all the molecules in cells is an ultimate goal of modern biology. An important facet is to understand the functional contributions from intermolecular interactions, both within a class of molecules (e.g. protein-protein) or between classes (e.g. protein-DNA). While the technologies for analyzing protein-protein and protein-DNA interactions are well established, the field of protein-lipid interactions is still relatively nascent. Here, we review the current status of the experimental and computational approaches for detecting and analyzing protein-lipid interactions. Experimental technologies fall into two principal categories, namely solution-based and array-based methods. Computational methods include large-scale data-driven analyses and predictions/dynamic simulations based on prior knowledge of experimentally identified interactions. Advances in the experimental technologies have led to improved computational analyses and vice versa, thereby furthering our understanding of protein-lipid interactions and their importance in biological systems.

Label-free strategy for in-situ analysis of protein binding interaction based on attenuated total reflection surface enhanced infrared absorption spectroscopy (ATR-SEIRAS)

A versatile ATR-SEIRAS methodology is described herein for highly sensitive analysis of immunoglobulin (IgG) recognition. This strategy allows in situ tracking of specific protein binding at the liquid-solid interface. Most importantly, interferential signal from environmental molecules (e.g., water, nonspecific binding molecules, and bulk molecules) can be eliminated to negligible levels by using the ATR analysis mode, and the sensitive IR structural information of target proteins is obtained simultaneously. A simplified numerical model has been established to quantitatively describe the kinetics and thermodynamics of protein recognition processes at surfaces. Compared with conventional label-free methods for protein binding study, experimental results obtained from IR spectroscopic information are more reliable. The presented ATR-SEIRAS method is powerful in studying surface limited protein binding reactions.

Tackling reproducibility in microcantilever biosensors: a statistical approach for sensitive and specific end-point detection of immunoreactions

In the last decade, microcantilever biosensors have shown enormous potential for highly sensitive label-free detection of nucleic acid and proteins. Despite the enormous advances, the promise of applications of this technology in the biomedical field has been frustrated because of its low reproducibility. Here we tackle the reproducibility issue in microcantilever biosensors and provide the guidelines to minimize the deviations in the biosensor response between different assays. We use as a model system the label-free end-point detection of horseradish peroxidase. We choose the end-point detection mode because of its suitability for implementation in the clinical field that requires simplicity and point-of-care capability. Our study comprises the analysis of 1012 cantilevers with different antibody surface densities, two blocking strategies based on polyethylene-glycol (PEG) and bovine serum albumin (BSA) and stringent controls. The study reveals that the performance of the assay critically depends on both antibody surface density and blocking strategies. We find that the optimal conditions involve antibody surface densities near but below saturation and blocking with PEG. We find that the surface stress induced by the antibody-antigen binding is significantly correlated with the surface stress generated during the antibody attachment and blocking steps. The statistical correlation is harnessed to identify immobilization failure or success, and thus enhancing the specificity and sensitivity of the assay. This procedure enables achieving rates of true positives and true negatives of 90% and 91% respectively. The detection limit is of 10 ng mL(-1) (250 pM) that is similar to the detection limit obtained in our enzyme-linked immunosorbent assay (ELISA) and at least two orders of magnitude smaller than that achieved with well-established label-free biosensors such as a quartz crystal microbalance (QCM) and surface plasmon resonance (SPR) sensor.