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

Realizing the label-free sensitive detection of carcinoembryogenic antigen (CEA) in blood serum via a MNC-decorated flexible immunosensor

A label-free electrochemical immunosensor utilising nitrogen-rich mesoporous carbon (MNC) as the substrate material was developed for the sensitive quantification of carcinoembryonic antigen (CEA). The synergic interactions between MNC and AbCEA also eliminated the need for coupling agents such as EDC/NHS. The novel immunosensor demonstrated a wide detection range from 500 fM (9.04 pg mL-1) to 50 nM (1 μg mL-1) and a low detection limit (LOD) of 500 fM. Moreover, the immunosensor showed sensitivities of 12.27 mA nM-1 cm-2 and 0.066 mA nM-1 cm-2 for detecting CEA in the linear ranges 10 pM to 1 nM and 2 nM to 50 nM, respectively, while maintaining long-term storage stability of 6 weeks. Analysis of real serum sample analysis yielded highly accurate results with recovery rates ranging from 99.3% to 103.7%. Furthermore, the developed paper-based screen-printed electrode exhibited a similar detection range, suggesting its potential for use in point-of-care detection devices in future applications.

Fluorescence-Based Protein Stability Monitoring-A Review

Proteins are large biomolecules with a specific structure that is composed of one or more long amino acid chains. Correct protein structures are directly linked to their correct function, and many environmental factors can have either positive or negative effects on this structure. Thus, there is a clear need for methods enabling the study of proteins, their correct folding, and components affecting protein stability. There is a significant number of label-free methods to study protein stability. In this review, we provide a general overview of these methods, but the main focus is on fluorescence-based low-instrument and -expertise-demand techniques. Different aspects related to thermal shift assays (TSAs), also called differential scanning fluorimetry (DSF) or ThermoFluor, are introduced and compared to isothermal chemical denaturation (ICD). Finally, we discuss the challenges and comparative aspects related to these methods, as well as future opportunities and assay development directions.

Identification of differentially expressed proteins in heart of mouse death from smother based on label-free proteomics

Identification of mechanical asphyxia deaths without obvious injuries is a difficult problem for forensic medicine. This study aimed to identify molecular biological markers to predict death from mechanical asphyxia (smother). We established a smother model of mice by over the head with plastic bag tightly until the mice died and applied label-free proteomic technology to identify differentially expressed proteins (DEPs) in heart. A total of 3307 proteins were quantified, and a Fold Change (FC) > 1.2 (or <1/1.2) and Q value < 0.05 were considered as DEPs. Through comparative analysis, we identified 606 DEPs compared to the control group, comprising 219 upregulated and 387 downregulated proteins. Bioinformatics analysis (MCODE analysis) showed that the candidate proteins were mainly involved in regulation of ribosome function, myocardial contraction and calcium regulation, regulation of coagulation and regulation of mitochondrial oxidative respiration. Seven of these proteins were validated using parallel reaction monitoring (PRM), including fibrinogen alpha chain (FIBA), fibrinogen gamma chain (FIBG), Calsequestrin-2 (CASQ2), NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 (NDUAB), NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 (NDUA3), NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 (NDUAD) and Rab7 (RAB7A). CASQ2 and FIBG were further validated by immunohistochemistry. In conclusion, our results may provide some auxiliary indices for identifying the death from mechanical asphyxia.

Highly sensitive label-free biosensor: graphene/CaF2 multilayer for gas, cancer, virus, and diabetes detection with enhanced quality factor and figure of merit

One of the primary goals for the researchers is to create a high-quality sensor with a simple structure because of the urgent requirement to identify biomolecules at low concentrations to diagnose diseases and detect hazardous chemicals for health early on. Recently graphene has attracted much interest in the field of improved biosensors. Meanwhile, graphene with new materials such as CaF2 has been widely used to improve the applications of graphene-based sensors. Using the fantastic features of the graphene/CaF2 multilayer, this article proposes an improvement sensor in the sensitivity (S), the figure of merit (FOM), and the quality factor (Q). The proposed sensor is based on the five-layers graphene/dielectric grating integrated with a Fabry-Perot cavity. By tuning graphene chemical potential (µc), due to the semi-metal features of graphene, the surface plasmon resonance (SPR) waves excited at the graphene/dielectric boundaries. Due to the vertical polarization of the source to the gratings and the symmetry of the electric field, both corners of the grating act as electric dipoles, and this causes the propagation of plasmonic waves on the graphene surface to propagate towards each other. Finally, it causes Fabry-Perot (FP) interference on the surface of graphene in the proposed structure's active medium (the area where the sample is located). In this article, using the inherent nature of FP interference and its S to the environment's refractive index (RI), by changing a minimal amount in the RI of the sample, the resonance wavelength (interferometer order) shifts sharply. The proposed design can detect and sense some cancers, such as Adrenal Gland Cancer, Blood Cancer, Breast Cancer I, Breast Cancer II, Cervical Cancer, and skin cancer precisely. By optimizing the structure, we can achieve an S as high as 9000 nm/RIU and a FOM of about 52.14 for the first resonance order (M1). Likewise, the remarkable S of 38,000 nm/RIU and the FOM of 81 have been obtained for the second mode (M2). In addition, the proposed label-free SPR sensor can detect changes in the concentration of various materials, including gases and biomolecules, hemoglobin, breast cancer, diabetes, leukemia, and most alloys, with an accuracy of 0.001. The proposed sensor can sense urine concentration with a maximum S of 8500 nm/RIU and cancers with high S in the 6000 nm/RIU range to 7000 nm/RIU. Also, four viruses, such as M13 bacteriophage, HIV type one, Herpes simplex type 1, and influenza, have been investigated, showing Maximum S (for second resonance mode of λR(M2) of 8000 nm/RIU (λR(M2) = 11.2 µm), 12,000 nm/RIU (λR(M2) = 10.73 µm), 38,000 nm/RIU (λR(M2) = 11.78 µm), and 12,000 nm/RIU (λR(M2) = 10.6 µm), respectively, and the obtained S for first resonance mode (λR(M1)) for mentioned viruses are 4740 nm/RIU (λR(M1) = 8.7 µm), 8010 nm/RIU (λR(M1) = 8.44 µm), 8100 nm/RIU (λR(M1) = 10.15 µm), and 9000 (λR(M1) = 8.36 µm), respectively.

Plasmon- and Waveguide-Coupled Fluorescence at the Ultraviolet Region

Surface plasmon-coupled emission (SPCE) has been well studied for its coupled, directional, and enhanced P-polarized radiation due to the interactions of fluorophores with surface plasmon polaritons (SPPs) on thin metal films. Such surface plasmon polariton-assisted directional fluorescence has various applications in biosensing. Herein, we demonstrate 2-aminopurine (2AP, a UV-absorbing and -emitting fluorophore) emission coupling to modes in aluminum-based plasmon-coupled waveguides (Al-PCWs). Directional emission from 2-aminopurine on plasmon-coupled waveguides was observed at specific angles as P-polarized SPCE and/or as P- or S-polarized waveguide-coupled emission (WGCE). All S-polarized waveguide modes showed clear angularly resolved emission as compared to that of P-polarized surface plasmon-coupled emission or P-polarized waveguide-coupled emission. The coupling angles, efficiencies, and polarizations of the modes were sensitive to the optical properties and overall dimensions of the top dielectric layer in PCWs. The effective plasmon-coupled waveguide can consist of either a thin probe-containing layer on top of the undoped silica film, or a single dielectric PVA layer with probes distributed throughout the film on the Al layer. The former structures with probes confined to the top of the undoped silica layer showed much higher angular resolutions and coupling efficiencies, as well as mode-dependent changes in lifetimes. These results demonstrate that the plasmon and waveguide modes can be used for selective detection of surface-bound and bulk fluorophores, simultaneously.

Planar Junctionless Field-Effect Transistor for Detecting Biomolecular Interactions

Label-free field-effect transistor-based immunosensors are promising candidates for proteomics and peptidomics-based diagnostics and therapeutics due to their high multiplexing capability, fast response time, and ability to increase the sensor sensitivity due to the short length of peptides. In this work, planar junctionless field-effect transistor sensors (FETs) were fabricated and characterized for pH sensing. The device with SiO₂ gate oxide has shown voltage sensitivity of 41.8 ± 1.4, 39.9 ± 1.4, 39.0 ± 1.1, and 37.6 ± 1.0 mV/pH for constant drain currents of 5, 10, 20, and 50 nA, respectively, with a drain to source voltage of 0.05 V. The drift analysis shows a stability over time of −18 nA/h (pH 7.75), −3.5 nA/h (pH 6.84), −0.5 nA/h (pH 4.91), 0.5 nA/h (pH 3.43), corresponding to a pH drift of −0.45, −0.09, −0.01, and 0.01 per h. Theoretical modeling and simulation resulted in a mean value of the surface states of 3.8 × 10¹⁵/cm² with a standard deviation of 3.6 × 10¹⁵/cm². We have experimentally verified the number of surface sites due to APTES, peptide, and protein immobilization, which is in line with the theoretical calculations for FETs to be used for detecting peptide-protein interactions for future applications.

A microwell-based impedance sensor on an insertable microneedle for real-time in vivo cytokine detection

Impedance-based protein detection sensors for point-of-care diagnostics require quantitative specificity, as well as rapid or real-time operation. Furthermore, microfabrication of these sensors can lead to the formation of factors suitable for in vivo operation. Herein, we present microfabricated needle-shaped microwell impedance sensors for rapid-sample-to-answer, label-free detection of cytokines, and other biomarkers. The microneedle form factor allows sensors to be utilized in transcutaneous or transvascular sensing applications. In vitro, experimental characterization confirmed sensor specificity and sensitivity to multiple proteins of interest. Mechanical characterization demonstrated sufficient microneedle robustness for transcutaneous insertion, as well as preserved sensor function postinsertion. We further utilized these sensors to carry out real-time in vivo quantification of human interleukin 8 (hIL8) concentration levels in the blood of transgenic mice that endogenously express hIL8. To assess sensor functionality, hIL8 concentration levels in serum samples from the same mice were quantified by ELISA. Excellent agreement between real-time in vivo sensor readings in blood and subsequent ELISA serum assays was observed over multiple transgenic mice expressing hIL8 concentrations from 62 pg/mL to 539 ng/mL.

Microfluidic devices for glycobiomarker detection in cancer

During oncogenesis, several alterations occur within cells, one of them being the abnormal glycosylation of proteins, resulting in the formation of glycoproteins with aberrant glycan structures, which can be secreted into the blood stream. Their specific association to tumour cells makes them useful indicators (biomarkers) of the oncogenic process and their detection in blood can be employed in different stages of tumour development for early detection, prognosis and therapeutic drug monitoring. Due to the importance of detecting cancer-associated glycoproteins with aberrant glycosylation in blood or serum, analytical methodologies with improved performance are required to ameliorate the laboratorial tests currently used for the detection of these analytes. Microfluidics was created to facilitate the implementation of simple and point-of-care analysis, away from a centralized laboratory. The massive use of microfluidic systems in clinical settings can be seen in pregnancy tests and diabetes control, for example. But what about other clinical domains, such as the detection of glycoproteins with aberrant glycans secreted by tumour cells? Are microfluidic systems helpful in this case? This review analyses the requirements of a microfluidic assay for the detection of low-abundant blood/serum cancer-associated glycoproteins with abnormal glycans and the progresses that have been made in the last years to develop integrated microfluidic devices for this particular application. The diverse microfluidic systems found in literature present, in general, the same analytical performance as the conventional assays but have additional advantages, namely a reduction in assay times, a decrease of sample and reagent consumption and lower costs. The review will also focus on the improvements that are still needed for better biosensing of this type of cancer biomarkers using microfluidic devices.

New applications of advanced instrumental techniques for the characterization of food allergenic proteins

Current approaches based on electrophoretic, chromatographic or immunochemical principles have allowed characterizing multiple allergens, mapping their epitopes, studying their mechanisms of action, developing detection and diagnostic methods and therapeutic strategies for the food and pharmaceutical industry. However, some of the common structural features related to the allergenic potential of food proteins remain unknown, or the pathological mechanism of food allergy is not yet fully understood. In addition, it is also necessary to evaluate new allergens from novel protein sources that may pose a new risk for consumers. Technological development has allowed the expansion of advanced technologies for which their whole potential has not been entirely exploited and could provide novel contributions to still unexplored molecular traits underlying both the structure of food allergens and the mechanisms through which they sensitize or elicit adverse responses in human subjects, as well as improving analytical techniques for their detection. This review presents cutting-edge instrumental techniques recently applied when studying structural and functional aspects of proteins, mechanism of action and interaction between biomolecules. We also exemplify their role in the food allergy research and discuss their new possible applications in several areas of the food allergy field.

Label-Free Immunoassay Using Droplet-Based Brewster's Angle Straddle Interferometry

We report the detection of antigen capture by immobilized antibodies using a simple, label-free version of monochromatic reflective interferometry. The technique is implemented on silicon with its native oxide and relies on choosing an incident angle between the Brewster angles for the air/oxide and oxide/silicon interfaces. We demonstrate sensitivity to anti-human and anti-rabbit immunoglobulin (anti-IgG) concentrations less than 100 nM using only 10 nL droplets of the analyte. We have introduced a protocol using a model sugar to reduce nonspecific binding and have been able to detect anti-IgG even in the presence of 100-fold larger concentrations of bovine serum albumin. The limit of detection is not yet associated with the optical method but is imposed by nonspecific binding. Evaluated in terms of pg/mm², our sensors are comparable in sensitivity to surface plasmon resonance (SPR) but are advantaged with respect to SPR in the tolerance of the optical components and alignment, the low material usage, and the ability to exploit multiplex detection without modification. The simplicity and convenience of the method are promising for eventual application to portable diagnostic applications.

Label-free capacitive assaying of biomarkers for molecular diagnostics

The label-free analysis of biomarkers offers important advantages in developing point-of-care (PoC) biosensors. In contrast to label-based methodologies, such as ELISA, label-free analysis enables direct detection of targets without additional steps and labeled reagents. Nonetheless, label-free approaches require high sensitivity to detect the intrinsic features of a biomarker and low levels of nonspecific signals. Electrochemical capacitance, [Formula: see text], is a feature of electroactive nanoscale films that can be measured using electrochemical impedance spectroscopy. [Formula: see text] is promising as an electrochemical transducing signal for the development of high-sensitivity, reagentless and label-free molecular diagnostic assays. We used a proprietary ferrocene (Fc)-tagged peptide that is able to self-assemble onto gold electrodes (thicknesses <2 nm) to which any biological receptor can be coupled. When coupled with biological receptors (e.g., a monoclonal antibody), [Formula: see text] exhibited by the redox-tagged peptide changes as a function of the target concentration. We provide herein the steps for the qualitative and quantitative detection of dengue non-structural protein 1 (NS1) biomarker. Detection of NS1 can be used to diagnose dengue virus infection, which causes epidemics each year in tropical and subtropical regions of the world. Including the pre-treatment of the electrode surface, the analysis takes ~25 h. This time can be reduced to minutes if the electrode surface is fabricated separately, demonstrating that [Formula: see text] is promising for PoC applications. We hope this protocol will serve as a reference point for researchers and companies that intend to further develop capacitive devices for molecular diagnostic assays.

A ten-minute, single step, label-free, sample-to-answer assay for qualitative detection of cytokines in serum at femtomolar levels

Label-free electronic affinity based immuno-sensing is an attractive candidate as a platform technology for analyzing biomarkers due to the ease of miniaturization and minimal use of reagents. Electronic based sensing approaches, however, have lagged behind their optical counterparts in terms of detection limit, selectivity, and reliability. Also, the matrix dependent nature of electronic sensing modalities makes difficult the analysis of biomarkers in high salt concentration samples such as serum due to charge screening. We present a novel sensing platform, the micro-well sensor, that works by functionalizing nanoscale volume wells with antibodies and monitoring the impedance change inside the wells due binding of target protein. This detection modality is advantageous to many label-free electronic sensors in that signal power scales with increase in salt concentration, thus improving the sensitivity of the platform. We demonstrate rapid label-free qualitative detection of cytokines within ten minutes at femtoMolar concentrations and a dynamic range of 3 orders of magnitude in serum samples. We describe the design, fabrication, and characterization of the micro-well sensor in serum samples using inflammatory protein biomarkers.

Technological Advances in Preclinical Drug Evaluation: The Role of -Omics Methods

Preclinical drug development is an essential step in the drug development process where the evaluation of new chemical entities occurs. In particular, preclinical drug development phases include deep analysis of drug candidates' interactions with biomolecules/targets, their safety, toxicity, pharmacokinetics, metabolism by use of assays in vitro and in vivo animal assays. Legal aspects of the required procedures are well-established. Herein, we present a comprehensive summary of current state-of-the art approaches and techniques used in preclinical studies. In particular, we will review the potential of new, -omics methods and platforms for mechanistic evaluation of drug candidates and speed-up of the preclinical evaluation steps.

Electrospun Nanofibers for Label-Free Sensor Applications

Electrospinning is a simple, low-cost and versatile method for fabricating submicron and nano size fibers. Due to their large surface area, high aspect ratio and porous structure, electrospun nanofibers can be employed in wide range of applications. Biomedical, environmental, protective clothing and sensors are just few. The latter has attracted a great deal of attention, because for biosensor application, nanofibers have several advantages over traditional sensors, including a high surface-to-volume ratio and ease of functionalization. This review provides a short overview of several electrospun nanofibers applications, with an emphasis on biosensor applications. With respect to this area, focus is placed on label-free sensors, pertaining to both recent advances and fundamental research. Here, label-free sensor properties of sensitivity, selectivity, and detection are critically evaluated. Current challenges in this area and prospective future work is also discussed.

Probing the interaction of nanoparticles with small molecules in real time via quartz crystal microbalance monitoring

Despite extensive advances in the field of molecular recognition, the real-time monitoring of small molecule binding to nanoparticles (NP) remains a challenge. To this end, we report on a versatile approach, based on quartz crystal microbalance with dissipation monitoring, for the stepwise in situ quantification of gold nanoparticle (AuNPs) immobilisation and subsequent uptake and release of binding partners. AuNPs stabilised by thiol-bound ligand shells of prescribed chemical composition were densely immobilised onto gold surfaces via dithiol linkers. The boronate ester formation between salicylic acid derivatives in solution and boronic acids in the AuNP ligand shell was then studied in real time, revealing a drastic effect of both ligand architecture and Lewis base concentration on the interaction strength. The binding kinetics were analysed with frequency response modelling for a thorough comparison of binding parameters including relaxation time as well as association rate constant. The results directly mirror those from previously reported in-depth studies using nuclear magnetic resonance spectroscopy. By achieving quantitative characterisation of selective binding of analytes with molecular weight below 300 Da, this new method enables rapid, low cost, rational screening of AuNP candidates for molecular recognition.

Label-free tomography of living cellular nanoarchitecture using hyperspectral self-interference microscopy

Quantitative phase imaging (QPI) is the most ideal method for achieving long-term cellular tomography because it is label free and quantitative. However, for current QPI instruments, interference signals from different layers overlay with each other and impede nanoscale optical sectioning. Integrated incubators and improved configurations also require further investigation for QPI instruments. In this work, hyperspectral self-reflectance microscopy is proposed to achieve label-free tomography of living cellular nanoarchitecture. The optical description and tomography reconstruction algorithm were proposed so that the quantitative morphological structure of the entire living cell can be acquired with 89.2 nm axial resolution and 1.91 nm optical path difference sensitivity. A cell incubator was integrated to culture living cells for in situ measurement and expensive precise optical components were not needed. The proposed system can reveal native and dynamic cellular nanoscale structure, providing an alternative approach for long-term monitoring and quantitative analysis of living cells.

Towards Portable Nanophotonic Sensors

A range of nanophotonic sensors composed of different materials and device configurations have been developed over the past two decades. These sensors have achieved high performance in terms of sensitivity and detection limit. The size of onchip nanophotonic sensors is also small and they are regarded as a strong candidate to provide the next generation sensors for a range of applications including chemical and biosensing for point-of-care diagnostics. However, the apparatus used to perform measurements of nanophotonic sensor chips is bulky, expensive and requires experts to operate them. Thus, although integrated nanophotonic sensors have shown high performance and are compact themselves their practical applications are limited by the lack of a compact readout system required for their measurements. To achieve the aim of using nanophotonic sensors in daily life it is important to develop nanophotonic sensors which are not only themselves small, but their readout system is also portable, compact and easy to operate. Recognizing the need to develop compact readout systems for onchip nanophotonic sensors, different groups around the globe have started to put efforts in this direction. This review article discusses different works carried out to develop integrated nanophotonic sensors with compact readout systems, which are divided into two categories; onchip nanophotonic sensors with monolithically integrated readout and onchip nanophotonic sensors with separate but compact readout systems.

Exploring the protein-protein interaction landscape in plants

Protein-protein interactions (PPIs) represent an essential aspect of plant systems biology. Identification of key protein players and their interaction networks provide crucial insights into the regulation of plant developmental processes and into interactions of plants with their environment. Despite the great advance in the methods for the discovery and validation of PPIs, still several challenges remain. First, the PPI networks are usually highly dynamic, and the in vivo interactions are often transient and difficult to detect. Therefore, the properties of the PPIs under study need to be considered to select the most suitable technique, because each has its own advantages and limitations. Second, besides knowledge on the interacting partners of a protein of interest, characteristics of the interaction, such as the spatial or temporal dynamics, are highly important. Hence, multiple approaches have to be combined to obtain a comprehensive view on the PPI network present in a cell. Here, we present the progress in commonly used methods to detect and validate PPIs in plants with a special emphasis on the PPI features assessed in each approach and how they were or can be used for the study of plant interactions with their environment.

Label-Free Capacitive Biosensor for Detection of Cryptosporidium

Cryptosporidium, an intestinal protozoan pathogen, is one of the leading causes of diarrhea in healthy adults and death in children. Detection of Cryptosporidium oocysts has become a high priority to prevent potential outbreaks. In this paper, a label-free interdigitated-based capacitive biosensor has been introduced for the detection of Cryptosporidium oocysts in water samples. Specific anti-Cryptosporidium monoclonal antibodies (IgG3) were covalently immobilized onto interdigitated gold electrodes as the capture probes, and bovine serum albumin was used to avoid non-specific adsorption. The immobilization of the antibodies was confirmed by measuring the change in the contact angle. The detection was achieved by measuring the relative change in the capacitive/dielectric properties due to the formation of Cryptosporidium-antibody complex. The biosensor has been tested for different concentrations of Cryptosporidium. The results show that the biosensor developed can accurately distinguish different numbers of captured cells and densities on the surface of the biosensor. The number of Cryptosporidium oocysts captured on the electrode surface was confirmed using a fluorescein isothiocyanate (FITC) immunofluorescence assay. The response from the developed biosensor has been mainly dependent on the concentration of Cryptosporidium under optimized conditions. The biosensor showed a linear detection range between 15 and 153 cells/mm² and a detection limit of 40 cells/mm². The label-free capacitive biosensor developed has a great potential for detecting Cryptosporidium in environmental water samples. Furthermore, under optimized conditions, this label-free biosensor can be extended for detection of other biomarkers for biomedical and environmental analyses.

Towards precision medicine: the role and potential of protein and peptide microarrays

Techniques to comprehensively analyze protein signatures are pivotal to unravel disease mechanisms, develop novel biomarkers and targeted therapies. In this frame, protein and peptide microarrays can play a major role in fuelling precision medicine.

Microfluidic Devices for Label-Free DNA Detection

Sensitive and specific DNA biomarker detection is critical for accurately diagnosing a broad range of clinical conditions. However, the incorporation of such biosensing structures in integrated microfluidic devices is often complicated by the need for an additional labelling step to be implemented on the device. In this review we focused on presenting recent advances in label-free DNA biosensor technology, with a particular focus on microfluidic integrated devices. The key biosensing approaches miniaturized in flow-cell structures were presented, followed by more sophisticated microfluidic devices and higher integration examples in the literature. The option of full DNA sequencing on microfluidic chips via nanopore technology was highlighted, along with current developments in the commercialization of microfluidic, label-free DNA detection devices.

pH-Based Detection of Target Analytes in Diluted Serum Samples Using Surface Plasmon Resonance Immunosensor

Detection of minute quantities of target antigens in serum samples (consisting of a mixture of proteins/biomolecules) can be achieved by enhancement of the capture efficiencies of heterogeneous immunosensors. An important process parameter which affects the capture of target analytes in such immunosensors is the pH of the solution as the target proteins present in the serum samples are charged molecules. Here, we investigated the capture of prostate-specific antigens (PSAs), first in a mixed-analyte system wherein the solution contained two other non-specific proteins along with the target analyte, using the surface plasmon resonance spectroscopy. There are no reports on the detection of antigens in a mixed system based on the optimization of the pH values of the carrier fluid, and this is the motivation of the present work. Further, we studied interference effects caused by the presence of these non-specific proteins in the mixed-analyte systems by artificially increasing the ratio of the interfering proteins to that of the target protein. Eventually PSA spiked into the rabbit serum samples was captured through the optimization of the pH of the solution. We could detect PSA in the serum samples when diluted to 100 times or more, where the amounts of other interfering proteins were ~ 66 times that of the amount of PSA. This study proposes a heterogeneous immunosensor to detect the target analytes in the diluted serum samples by tuning pH the of solution mixture, which can be utilized to detect disease biomarkers in serum samples.

Analysis of Multiplexed Nanosensor Arrays Based on Near-Infrared Fluorescent Single-Walled Carbon Nanotubes

The high-throughput, label-free detection of biomolecules remains an important challenge in analytical chemistry with the potential of nanosensors to significantly increase the ability to multiplex such assays. In this work, we develop an optical sensor array, printable from a single-walled carbon nanotube/chitosan ink and functionalized to enable a divalent ion-based proximity quenching mechanism for transducing binding between a capture protein or an antibody with the target analyte. Arrays of 5 × 6, 200 μm near-infrared (nIR) spots at a density of ≈300 spots/cm² are conjugated with immunoglobulin-binding proteins (proteins A, G, and L) for the detection of human IgG, mouse IgM, rat IgG2a, and human IgD. Binding kinetics are measured in a parallel, multiplexed fashion from each sensor spot using a custom laser scanning imaging configuration with an nIR photomultiplier tube detector. These arrays are used to examine cross-reactivity, competitive and nonspecific binding of analyte mixtures. We find that protein G and protein L functionalized sensors report selective responses to mouse IgM on the latter, as anticipated. Optically addressable platforms such as the one examined in this work have potential to significantly advance the real-time, multiplexed biomolecular detection of complex mixtures.

Label-Free Detection of Microvesicles and Proteins by the Bundling of Gliding Microtubules

Development of miniaturized devices for the rapid and sensitive detection of analyte is crucial for various applications across healthcare, pharmaceutical, environmental, and other industries. Here, we report on the detection of unlabeled analyte by using fluorescently labeled, antibody-conjugated microtubules in a kinesin-1 gliding motility assay. The detection principle is based on the formation of fluorescent supramolecular assemblies of microtubule bundles and spools in the presence of multivalent analytes. We demonstrate the rapid, label-free detection of CD45+ microvesicles derived from leukemia cells. Moreover, we employ our platform for the label-free detection of multivalent proteins at subnanomolar concentrations, as well as for profiling the cross-reactivity between commercially available secondary antibodies. As the detection principle is based on the molecular recognition between antigen and antibody, our method can find general application where it identifies any analyte, including clinically relevant microvesicles and proteins.

Dual-Mode Electro-Optical Techniques for Biosensing Applications: A Review

The monitoring of biomolecular interactions is a key requirement for the study of complex biological processes and the diagnosis of disease. Technologies that are capable of providing label-free, real-time insight into these interactions are of great value for the scientific and clinical communities. Greater understanding of biomolecular interactions alongside increased detection accuracy can be achieved using technology that can provide parallel information about multiple parameters of a single biomolecular process. For example, electro-optical techniques combine optical and electrochemical information to provide more accurate and detailed measurements that provide unique insights into molecular structure and function. Here, we present a comparison of the main methods for electro-optical biosensing, namely, electrochemical surface plasmon resonance (EC-SPR), electrochemical optical waveguide lightmode spectroscopy (EC-OWLS), and the recently reported silicon-based electrophotonic approach. The comparison considers different application spaces, such as the detection of low concentrations of biomolecules, integration, the tailoring of light-matter interaction for the understanding of biomolecular processes, and 2D imaging of biointeractions on a surface.

Surface Plasmon Resonance or Biocompatibility-Key Properties for Determining the Applicability of Noble Metal Nanoparticles

Metal and in particular noble metal nanoparticles represent a very special class of materials which can be applied as prepared or as composite materials. In most of the cases, two main properties are exploited in a vast number of publications: biocompatibility and surface plasmon resonance (SPR). For instance, these two important properties are exploitable in plasmonic diagnostics, bioactive glasses/glass ceramics and catalysis. The most frequently applied noble metal nanoparticle that is universally applicable in all the previously mentioned research areas is gold, although in the case of bioactive glasses/glass ceramics, silver and copper nanoparticles are more frequently applied. The composite partners/supports/matrix/scaffolds for these nanoparticles can vary depending on the chosen application (biopolymers, semiconductor-based composites: TiO₂, WO₃, Bi₂WO₆, biomaterials: SiO₂ or P₂O₅-based glasses and glass ceramics, polymers: polyvinyl alcohol (PVA), Gelatin, polyethylene glycol (PEG), polylactic acid (PLA), etc.). The scientific works on these materials' applicability and the development of new approaches will be targeted in the present review, focusing in several cases on the functioning mechanism and on the role of the noble metal.

Label-free biosensing of Salmonella enterica serovars at single-cell level

BACKGROUND

The emerging nanotechnologies have greatly facilitated the development of label-free biosensors. The atomic force microscopy (AFM) has been used to study the molecular mechanism of the reactions for protein and aptamers. The surface plasmon resonance (SPR) have been used in fast detections of various pathogens such as bacteria. This study used both AFM and SPR to investigate the complex reactions between aptamers and outer membrane proteins (OMPs) on the surface of S. typhimurium.

RESULTS

Two DNA aptamers were used for the label-free detections of S. typhimurium by AFM and SPR. The aptamers have specific binding affinities to the OMPs of S. typhimurium. At single-molecule level, the high resolution AFM topography and recognition images distinguished the OMPs on the bacteria surface, which is the first time the location of individual outer membrane protein have been determined on Salmonella surface. E. coli in the control experiments didn't generate recognition signals, which proved the specificity of these two aptamers to S. typhimurium. The off-rate values for the interactions of these two aptamers to the OMPs were estimated as 5.2 × 10-3 and 7.4 × 10-3 s-1, respectively, by the AFM dynamic force microscopy (DFS). The force and extension values form DFS measurements were used to distinguish the two aptamers. The surface membrane model was proposed to explain the complex correlations among force and extension values. Next, these two aptamers were used in the bulk solution detections of S. typhimurium. The gold chips in SPR experiments were modified with carboxymethylated-dextran (CD), followed by aptamers immobilization, to reduce the non-specific binding signals. The limit of detection (LOD) was determined as 3 × 104 CFU mL-1.

CONCLUSIONS

The AFM single-molecule study revealed detailed information about the unbinding force and extension of the aptamer in complex biological reactions. The careful analysis of the experimental results provide better understanding of the molecular mechanism of OMPs reactions. The single-molecule measurements are helpful in evaluating the specificity of binding reagents, such as aptamers, in bulk solution detections. The protocols used in the SPR detections can be expanded into the label-free detections of other bacterial pathogens.

Fluorescence Sensing of Circulating Diagnostic Biomarkers Using Molecular Probes and Nanoparticles

The interplay of photonics, nanotechnology, and biochemistry has significantly improved the identification and characterization of multiple types of biomarkers by optical biosensors. Great achievements in fluorescence-based technologies have been realized, for example, by the advancement of multiplexing techniques or the introduction of nanoparticles to biochemical and clinical research. This review presents a concise overview of recent advances in fluorescence sensing techniques for the detection of circulating disease biomarkers. Detection principles of representative approaches, including fluorescence detection using molecular fluorophores, quantum dots, and metallic and silica nanoparticles, are explained and illustrated by pertinent examples from the recent literature. Advanced detection technologies and material development play a major role in modern biosensing and consistently provide significant improvements toward robust, sensitive, and versatile platforms for early detection of circulating diagnostic biomarkers.

Antigen arrays for profiling autoantibody repertoires

Autoantibodies are a key component for the diagnosis, prognosis and monitoring of various diseases. In order to discover novel autoantibody targets, highly multiplexed assays based on antigen arrays hold a great potential and provide possibilities to analyze hundreds of body fluid samples for their reactivity pattern against thousands of antigens in parallel. Here, we provide an overview of the available technologies for producing antigen arrays, highlight some of the technical and methodological considerations and discuss their applications as discovery tools. Together with recent studies utilizing antigen arrays, we give an overview on how the different types of antigen arrays have and will continue to deliver novel insights into autoimmune diseases among several others.

Clinical proteomics-driven precision medicine for targeted cancer therapy: current overview and future perspectives

Cancer is a common disease that is a leading cause of death worldwide. Currently, early detection and novel therapeutic strategies are urgently needed for more effective management of cancer. Importantly, protein profiling using clinical proteomic strategies, with spectacular sensitivity and precision, offer excellent promise for the identification of potential biomarkers that would direct the development of targeted therapeutic anticancer drugs for precision medicine. In particular, clinical sample sources, including tumor tissues and body fluids (blood, feces, urine and saliva), have been widely investigated using modern high-throughput mass spectrometry-based proteomic approaches combined with bioinformatic analysis, to pursue the possibilities of precision medicine for targeted cancer therapy. Discussed in this review are the current advantages and limitations of clinical proteomics, the available strategies of clinical proteomics for the management of precision medicine, as well as the challenges and future perspectives of clinical proteomics-driven precision medicine for targeted cancer therapy.

Aryl Diazonium Chemistry for the Surface Functionalization of Glassy Biosensors

Nanostring resonator and fiber-optics-based biosensors are of interest as they offer high sensitivity, real-time measurements and the ability to integrate with electronics. However, these devices are somewhat impaired by issues related to surface modification. Both nanostring resonators and photonic sensors employ glassy materials, which are incompatible with electrochemistry. A surface chemistry approach providing strong and stable adhesion to glassy surfaces is thus required. In this work, a diazonium salt induced aryl film grafting process is employed to modify a novel SiCN glassy material. Sandwich rabbit IgG binding assays are performed on the diazonium treated SiCN surfaces. Fluorescently labelled anti-rabbit IgG and anti-rabbit IgG conjugated gold nanoparticles were used as markers to demonstrate the absorption of anti-rabbit IgG and therefore verify the successful grafting of the aryl film. The results of the experiments support the effectiveness of diazonium chemistry for the surface functionalization of SiCN surfaces. This method is applicable to other types of glassy materials and potentially can be expanded to various nanomechanical and optical biosensors.

Detection, quantification, and profiling of PSA: current microarray technologies and future directions

The death rate of 13% among the men diagnosed with prostate cancer makes it a second leading cause of cancer death. This critical review evaluates DNA and protein microarray based methods for detection, quantification, and profiling of PSA.

Recent advances in optical fiber devices for microfluidics integration

This paper examines the recent emergence of miniaturized optical fiber based sensing and actuating devices that have been successfully integrated into fluidic microchannels that are part of microfluidic and lab-on-chip systems. Fluidic microsystems possess the advantages of reduced sample volumes, faster and more sensitive biological assays, multi-sample and parallel analysis, and are seen as the de facto bioanalytical platform of the future. This paper considers the cases where the optical fiber is not merely used as a simple light guide delivering light across a microchannel, but where the fiber itself is engineered to create a new sensor or tool for use within the environment of the fluidic microchannel.

Molecularly imprinted polymer film interfaced with Surface Acoustic Wave technology as a sensing platform for label-free protein detection

Molecularly imprinted polymer (MIP)-based synthetic receptors integrated with Surface Acoustic Wave (SAW) sensing platform were applied for the first time for label-free protein detection. The ultrathin polymeric films with surface imprints of immunoglobulin G (IgG-MIP) were fabricated onto the multiplexed SAW chips using an electrosynthesis approach. The films were characterized by analyzing the binding kinetics recorded by SAW system. It was revealed that the capability of IgG-MIP to specifically recognize the target protein was greatly influenced by the polymer film thickness that could be easily optimized by the amount of the electrical charge consumed during the electrodeposition. The thickness-optimized IgG-MIPs demonstrated imprinting factors towards IgG in the range of 2.8-4, while their recognition efficiencies were about 4 and 10 times lower toward the interfering proteins, IgA and HSA, respectively. Additionally, IgG-MIP preserved its capability to recognize selectively the template after up to four regeneration cycles. The presented approach of the facile integration of the protein-MIP sensing layer with SAW technology allowed observing the real-time binding events of the target protein at relevant sensitivity levels and can be potentially suitable for cost effective fabrication of a biosensor for analysis of biological samples in multiplexed manner.

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.