Elena Pérez-Ruiz

Label-free Protein Detection Based on the Heat-Transfer Method-A Case Study with the Peanut Allergen Ara h 1 and Aptamer-Based Synthetic Receptors

Aptamers are an emerging class of molecules that, because of the development of the systematic evolution of ligands by exponential enrichment (SELEX) process, can recognize virtually every target ranging from ions, to proteins, and even whole cells. Although there are many techniques capable of detecting template molecules with aptamer-based systems with high specificity and selectivity, they lack the possibility of integrating them into a compact and portable biosensor setup. Therefore, we will present the heat-transfer method (HTM) as an interesting alternative because this offers detection in a fast and low-cost manner and has the possibility of performing experiments with a fully integrated device. This concept has been demonstrated for a variety of applications including DNA mutation analysis and screening of cancer cells. To the best our knowledge, this is the first report on HTM-based detection of proteins, in this case specifically with aptamer-type receptors. For proof-of-principle purposes, measurements will be performed with the peanut allergen Ara h 1 and results indicate detection limits in the lower nanomolar regime in buffer liquid. As a first proof-of-application, spiked Ara h 1 solutions will be studied in a food matrix of dissolved peanut butter. Reference experiments with the quartz-crystal microbalance will allow for an estimate of the areal density of aptamer molecules on the sensor-chip surface.

Building bio-assays with magnetic particles on a digital microfluidic platform

Digital microfluidics (DMF) has emerged as a promising liquid handling technology for a variety of applications, demonstrating great potential both in terms of miniaturization and automation. DMF is based on the manipulation of discrete, independently controllable liquid droplets, which makes it highly reconfigurable and reprogrammable. One of its most exclusive advantages, compared to microchannel-based microfluidics, is its ability to precisely handle solid nano- and microsized objects, such as magnetic particles. Magnetic particles have become very popular in the last decade, since their high surface-to-volume ratio and the possibility to magnetically separate them from the matrix make them perfect suitable as a solid support for bio-assay development. The potential of magnetic particles in DMF-based bio-assays has been demonstrated for various applications. In this review we discuss the latest developments of magnetic particle-based DMF bio-assays with the aim to present, identify and analyze the trends in the field. We also discuss the state-of-the art of device integration, current status of commercialization and issues that still need to be addressed. With this paper we intend to stimulate researchers to exploit and unveil the potential of these exciting tools, which will shape the future of modern biochemistry, microbiology and biomedical diagnostics.

Bioassay development for ultrasensitive detection of influenza A nucleoprotein using digital ELISA

Flu is caused by the influenza virus that, due to mutations, keeps our body vulnerable for infections, making early diagnosis essential. Although immuno-based diagnostic tests are available, they have low sensitivity and reproducibility. In this paper, the prospect of detecting influenza A virus using digital ELISA has been studied. To appropriately select bioreceptors for this bioassay, seven commercial antibodies against influenza A nucleoprotein were methodically tested for their reactivity and binding affinity. The study has been performed on two markedly different platforms, being an enzyme-linked immunosorbent assay and a surface plasmon resonance system. The selected antibodies displayed completely different behavior on the two platforms and in various assay configurations. Surprisingly, the antibodies that showed overall good reactivity on both platforms had the highest dissociation constant among the tested antibodies, suggesting that, although important, binding affinity is not the only parameter to be considered when selecting antibodies. Moreover, only one antibody had the capacity to capture the nucleoprotein directly in lysis buffer used for releasing this viral protein, which might pose a huge advantage when developing assays with a fast time-to-result. This antibody was implemented on an in-house developed digital ELISA platform for ultrasensitive detection of recombinant nucleoprotein, reaching a detection limit of 4 ± 1 fM in buffer and 10 ± 2 fM in 10-fold diluted nasopharyngeal swabs, which is comparable to currently available fast molecular detection techniques. These results point to a great potential for ultrasensitive immuno-based influenza detection.

Probing the force-induced dissociation of aptamer-protein complexes.

Aptamers are emerging as powerful synthetic bioreceptors for fundamental research, diagnostics, and therapeutics. For further advances, it is important to gain a better understanding of how aptamers interact with their targets. In this work, we have used magnetic force-induced dissociation experiments to study the dissociation process of two different aptamer-protein complexes, namely for hIgE and Ara h 1. The measurements show that both complexes exhibit dissociation with two distinct regimes: the dissociation rate depends weakly on the applied force at high forces but depends stronger on force at low forces. We attribute these observations to the existence of at least one intermediate state and at least two energy barriers in the aptamer-protein interaction. The measured spontaneous dissociation rate constants were validated with SPR using both Biacore and fiber optic technology. This work demonstrates the potential of the magnetic force-induced dissociation approach for an in-depth study of the dissociation kinetics of aptamer-protein bonds, which is not possible with SPR technologies. The results will help in the development and expansion of aptamers as bioaffinity probes.

Real-Time Monitoring of Aptamer Functionalization and Detection of Ara H1 by Electrochemical Impedance Spectroscopy and Dissipation-Mode Quartz Crystal Microbalance

Peanut allergy, the most common cause of fatal-food-related anaphylaxis, is a lifelong disorder and the only existing therapy is avoidance of allergen-containing food. Detection of Ara h 1, the most important peanut allergen, is commonly performed by immunoassay techniques relying on the use of expensive and relatively unstable antibodies. Aptamers can overcome these drawbacks and offer a great potential for the development of reliable biosensors. Therefore, we will present a novel aptamer-based sensor for the label-free detection of Ara h 1. Amino (NH2)-terminated Ara h 1 aptamers were covalently attached to carboxylated gold surfaces employing carbodiimide chemistry. This functionalization procedure was followed in real time by electrochemical impedance spectroscopy and quartz crystal microbalance with dissipation monitoring. Subsequently, the functionalized surfaces were exposed to Ara h 1 solutions in TGK buffer. By combining the two techniques, we can measure in a wide concentration regime varying from the low nanomolar range (1-15 nM) via electrochemical impedance spectroscopy to the higher concentrations (25-250 nM) by microgravimetric detection. In summary, a fast, low-cost and sensitive sensor platform for Ara h 1 detection has been developed, which can be operated as a ‘stand-alone device’, making it well suited for applications such as the screening of trace allergens.

Evaluation of different strategies for magnetic particle functionalization with DNA aptamers

The optimal bio-functionalization of magnetic particles is essential for developing magnetic particle-based bioassays. Whereas functionalization with antibodies is generally well established, immobilization of DNA probes, such as aptamers, is not yet fully explored. In this work, four different types of commercially available magnetic particles, coated with streptavidin, maleimide or carboxyl groups, were evaluated for their surface coverage with aptamer bioreceptors, efficiency in capturing target protein and non-specific protein adsorption on their surface. A recently developed aptamer against the peanut allergen, Ara h 1 protein, was used as a model system. Conjugation of biotinylated Ara h 1 aptamer to the streptavidin particles led to the highest surface coverage, whereas the coverage of maleimide particles was 25% lower. Carboxylated particles appeared to be inadequate for DNA functionalization. Streptavidin particles also showed the greatest target capturing efficiency, comparable to the one of particles functionalized with anti-Ara h 1 antibody. The performance of streptavidin particles was additionally tested in a sandwich assay with the aptamer as a capture receptor on the particle surface. While the limit of detection obtained was comparable to the same assay system with antibody as capture receptor, it was superior to previously reported values using the same aptamer in similar assay schemes with different detection platforms. These results point to the promising application of the Ara h 1 aptamer-functionalized particles in bioassay development.

Digital ELISA for the quantification of attomolar concentrations of Alzheimer's disease biomarker protein Tau in biological samples

The close correlation between Tau pathology and Alzheimers disease (AD) progression makes this protein a suitable biomarker for diagnosis and monitoring of the disorder evolution. However, the use of Tau in diagnostics has been hampered, as it currently requires collection of cerebrospinal fluid (CSF), which is an invasive clinical procedure. Although measuring Tau-levels in blood plasma would be favorable, the concentrations are below the detection limit of a conventional ELISA. In this work, we developed a digital ELISA for the quantification of attomolar protein Tau concentrations in both buffer and biological samples. Individual Tau molecules were first captured on the surface of magnetic particles using in-house developed antibodies and subsequently isolated into the femtoliter-sized wells of a 2 × 2 mm2 microwell array. Combination of high-affinity antibodies, optimal assay conditions and a digital quantification approach resulted in a 24 ± 7 aM limit of detection (LOD) in buffer samples. Additionally, a dynamic range of 6 orders of magnitude was achieved by combining the digital readout with an analogue approach, allowing quantification from attomolar to picomolar levels of Tau using the same platform. This proves the compatibility of the presented assay with the wide range of Tau concentrations encountered in different biological samples. Next, the developed digital assay was applied to detect total Tau levels in spiked blood plasma. A similar LOD (55 ± 29 aM) was obtained compared to the buffer samples, which was 5000-fold more sensitive than commercially available ELISAs and even outperformed previously reported digital assays with 10-fold increase in sensitivity. Finally, the performance of the developed digital ELISA was assessed by quantifying protein Tau in three clinical CSF samples. Here, a high correlation (i.e. Pearson coefficient of 0.99) was found between the measured percentage of active particles and the reference protein Tau values. The presented digital ELISA technology has great capacity in unlocking the potential of Tau as biomarker for early AD diagnosis.

Ara h 1 protein–antibody dissociation study: evidence for binding inhomogeneities on a molecular scale

The characterization of biomolecular interactions is essential when designing novel biosensors, since the interaction between the bioreceptor and the ligand determines important biosensing parameters such as sensitivity and selectivity. In this paper we study the interaction of the trimeric Ara h 1 protein with a monoclonal anti-Ara h 1 antibody by means of magnetic force-induced dissociation. The proteins were bound to magnetic particles and polystyrene surfaces by EDC/NHS reaction chemistry and by physisorption, respectively. Two different molecular configurations have been investigated, with either the Ara h 1 protein on the particles or the Ara h 1 protein on the polystyrene surface. A model with a Gaussian distribution of energy barriers for dissociation gives an adequate description for the measured multi-exponential decays. We hypothesize that distributions of molecular orientations as well as experimentally induced variations may underlay the observed distributions. The two molecular configurations show a different peak value of the energy distribution. Similarly, SPR experiments for two distinct configurations (either Ara h 1 protein on the surface, or anti-Ara h 1 antibody on the surface) also show clear differences in dissociation behavior. We hypothesize that the multivalency of the involved molecules leads to different modes of binding. The results of this work highlight the importance of molecular inhomogeneities when studying the interaction processes of biomolecular complexes.

Integration of heat-transfer resistance measurements onto a digital microfluidic platform towards the miniaturized and automated label-free detection of biomolecular interactions

In this paper the successful integration of heat-transfer resistance measurements with a digital microfluidic chip is shown. The integrated miniaturized platform allows the automated label-free detection of biomolecular interactions. To immobilize biomolecules on the hydrophobic chip surface, hydrophilic gold sensing patches are created by means of a recently described dry lift-off technique that leaves the chip surface unaffected. DNA melting analysis was performed for validating the integrated device.