Correction of 2π Phase Jumps for Silicon Photonic Sensors Based on Mach Zehnder Interferometers with Application in Gas and Biosensing.

Silicon photonic sensors based on Mach Zehnder Interferometers (MZIs) have applications spanning from biological and olfactory sensors to temperature and ultrasound sensors. Although a coherent detection scheme can solve the issues of sensitivity fading and ambiguity in phase direction, the measured phase remains 2π periodic. This implies that the acquisition frequency should ensure a phase shift lower than π between each measurement point to prevent 2π phase jumps. Here, we describe and experimentally characterize two methods based on reference MZIs with lower sensitivities to alleviate this drawback. These solutions improve the measurement robustness and allow the lowering of the acquisition frequency. The first method is based on the phase derivative sign comparison. When a discrepancy is detected, the reference MZI is used to choose whether 2π should be added or removed from the nominal MZI. It can correct 2π phase jumps regardless of the sensitivity ratio, so that a single reference MZI can be used to correct multiple nominal MZIs. This first method relaxes the acquisition frequency requirement by a factor of almost two. However, it cannot correct phase jumps of 4π, 6π or higher between two measurement points. The second method is based on the comparison between the measured phase from the nominal MZI and the phase expected from the reference MZI. It can correct multiple 2π phase jumps but requires at least one reference MZI per biofunctionalization. It will also constrain the corrected phase to lie in a limited interval of [-π, +π] around the expected value, and might fail to correct phase shifts above a few tens of radians depending on the disparity of the nominal sensors responses. Nonetheless, for phase shift lower than typically 20 radians, this method allows the lowering of the acquisition frequency almost arbitrarily.

Silicon photonic olfactory sensor based on an array of 64 biofunctionalized Mach-Zehnder interferometers.

Silicon photonics can address a variety of applications, from datacom and biosensing to lidars. Recently, this technology has been explored for gas sensing. Detection and identification of odors remains a critical challenge in diverse areas such as air quality, food spoilage, or personal well-being. In this work, we present an olfactory sensor based on an array of 64 biofunctionalized Mach-Zehnder interferometers integrated on a silicon nitride platform. The ability to analyze odors at ppm level is demonstrated for several volatile organic compounds.

Discrimination of deletion to point cytokine mutants based on an array of cross-reactive receptors mimicking protein recognition by heparan sulfate.

Differential sensing of proteins based on cross-reactive arrays and pattern recognition is a promising technique for the detection and identification of proteins. In this study, a rational biomimetic strategy has been used to prepare sensing materials capable of discriminating structurally similar proteins, such as deletion and point mutants of a cytokine, by mimicking the biological properties of heparan sulfate (HS). Using the self-assembly of two disaccharides, lactose and sulfated lactose at various ratios on the surface of a chip, an array of combinatorial cross-reactive receptors has been prepared. Coupling with surface plasmon resonance imaging (SPRi), the obtained cross-reactive array is very efficient for protein sensing. It is able to detect HS binding proteins (HSbps) such as IFNγ at nanomolar concentrations. Moreover, such a system is capable of discriminating between IFNγ and its mutants with good selectivity.

Enhancing the sensitivity of plasmonic optical fiber sensors by analyzing the distribution of the optical modes intensity.

Improving the sensitivity of plasmonic optical fiber sensors constitutes a major challenge as it could significantly enhance their sensing capabilities for the label-free detection of biomolecular interactions or chemical compounds. While many efforts focus on developing more sensitive structures, we present here how the sensitivity of a sensor can be significantly enhanced by improving the light analysis. Contrary to the common approach where the global intensity of the light coming from the core is averaged, our approach is based on the full analysis of the retro-reflected intensity distribution that evolves with the refractive index of the medium being analyzed. Thanks to this original and simple approach, the refractive index sensitivity of a plasmonic optical fiber sensor used in reflection mode was enhanced by a factor of 25 compared to the standard method. The reported approach opens exciting perspectives for improving the remote detection as well as for developing new sensing strategies.

Enhanced Bipolar Electrochemistry at Solid-State Micropores: Demonstration by Wireless Electrochemiluminescence Imaging.

Bipolar electrochemistry (BPE) is a powerful method based on the wireless polarization of a conductive object that induces the asymmetric electroactivity at its two extremities. A key physical limitation of BPE is the size of the conductive object because the shorter the object, the larger is the potential necessary for sufficient polarization. Micrometric and nanometric objects are thus extremely difficult to address by BPE due to the very high potentials required, in the order of tens of kV or more. Herein, the synergetic actions of BPE and of planar micropores integrated in a microfluidic device lead to the spatial confinement of the potential drop at the level of the solid-state micropore, and thus to a locally enhanced polarization of a bipolar electrode. Electrochemiluminescence (ECL) is emitted in half of the electroactive micropore and reveals the asymmetric polarization in this spatial restriction. Micrometric deoxidized silicon electrodes located in the micropore are polarized at a very low potential (7 V), which is more than 2 orders of magnitude lower compared to the classic bipolar configurations. This behavior is intrinsically associated with the unique properties of the micropores, where the sharp potential drop is focused. The presented approach offers exciting perspectives for BPE of micro/nano-objects, such as dynamic BPE with objects passing through the pores or wireless ECL-emitting micropores.

Highly parallel remote SPR detection of DNA hybridization by micropillar optical arrays.

Remote detection by surface plasmon resonance (SPR) is demonstrated through microstructured optical arrays of conical nanotips or micropillars. Both geometries were fabricated by controlled wet chemical etching of bundles comprising several thousands of individual optical fibers. Their surface was coated by a thin gold layer in order to confer SPR properties. The sensitivity and resolution of both shapes were evaluated as a function of global optical index changes in remote detection mode performed by imaging through the etched optical fiber bundle itself. With optimized geometry of micropillar arrays, resolution was increased up to 10-4 refractive index units. The gold-coated micropillar arrays were functionalized with DNA and were able to monitor remotely the kinetics of DNA hybridization with complementary strands. We demonstrate for the first time highly parallel remote SPR detection of DNA via microstructured optical arrays. The obtained SPR sensitivity combined with the remote intrinsic properties of the optical fiber bundles should find promising applications in biosensing, remote SPR imaging, a lab-on-fiber platform dedicated to biomolecular analysis, and in vivo endoscopic diagnosis. Graphical abstract We present a single fabrication step to structure simultaneously all the individual cores of an optical fiber bundle composed of thousands of fibers. The resulting sensor is optimized for reflection mode (compatible with in vivo applications) and is used to perform for the first time highly parallel remote SPR detection of DNA via several thousands of individual optical fiber SPR sensors paving the way for multiplexed biological detection.

Highly-Selective Optoelectronic Nose Based on Surface Plasmon Resonance Imaging for Sensing Volatile Organic Compounds.

Monitoring volatile organic compounds (VOCs) is an important issue, but difficult to achieve on a large scale and on the field using conventional analytical methods. Electronic noses (eNs), as promising alternatives, are still compromised by their performances due to the fact that most of them rely on a very limited number of sensors and use databases devoid of kinetic information. To narrow the performance gap between human and electronic noses, we developed a novel optoelectronic nose, which features a large sensor microarray that enables multiplexed monitoring of binding events in real-time with a temporal response. For the first time, surface plasmon resonance imaging is demonstrated as a promising novel analytical tool for VOC detection in the gas phase. By combining it with cross-reactive sensor microarrays, the obtained optoelectronic nose shows a remarkably high selectivity, capable of discriminating between homologous VOCs differing by only a single carbon atom. In addition, the optoelectronic nose has good repeatability and stability. Finally, the preliminary assays using VOC binary and ternary mixtures show that it is also very efficient for the analysis of more complex samples, opening up the exciting perspective of applying it to "real-world" samples in diverse domains.

A Versatile Electronic Tongue Based on Surface Plasmon Resonance Imaging and Cross-Reactive Sensor Arrays-A Mini-Review.

Nowadays, there is a strong demand for the development of new analytical devices with novel performances to improve the quality of our daily lives. In this context, multisensor systems such as electronic tongues (eTs) have emerged as promising alternatives. Recently, we have developed a new versatile eT system by coupling surface plasmon resonance imaging (SPRi) with cross-reactive sensor arrays. In order to largely simplify the preparation of sensing materials with a great diversity, an innovative combinatorial approach was proposed by combining and mixing a small number of easily accessible molecules displaying different physicochemical properties. The obtained eT was able to generate 2D continuous evolution profile (CEP) and 3D continuous evolution landscape (CEL), which is also called 3D image, with valuable kinetic information, for the discrimination and classification of samples. Here, diverse applications of such a versatile eT have been summarized. It is not only effective for pure protein analysis, capable of differentiating protein isoforms such as chemokines CXCL12α and CXCL12γ, but can also be generalized for the analysis of complex mixtures, such as milk samples, with promising potential for monitoring the deterioration of milk.

Carbohydrates as new probes for the identification of closely related Escherichia coli strains using surface plasmon resonance imaging.

Prevention of foodborne diseases depends highly on our ability to control rapidly and accurately a possible contamination of food. So far, standard procedures for bacterial detection require time-consuming bacterial cultures on plates before the pathogens can be detected and identified. We present here an innovative biochip, based on direct differential carbohydrate recognitions of five closely related Escherichia coli strains, including the enterohemorragic E. coli O157:H7. Our device relies on efficient grafting of simple carbohydrates on a gold surface and on the monitoring of their interactions with bacteria during their culture using surface plasmon resonance imaging. We show that each of the bacteria interacts in a different way with the carbohydrate chip. This allows the detection and discrimination of the tested bacterial strains in less than 10 h from an initial bacterial concentration of 10(2) CFU·mL(-1). This is an improvement over previously described systems in terms of cost, easiness to use, and stability. Easily conceived and easily regenerated, this tool is promising for the future of food safety.

On the use of aptamer microarrays as a platform for the exploration of human prothrombin/thrombin conversion.

Microarrays are particular biosensors with multiple grafted probes that are generally used for parallel and simultaneous detection of various targets. In this study, we used microarrays with aptamer probes in order to follow up the different biomolecular interactions of a single enzyme, the thrombin protein, involved in the complex coagulation cascade. More precisely, thanks to label-free surface plasmon resonance imaging, we were able to monitor in real time an important step in the firing of the coagulation cascade in situ-the enzymatic transformation of prothrombin into thrombin, catalyzed by factor Xa. We were also able to appraise the influence of other biochemical factors and their corresponding inhibiting or enhancing behaviors on thrombin activation. Our study opens the door for the development of a complete microarray-based platform not only for the whole coagulation cascade analysis but also for novel drug screening assays in pharmacology.

Spatial resolution in prism-based surface plasmon resonance microscopy.

Several optical surface sensing techniques, such as Surface Plasmon Resonance (SPR), work by imaging the base of a prism by one of its faces. However, such a fundamental optical concern has not been fully analyzed and understood so far, and spatial resolution remains a critical and controversial issue. In SPR, the propagation length L(x) of the surface plasmon waves has been considered as the limiting factor. Here, we demonstrate that for unoptimized systems geometrical aberrations caused by the prism can be more limiting than the propagation length. By combining line-scan imaging mode with optimized prisms, we access the ultimate lateral resolution which is diffraction-limited by the object light diffusion. We describe several optimized configurations in water and discuss the trade-off between L(x) and sensitivity. The improvement of resolution is confirmed by imaging micro-structured PDMS stamps and individual living eukaryote cells and bacteria on field-of-view from 0.1 to 20 mm(2).

Cell specific electrodes for neuronal network reconstruction and monitoring.

Direct interfacing of neurons with electronic devices has been investigated for both prosthetic and neuro-computing applications. In vitro neuronal networks provide great tools not only for improving neuroprostheses but also to take advantage of their computing abilities. However, it is often difficult to organize neuronal networks according to specific cell distributions. Our aim was to develop a cell-type specific immobilization of neurons on individual electrodes to produce organized in vitro neuronal networks on multi-electrode arrays (MEAs). We demonstrate the selective capture of retinal neurons on antibody functionalized surfaces following the formation of self-assembled monolayers from protein-thiol conjugates by simple contact and protein-polypyrrole deposits by electrochemical functionalization. This neuronal selection was achieved on gold for either cone photoreceptors or retinal ganglion neurons using a PNA lectin or a Thy1 antibody, respectively. Anti-fouling of un-functionalized gold surfaces was optimized to increase the capture efficiencies. The technique was extended to electrode arrays by addressing electropolymerization of pyrrole monomers and pyrrole-protein conjugates to active electrodes. Retinal ganglion cell recording on the array further demonstrated the integrity of these neurons following their selection on polypyrrole-coated electrodes. Therefore, this protein-polypyrrole electrodeposition could provide a new approach to generate organized in vitro neuronal networks.

Electrochemical transduction of DNA hybridization at modified electrodes by using an electroactive pyridoacridone intercalator.

A synthetic redox probe structurally related to natural pyridoacridones was designed and electrochemically characterised. These heterocycles behave as DNA intercalators due to their extended planar structure that promotes stacking in between nucleic acid base pairs. Electrochemical characterization by cyclic voltammetry revealed a quasi-reversible electrochemical behaviour occurring at a mild negative potential in aqueous solution. The study of the mechanism showed that the iminoquinone redox moiety acts similarly to quinone involving a two-electron reduction coupled with proton transfer. The easily accessible potential region with respect to aqueous electro-inactive window makes the pyridoacridone ring suitable for the indirect electrochemical detection of chemically unlabelled DNA. Its usefulness as electrochemical hybridization indicator was assessed on immobilised DNA and compared to doxorubicin. The voltamperometric response of the intercalator acts as an indicator of the presence of double-stranded DNA at the electrode surface and allows the selective transduction of immobilised oligonucleotide hybridization at both macro- and microscale electrodes.

Binding of chondroitin 4-sulfate to cathepsin S regulates its enzymatic activity.

Human cysteine cathepsin S (catS) participates in distinct physiological and pathophysiological cellular processes and is considered as a valuable therapeutic target in autoimmune diseases, cancer, atherosclerosis, and asthma. We evaluated the capacity of negatively charged glycosaminoglycans (heparin, heparan sulfate, chondroitin 4/6-sulfates, dermatan sulfate, and hyaluronic acid) to modulate the activity of catS. Chondroitin 4-sulfate (C4-S) impaired the collagenolytic activity (type IV collagen) and inhibited the peptidase activity (Z-Phe-Arg-AMC) of catS at pH 5.5, obeying a mixed-type mechanism (estimated Ki = 16.5 ± 6 µM). Addition of NaCl restored catS activity, supporting the idea that electrostatic interactions are primarly involved. Furthermore, C4-S delayed in a dose-dependent manner the maturation of procatS at pH 4.0 by interfering with the intermolecular processing pathway. Binding of C4-S to catS was demonstrated by gel-filtration chromatography, and its affinity was measured by surface plasmon resonance (equilibrium dissociation constant Kd = 210 ± 40 nM). Moreover, C4-S induced subtle conformational changes in mature catS as observed by intrinsic fluorescence spectroscopy analysis. Molecular docking predicted three specific binding sites on catS for C4-S that are different from those found in the crystal structure of the cathepsin K-C4-S complex. Overall, these results describe a novel glycosaminoglycan-mediated mechanism of catS inhibition and suggest that C4-S may modulate the collagenase activity of catS in vivo.

Antibody microarrays for label-free cell-based applications.

The recent advances in microtechnologies have shown the interest of developing microarrays dedicated to cell analysis. In this way, miniaturized cell analyzing platforms use several detection techniques requiring specific solid supports for microarray read-out (colorimetric, fluorescent, electrochemical, acoustic, optical…). Real-time and label-free techniques, such as Surface Plasmon Resonance imaging (SPRi), arouse increasing interest for applications in miniaturized formats. Thus, we focused our study on chemical methods for antibody-based microarray fabrication dedicated to the SPRi analysis of cells or cellular activity. Three different approaches were designed and developed for specific applications. In the first case, a polypyrrole-based chemistry was used to array antibody-microarray for specific capture of whole living cells. In the second case, the polypyrrole-based chemistry was complexified in a three molecular level assembly using DNA and antibody conjugates to allow the specific release of cells after their capture. Finally, in the third case, a thiol-based chemistry was developed for long incubation times of biological samples of high complexity. This last approach was focused on the simultaneous study of both cell type characterization and secretory activity (detection of proteins secreted by cells). This paper describes three original methods allowing a rapid and efficient analysis of cellular sample on-chip using immunoaffinity-based assays.

Polarization-induced local pore-wall functionalization for biosensing: from micropore to nanopore.

The use of biological-probe-modified solid-state pores in biosensing is currently hindered by difficulties in pore-wall functionalization. The surface to be functionalized is small and difficult to target and is usually chemically similar to the bulk membrane. Herein, we demonstrate the contactless electrofunctionalization (CLEF) approach and its mechanism. This technique enables the one-step local functionalization of the single pore wall fabricated in a silica-covered silicon membrane. CLEF is induced by polarization of the pore membrane in an electric field and requires a sandwich-like composition and a conducting or semiconducting core for the pore membrane. The defects in the silica layer of the micropore wall enable the creation of an electric pathway through the silica layer, which allows electrochemical reactions to take place locally on the pore wall. The pore diameter is not a limiting factor for local wall modification using CLEF. Nanopores with a diameter of 200 nm fabricated in a silicon membrane and covered with native silica layer have been successfully functionalized with this method, and localized pore-wall modification was obtained. Furthermore, through proof-of-concept experiments using ODN-modified nanopores, we show that functionalized nanopores are suitable for translocation-based biosensing.

Electrochemically induced maskless metal deposition on micropore wall.

By applying an external electric field across a micropore via an electrolyte, metal ions in the electrolyte can be reduced locally onto the inner wall of the micropore, which was fabricated in a silica-covered silicon membrane. This maskless metal deposition on the silica surface is a result of the pore membrane polarization in the electric field.

Surfactant-like Peptide Self-Assembled into Hybrid Nanostructures for Electronic Nose Applications.

An electronic nose (e-nose) utilizes a multisensor array, which relies on the vector contrast of combinatorial responses, to effectively discriminate between volatile organic compounds (VOCs). In recent years, hierarchical structures made of nonbiological materials have been used to achieve the required sensor diversity. With the advent of self-assembling peptides, the ability to tune nanostructuration, surprisingly, has not been exploited for sensor array diversification. In this work, a designer surfactant-like peptide sequence, CG7-NH2, is used to fabricate morphologically and physicochemically heterogeneous "biohybrid" surfaces on Au-covered chips. These multistructural sensing surfaces, containing immobilized hierarchical nanostructures surrounded by self-assembled monolayers, are used for the detection and discrimination of VOCs. Through a simple and judicious design process, involving changes in pH and water content of peptide solutions, a five-element biohybrid sensor array coupled with a gas-phase surface plasmon resonance imaging system is shown to achieve sufficient discriminatory capabilities for four VOCs. Moreover, the limit of detection of the multiarray system is bench-marked at <1 and 6 ppbv for hexanoic acid and phenol (esophago-gastric biomarkers), respectively. Finally, the humidity effects are characterized, identifying the dissociation rate constant as a robust descriptor for classification, further exemplifying their efficacy as biomaterials in the field of artificial olfaction.

TOX4 and its binding partners recognize DNA adducts generated by platinum anticancer drugs.

Platinating agents are commonly prescribed anticancer drugs damaging DNA. Induced lesions are recognized by a wide range of proteins. These are involved in cellular mechanisms such as DNA repair, mediation of cytotoxicity or chromatin remodeling. They therefore constitute crucial actors to understand pharmacology of these drugs. To expand our knowledge about this subproteome, we developed a ligand fishing trap coupled to high throughput proteomic tools. This trap is made of damaged plasmids attached to magnetic beads, and was exposed to cell nuclear extracts. Retained proteins were identified by nanoHPLC coupled to tandem mass spectrometry. This approach allowed us to establish a list of 38 proteins interacting with DNA adducts generated by cisplatin, oxaliplatin and satraplatin. Some of them were already known interactome members like high mobility group protein 1 (HMGB1) or the human upstream binding factor (hUBF), but we also succeeded in identifying unexpected proteins such as TOX HMG box family member 4 (TOX4), phosphatase 1 nuclear targeting subunit (PNUTS), and WD repeat-containing protein 82 (WDR82), members of a recently discovered complex. Interaction between TOX4 and platinated DNA was subsequently validated by surface plasmon resonance imaging (SPRi). These interactions highlight new cellular responses to DNA damage induced by chemotherapeutic agents.

Opto-electrochemical nanosensor array for remote DNA detection.

A high-density array of opto-electrochemical nanosensors is presented for remote DNA detection. It was fabricated by chemical etching of a coherent optical fibre bundle to produce a nanotip array. The surface of the etched bundle was sputter-coated with a thin ITO layer which was eventually insulated by an electrophoretic paint. The fabrication steps produced a high-density array of electrochemical nanosensors which retains the optical fibre bundle architecture and its imaging properties. A DNA probe was then immobilized on the nanosensor array surface in a polypyrrole film by electropolymerisation. After hybridisation with the complementary sequence, detection of the strepavidin-R-phycoerythrin label is performed by fluorescence imaging through the optical fibre bundle itself. Control experiments and regeneration steps have also been successfully demonstrated on this nanostructured opto-electrochemical platform.