Nanostructured optical fibre arrays for high-density biochemical sensing and remote imaging

Optical fiber biosensors toward in vivo detection

This review takes stock of the various optical fiber-based biosensors that could be used for in vivo applications. We discuss the characteristics that biosensors must have to be suitable for such applications and the corresponding transduction modes. In particular, we focus on optical fiber biosensors based on fluorescence, evanescent wave, plasmonics, interferometry, and Raman phenomenon. The operational principles, implemented solutions, and performances are described and debated. The different sensing configurations, such as the side- and tip-based fiber biosensors, are illustrated, and their adaptation for in vivo measurements is discussed. The required implementation of multiplexed biosensing on optical fibers is shown. In particular, the use of multi-fiber assemblies, one of the most optimal configurations for multiplexed detection, is discussed. Different possibilities for multiple localized functionalizations on optical fibers are presented. A final section is devoted to the practical in vivo use of fiber-based biosensors, covering regulatory, sterilization, and packaging aspects. Finally, the trends and required improvements in this promising and emerging field are analyzed and discussed.

Design of optoelectrodes for the remote imaging of cells and in situ electrochemical detection of neurosecretory events

Optical fibers have opened avenues for remote imaging, bioanalyses and recently optogenetics. Besides, miniaturized electrochemical sensors have offered new opportunities in sensing directly redox neurotransmitters. The combination of both optical and electrochemical approaches was usually performed on the platform of microscopes or within microsystems. In this work, we developed optoelectrodes which features merge the advantages of both optical fibers and microelectrodes. Optical fiber bundles were modified at one of their extremity by a transparent ITO deposit. The electrochemical responses of these ITO-modified bundles were characterized for the detection of dopamine, epinephrine and norepinephrine. The analytical performances of the optoelectrodes were equivalent to the ones reported for carbon microelectrodes. The remote imaging of model neurosecretory PC12 cells by optoelectrodes was performed upon cell-staining with common fluorescent dyes: acridine orange and calcein-AM. An optoelectrode placed by micromanipulation at a few micrometers-distance from the cells offered remote images with single cell resolution. Finally, in situ electrochemical sensing was demonstrated by additions of K⁺-secretagogue solutions near PC12 cells under observation, leading to exocytotic events detected as amperometric spikes at the ITO surface. Such dual sensors should pave the way for in vivo remote imaging, optogenetic stimulation, and simultaneous detection of neurosecretory activities.

Long Spiky Au-Ag Nanostar Based Fiber Probe for Surface Enhanced Raman Spectroscopy

The detection performances of noble metal-based surface enhanced Raman spectroscopy (SERS) devices are determined by the compositions and geometries of the metal nanostructures, as well as the substrates. In the current study, long spiky Au-Ag alloy nanostars were synthesized, and both core diameters and spike lengths were controlled by Lauryl sulfobetaine concentrations (as the nanostructure growth skeleton). The long spiky star geometries were confirmed by transmission electron micrograph images. Elements energy dispersive spectrometer mapping confirmed that Au and Ag elements were inhomogeneously distributed in the nanostructures and demonstrated a higher Ag content at surface for potential better SERS performance. Selected synthesized spiky nanostars were uniformly assembled on multi-mode silica fiber for probe fabrication by silanization. The SERS performance were characterized using crystal violet (CV) and rhodamine 6G (R6G) as analyte molecules. The lowest detection limit could reach as low as 10^-8 M, with a 6.23 × 10⁶ enhancement factor, and the relationship between analyte concentrations and Raman intensities was linear for both CV and R6G, which indicated the potential qualitative and quantitative molecule detection applications. Moreover, the fiber probes also showed good reproducibility and stability in the ambient atmosphere.

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.

Multiplexed Remote SPR Detection of Biological Interactions through Optical Fiber Bundles

The development of sensitive methods for in situ detection of biomarkers is a real challenge to bring medical diagnosis a step forward. The proof-of-concept of a remote multiplexed biomolecular interaction detection through a plasmonic optical fiber bundle is demonstrated here. The strategy relies on a fiber optic biosensor designed from a 300 µm diameter bundle composed of 6000 individual optical fibers. When appropriately etched and metallized, each optical fiber exhibits specific plasmonic properties. The surface plasmon resonance phenomenon occurring at the surface of each fiber enables to measure biomolecular interactions, through the changes of the retro-reflected light intensity due to light/plasmon coupling variations. The functionalization of the microstructured bundle by multiple protein probes was performed using new polymeric 3D-printed microcantilevers. Such soft cantilevers allow for immobilizing the probes in micro spots, without damaging the optical microstructures nor the gold layer. We show here the potential of this device to perform the multiplexed detection of two different antibodies with limits of detection down to a few tenths of nanomoles per liter. This tool, adapted for multiparametric, real-time, and label free monitoring is minimally invasive and could then provide a useful platform for in vivo targeted molecular analysis.

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.

Flexible, transparent and robust SERS tapes through a two-step block copolymer self-assembly process

We demonstrate a simple and economical method for fabricating flexible, transparent and robust large area SERS-active tapes using a two-step process: the fabrication of gold nanoclusters on a flat chip and the transfer of the resulting metal nanoclusters onto a thermal tape.

Supramolecular electron transfer-based switching involving pyrrolic macrocycles. A new approach to sensor development?

The potential utility of energy transfer in the design of pyrrolic macrocycle-based molecular switches and ability to serve as the readout motif for molecular sensors development is discussed.

Optical microwell arrays for large-scale studies of single mitochondria metabolic responses

Most of the methods dedicated to the monitoring of metabolic responses from isolated mitochondria are based on whole-population analyses. They rarely offer an individual resolution though fluorescence microscopy allows it, as demonstrated by numerous studies on single mitochondria activities in cells. Herein, we report on the preparation and use of microwell arrays for the entrapment and fluorescence microscopy of single isolated mitochondria. Highly dense arrays of 3 μm mean diameter wells were obtained by the chemical etching of optical fiber bundles (850 μm whole diameter). They were manipulated by a micro-positioner and placed in a chamber made of a biocompatible elastomer (polydimethylsiloxane or PDMS) and a glass coverslip, on the platform of an inverted microscope. The stable entrapment of individual mitochondria (extracted from Saccharomyces cerevisiae yeast strains, inter alia, expressing a green fluorescent protein) within the microwells was obtained by pretreating the optical bundles with an oxygen plasma and dipping the hydrophilic surface of the array in a concentrated solution of mitochondria. Based on the measurement of variations of the intrinsic NADH fluorescence of each mitochondrion in the array, their metabolic status was analyzed at different energetic respiratory stages: under resting state, following the addition of an energetic substrate to stimulate respiration (ethanol herein) and the addition of a respiratory inhibitor (antimycin A). Statistical analyses of mean variations of mitochondrial NADH in the population were subsequently achieved with a single organelle resolution.

Evaluation of optical detection platforms for multiplexed detection of proteins and the need for point-of-care biosensors for clinical use

This review investigates optical sensor platforms for protein multiplexing, the ability to analyze multiple analytes simultaneously. Multiplexing is becoming increasingly important for clinical needs because disease and therapeutic response often involve the interplay between a variety of complex biological networks encompassing multiple, rather than single, proteins. Multiplexing is generally achieved through one of two routes, either through spatial separation on a surface (different wells or spots) or with the use of unique identifiers/labels (such as spectral separation-different colored dyes, or unique beads-size or color). The strengths and weaknesses of conventional platforms such as immunoassays and new platforms involving protein arrays and lab-on-a-chip technology, including commercially-available devices, are discussed. Three major public health concerns are identified whereby detecting medically-relevant markers using Point-of-Care (POC) multiplex assays could potentially allow for a more efficient diagnosis and treatment of diseases.

The optical fiber tip: an inherently light-coupled microscopic platform for micro- and nanotechnologies

The flat tip of an optical fiber is a unique and unconventional platform for micro and nanotechnologies. The small cross-section and large aspect ratio of the fiber provide an inherently light-coupled substrate that is uniquely suited to remote, in vivo and in situ applications. However, these same characteristics challenge established fabrication technologies, which are best suited to large planar substrates. This review presents a broad overview of strategies for patterning the flat tip of an optical fiber. Techniques discussed include self-assembly, numerous lithographies, through-fiber patterning, hybrid techniques, and strategies for mass manufacture, while the diverse applications are discussed in context throughout.

Diffraction-limited ultrasensitive molecular nano-arrays with singular nano-cone scattering

Large-library fluorescent molecular arrays remain limited in sensitivity (1 × 10(6) molecules) and dynamic range due to background auto-fluorescence and scattering noise within a large (20-100 μm) fluorescent spot. We report an easily fabricated silica nano-cone array platform, with a detection limit of 100 molecules and a dynamic range that spans 6 decades, due to point (10 nm to 1 μm) illumination of preferentially absorbed tagged targets by singular scattering off wedged cones. Its fluorescent spot reaches diffraction-limited submicron dimensions, which are 10(4) times smaller in area than conventional microarrays, with comparable reduction in detection limit and amplification of dynamic range.

Functionalization of optical nanotip arrays with an electrochemical microcantilever for multiplexed DNA detection

Optical nanotip arrays fabricated on etched fiber bundles were functionalized with DNA spots. Such unconventional substrates (3D and non-planar) are difficult to pattern with standard microfabrication techniques but, using an electrochemical cantilever, up to 400 spots were electrodeposited on the nanostructured optical surface in 5 min. This approach allows each spot to be addressed individually and multiplexed fluorescence detection is demonstrated. Finally, remote fluorescence detection was performed by imaging through the optical fiber bundle itself after hybridisation with the complementary sequence.

Optical microwell array for large scale studies of single mitochondria metabolic responses

Microsystems based on microwell arrays have been widely used for studies on single living cells. In this work, we focused on the subcellular level in order to monitor biological responses directly on individual organelles. Consequently, we developed microwell arrays for the entrapment and fluorescence microscopy of single isolated organelles, mitochondria herein. Highly dense arrays of 3-μm mean diameter wells were obtained by wet chemical etching of optical fiber bundles. Favorable conditions for the stable entrapment of individual mitochondria within a majority of microwells were found. Owing to NADH auto-fluorescence, the metabolic status of each mitochondrion was analyzed at resting state (Stage 1), then following the addition of a respiratory substrate (Stage 2), ethanol herein, and of a respiratory inhibitor (Stage 3), antimycin A. Mean levels of mitochondrial NADH were increased by 29% and 35% under Stages 2 and 3, respectively. We showed that mitochondrial ability to generate higher levels of NADH (i.e., its metabolic performance) is not correlated either to the initial energetic state or to the respective size of each mitochondrion. This study demonstrates that microwell arrays allow metabolic studies on populations of isolated mitochondria with a single organelle resolution.

A review on the fabrication of substrates for surface enhanced Raman spectroscopy and their applications in analytical chemistry

This work reviews different types of substrates used for surface-enhanced Raman scattering (SERS) that have been developed in the last 10 years. The different techniques of self-assembly to immobilize metallic nanoparticles on solid support are covered. An overview of SERS platforms developed using nanolithography methods, including electron-beam (e-beam) lithography and focused ion beam (FIB) milling are also included, together with several examples of template-based methodologies to generate metallic nano-patterns. The potential of SERS to impact several aspects of analytical chemistry is demonstrated by selected examples of applications in electrochemistry, biosensing, environmental analysis, and remote sensing. This review shows that highly enhancing SERS substrates with a high degree of reliability and reproducibility can now be fabricated at relative low cost, indicating that SERS may finally realize its full potential as a very sensitive tool for routine analytical applications.

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.