Label-Free Tracking of Proteins through Plasmon-Enhanced Interference

Single unmodified biomolecules in solution can be observed and characterized by interferometric imaging approaches; however, Rayleigh scattering limits this to larger proteins (typically >30 kDa). We observe real-time image tracking of unmodified proteins down to 14 kDa using interference imaging enhanced by surface plasmons launched at an aperture in a metal film. The larger proteins show slower diffusion, quantified by tracking. When the diffusing protein is finally trapped by the nanoaperture, we perform complementary power spectral density and noise amplitude analysis, which gives information about the protein. This approach allows for rapid protein characterization with minimal sample preparation and opens the door to characterizing protein interactions in real time.

Biosensing by Polymer-Coated Etched Long-Period Fiber Gratings Working near Mode Transition and Turn-around Point

A methodology to enhance the sensitivity of long-period fiber gratings (LPFGs) based on the combination of three different enhancement approaches is presented; the methods here adopted are the working near mode transition (MT) of a cladding mode (CM), working near the turn-around point of a CM and the enhancement of the evanescent field of CMs by reducing the cladding diameter or by increasing the order number of CMs. In order to combine these enhancement methodologies, an electrostatic self-assembly (ESA) process was used to deposit a polymeric overlay, with a chosen thickness, onto the etched fiber. The add-layer sensitivity of the sensor was theoretically calculated, and the demonstration of the real applicability of the developed LPFG as a biosensor was performed by means of an IgG/anti-IgG immunoassay in human serum in a thermostated microfluidic system. The limits of detection (LODs) calculated by following different procedures (three times the standard deviation of the blank and the mean value of the residuals) were 6.9 × 10^-8 µg/mL and 4.5 × 10^-6 µg/mL, respectively. The calculated LODs demonstrate the effectiveness of the applied methodology for sensitivity enhancement.

Label-Free Direct Detection of Cylindrospermopsin via Graphene-Enhanced Surface Plasmon Resonance Aptasensor

In this work, we report a novel method for the label-free detection of cyanotoxin molecules based on a direct assay utilizing a graphene-modified surface plasmon resonance (SPR) aptasensor. Molecular dynamic simulation of the aptamer's interaction with cylindrospermopsin (CYN) reveals the strongest binding sites between C18-C26 pairs. To modify the SPR sensor, the wet transfer method of CVD monolayer graphene was used. For the first time, we report the use of graphene functionalized by an aptamer as a bioreceptor in conjunction with SPR for the detection of CYN. In a direct assay with an anti-CYN aptamer, we demonstrated a noticeable change in the optical signal in response to the concentrations far below the maximum tolerable level of 1 µg/L and high specificity.

Label-Free Multiplexed Microfluidic Analysis of Protein Interactions Based on Photonic Crystal Surface Mode Imaging

High-throughput protein assays are crucial for modern diagnostics, drug discovery, proteomics, and other fields of biology and medicine. It allows simultaneous detection of hundreds of analytes and miniaturization of both fabrication and analytical procedures. Photonic crystal surface mode (PC SM) imaging is an effective alternative to surface plasmon resonance (SPR) imaging used in conventional gold-coated, label-free biosensors. PC SM imaging is advantageous as a quick, label-free, and reproducible technique for multiplexed analysis of biomolecular interactions. PC SM sensors are characterized by a longer signal propagation at the cost of a lower spatial resolution, which makes them more sensitive than classical SPR imaging sensors. We describe an approach for designing label-free protein biosensing assays employing PC SM imaging in the microfluidic mode. Label-free, real-time detection of PC SM imaging biosensors using two-dimensional imaging of binding events has been designed to study arrays of model proteins (antibodies, immunoglobulin G-binding proteins, serum proteins, and DNA repair proteins) at 96 points prepared by automated spotting. The data prove feasibility of simultaneous PC SM imaging of multiple protein interactions. The results pave the way to further develop PC SM imaging as an advanced label-free microfluidic assay for the multiplexed detection of protein interactions.

Refractive Index Measurement Using SOI Photodiode with SP Antenna toward SOI CMOS-Compatible Integrated Optical Biosensor

This paper proposes a new optical biosensor composed of a silicon-on-insulator (SOI) p-n junction photodiode (PD) with a surface plasmon (SP) antenna. When the phase-matching condition between two lateral wavelengths of the diffracted light from the SP antenna and the waveguiding mode in the SOI PD is satisfied, we observe sharp peaks in the spectroscopic light sensitivity. Since the peak wavelength depends on the RI change around the SP antenna corresponding to the phase-matching condition, the SOI PDs with an SP antenna can be applied to the optical biosensor. The RI detection limit is evaluated in the measurements with bulk solutions, and 1.11 × 10^-5 RIU (refractive index unit) can be obtained, which is comparable to that of a surface plasmon resonance (SPR) sensor, which is well known as a representative optical biosensor. In addition, the response for intermolecular bonds is estimated by the electromagnetic simulations using the finite-difference time-domain (FDTD) method to clarify its ability to detect biomolecular interactions. The results of this paper will provide new ground for high-throughput label-free biosensing, since a large number of SOI PDs with an SP antenna can be easily integrated on a single chip via an SOI complementary metal-oxide-semiconductor (CMOS) fabrication process.

The Effects of Three-Dimensional Ligand Immobilization on Kinetic Measurements in Biosensors

The field of biosensing is in constant evolution, propelled by the need for sensitive, reliable platforms that provide consistent results, especially in the drug development industry, where small molecule characterization is of uttermost relevance. Kinetic characterization of small biochemicals is particularly challenging, and has required sensor developers to find solutions to compensate for the lack of sensitivity of their instruments. In this regard, surface chemistry plays a crucial role. The ligands need to be efficiently immobilized on the sensor surface, and probe distribution, maintenance of their native structure and efficient diffusion of the analyte to the surface need to be optimized. In order to enhance the signal generated by low molecular weight targets, surface plasmon resonance sensors utilize a high density of probes on the surface by employing a thick dextran matrix, resulting in a three-dimensional, multilayer distribution of molecules. Despite increasing the binding signal, this method can generate artifacts, due to the diffusion dependence of surface binding, affecting the accuracy of measured affinity constants. On the other hand, when working with planar surface chemistries, an incredibly high sensitivity is required for low molecular weight analytes, and furthermore the standard method for immobilizing single layers of molecules based on self-assembled monolayers (SAM) of epoxysilane has been demonstrated to promote protein denaturation, thus being far from ideal. Here, we will give a concise overview of the impact of tridimensional immobilization of ligands on label-free biosensors, mostly focusing on the effect of diffusion on binding affinity constants measurements. We will comment on how multilayering of probes is certainly useful in terms of increasing the sensitivity of the sensor, but can cause steric hindrance, mass transport and other diffusion effects. On the other hand, probe monolayers on epoxysilane chemistries do not undergo diffusion effect but rather other artifacts can occur due to probe distortion. Finally, a combination of tridimensional polymeric chemistry and probe monolayer is presented and reviewed, showing advantages and disadvantages over the other two approaches.

Refractive Index Sensing for Measuring Single Cell Growth

Accessing cell growth on adhesive substrates is critical for identifying biophysical properties of cells and their therapeutic response to drug therapies. However, optical techniques have low sensitivity, and their reliability varies with cell type, whereas microfluidic technologies rely on cell suspension. In this paper, we introduced a plasmonic functional assay platform that can precisely measure cell weight and the dynamic change in real-time for adherent cells. Possessing this ability, our platform can determine growth rates of individual cells within only 10 min to map the growth profile of populations in short time intervals. The platform could successfully determine heterogeneity within the growth profile of populations and assess subpopulations exhibiting distinct growth profiles. As a proof of principle, we investigated the growth profile of MCF-7 cells and the effect of two intracellular metabolisms critical for their proliferation. We first investigated the negative effect of serum starvation on cell growth. We then studied ornithine decarboxylase (ODC) activity, a key enzyme which is involved in proliferation, and degraded under low osmolarity that inhibits cell growth. We successfully determined the significant distinction between growth profiles of MCF-7 cells and their ODC-overproducing variants that possess strong resistance to the negative effects of low osmolarity. We also demonstrated that an exogenous parameter, putrescine, could rescue cells from ODC inhibition under hypoosmotic conditions. In addition to the ability of accessing intracellular activities through ex vivo measurements, our platform could also determine therapeutic behaviors of cancer cells in response to drug treatments. Here, we investigated difluoromethylornithine (DFMO), which has antitumor effects on MCF-7 cells by inhibiting ODC activity. We successfully demonstrated the susceptibility of MCF-7 cells to such drug treatment, while its DFMO-resistant subpopulation could survive in the presence of this antigrowth agent. By rapidly determining cell growth kinetics in small samples, our plasmonic platform may be of broad use to basic research and clinical applications.

Studying Soft Interfaces with Shear Waves: Principles and Applications of the Quartz Crystal Microbalance (QCM)

The response of the quartz crystal microbalance (QCM, also: QCM-D for "QCM with Dissipation monitoring") to loading with a diverse set of samples is reviewed in a consistent frame. After a brief introduction to the advanced QCMs, the governing equation (the small-load approximation) is derived. Planar films and adsorbates are modeled based on the acoustic multilayer formalism. In liquid environments, viscoelastic spectroscopy and high-frequency rheology are possible, even on layers with a thickness in the monolayer range. For particulate samples, the contact stiffness can be derived. Because the stress at the contact is large, the force is not always proportional to the displacement. Nonlinear effects are observed, leading to a dependence of the resonance frequency and the resonance bandwidth on the amplitude of oscillation. Partial slip, in particular, can be studied in detail. Advanced topics include structured samples and the extension of the small-load approximation to its tensorial version.

Bioconjugation of a PNA Probe to Zinc Oxide Nanowires for Label-Free Sensing

Zinc oxide nanowires (ZnONWs) are largely used in biosensing applications due to their large specific surface area, photoluminescence emission and electron mobility. In this work, the surfaces of ZnONWs are modified by covalent bioconjugation of a peptidic nucleic acid (PNA) probe whose sequence is properly chosen to recognize a complementary DNA (cDNA) strand corresponding to a tract of the CD5 mRNA, the main prognostic marker of chronic lymphatic leukemia. The interaction between PNA and cDNA is preliminarily investigated in solution by circular dichroism, CD melting, and polyacrylamide gel electrophoresis. After the immobilization of the PNA probe on the ZnONW surface, we demonstrate the ability of the PNA-functionalized ZnONW platform to detect cDNA in the μM range of concentration by electrical, label-free measurements. The specificity of the sensor is also verified against a non-complementary DNA sequence. These preliminary results highlight the potential application of PNA-bioconjugated ZnONWs to label-free biosensing of tumor markers.

Spectral-Phase Interferometry Detection of Ochratoxin A via Aptamer-Functionalized Graphene Coated Glass

In this work, we report a novel method of label-free detection of small molecules based on direct observation of interferometric signal change in graphene-modified glasses. The interferometric sensor chips are fabricated via a conventional wet transfer method of CVD-grown graphene onto the glass coverslips, lowering the device cost and allowing for upscaling the sensor fabrication. For the first time, we report the use of graphene functionalized by the aptamer as the bioreceptor, in conjunction with Spectral-Phase Interferometry (SPI) for detection of ochratoxin A (OTA). In a direct assay with an OTA-specific aptamer, we demonstrated a quick and significant change of the optical signal in response to the maximum tolerable level of OTA concentration. The sensor regeneration is possible in urea solution. The developed platform enables a direct method of kinetic analysis of small molecules using a low-cost optical chip with a graphene-aptamer sensing layer.

Long-Period Gratings and Microcavity In-Line Mach Zehnder Interferometers as Highly Sensitive Optical Fiber Platforms for Bacteria Sensing

Selected optical fiber sensors offer extraordinary sensitivity to changes in external refractive (RI), which make them promising for label-free biosensing. In this work the most sensitive ones, namely long-period gratings working at (DTP-LPG) and micro-cavity in-line Mach-Zehnder interferometers (µIMZI) are discussed for application in bacteria sensing. We describe their working principles and RI sensitivity when operating in water environments, which is as high as 20,000 nm/RIU (Refractive index unit) for DTP-LPGs and 27,000 nm/RIU for µIMZIs. Special attention is paid to the methods to enhance the sensitivity by etching and nano-coatings. While the DTP-LPGs offer a greater interaction length and sensitivity to changes taking place at their surface, the µIMZIs are best suited for investigations of sub-nanoliter and picoliter volumes. The capabilities of both the platforms for bacteria sensing are presented and compared for strains of Escherichia coli, lipopolysaccharide E. coli, outer membrane proteins of E. coli, and Staphylococcus aureus. While DTP-LPGs have been more explored for bacteria detection in 10²–10⁶ Colony Forming Unit (CFU)/mL for S. aureus and 10³–10⁹ CFU/mL for E. coli, the µIMZIs reached 10²–10⁸ CFU/mL for E. coli and have a potential for becoming picoliter bacteria sensors.

Biohybrid Triboelectric Nanogenerator for Label-Free Pharmacological Fingerprinting in Cardiomyocytes

The development of new drugs requires high-throughput and cost-effective pharmacological assessment in relevant biological models. Here, we introduce a novel pharmacological screening platform that combines a biohybrid triboelectric nanogenerator (TENG) and informatic analysis for self-powered, noninvasive, and label-free biosensing in cardiac cells. The cyclic mechanical activity of functional cardiomyocytes is dynamically captured by a specially designed biohybrid TENG device and is analyzed by a custom-made machine learning algorithm to reveal distinctive fingerprints in response to different pharmacological treatment. The core of the TENG device is a multilayer mesh substrate with microscale-gapped triboelectric layers, which are induced to generate electrical outputs by the characteristic motion of cardiomyocytes upon pharmaceutical treatment. Later bioinformatic extraction from the recorded TENG signal is sufficient to predict a drug's identity and efficacy, demonstrating the great potential of this platform as a biocompatible, low-cost, and highly sensitive drug screening system.

Ultraflexible Nanowire Array for Label- and Distortion-Free Cellular Force Tracking

Living cells interact with their immediate environment by exerting mechanical forces, which regulate important cell functions. Elucidation of such force patterns yields deep insights into the physics of life. Here we present a top-down nanostructured, ultraflexible nanowire array biosensor capable of probing cell-induced forces. Its universal building block, an inverted conical semiconductor nanowire, greatly enhances both the functionality and the sensitivity of the device. In contrast to existing cellular force sensing architectures, microscopy is performed on the nanowire heads while cells deflecting the nanowires are confined within the array. This separation between the optical path and the cells under investigation excludes optical distortions caused by cell-induced refraction, which can give rise to feigned displacements on the 100 nm scale. The undistorted nanowire displacements are converted into cellular forces via the nanowire spring constant. The resulting distortion-free cellular force transducer realizes a high-resolution and label-free biosenor based on optical microscopy. Its performance is demonstrated in a proof-of-principle experiment with living Dictyostelium discoideum cells migrating through the nanowire array. Cell-induced forces are probed with a resolution of 50 piconewton, while the most flexible nanowires promise to enter the 100 femtonewton realm.

One Hour In Vivo-like Phenotypic Screening System for Anti-cancer Drugs Using a High Precision Surface Plasmon Resonance Device

In anti-cancer drug (candidate) screening, there is the need for evaluation at physiological concentrations similar to in vivo. This is often performed by three-dimensionally (3D) cultured cells; however, it requires a long culture period of 2 - 4 weeks with tedious experimental procedures. Here, we report on a high precision surface plasmon resonance (HP-SPR)-3D system. We developed the system with average fluctuation of 50 ndeg s^-1 using two-dimensionally cultured cells attached onto a sensor chip by applying collagen on the top to change their activity into in vivo-like conditions without cell division. It allowed in vivo-like phenotypic screening for anti-cancer drugs within 1 h of drug addition. The data were collected as the stable linear signal change parts for at least 5 min after 25 min following drug addition. The results provided compatibility to clinically related chemosensitivity test for anti-cancer (P <0.001) using two cell lines of pancreatic cancer and three anti-cancer drugs to represent differences in individual gene expression and drug mode of action.

Capacitive Sensing of Glucose in Electrolytes Using Graphene Quantum Capacitance Varactors

A novel graphene-based variable capacitor (varactor) that senses glucose based on the quantum capacitance effect was successfully developed. The sensor utilizes a metal-oxide-graphene varactor device structure that is inherently compatible with passive wireless sensing, a key advantage for in vivo glucose sensing. The graphene varactors were functionalized with pyrene-1-boronic acid (PBA) by self-assembly driven by π-π interactions. Successful surface functionalization was confirmed by both Raman spectroscopy and capacitance-voltage characterization of the devices. Through glucose binding to the PBA, the glucose concentration in the buffer solutions modulates the level of electrostatic doping of the graphene surface to different degrees, which leads to capacitance changes and Dirac voltage shifts. These responses to the glucose concentration were shown to be reproducible and reversible over multiple measurement cycles, suggesting promise for eventual use in wireless glucose monitoring.

Nanoplasmonic mid-infrared biosensor for in vitro protein secondary structure detection

Plasmonic nanoantennas offer new applications in mid-infrared (mid-IR) absorption spectroscopy with ultrasensitive detection of structural signatures of biomolecules, such as proteins, due to their strong resonant near-fields. The amide I fingerprint of a protein contains conformational information that is greatly important for understanding its function in health and disease. Here, we introduce a non-invasive, label-free mid-IR nanoantenna-array sensor for secondary structure identification of nanometer-thin protein layers in aqueous solution by resolving the content of plasmonically enhanced amide I signatures. We successfully detect random coil to cross β-sheet conformational changes associated with α-synuclein protein aggregation, a detrimental process in many neurodegenerative disorders. Notably, our experimental results demonstrate high conformational sensitivity by differentiating subtle secondary-structural variations in a native β-sheet protein monolayer from those of cross β-sheets, which are characteristic of pathological aggregates. Our nanoplasmonic biosensor is a highly promising and versatile tool for in vitro structural analysis of thin protein layers.

Direct and label-free detection of the human growth hormone in urine by an ultrasensitive bimodal waveguide biosensor

A label-free interferometric transducer showing a theoretical detection limit for homogeneous sensing of 5 × 10^-8 RIU, being equivalent to a protein mass coverage resolution of 2.8 fg mm^-2 , is used to develop a high sensitive biosensor for protein detection. The extreme sensitivity of this transducer combined with a selective bioreceptor layer enables the direct evaluation of the human growth hormone (hGH) in undiluted urine matrix in the 10 pg mL^-1 range.

Flexible Molybdenum Electrodes towards Designing Affinity Based Protein Biosensors

Molybdenum electrode based flexible biosensor on porous polyamide substrates has been fabricated and tested for its functionality as a protein affinity based biosensor. The biosensor performance was evaluated using a key cardiac biomarker; cardiac Troponin-I (cTnI). Molybdenum is a transition metal and demonstrates electrochemical behavior upon interaction with an electrolyte. We have leveraged this property of molybdenum for designing an affinity based biosensor using electrochemical impedance spectroscopy. We have evaluated the feasibility of detection of cTnI in phosphate-buffered saline (PBS) and human serum (HS) by measuring impedance changes over a frequency window from 100 mHz to 1 MHz. Increasing changes to the measured impedance was correlated to the increased dose of cTnI molecules binding to the cTnI antibody functionalized molybdenum surface. We achieved cTnI detection limit of 10 pg/mL in PBS and 1 ng/mL in HS medium. The use of flexible substrates for designing the biosensor demonstrates promise for integration with a large-scale batch manufacturing process.

Real-Time Label-Free Direct Electronic Monitoring of Topoisomerase Enzyme Binding Kinetics on Graphene

Monolayer graphene field-effect sensors operating in liquid have been widely deployed for detecting a range of analyte species often under equilibrium conditions. Here we report on the real-time detection of the binding kinetics of the essential human enzyme, topoisomerase I interacting with substrate molecules (DNA probes) that are immobilized electrochemically on to monolayer graphene strips. By monitoring the field-effect characteristics of the graphene biosensor in real-time during the enzyme-substrate interactions, we are able to decipher the surface binding constant for the cleavage reaction step of topoisomerase I activity in a label-free manner. Moreover, an appropriate design of the capture probes allows us to distinctly follow the cleavage step of topoisomerase I functioning in real-time down to picomolar concentrations. The presented results are promising for future rapid screening of drugs that are being evaluated for regulating enzyme activity.

Optical Microfibre Based Photonic Components and Their Applications in Label-Free Biosensing

Optical microfibre photonic components offer a variety of enabling properties, including large evanescent fields, flexibility, configurability, high confinement, robustness and compactness. These unique features have been exploited in a range of applications such as telecommunication, sensing, optical manipulation and high Q resonators. Optical microfibre biosensors, as a class of fibre optic biosensors which rely on small geometries to expose the evanescent field to interact with samples, have been widely investigated. Due to their unique properties, such as fast response, functionalization, strong confinement, configurability, flexibility, compact size, low cost, robustness, ease of miniaturization, large evanescent field and label-free operation, optical microfibres based biosensors seem a promising alternative to traditional immunological methods for biomolecule measurements. Unlabeled DNA and protein targets can be detected by monitoring the changes of various optical transduction mechanisms, such as refractive index, absorption and surface plasmon resonance, since a target molecule is capable of binding to an immobilized optical microfibre. In this review, we critically summarize accomplishments of past optical microfibre label-free biosensors, identify areas for future research and provide a detailed account of the studies conducted to date for biomolecules detection using optical microfibres.