High-Throughput Surface Plasmon Resonance Biosensors for Identifying Diverse Therapeutic Monoclonal Antibodies.

Identification of antibodies targeting diverse functional epitopes on an antigen is highly crucial for discovering effective therapeutic candidates. Employing a traditional stepwise antibody "screening funnel" as well as prioritizing affinity-based selections over epitope-based selections, result in lead antibody panels lacking epitope diversity. In the present study, we employed an array-based surface plasmon resonance (SPR) platform to perform high-throughput epitope binning analysis on a large number of monoclonal antibodies (mAbs) generated in the early drug discovery process. The mAb panel contained clones from different antibody generation techniques and diverse transgenic mouse strains. The epitope binning results were analyzed in unique ways using various visualizations in the form of dendrograms and network plots, which assisted in determining diversity and redundancy in the mAb sample set. The binning data were further integrated with affinity information to evaluate the performance of seven different transgenic mouse strains. The combination of epitope binning results with binding kinetics and sequence analysis provided an effective and efficient way of selecting high affinity antibodies representing a diverse set of sequence families and epitopes.

A three-dimensional electrochemical paper-based analytical device for low-cost diagnostics.

Paper-based microfluidic devices with screen-printed electrodes (SPEs) for electrochemical sensing are popular for low-cost point-of-care diagnostics. The electroactive sensing area in these devices is always the irregular, bottom-SPE surface which is in contact with the analyte flowing within the paper substrate. Unfortunately, this results in an electroactive area which varies widely from sensor to sensor. In this paper, we present a three-dimensional paper-based analytical device with a hollow 3D fluid reservoir which allows for use of a more uniform top-SPE surface as the electroactive sensing area. The use of this isolated reservoir eliminates the need for dielectric inks used in conventional SPEs on paper. Our sensors are fabricated using a combination of wax-printing, screen-printing and simple folding via a cleanroom free process without the need for expensive equipment. Additionally, for the first time, we demonstrate an electrochemical paper-based analytical device with a custom designed potentiostat integrated circuit (IC) as a miniaturized reader. The versatility of the sensor is demonstrated through voltammetric, amperometric and potentiometric measurements of important biochemical analytes such as dopamine, glucose and pH. The 3D ePAD together with a custom CMOS potentiostat demonstrates a low-cost, versatile, self-contained system suitable for point-of-care diagnostic devices.

Sequence-Specific Electrical Purification of Nucleic Acids with Nanoporous Gold Electrodes.

Nucleic-acid-based biosensors have enabled rapid and sensitive detection of pathogenic targets; however, these devices often require purified nucleic acids for analysis since the constituents of complex biological fluids adversely affect sensor performance. This purification step is typically performed outside the device, thereby increasing sample-to-answer time and introducing contaminants. We report a novel approach using a multifunctional matrix, nanoporous gold (np-Au), which enables both detection of specific target sequences in a complex biological sample and their subsequent purification. The np-Au electrodes modified with 26-mer DNA probes (via thiol-gold chemistry) enabled sensitive detection and capture of complementary DNA targets in the presence of complex media (fetal bovine serum) and other interfering DNA fragments in the range of 50-1500 base pairs. Upon capture, the noncomplementary DNA fragments and serum constituents of varying sizes were washed away. Finally, the surface-bound DNA-DNA hybrids were released by electrochemically cleaving the thiol-gold linkage, and the hybrids were iontophoretically eluted from the nanoporous matrix. The optical and electrophoretic characterization of the analytes before and after the detection-purification process revealed that low target DNA concentrations (80 pg/µL) can be successfully detected in complex biological fluids and subsequently released to yield pure hybrids free of polydisperse digested DNA fragments and serum biomolecules. Taken together, this multifunctional platform is expected to enable seamless integration of detection and purification of nucleic acid biomarkers of pathogens and diseases in miniaturized diagnostic devices.

Effect of nanoporous gold thin film morphology on electrochemical DNA sensing.

Advances in materials science and chemistry have led to the development of a wide range of nanostructured materials for building novel electrochemical biosensors. A systematic understanding of the challenges related to electrode morphology involved in designing such sensors is essential for developing effective biosensing tools. In this study, we use nanoporous gold (np-Au) thin film electrode coatings with submicrometer thicknesses, as a model system to investigate the influence of nanostructuring on DNA-methylene blue (MB) interactions and their application to DNA biosensors. The interaction of single- and double-stranded DNA immobilized onto morphologically different np-Au films with MB was electrochemically interrogated via square wave voltammetry (SWV). The electrochemical signal from these electrodes in response to MB decayed progressively with each SWV scan. The decay rate was governed by accessibility of the electrochemically active np-Au surface by the analyte. The optimum frequency for extracting the maximum signal via SWV was influenced by the film morphology, where the optimum frequency was lower for the nanoporous morphology with lower density of molecular access points into the porous coating. Overall, the np-Au electrodes exhibited a 10-fold enhancement in probe grafting density and approximately 10-fold higher electrochemical current upon probe-target hybridization as compared to the planar Au electrodes. The np-Au electrodes enabled sensitive detection with a dynamic range of 10 to 100 nM that shifts by 1 order of magnitude for coarsened np-Au morphology due to increased target penetration into the porous network and hence enhanced hybridization efficiency. These findings provide insight into the influence of nanostructuring on the transport mechanisms of small molecules and nucleic acids, and yield an understanding of diverse sensor performance parameters such as DNA grafting density, hybridization efficiency, sensitivity and dynamic range.

Biofouling-resilient nanoporous gold electrodes for DNA sensing.

Electrochemical nucleic acid sensors are promising tools for point-of-care diagnostic platforms with their facile integration with electronics and scalability. However, nucleic acid detection in complex biological fluids is challenging as biomolecules nonspecifically adsorb on the electrode surface and adversely affect the sensor performance by obscuring the transport of analytes and redox species to the electrode. We report that nanoporous gold (np-Au) electrodes, prepared by a microfabrication-compatible self-assembly process and functionalized with DNA probes, enabled detection of target DNA molecules (10-200 nM) in physiologically relevant complex media (bovine serum albumin and fetal bovine serum). In contrast, the sensor performance was compromised for planar gold electrodes in the same conditions. Hybridization efficiency decreased by 10% for np-Au with coarser pores revealing a pore-size dependence of sensor performance in biofouling conditions. This nanostructure-dependent functionality in complex media suggests that the pores with the optimal size and geometry act as sieves for blocking the biomolecules from inhibiting the surfaces within the porous volume while allowing the transport of nucleic acid analytes and redox molecules.

Detecting transforming growth factor-ß release from liver cells using an aptasensor integrated with microfluidics.

We developed a cell-culture/biosensor platform consisting of aptamer-modified Au electrodes integrated with reconfigurable microfluidics for monitoring of transforming growth factor-beta 1 (TGF-ß1), an important inflammatory and pro-fibrotic cytokine. Aptamers were thiolated, labeled with redox reporters, and self-assembled on gold surfaces. The biosensor was determined to be specific for TGF-ß1 with an experimental detection limit of 1 ng/mL and linear range extending to 250 ng/mL. Upon determining figures of merit, aptasensor was miniaturized and integrated with human hepatic stellate cells inside microfluidic devices. Reconfigurable microfluidics were developed to ensure that seeding of "sticky" stromal cells did not foul the electrode and compromise sensor performance. This microsystem with integrated aptasensors was used to monitor TGF-ß1 release from activated stellate cells over the course of 20 h. The electrochemical response went down upon infusing anti-TGF-ß1 antibodies into the microfluidic devices containing activated stellate cells. To further validate aptasensor responses, stellate cells were stained for markers of activation (e.g., alpha smooth muscle actin) and were also tested for presence of TGF-ß1 using enzyme linked immunosorbent assay (ELISA). Given the importance of TGF-ß1 as a fibrogenic signal, a microsystem with integrated biosensors for local and continuous detection of TGF-ß1 may prove to be an important tool to study fibrosis of the liver and other organs.

Miniature enzyme-based electrodes for detection of hydrogen peroxide release from alcohol-injured hepatocytes.

Alcohol insult to the liver sets off a complex sequence of inflammatory and fibrogenic responses. There is increasing evidence that hepatocytes play a key role in triggering these responses by producing inflammatory signals such as cytokines and reactive oxygen species (ROS). In the present study, we employed a cell culture/biosensor platform consisting of electrode arrays integrated with microfluidics to monitor extracellular H(2)O(2), one of the major ROS types, produced by primary rat hepatocytes during alcohol injury. The biosensor consisted of hydrogel microstructures with entrapped horseradish peroxidase (HRP) immobilized on an array of miniature gold electrodes. These arrays of sensing electrodes were integrated into microfluidic devices and modified with collagen (I) to promote hepatocyte adhesion. Once seeded into the microfluidic devices, hepatocytes were exposed to 100 mM ethanol and the signal at the working electrode was monitored by cyclic voltammetry (CV) over the course of 4 h. The CV experiments revealed that hepatocytes secreted up to 1.16 µM H(2)O(2) after 3 h of stimulation. Importantly, when hepatocytes were incubated with antioxidants or alcohol dehydrogenase inhibitor prior to alcohol exposure, the H(2)O(2) signal was decreased by ~5-fold. These experiments further confirmed that the biosensor was indeed monitoring oxidative stress generated by the hepatocytes and also pointed to one future use of this technology for screening hepatoprotective effects of antioxidants.

Micropatterned surfaces functionalized with electroactive peptides for detecting protease release from cells.

Matrix metalloproteinases (MMPs) regulate composition of the extracellular matrix and play a critical role in cancer, fibrosis, and wound healing. This article describes a novel peptide-based electrochemical biosensor for detecting activity of cell-secreted protease MMP9. In this sensing strategy, a peptide specific to MMP9 was modified with a redox label (methylene blue (MB)) and immobilized on microfabricated 300 µm diameter Au electrodes. Challenging the electrodes with known concentrations of MMP9 resulted in the cleavage of the MB containing peptide fragment and caused a decrease in electrical signal measured by square wave voltammetry (SWV). The limit of detection for MMP9 was determined to be 60 pM with a linear range extending to 50 nM. In preparation to detect cell-secreted MMP9, glass surfaces with Au electrode arrays were further micropatterned with poly(ethylene glycol) (PEG) gel to define annular cell adhesive regions next to electrodes and render the remainder of the surface nonfouling. The surfaces were further modified with CD14 antibody to promote attachment of monocytes. The peptide-modified electrode arrays were integrated into PDMS microfluidic devices and incubated with U-937 cells, transformed monocytes known to produce MMPs. These studies revealed a 3-fold higher electrochemical signal from ∼400 activated monocytes after 10 min activation compared to nonactivated monocytes. Whereas this article focuses on MMP9 detection, the general strategy of employing redox-labeled peptides on electrodes should be broadly applicable for detection of other proteases and should have clinical as well as basic science applications.

Fundamentals and application of ordered molecular assemblies to affinity biosensing.

Organization of biomolecules in two/three dimensional assemblies has recently aroused much interest in nanobiotechnology. In this context, the development of techniques for controlling spatial arrangement and orientation of the desired molecules to generate highly-ordered nanostructures in the form of a mono/multi layer is considered highly significant. The studies of monolayer films to date have focused on three distinct methods of preparation: (i) the Langmuir-Blodgett (LB) technique, involving the transfer of a monolayer assembled at the gas-liquid interface; (ii) self-assembly at the liquid-solid interface, based on spontaneous adsorption of desired molecules from a solution directly onto a solid surface; and (iii) Layer-by-layer (LBL) self-assembly at a liquid-solid interface, based on inter-layer electrostatic attractions for fabrication of multilayers. A variety of monolayers have been utilized to fabricate biomolecular electronic devices including biosensors. The composition of a monolayer based matrix has been found to influence the activity(ies) of biomolecule(s). We present comprehensive and critical analysis of ordered molecular assemblies formed by LB and self-assembly with potential applications to affinity biosensing. This critical review on fundamentals and application of ordered molecular assemblies to affinity biosensing is likely to benefit researchers working in this as well as related fields of research (401 references).

Nanopatterned cadmium selenide Langmuir-Blodgett platform for leukemia detection.

We present results of the studies relating to preparation of Langmuir-Blodgett (LB) monolayers of tri-n-octylphosphine oxide-capped cadmium selenide quantum dots (QCdSe) onto indium-tin oxide (ITO) coated glass substrate. The monolayer behavior has been studied at the air-water interface under various subphase conditions. This nanopatterned platform has been explored to fabricate an electrochemical DNA biosensor for detection of chronic myelogenous leukemia (CML) by covalently immobilizing the thiol-terminated oligonucleotide probe sequence via a displacement reaction. The results of electrochemical response studies reveal that this biosensor can detect target DNA in the range of 10(-6) to 10(-14) M within 120 s, has a shelf life of 2 months, and can be used about 8 times. Further, this nucleic acid sensor has been found to distinguish the CML-positive and the control negative clinical patient samples.

Mediator free cholesterol biosensor based on self-assembled monolayer platform.

Self-assembled monolayer (SAM) of 4-aminothiophenol (4-ATP) has been investigated for immobilization of bi-enzymes (ChOx and ChEt) towards development of enzyme biosensors for detection of free and total cholesterol. This enzyme immobilized SAM surface has been characterized by scanning electron microscopy and electrochemical measurements. The results of electrochemical response studies reveal fast enzymatic reaction in phosphate buffer saline solution without using any artificial mediator. This may be attributed to the molecular wire type behavior of short 4-ATP molecule that promotes electron transfer between enzyme and the electrode surface due to its conjugated structure. Interference free estimation of free and total cholesterol has been realized at low operating potential of 0.33 V with range of detection as 25 to 400 mg dl(-1), sensitivity of 542.3 nA mM(-1) (for ChOx/4-ATP/Au) and 886.6 nA mM(-1) (for ChEt-ChOx/4-ATP/Au) with a response time of 20 s at pH 7.4.

Affinity and enzyme-based biosensors: recent advances and emerging applications in cell analysis and point-of-care testing.

The applications of biosensors range from environmental testing and biowarfare agent detection to clinical testing and cell analysis. In recent years, biosensors have become increasingly prevalent in clinical testing and point-of-care testing. This is driven in part by the desire to decrease the cost of health care, to shift some of the analytical tests from centralized facilities to "frontline" physicians and nurses, and to obtain more precise information more quickly about the health status of a patient. This article gives an overview of recent advances in the field of biosensors, focusing on biosensors based on enzymes, aptamers, antibodies, and phages. In addition, this article attempts to describe efforts to apply these biosensors to clinical testing and cell analysis.

Nanoporous-Gold-Based Electrode Morphology Libraries for Investigating Structure-Property Relationships in Nucleic Acid Based Electrochemical Biosensors.

Nanoporous gold (np-Au) electrode coatings significantly enhance the performance of electrochemical nucleic acid biosensors because of their three-dimensional nanoscale network, high electrical conductivity, facile surface functionalization, and biocompatibility. Contrary to planar electrodes, the np-Au electrodes also exhibit sensitive detection in the presence of common biofouling media due to their porous structure. However, the pore size of the nanomatrix plays a critical role in dictating the extent of biomolecular capture and transport. Small pores perform better in the case of target detection in complex samples by filtering out the large nonspecific proteins. On the other hand, larger pores increase the accessibility of target nucleic acids in the nanoporous structure, enhancing the detection limits of the sensor at the expense of more interference from biofouling molecules. Here, we report a microfabricated np-Au multiple electrode array that displays a range of electrode morphologies on the same chip for identifying feature sizes that reduce the nonspecific adsorption of proteins but facilitate the permeation of target DNA molecules into the pores. We demonstrate the utility of the electrode morphology library in studying DNA functionalization and target detection in complex biological media with a special emphasis on revealing ranges of electrode morphologies that mutually enhance the limit of detection and biofouling resilience. We expect this technique to assist in the development of high-performance biosensors for point-of-care diagnostics and facilitate studies on the electrode structure-property relationships in potential applications ranging from neural electrodes to catalysts.

Sensing Conductive Hydrogels for Rapid Detection of Cytokines in Blood.

Conducting polymer hydrogel is fabricated atop gold or ITO electrodes and is functionalized with monoclonal antibodies. Binding of interferon-γ molecules causes redox properties of conductive hydrogel to change in a concentration-dependent fashion without the need for washing or sample handling steps. This conductive hydrogel remains functional in a fouling media such as whole blood.

Detecting multiple cell-secreted cytokines from the same aptamer-functionalized electrode.

Inflammatory cytokines are secreted by immune cells in response to infection or injury. Quantification of multiple cytokines in parallel may help with disease diagnosis by illuminating inflammatory pathways related to disease onset and progression. This paper describes development of an electrochemical aptasensor for simultaneous detection of two important inflammatory cytokines, interferon gamma (IFN-γ) and tumor necrosis factor alpha (TNF-α). To enable multiplexing, IFN-γ and TNF-α aptamers were labeled with anthraquinone (AQ) and methylene blue (MB) redox reporters respectively. Random immobilization of two aptamer on gold exhibited redox peaks at -0.37 V (AQ) and -0.15 V (MB) vs. Ag/AgCl reference. When challenged with either IFN-γ or TNF-α, redox signal of the appropriate reporter changed in concentration dependent manner. To demonstrate one possible application of this sensing approach, electrodes were integrated into microfluidic devices and used to dynamically monitor cytokine release from immune cells. Two cell types, primary human CD4 T-cells and U937 monocytic cells, were used to compare differences in cytokine secretions upon stimulation. These cells were infused into the microfluidic devices and stimulated to commence cytokine production. Release of IFN-γ and TNF-α was monitored concurrently from the same small group of cells over the course of 2h. The strategy of encoding specific aptamer types with unique redox reporters allows sensitive and specific detection of multiple protein biomarkers from the same electrode.

Liver injury-on-a-chip: microfluidic co-cultures with integrated biosensors for monitoring liver cell signaling during injury.

Tissue injury triggers complex communication between cells via secreted signaling molecules such as cytokines and growth factors. Discerning when and where these signals begin and how they propagate over time is very challenging with existing cell culture and analysis tools. The goal of this study was to develop new tools in the form of microfluidic co-cultures with integrated biosensors for local and continuous monitoring of secreted signals. Specifically, we focused on how alcohol injury affects TGF-ß signaling between two liver cell types, hepatocytes and stellate cells. Activation of stellate cells happens early during liver injury and is at the center of liver fibrosis. We demonstrated that alcohol injury to microfluidic co-cultures caused significantly higher levels of stellate cell activation compared to conditioned media and transwell injury experiments. This highlighted the advantage of the microfluidic co-culture: placement of two cell types in close proximity to ensure high local concentrations of injury-promoting secreted signals. Next, we developed a microsystem consisting of five chambers, two for co-culturing hepatocytes with stellate cells and three additional chambers containing miniature aptamer-modified electrodes for monitoring secreted TGF-ß. Importantly, the walls separating microfluidic chambers were actuatable; they could be raised or lowered to create different configurations of the device. The use of reconfigurable microfluidics and miniature biosensors revealed that alcohol injury causes hepatocytes to secrete TGF-ß molecules, which diffuse over to neighboring stellate cells and trigger production of additional TGF-ß from stellate cells. Our results lend credence to the emerging view of hepatocytes as active participants of liver injury. Broadly speaking, our microsystem makes it possible to monitor paracrine crosstalk between two cell types communicating via the same signaling molecule (e.g. TGF-ß).

A mathematical method for extracting cell secretion rate from affinity biosensors continuously monitoring cell activity.

Our laboratory has previously developed miniature aptasensors that may be integrated at the site of a small group of cells for continuous detection of cell secreted molecules such as inflammatory cytokine interferon gamma (IFN-γ). In a system such as this, the signal measured at the sensor surfaces is a complex function of transport, reaction, as well as of cellular activity. Herein, we report on the development of a mathematical framework for extracting cell production rates from binding curves generated with affinity biosensors. This framework consisted of a diffusion-reaction model coupled to a root finding algorithm for determining cell production rates values causing convergence of a predetermined criterion. To experimentally validate model predictions, we deployed a microfluidic device with an integrated biosensor for measuring the IFN-γ release from CD4 T cells. We found close agreement between secretion rate observed theoretically and those observed experimentally. After taking into account the differences in sensor geometry and reaction kinetics, the method for cell secretion rate determination described in this paper may be broadly applied to any biosensor continuously measuring cellular activity.

Electrochemical biosensors for on-chip detection of oxidative stress from cells.

The production of reactive oxygen species (ROS) in the body has been shown to play a significant role in the development and progression of numerous diseases. This makes it important to develop a method of detection for hydrogen peroxide (H2O2), the most stable ROS. Several methods such as the use of fluorescent probes and electrochemistry have been utilized in the past to detect the imbalance in ROS levels generated from injured or stimulated cells. An imbalance in the levels of ROS leads to a state of oxidative stress within the body. Different enzymes such as horseradish peroxidase (HRP) and superoxide dismutase have been used in the detection of ROS. HRP is commonly used as the biorecognition element in many H2O2 sensors. Researchers have looked into immobilizing these enzymes onto carbon nanotubes and nanoparticles to increase sensor sensitivity. In this chapter, we present experimental procedures to perform electrochemical quantification of H2O2, one of the major ROS release from injured cells (macrophages and hepatocytes).

Polyaniline Langmuir-Blodgett film based aptasensor for ochratoxin A detection.

Ochratoxin A (OTA) produced by Aspergillus Ochraceus and Penicillium verrucosum is a very dangerous toxin due to its toxic effects in human beings and its presence in a wide range of food products and cereals. A Langmuir-Blodgett (polyaniline (PANI)-stearic acid (SA)) film based highly sensitive and robust impedimetric aptasensor has been developed for ochratoxin A (OTA) detection. DNA Aptamer (Apt-DNA) specific to OTA has been covalently immobilized onto mixed Langmuir-Blodgett (LB) monolayer comprising of PANI-SA deposited onto indium tin-oxide (ITO) coated glass plates. This Apt-DNA/PANI-SA/ITO aptaelectrode has been characterized using scanning electron microscopy, Fourier transform-infrared spectroscopy, contact angle measurements, cyclic voltammetry and electrochemical impedance spectroscopy, respectively. The Apt-DNA/PANI-SA/ITO aptasensor shows detection of OTA by electrochemical impedance spectroscopy in the linear range of 0.0001 µg/ml (0.1 ng/ml) to 0.01 µg/ml (10 ng/ml) and 1 µg/ml-25 µg/ml with detection limit of 0.1 ng/ml in 15 min. The Apt-DNA/PANI-SA/ITO aptasensor can be reused ∼13 times. The binding or affinity constant (K(a)) of aptamer with OTA, calculated using Langmuir adsorption isotherm, is found be 1.21×10(7) M(-1).

Langmuir-Blodgett film based on MEH-PPV for cholesterol biosensor.

Cholesterol oxidase (ChOx) has been immobilized onto conducting poly[2-methoxy,5-(2'-ethyl-hexyloxy)-1,4-phenylene vinylene] (MEH-PPV)/stearic acid (SA) Langmuir-Blodgett film transferred onto octadecanethiol (ODT) modified gold plate. The ChOx/MEH-PPV/SA LB film bioelectrode exhibits has been characterized by FT-IR, contact angle, and atomic force microscopy. The response of the ChOx/MEH-PPV/SA LB film bioelectrode carried out using differential pulse voltammetry (DPV) studies reveal linearity from 1.29 to 12.91 mM of cholesterol concentration and response time as 30 s. This ChOx/MEH-PPV/SA bioelectrode exhibits values of correlation coefficient as 0.9939, standard deviation as 0.0029 microA and limit of detection as 1.66 mM. UV-visible spectrophotometer studies reveal that 5.2x10(-3) U of ChOx are actively working per cm(2) area of ChOx/MEH-PPV/SA LB film bioelectrode and this bioelectrode is thermally stable upto 55 degrees C with reusability of about 60 times.