Optical microarray biosensing techniques

Development of multiple genome-wide proteome microarrays comprised wafer substrate-based chip and its scanner: An advanced high-throughput and sensitivity for molecular interactions studies

Proteome microarray technology enables high-throughput analysis of protein interactions with all kinds of molecules. Wafer (6-inch) substrates offer a promising alternative to conventional glass (2.6 × 7.6 cm) substrates for carrying proteomes. This study aims to develop high-density wafer-based proteome microarrays and a corresponding fluorescence scanner. We constructed E. coli proteome microarrays and probed them with the antimicrobial peptide indolicidin to identify its protein targets, revealing its antimicrobial mechanisms. Compared to glass substrates, wafer substrates showed a detectable fluorescence signal of the immobilized Dylight 550-labeled antibody at a lower concentration (200 ng/mL vs. 5000 ng/mL), indicating greater sensitivity. Spot images on wafers also exhibited a more uniform circular profile. We fabricated a wafer holder compatible with a regular glass microarray printer and successfully printed six entire genome-wide E. coli proteome microarrays, totaling approximately 52,000 protein spots, on one wafer. Probing the wafer array with indolicidin and its control in triplicate, we identified 75 E. coli K12 protein targets, many of which are enriched in transport functions. Notably, we also found that two proteins crucial for DNA synthesis (nrdF and nrdB) were targeted by indolicidin. This explains the earlier finding that indolicidin inhibits DNA synthesis in E. coli. This study introduces the first wafer-based proteome microarrays, demonstrating enhanced sensitivity and the ability to perform simultaneous multiplexed probing compared to regular glass slide-based proteome microarrays.

Recent Progress in Development and Application of DNA, Protein, Peptide, Glycan, Antibody, and Aptamer Microarrays

Microarrays are one of the trailblazing technologies of the last two decades and have displayed their importance in all the associated fields of biology. They are widely explored to screen, identify, and gain insights on the characteristics traits of biomolecules (individually or in complex solutions). A wide variety of biomolecule-based microarrays (DNA microarrays, protein microarrays, glycan microarrays, antibody microarrays, peptide microarrays, and aptamer microarrays) are either commercially available or fabricated in-house by researchers to explore diverse substrates, surface coating, immobilization techniques, and detection strategies. The aim of this review is to explore the development of biomolecule-based microarray applications since 2018 onwards. Here, we have covered a different array of printing strategies, substrate surface modification, biomolecule immobilization strategies, detection techniques, and biomolecule-based microarray applications. The period of 2018-2022 focused on using biomolecule-based microarrays for the identification of biomarkers, detection of viruses, differentiation of multiple pathogens, etc. A few potential future applications of microarrays could be for personalized medicine, vaccine candidate screening, toxin screening, pathogen identification, and posttranslational modifications.

Applications of liquid crystals in biosensing

Liquid crystals (LCs), as a promising branch of highly-sensitive, quick-response, and low-cost materials, are widely applied to the detection of weak external stimuli and have attracted significant attention. Over the past decade, many research groups have been devoted to developing LC-based biosensors due to their self-assembly potential and functional diversity. In this paper, recent investigations on the design and application of LC-based biosensors are reviewed, based on the phenomenon that the orientation of LCs can be directly influenced by the interactions between biomolecules and LC molecules. The sensing principle of LC-based biosensors, as well as their signal detection by probing interfacial interactions, is described to convert, amplify, and quantify the information from targets into optical and electrical parameters. Furthermore, commonly-used LC biosensing targets are introduced, including glucose, proteins, enzymes, nucleic acids, cells, microorganisms, ions, and other micromolecules that are critical to human health. Due to their self-assembly potential, chemical diversity, and high sensitivity, it has been reported that tunable stimuli-responsive LC biosensors show bright perspectives and high superiorities in biological applications. Finally, challenges and future prospects are discussed for the fabrication and application of LC biosensors to both enhance their performance and to realize their promise in the biosensing industry.

Controlling the immobilization process of an optically enhanced protein microarray for highly reproducible immunoassay

By virtue of its high throughput multiplex detection capability, superior read-out sensitivity, and tiny analyte consumption, an optically enhanced protein microarray assay has been developed as a promising diagnostic tool for various applications, ranging from the field of pharmacology to diagnostics. However, so far, the development of an optically enhanced protein microarray (OEPM) toward widespread commercial availability is mainly hampered by insufficient detection reproducibility. Here, we develop an OEPM platform with an order of magnitude optical enhancement induced by the interference effect. High assay reproducibility of the OEPM is achieved by optimizing the protein immobilization schemes, linking to the surface energy of the substrate, surfactant-tuned wetting ability, and the washing and drying dynamics. As a result, smearing-free and uniform spot arrays with a coefficient of variation less than 7% can be achieved. Furthermore, we demonstrate the assay performance of the OEPM by detecting five biomarkers, showing an order of magnitude higher sensitivity, many-fold higher throughput, and 10 times less analyte consumption than those of the commercial enzyme-linked immunosorbent assay kits. Our results provide new insight for improving the reproducibility of OEPMs toward practical and commercial diagnostic assays.

Critical assessment of relevant methods in the field of biosensors with direct optical detection based on fibers and waveguides using plasmonic, resonance, and interference effects

Direct optical detection has proven to be a highly interesting tool in biomolecular interaction analysis to be used in drug discovery, ligand/receptor interactions, environmental analysis, clinical diagnostics, screening of large data volumes in immunology, cancer therapy, or personalized medicine. In this review, the fundamental optical principles and applications are reviewed. Devices are based on concepts such as refractometry, evanescent field, waveguides modes, reflectometry, resonance and/or interference. They are realized in ring resonators; prism couplers; surface plasmon resonance; resonant mirror; Bragg grating; grating couplers; photonic crystals, Mach-Zehnder, Young, Hartman interferometers; backscattering; ellipsometry; or reflectance interferometry. The physical theories of various optical principles have already been reviewed in detail elsewhere and are therefore only cited. This review provides an overall survey on the application of these methods in direct optical biosensing. The "historical" development of the main principles is given to understand the various, and sometimes only slightly modified variations published as "new" methods or the use of a new acronym and commercialization by different companies. Improvement of optics is only one way to increase the quality of biosensors. Additional essential aspects are the surface modification of transducers, immobilization strategies, selection of recognition elements, the influence of non-specific interaction, selectivity, and sensitivity. Furthermore, papers use for reporting minimal amounts of detectable analyte terms such as value of mass, moles, grams, or mol/L which are difficult to compare. Both these essential aspects (i.e., biochemistry and the presentation of LOD values) can be discussed only in brief (but references are provided) in order to prevent the paper from becoming too long. The review will concentrate on a comparison of the optical methods, their application, and the resulting bioanalytical quality.

Plasma Fabrication and SERS Functionality of Gold Crowned Silicon Submicrometer Pillars

Sequential plasma processes combined with specific lithographic methods allow for the fabrication of advanced material structures. In the present work, we used self-assembled colloidal monolayers as lithographic structures for the conformation of ordered Si submicrometer pillars by reactive ion etching. We explored different discharge conditions to optimize the Si pillar geometry. Selected structures were further decorated with gold by conventional sputtering, prior to colloidal monolayer lift-off. The resulting structures consist of a gold crown, that is, a cylindrical coating on the edge of the Si pillar and a cavity on top. We analysed the Au structures in terms of electronic properties by using X-ray absorption spectroscopy (XAS) prior to and after post-processing with thermal annealing at 300 °C and/or interaction with a gold etchant solution (KI). The angular dependent analysis of the plasmonic properties was studied with Fourier transformed UV-vis measurements. Certain conditions were selected to perform a surface enhanced Raman spectroscopy (SERS) evaluation of these platforms with two model dyes, prior to confirming the potential interest for a well-resolved analysis of filtered blood plasma.

Ultrasensitive and simple fluorescence biosensor for detection of the mecA gene of Staphylococcus aureus by using an exonuclease III-assisted cascade signal amplification strategy

In this work, a label-free fluorescence biosensor for ultrasensitive and simple detection of the mecA gene of Staphylococcus aureus was proposed by using an exonuclease III (Exo III)-assisted cascade signal amplification strategy. The 3' end-extruding hairpin probe (HP) acted as the target recognition element and the caged G-quadruplex was used as the signal reporter. Without the mecA gene, the HP probe cannot be digested by Exo III, as the G-rich sequences are blocked in the stem of the HP probe. In the presence of the mecA gene, the hybridization of the mecA gene with the 3' end-extruding HP probe triggers the digestion reaction of Exo III, liberating the mecA gene and the mecA gene analogue. Both the released mecA gene and the mecA gene analogue can hybridize with other HP probes and activate another round of the cleavage reaction. Consequently, the released free G-quadruplex is "lit up" by N-methylmesoporphyrin IX (NMM), displaying a dramatically enhanced fluorescence intensity. This sensing platform showed a high sensitivity towards the mecA gene with a detection limit as low as 2.4 fM without any labelling, immobilization, or washing steps. The designed sensing system also exhibits excellent selectivity for the mecA gene in the presence of other interfering DNA sequences. Furthermore, the presented biosensor is robust and has been successfully applied for the detection of the mecA gene in a real food sample with satisfactory results. Owing to its simplicity, cost-effectiveness and ultrasensitivity, our proposed sensing strategy provides a promising platform for the detection of other genes by substituting the target-recognition element.

Fluorescence-based kinetic analysis of miniaturized protein microarrays

Ideal monitoring devices should enjoy a combination of characteristics, e.g. high sensitivity, multiplexing, portability, short time-to-result (TTR). Typically, no device meets all of these demands since some of them are contradictory, to some extent. Herein, we present a miniaturized platform based on fluorescent detection, which is sensitive, readily allows multiplexing, and allows real-time monitoring of the signal, thus allowing extraction of kinetic information as well as drastic reduction of TTR. This is achieved via miniaturization of active spots, integration with microfluidics, and algorithmic approaches. We validate its performance by comparing with evanescent field excitation, which obtains similar results, however without the addition of the necessary complex hardware.

Surface Plasmon Resonance Sensors on Raman and Fluorescence Spectroscopy

The performance of chemical reactions has been enhanced immensely with surface plasmon resonance (SPR)-based sensors. In this review, the principle and application of SPR sensors are introduced and summarized thoroughly. We introduce the mechanism of the SPR sensors and present a thorough summary about the optical design, including the substrate and excitation modes of the surface plasmons. Additionally, the applications based on SPR sensors are described by the Raman and fluorescence spectroscopy in plasmon-driven surface catalytic reactions and the measurement of refractive index sensing, especially.

Plasmonically amplified bioassay - Total internal reflection fluorescence vs. epifluorescence geometry

This paper investigates plasmonic amplification in two commonly used optical configurations for fluorescence readout of bioassays - epifluorescence (EPF) and total internal reflection fluorescence (TIRF). The plasmonic amplification in the EPF configuration was implemented by using crossed gold diffraction grating and Kretschmann geometry of attenuated total reflection method (ATR) was employed in the TIRF configuration. Identical assay, surface architecture for analyte capture, and optics for the excitation, collection and detection of emitted fluorescence light intensity were used in both TIRF and EPF configurations. Simulations predict that the crossed gold diffraction grating (EPF) can amplify the fluorescence signal by a factor of 10(2) by the combination of surface plasmon-enhanced excitation and directional surface plasmon-coupled emission in the red part of spectrum. This factor is about order of magnitude higher than that predicted for the Kretschmann geometry (TIRF) which only took advantage of the surface plasmon-enhanced excitation. When applied for the readout of sandwich interleukin 6 (IL-6) immunoassay, the plasmonically amplified EPF geometry designed for Alexa Fluor 647 labels offered 4-times higher fluorescence signal intensity compared to TIRF. Interestingly, both geometries allowed reaching the same detection limit of 0.4pM despite of the difference in the fluorescence signal enhancement. This is attributed to inherently lower background of fluorescence signal for TIRF geometry compared to that for EPF which compensates for the weaker fluorescence signal enhancement. The analysis of the inflammation biomarker IL-6 in serum at medically relevant concentrations and the utilization of plasmonic amplification for the fluorescence measurement of kinetics of surface affinity reactions are demonstrated for both EPF and TIRF readout.

A compact imaging spectroscopic system for biomolecular detections on plasmonic chips

In this study, we demonstrate a compact imaging spectroscopic system for high-throughput detection of biomolecular interactions on plasmonic chips, based on a curved grating as the key element of light diffraction and light focusing.

Total internal reflection fluorescence quantification of receptor pharmacology

Total internal reflection fluorescence (TIRF) microscopy has been widely used as a single molecule imaging technique to study various fundamental aspects of cell biology, owing to its ability to selectively excite a very thin fluorescent volume immediately above the substrate on which the cells are grown. However, TIRF microscopy has found little use in high content screening due to its complexity in instrumental setup and experimental procedures. Inspired by the recent demonstration of label-free evanescent wave biosensors for cell phenotypic profiling and drug screening with high throughput, we had hypothesized and demonstrated that TIRF imaging is also amenable to receptor pharmacology profiling. This paper reviews key considerations and recent applications of TIRF imaging for pharmacology profiling.

Long-range surface plasmons supported by a bilayer metallic structure for sensing applications

We show, both theoretically and experimentally, that long-range surface plasmons (LRSPs) are supported by asymmetric structure, consisting of a thin silver/gold bilayer metallic film sandwiched between a magnesium fluoride (i.e., MgF₂) buffer layer and a sensing medium (water). The geometrical parameters of the structure are optimized to yield efficient excitation of LRSPs by using transfer matrix method based on Fresnel reflection. The excitation of LRSPs was performed by using a custom-made automated optical setup based on angular interrogation with the precision of 0.01°. We demonstrate that the bimetallic asymmetric structure achieves better minimum reflectivity resolution than monometallic (gold) asymmetric structure. Finally, figures of merit are compared for bimetallic, monometallic, and conventional SPR structures, and we found that the bimetallic asymmetric structure provides a higher figure of merit; e.g., more than double for monometallic LRSP configuration and 8 times as compared to the conventional surface plasmon resonance sensor.

An integrated microspectrometer for localised multiplexing measurements

We describe the development of an integrated lensed Arrayed Waveguide Grating (AWG) microspectrometer for localized multiplexing fluorescence measurements. The device, which has a footprint that is only 1 mm wide and 1 cm long, is capable of spectroscopic measurements on chip. Multiple fluorescence signals were measured simultaneously based upon simple intensity readouts from a CCD camera. We also demonstrate the integration of the AWG spectrometer with a microfluidic platform using a lensing function to confine the beam shape for focused illumination. This capability enhances signal collection, gives better spatial resolution, and provides a route for the analysis of small volume samples (e.g. cells) in flow. To show these capabilities we developed a novel "bead-AWG" platform with which we demonstrate localized multiplexed fluorescence detection either simultaneously or successively. Such an integrated system provides the basis for a portable system capable of optical detection of multi-wavelength fluorescence from a single defined location.

Qualifying label components for effective biosensing using advanced high-throughput SEIRA methodology

The multiplexed SEIRA analysis of antibody-functionalized NP biolabels that can be exploited for specific assay platforms in view of high-performance readout.

A simple cyanide sensing probe based on Ag/Fe3O4nanoparticles

The first direct approach in ultra-trace cyanide determination through a simple, selective and rapid reaction by simply-synthesized recyclable Ag/Fe₃O₄nanostructures.

A fluorescence resonance energy transfer (FRET) biosensor based on graphene quantum dots (GQDs) and gold nanoparticles (AuNPs) for the detection of mecA gene sequence of Staphylococcus aureus

In this work, a novel fluorescence resonance energy transfer (FRET) biosensor based on graphene quantum dots (GQDs) and gold nanoparticles (AuNPs) pairs was developed for Staphylococcus aureus specific gene sequence detection. This FRET biosensor platform was realized by immobilization of capture probes on GQDs and conjugation of reporter probes on AuNPs. Target oligos then co-hybridized with capture probes and reporter probes to form a sandwich structure which brought GQDs and AuNPs to close proximity to trigger FRET effect. The fluorescence signals before and after addition of targets were measured and the fluorescence quenching efficiency could reach around 87% with 100 nM target oligo. The limit of detection (LOD) of this FRET biosensor was around 1 nM for S.aureus gene detection. Experiments with both single-base mismatched oligos and double-base mismatched oligos demonstrated the good sequence selectivity of this FRET biosensor.

Optimization of multiple-slot waveguides for biochemical sensing

In this work, we analyze and optimize an optical biochemical sensor using silicon multiple-slot waveguides. The rigorous optimization procedure considers parameters such as ridge width, slot width, the number of slots, and the effect of residual silicon left at the bottom of the slot region. These parameters are then optimized using a figure of merit to achieve the highest possible sensitivity to bulk and surface changes in the upper cladding of the sensor. The multiple-slot structure is then studied in a bend configuration in order to construct ring-resonator-based sensors. A bulk sensitivity of 912 nm/refractive index unit is achieved for a change in bulk refractive index, which is three times better than single-slot waveguides.

A polymeric waveguide resonant mirror (RM) device for detection in microfluidic flow cells

A novel resonant mirror (RM) device, which consisted of silica sol-gel spacer and polystyrene waveguide layers on a standard microscope slide glass substrate, was developed in this work. The device was successfully used to measure the absorption spectrum of methylene blue with a limit of detection (LOD) of at most 20.8 μM at 635 nm and a minimum detectable absorption coefficient of 0.94 cm(-1). A RM device consisting of dye-doped polystyrene waveguide layer was then demonstrated to be suitable to monitor antibody-antigen (in this case, anti-IgG and IgG) binding and was shown to be capable of detecting at least 100 nM IgG. The sensitivity of the device was estimated to be 17.27° per refractive index unit (RIU), which corresponds to a resolution of 1.45 × 10(-4) RIU for the set-up used. The RM device developed in this work can be easily integrated with microfluidic devices to identify and quantify (bio) chemical species by either absorption spectroscopy or measurement of effective optical thickness or both. In addition, the device was fabricated using a simple and low cost fabrication technique, spin coating. Hence, it can be easily mass produced.

Effect of biointerfacing linker chemistries on the sensitivity of silicon nanowires for protein detection

Point-of-care diagnostics show promise in removing reliance on centralized lab testing facilities and may help increase both the survival rate for infectious diseases as well as monitoring of chronic illnesses. CMOS compatible diagnostic platforms are currently being considered as possible solutions as they can be easily miniaturized and can be cost-effective. Top-down fabricated silicon nanowires are a CMOS-compatible technology which have demonstrated high sensitivities in detecting biological analytes, such as proteins, DNA, and RNA. However, the reported response of nanowires to these analytes has varied widely since several different functionalization protocols have been attempted with little characterization and comparison. Here we report protocols for fabrication and functionalization of silicon nanowires which yield highly stable nanowires in aqueous solutions and limits of detection to ∼1 pg/mL of the model protein used in the study. A thorough characterization was done into optimizing the release of the silicon nanowires using combined dry and wet etch techniques, which yielded nanowires that could be directly compared to increase output statistics. Moreover, a range of different linker chemistries were tried for reacting the primary antibody, and its response to target and nonspecific antigens, with polyethylene glycol based linker BS(PEG)5 providing the best response. Consequently, this chemistry was used to characterize different oxide thicknesses and their responses to the mouse IgG antigen, which with the smallest oxide thickness yielded 0.1-1 pg/mL limits of detection and a dynamic range over 3 orders of magnitude.

A novel handheld fluorescent microarray reader for point-of-care diagnostic

A novel handheld optical sensor for quantification of fluorescent microarrays, the so-called portMD-113 has been developed. On the surface of a planar waveguide, the spots of different fluorescently labeled biological complexes are excited by the evanescent field of the guided light. The emitted fluorescence signals of the spots are independently and simultaneously detected applying our system, which consists of a pinehole array, a microlens array, an interference filter and a detector array. As it is demonstrated in comparative measurements, the detection limit of this sensor is close to that of commercial top microarray readers, e.g. of modern laser scanners, while it has remarkable and important advantages over them. Namely, the device comprises only a few low-cost, lightweight and small components without applying any moving or energy-intensive elements, which results in turn in a commercially competitive, handheld and compact design and in the possibility to be supplied simply by a battery or a personal computer. These advantageous properties open prospects e.g. for point-of-care medical checks, as well.

Thymine/adenine diblock-oligonucleotide monolayers and hybrid brushes on gold: a spectroscopic study

BACKGROUND

The establishment of spectroscopic analysis techniques for complex, surface-bound biological systems is an important step toward the further application of these powerful experimental tools to new questions in biology and medicine.

METHODS

We use a combination of the complementary spectroscopic techniques of X-ray photoelectron spectroscopy, Infrared reflection-absorption spectroscopy, and near-edge x-ray absorption fine structure spectroscopy to monitor the composition and molecular orientation in adenine/thymine diblock oligonucleotide films and their hybridized brushes on gold.

RESULTS

We demonstrate that the surface-bound probe molecules, consisting of a binding adenine block, d(A), and a sensing thymine block, d(T), deviate from the ideal L-shape model due to the internal intra- and intermolecular hybridization. This effect becomes more pronounced with increasing length of the d(A) block. Nevertheless, these films were found to hybridize well with the complementary target d(A) strands, especially if they were treated in advance to reduce internal interaction between the molecules. In spite of the structural complexity of these films, the hybridization efficiency correlated well with the potential accessibility of the sensing d(T) blocks, defined by their lateral spacing.

CONCLUSIONS

These findings are a good demonstration of the strength of multi-technique spectroscopic analysis when applied to assemblies of biological molecules intrinsically prone to complex interactions.

A virus biosensor with single virus-particle sensitivity based on fluorescent vesicle labels and equilibrium fluctuation analysis

Biosensors allowing for the rapid and sensitive detection of viral pathogens in environmental or clinical samples are urgently needed to prevent disease outbreaks and spreading. We present a bioanalytical assay for the detection of whole viral particles with single virus sensitivity. Specifically, we focus on the detection of human norovirus, a highly infectious virus causing gastroenteritis. In our assay configuration, virus-like particles are captured onto a supported lipid bilayer containing a virus-specific glycolipid and detected after recognition by a glycolipid-containing fluorescent vesicle. Read-out is performed after illumination of the vesicle labels by total internal reflection fluorescence microscopy. This allows for visualization of individual vesicles and for recording of their binding kinetics under equilibrium conditions (equilibrium fluctuation analysis), as demonstrated previously. In this work we extend the concept and demonstrate that this simple assay setup can be used as a bioanalytical assay for the detection of virus particles at a limit of detection of 16 fM. Furthermore, we demonstrate how the analysis of the single vesicle-virus-like particle interaction dynamics can contribute to increase the accuracy and sensitivity of the assay by discriminating specific from non-specific binding events. This method is suggested to be generally applicable, provided that these events display different interaction kinetics.

SERS-based immunoassay using a gold array-embedded gradient microfluidic chip

Here we report the development of a programmable and fully automatic gold array-embedded gradient microfluidic chip that integrates a gradient microfluidic device with gold-patterned microarray wells. This device provides a convenient and reproducible surface-enhanced Raman scattering (SERS)-based immunoassay platform for cancer biomarkers. We used hollow gold nanospheres (HGNs) as SERS agents because of their highly sensitive and reproducible characteristics. The utility of this platform was demonstrated by the quantitative immunoassay of alpha-fetoprotein (AFP) model protein marker. Our proposed SERS-based immunoassay platform has many advantages over other previously reported SERS immunoassay methods. The tedious manual dilution process of repetitive pipetting and inaccurate dilution is eliminated with this process because various concentrations of biomarker are automatically generated by microfluidic gradient generators with N cascade-mixing stages. The total assay time from serial dilution to SERS detection takes less than 60 min because all of the experimental conditions for the formation and detection of immunocomplexes can be automatically controlled inside the exquisitely designed microfluidic channel. Thus, this novel SERS-based microfluidic assay technique is expected to be a powerful clinical tool for fast and sensitive cancer marker detection.

Ligand-receptor interaction platforms and their applications for drug discovery

INTRODUCTION

The study of drug-target interactions is essential for the understanding of biological processes and for the efforts to develop new therapeutic molecules. Increased ligand-binding assays have coincided with the advances in reagents, detection and instrumentation technologies, the expansion in therapeutic targets of interest, and the increasingly recognized importance of biochemical aspects of drug-target interactions in determining the clinical performance of drug molecules. Nowadays, ligand-binding assays can determine every aspect of many drug-target interactions.

AREAS COVERED

Given that ligand-target interactions are very diverse, the author has decided to focus on the binding of small molecules to protein targets. This article first reviews the key biochemical aspects of drug-target interactions, and then discusses the detection principles of various ligand-binding techniques in the context of their primary applications for drug discovery and development.

EXPERT OPINION

Equilibrium-binding affinity should not be used as a solo indicator for the in vivo pharmacology of drugs. The clinical relevance of drug-binding kinetics demands high throughput kinetics early in drug discovery. The dependence of ligand binding and function on the conformation of targets necessitates solution-based and whole cell-based ligand-binding assays. The increasing need to examine ligand binding at the proteome level, driven by the clinical importance of the polypharmacology of ligands, has started to make the structure-based in silico binding screen an indispensable technique for drug discovery and development. Integration of different ligand-binding assays is important to improve the efficiency of the drug discovery and development process.

Using complementary acoustic and optical techniques for quantitative monitoring of biomolecular adsorption at interfaces

The great wealth of different surface sensitive techniques used in biosensing, most of which claim to measure adsorbed mass, can at first glance look unnecessary. However, with each technique relying on a different transducer principle there is something to be gained from a comparison. In this tutorial review, different optical and acoustic evanescent techniques are used to illustrate how an understanding of the transducer principle of each technique can be exploited for further interpretation of hydrated and extended polymer and biological films. Some of the most commonly used surface sensitive biosensor techniques (quartz crystal microbalance, optical waveguide spectroscopy and surface plasmon resonance) are briefly described and five case studies are presented to illustrate how different biosensing techniques can and often should be combined. The case studies deal with representative examples of adsorption of protein films, polymer brushes and lipid membranes, and describe e.g., how to deal with strongly vs. weakly hydrated films, large conformational changes and ordered layers of biomolecules. The presented systems and methods are compared to other representative examples from the increasing literature on the subject.

Interferometric silicon biochips for label and label-free DNA and protein microarrays

Protein and DNA microarrays hold the promise to revolutionize the field of molecular diagnostics. Traditional microarray applications employ labeled detection strategies based on the use of fluorescent and chemiluminescent secondary antibodies. However, the development of high throughput, sensitive, label-free detection techniques is attracting attention as they do not require labeled reactants and provide quantitative information on binding kinetics. In this article, we will provide an overview of the recent author's work in label and label-free sensing platforms employing silicon/silicon oxide (Si/SiO(2)) substrates for interferometric and/or fluorescence detection of microarrays. The review will focus on applications of Si/SiO(2) with controlled oxide layers to (i) enhance the fluorescence intensity by optical interferences, (ii) quantify with sub-nanometer accuracy the axial locations of fluorophore-labeled probes tethered to the surface, and (iii) detect protein-protein interactions label free. Different methods of biofunctionalization of the sensing surface will be discussed. In particular, organosilanization reactions for monodimensional coatings and polymeric coatings will be extensively reviewed. Finally, the importance of calibration of protein microarrays through the dual use of labeled and label-free detection schemes on the same chip will be illustrated.

A general method to determine ionization constants of responsive polymer thin films

A general method has been developed to determine the ionization constants of polymer thin films based on the stimuli-responsiveness of the polymer. Robust polymer films were fabricated on silicon wafers and gold slides using perfluorophenyl azide (PFPA) as the coupling agent. The ionization constants were measured by a number of techniques including ellipsometry, dynamic contact angle goniometry, and surface plasmon resonance imaging (SPRi). Using poly(4-vinylpyridine) (P4VP) as the model system, P4VP thin films were fabricated and the ionization constants of the films were measured taking advantage of the pH responsive property of the polymer. The pK(a) determined by ellipsometry, ~4.0, reflects the swelling of the polymer film in response to pH. The pK(a) value calculated from the dynamic contact angle measurements, ~5.0, relies on the change in hydrophilicity/hydrophobicity of the films as the polymer undergoes protonation/deprotonation. The pK(a) value measured by SPRi, ~4.9, monitors in situ the change of refractive index of the polymer thin film as it swells upon protonation. This was the first example where SPRi was used to measure the ionization constants of polymers.

Contact CMOS imaging of gaseous oxygen sensor array

We describe a compact luminescent gaseous oxygen (O₂) sensor microsystem based on the direct integration of sensor elements with a polymeric optical filter and placed on a low power complementary metal-oxide semiconductor (CMOS) imager integrated circuit (IC). The sensor operates on the measurement of excited-state emission intensity of O₂-sensitive luminophore molecules tris(4,7-diphenyl-1,10-phenanthroline) ruthenium(II) ([Ru(dpp)₃]²⁺) encapsulated within sol-gel derived xerogel thin films. The polymeric optical filter is made with polydimethylsiloxane (PDMS) that is mixed with a dye (Sudan-II). The PDMS membrane surface is molded to incorporate arrays of trapezoidal microstructures that serve to focus the optical sensor signals on to the imager pixels. The molded PDMS membrane is then attached with the PDMS color filter. The xerogel sensor arrays are contact printed on top of the PDMS trapezoidal lens-like microstructures. The CMOS imager uses a 32 × 32 (1024 elements) array of active pixel sensors and each pixel includes a high-gain phototransistor to convert the detected optical signals into electrical currents. Correlated double sampling circuit, pixel address, digital control and signal integration circuits are also implemented on-chip. The CMOS imager data is read out as a serial coded signal. The CMOS imager consumes a static power of 320 µW and an average dynamic power of 625 µW when operating at 100 Hz sampling frequency and 1.8 V DC. This CMOS sensor system provides a useful platform for the development of miniaturized optical chemical gas sensors.

Detection of DNA targets hybridized to solid surfaces using optical images of liquid crystals

In this paper, we report a method of detecting DNA targets hybridized to a solid surface by using liquid crystals (LC). The detection principle is based on different interference colors of LC supported on surfaces decorated with single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA). However, the contrast between the ssDNA and dsDNA is not obvious, unless DNA-streptavidin complexes are introduced to the dsDNA to increase the surface mass density. Two different approaches of introducing streptavidin to the system are studied and compared. We find that by premixing the biotin-labeled DNA targets with streptavidin prior to the DNA hybridization, branched-streptavidin complexes are formed and clear LC signal can be observed. This LC-based DNA detection principle represents an important step toward the development of a simple, instrument- and fluorophore-free DNA detection method.

Evaluation of photochemically immobilized poly(2-ethyl-2-oxazoline) thin films as protein-resistant surfaces

Poly(2-ethyl-2-oxazoline) (PEOX) of various molecular weights were covalently immobilized on silicon wafers and gold slides to form protein-resistant surfaces via a fast and general photocoupling chemistry based on the CH insertion reaction of light-activated perfluorophenyl azide (PFPA). The thicknesses of the immobilized PEOX films ranged from 23 to 80 Å for molecular weight of 5000 to 500,000, and the grafting density reached 3.2 × 10(-3) Å(-2) for PEOX 5000. The protein-resistant property of the films was studied using bovine serum albumin (BSA) by fluorescence imaging, ellipsometry, and surface plasmon resonance imaging (SPRi). The fluorescence imaging and ellipsometry studies showed the largest amount of BSA adsorbed on PEOX 5000 and the smallest on PEOX 500,000. This was consistent with the kinetic analysis of BSA adsorption by SPRi showing that PEOX 5000 exhibited the fastest association rate and the slowest dissociation rate whereas PEOX 500,000 had the slowest association rate and the fastest dissociation rate. The PEOX film was then applied in the fabrication of carbohydrate microarrays to reduce the nonspecific adsorption of lectins and thus the background noises. Results showed that the microarray signals were significantly enhanced when the PEOX film was used.

pH dependent elasticity of polystyrene-block-poly(acrylic acid) vesicle shell membranes by atomic force microscopy

We assess the elastic properties of PS-b-PAA vesicle membranes under different pH values by AFM force measurements. We find that based on the shell deformation theory, the values of the estimated apparent Young's modulus of the vesicle membranes decrease as the pH of the solution increases. The onset of the decrease of E coincides with the surface pK(a) determined from ζ-potential measurements. This decrease of E at higher pH is attributed to electrostatic repulsion between the deprotonated PAA chains resulting in the thinning of the vesicle membrane.

Protein microarray biosensors based on imaging ellipsometry techniques and their applications

After years of development, biosensors based on imaging ellipsometry and biosensors based on total internal reflection imaging ellipsometry have been successfully implemented in various engineering systems. Their experimental setups, detection principles, and biological and clinical applications are briefly reviewed.

Detecting DNA targets through the formation of DNA/CTAB complex and its interactions with liquid crystals

In this paper, we report the formation of a DNA/cetyl trimethylammonium bromide (CTAB) complex on a solid surface and its interaction with a thin layer of liquid crystals (LC) supported on the surface. Our results show that when the surface is decorated with DNA only, the LC gives a bright image, but when the surface is decorated with the DNA/CTAB complex, the LC becomes dark when the surface density of CTAB is above 5.25 ± 0.13 × 10(13)/cm(2). To exploit this phenomenon for detecting DNA targets, we used a surface decorated with electroneutral PNA probes for capturing DNA targets, and then treated the surface with 0.1 mM of CTAB. In the presence of DNA targets, a PNA/DNA/CTAB complex is formed and that leads to a dark image on the thin layer of the LC supported on the surface. Moreover, DNA targets with a complementary, 1-base mismatch and non-complementary sequence can be differentiated by using this method. This study provides a new principle for the label-free detection of DNA targets without any fluorescent labels.

Review of transducer principles for label-free biomolecular interaction analysis

Label-free biomolecular interaction analysis is an important technique to study the chemical binding between e.g., protein and protein or protein and small molecule in real-time. The parameters obtained with this technique, such as the affinity, are important for drug development. While the surface plasmon resonance (SPR) instruments are most widely used, new types of sensors are emerging. These developments are generally driven by the need for higher throughput, lower sample consumption or by the need of complimentary information to the SPR data. This review aims to give an overview about a wide range of sensor transducers, the working principles and the peculiarities of each technology, e.g., concerning the set-up, sensitivity, sensor size or required sample volume. Starting from optical technologies like the SPR and waveguide based sensors, acoustic sensors like the quartz crystal microbalance (QCM) and the film bulk acoustic resonator (FBAR), calorimetric and electrochemical sensors are covered. Technologies long established in the market are presented together with those newly commercially available and with technologies in the early development stage. Finally, the commercially available instruments are summarized together with their sensitivity and the number of sensors usable in parallel and an outlook for potential future developments is given.

Fluorescent vesicles for signal amplification in reverse phase protein microarray assays

Developments in microarray technology promise to lead to great advancements in the biomedical and biological field. However, implementation of these analytical tools often relies on signal amplification strategies that are essential to reach the sensitivity levels required for a variety of biological applications. This is true especially for reverse phase arrays where a complex biological sample is directly immobilized on the chip. We present a simple and generic method for signal amplification based on the use of antibody-tagged fluorescent vesicles as labels for signal generation. To assess the gain in assay sensitivity, we performed a model assay for the detection of rabbit immunoglobulin G (IgG) and compared the limit of detection (LOD) of the vesicle assay with the LOD of a conventional assay performed with fluorescent reporter molecules. We evaluated the improvements for two fluorescence-based transduction setups: a high-sensitivity microarray reader (ZeptoREADER) and a conventional confocal scanner. In all cases, our strategy led to an increase in sensitivity. However, gain in sensitivity widely depended on the type of illumination; whereas an approximately 2-fold increase in sensitivity was observed for readout based on evanescent field illumination, the contribution was as high as more than 200-fold for confocal scanning.

CMOS Imaging of Temperature Effects on Pin-Printed Xerogel Sensor Microarrays

In this paper, we study the effect of temperature on the operation and performance of a xerogel-based sensor microarrays coupled to a complementary metal-oxide semiconductor (CMOS) imager integrated circuit (IC) that images the photoluminescence response from the sensor microarray. The CMOS imager uses a 32 × 32 (1024 elements) array of active pixel sensors and each pixel includes a high-gain phototransistor to convert the detected optical signals into electrical currents. A correlated double sampling circuit and pixel address/digital control/signal integration circuit are also implemented on-chip. The CMOS imager data are read out as a serial coded signal. The sensor system uses a light-emitting diode to excite target analyte responsive organometallic luminophores doped within discrete xerogel-based sensor elements. As a proto type, we developed a 3 × 3 (9 elements) array of oxygen (O2) sensors. Each group of three sensor elements in the array (arranged in a column) is designed to provide a different and specific sensitivity to the target gaseous O2 concentration. This property of multiple sensitivities is achieved by using a mix of two O2 sensitive luminophores in each pin-printed xerogel sensor element. The CMOS imager is designed to be low noise and consumes a static power of 320.4 μW and an average dynamic power of 624.6 μW when operating at 100-Hz sampling frequency and 1.8-V dc power supply.

Fabrication and anti-fouling properties of photochemically and thermally immobilized poly(ethylene oxide) and low molecular weight poly(ethylene glycol) thin films

Poly(ethylene oxide) (PEO) and low molecular weight poly(ethylene glycol) (PEG) were covalently immobilized on silicon wafers and gold films by way of the CH insertion reaction of perfluorophenyl azides (PFPAs) by either photolysis or thermolysis. The immobilization does not require chemical derivatization of PEO or PEG, and polymers of different molecular weights were successfully attached to the substrate to give uniform films. Microarrays were also generated by printing polymer solutions on PFPA-functionalized wafer or Au slides followed by light activation. For low molecular weight PEG, the immobilization was highly dependent on the quality of the film deposited on the substrate. While the spin-coated and printed PEG showed poor immobilization efficiency, thermal treatment of the PEG melt on PFPA-functionalized surfaces resulted in excellent film quality, giving, for example, a grafting density of 9.2×10(-4)Å(-2) and an average distance between grafted chains of 33Å for PEG 20,000. The anti-fouling property of the films was evaluated by fluorescence microscopy and surface plasmon resonance imaging (SPRi). Low protein adsorption was observed on thermally-immobilized PEG whereas the photoimmobilized PEG showed increased protein adsorption. In addition, protein arrays were created using polystyrene (PS) and PEG based on the differential protein adsorption of the two polymers.