Label-free molecular interaction determinations with nanoscale interferometry

Gold nanoparticle-decorated fluorine-doped tin oxide substrate for sensitive label-free OIRD microarray chips

Oblique incidence reflectance difference (OIRD) is an emerging technique enabling real-time and label-free detection of bio-affinity binding events on microarrays. The interfacial architecture of the microarray chip is critical to the performance of OIRD detection. In this work, a sensitive label-free OIRD microarray chip was developed by using gold nanoparticle-decorated fluorine-doped tin oxide (AuNPs-FTO) slides as a chip substrate. This AuNPs-FTO chip demonstrates a higher signal-to-noise ratio and improved sensitivity compared to that built on FTO glass, showing a detection limit of as low as 10 ng mL-1 for the model target, HRP-conjugated streptavidin. On-chip ELISA experiments and optical calculations suggest that the enhanced performance is not only due to the higher probe density enabling a high capture efficiency toward the target, but most importantly, the AuNP layer arouses optical interference to improve the intrinsic sensitivity of OIRD. This work provides an effective strategy for constructing OIRD-based microarray chips with enhanced sensitivity, and may help extend their practical applications in various fields.

Label-free OIRD microarray chips with a nanostructured sensing interface: enhanced sensitivity and mechanism

Oblique-incidence reflectivity difference (OIRD) is a novel optical technique for protein microarray detection with the characteristics of being real-time, label-free, high-throughput and compatible with arbitrary chip substrates. It is necessary yet challenging to improve the sensitivity of the OIRD microarray and gain a clear understanding of the enhancement mechanism for practical applications. In this study, we report a microarray chip specifically designed for OIRD to improve its sensitivity by using an electrochemically etched nanostructured fluorine-doped tin oxide (FTO) slide as the substrate. Compared with chips printed on a conventional glass slide and pristine FTO, the OIRD sensitivity and signal-to-noise ratio of this microarray are significantly improved, reaching a limit of detection (LOD) as low as 50 ng mL^-1 for the streptavidin target in 10% human serum, which is one order of magnitude lower than that of the glass-based chip. On-chip ELISA and theoretical calculation reveal that the enhanced sensitivity is not only because of its higher capture efficiency towards the target, but also benefits from the optical enhancement enabled by its unique nanostructured sensing interface. This work provides a new universal strategy for designing high performance OIRD-based chips via rational interfacial engineering, thus paving the way to a label-free OIRD immunoassay and real-time analysis of biomolecular interactions.

An Analysis of Semicircular Channel Backscattering Interferometry through Ray Tracing Simulations

Recent backscattering interferometry studies utilise a single channel microfluidic system, typically approximately semicircular in cross-section. Here, we present a complete ray tracing model for on-chip backscattering interferometry with a semicircular cross-section, including the dependence upon polarisation and angle of incidence. The full model is validated and utilised to calculate the expected fringe patterns and sensitivities observed under both normal and oblique angles of incidence. Comparison with experimental data from approximately semicircular channels using the parameters stated shows that they cannot be explained using a semicircular geometry. The disagreement does not impact on the validity of the experimental data, but highlights that the optical mechanisms behind the various modalities of backscattering interferometry would benefit from clarification. From the analysis presented here, we conclude that for reasons of ease of analysis, data quality, and sensitivity for a given radius, capillary-based backscattering interferometry affords numerous benefits over on-chip backscattering interferometry.

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.

Laser interferometry of the hydrolytic changes in protein solutions: the refractive index and hydration shells

Using an original laser interferometer of enhanced sensitivity, an increase in the refractive index of a protein solution was observed during the reaction of proteolysis catalyzed by pepsin. The increase in the refractive index of the protein solution at a concentration of 4 mg/ml was [Formula: see text] for bovine serum albumin and [Formula: see text] for lysozyme. The observed effect disproves the existing idea that the refractive index of protein solutions is determined only by their amino acid composition and concentration. It is shown that the refractive index also depends on the state of protein fragmentation. A mathematical model of proteolysis and a real-time method for estimating the state of protein hydration based on the measurement of refractive index during the reaction are proposed. A good agreement between the experimental and calculated time dependences of the refractive index shows that the growth of the surface of protein fragments and the change in the number of hydration cavities during proteolysis can be responsible for the observed effect.

Control of the Nucleotide Cycle in Photoreceptor Cell Extracts by Retinal Degeneration Protein 3

Retinal degeneration protein 3 (RD3) is crucial for photoreceptor cell survival and linked to Leber Congenital Amaurosis type 12 (LCA12), a hereditary retinal disease in humans. RD3 inhibits photoreceptor guanylate cyclases GC-E and GC-F and is involved in transport of GCs from the inner to the outer segments. Otherwise, its role in photoreceptor physiology is poorly understood. Here, we describe a new function of RD3. Purified RD3 evoked an increase in guanylate kinase activity, an enzyme that is involved in the nucleotide cycle in photoreceptors. We demonstrate a direct interaction between guanylate kinase and RD3 using back-scattering interferometry and show by immunohistochemistry of mouse retina sections that RD3 and guanylate kinase co-localize in photoreceptor inner segments and to a lesser extent in the outer plexiform layer. Our findings point toward a more complex function of RD3 in photoreceptors. The RD3 – guanylate kinase interaction may also play a role in other cellular systems, while the GC – RD3 interaction is exclusive to photoreceptors.

Label-free quantification of calcium-sensor targeting to photoreceptor guanylate cyclase and rhodopsin kinase by backscattering interferometry

Quantification of protein binding to membrane proteins is challenging and a limited set of methods is available to study such systems. Here we employed backscattering interferometry (BSI), a free-solution label-free method with high sensitivity, to quantify the interaction of neuronal Ca²⁺-Sensor proteins with their targets operating in phototransduction. We tested direct binding of guanylate cyclase–activating proteins (GCAP1 and GCAP2) to their membrane target guanylate cyclase 1. The regulatory mechanism of GCAPs including their binding interface in the target is unresolved. Here we used a label-free, free-solution assay method based on BSI to determine binding constants of GCAP1 and GCAP2 to the full-length membrane-bound guanylate cyclase type 1. GCAP1 and GCAP2 bound to different regions on the target guanylate cyclase with submicromolar affinity (apparent K_D-values of 663 ± 121 nM and 231 ± 63 nM for Ca²⁺-free GCAP1 and GCAP2, respectively). A guanylate cyclase construct containing the juxta-membrane and kinase homology domain harbored an exclusive binding site for GCAP1 with similar affinities as the full-length protein, whereas GCAP2 did not bind to this region. We provide a model in which GCAP1 and GCAP2 do not share a single binding site to the target, thus cannot exchange upon fluctuating Ca²⁺ levels.

Systems for multiplexing homogeneous immunoassays

High-throughput multiplex protein biomarker assays continue to gain significance in the fields of biomarker discovery and drug development, due to their economical use of not only the precious clinical biological samples but also expensive reagents. Among these platforms, homogeneous multiplex systems have potential for short assay run times and cost-effective reagent consumptions. However, these systems must overcome challenges of signal cross talk and biochemical cross-reactivity. Despite these obstacles, several homogeneous multiplex immunoassays have been demonstrated. These include fluorescent polarization, fluorescent resonance energy transfer with quantum dots or graphene, luminescent oxygen-channeling immunoassay coupled with aqueous two-phase systems and DNA proximity assays. The balance between speed/simplicity and high multiplexing and robustness of these homogeneous multiplex immunoassays are discussed in this review.

Trimerization of the HIV Transmembrane Domain in Lipid Bilayers Modulates Broadly Neutralizing Antibody Binding

The membrane-proximal external region (MPER) of HIV gp41 is an established target of antibodies that neutralize a broad range of HIV isolates. To evaluate the role of the transmembrane (TM) domain, synthetic MPER-derived peptides were incorporated into lipid nanoparticles using natural and designed TM domains, and antibody affinity was measured using immobilized and solution-based techniques. Peptides incorporating the native HIV TM domain exhibit significantly stronger interactions with neutralizing antibodies than peptides with a monomeric TM domain. Furthermore, a peptide with a trimeric, three-helix bundle TM domain recapitulates the binding profile of the native sequence. These studies suggest that neutralizing antibodies can bind the MPER when the TM domain is a three-helix bundle and this presentation could influence the binding of neutralizing antibodies to the virus. Lipid-bilayer presentation of viral antigens in Nanodiscs is a new platform for evaluating neutralizing antibodies.

A smart device for label-free and real-time detection of gene point mutations based on the high dark phase contrast of vapor condensation

A smart device for label-free and real-time detection of gene point mutation-related diseases was developed based on the high dark phase contrast of vapor condensation. The main components of the device included a Peltier cooler and a mini PC board for image processing. Heat from the hot side of the Peltier cooler causes the fluid in a copper chamber to evaporate, and the vapor condenses on the surface of a microarray chip placed on the cold side of the cooler. The high dark phase contrast of vapor condensation relative to the analytes on the microarray chip was explored. Combined with rolling circle amplification, the device visualizes less-to-more hydrophilic transitions caused by gene trapping and DNA amplification. A lung cancer gene point mutation was analysed, proving the high selectivity and multiplex analysis capability of this low-cost device.

Toward rapid, high-sensitivity, volume-constrained biomarker quantification and validation using backscattering interferometry

Realizing personalized medicine, which promises to enable early disease detection, efficient diagnostic staging, and therapeutic efficacy monitoring, hinges on biomarker quantification in patient samples. Yet, the lack of a sensitive technology and assay methodology to rapidly validate biomarker candidates continues to be a bottleneck for clinical translation. In our first direct and quantitative comparison of backscattering interferometry (BSI) to fluorescence sensing by ELISA, we show that BSI could aid in overcoming this limitation. The analytical validation study was performed against ELISA for two biomarkers for lung cancer detection: Cyfra 21-1 and Galectin-7. Spiked serum was used for calibration and comparison of analytical figures of merit, followed by analysis of blinded patient samples. Using the ELISA antibody as the probe chemistry in a mix-and-read assay, BSI provided significantly lower detection limits for spiked serum samples with each of the biomarkers. The limit of quantification (LOQ) for Cyrfa-21-1 was measured to be 230 pg/mL for BSI versus 4000 pg/mL for ELISA, and for Galectin-7, it was 13 pg/mL versus 500 pg/mL. The coefficient of variation for 5 day, triplicate determinations was <15% for BSI and <10% for ELISA. The two techniques correlated well, ranging from 3-29% difference for Cyfra 21-1 in a blinded patient sample analysis. The label-free and free-solution operation of BSI allowed for a significant improvement in analysis speed, with greater ease, improved LOQ values, and excellent day-to-day reproducibility. In this unoptimized format, BSI required 5.5-fold less sample quantity needed for ELISA (a 10 point calibration curve measured in triplicate required 36 μL of serum for BSI vs 200 μL for ELISA). The results indicate that the BSI platform can enable rapid, sensitive analytical validation of serum biomarkers and should significantly impact the validation bottleneck of biomarkers.

Real-time study of protein adsorption kinetics in porous silicon

This paper presents an optical method for real-time monitoring of protein adsorption using porous silicon self-supported microcavities as a label-free detection platform. The study combines an experimental approach with a physical model for the adsorption process. The proposed model agrees well with experimental observations, and provides information about the kinetics of diffusion and adsorption of proteins within the pores, which will be useful for future experimental designs.

Protein immobilization techniques for microfluidic assays

Microfluidic systems have shown unequivocal performance improvements over conventional bench-top assays across a range of performance metrics. For example, specific advances have been made in reagent consumption, throughput, integration of multiple assay steps, assay automation, and multiplexing capability. For heterogeneous systems, controlled immobilization of reactants is essential for reliable, sensitive detection of analytes. In most cases, protein immobilization densities are maximized, while native activity and conformation are maintained. Immobilization methods and chemistries vary significantly depending on immobilization surface, protein properties, and specific assay goals. In this review, we present trade-offs considerations for common immobilization surface materials. We overview immobilization methods and chemistries, and discuss studies exemplar of key approaches-here with a specific emphasis on immunoassays and enzymatic reactors. Recent "smart immobilization" methods including the use of light, electrochemical, thermal, and chemical stimuli to attach and detach proteins on demand with precise spatial control are highlighted. Spatially encoded protein immobilization using DNA hybridization for multiplexed assays and reversible protein immobilization surfaces for repeatable assay are introduced as immobilization methods. We also describe multifunctional surface coatings that can perform tasks that were, until recently, relegated to multiple functional coatings. We consider the microfluidics literature from 1997 to present and close with a perspective on future approaches to protein immobilization.

Label-free microcavity biosensors: steps towards personalized medicine

Personalized medicine has the potential to improve our ability to maintain health and treat disease, while ameliorating continuously rising healthcare costs. Translation of basic research findings to clinical applications within regulatory compliance is required for personalized medicine to become the new foundation for practice of medicine. Deploying even a few of the thousands of potential diagnostic biomarkers identified each year as part of personalized treatment workflows requires clinically efficient biosensor technologies to monitor multiple biomarkers in patients in real time. This paper discusses a critical component of a regulatory system, a microcavity optical biosensor for label-free monitoring of biomolecular interactions at physiologically-relevant concentrations. While most current biosensor research focuses on improving sensitivity, this paper emphasizes other characteristics a biosensor technology requires to be practical in a clinical setting, presenting robust microcavity biosensors which are easy to manufacture and integrate with microfluidics into flexible and redesignable platforms making the microcavity biosensors deployable for continuous monitoring of biomarkers in body fluids in the clinic, in dense 2D random arrays for high-throughput applications like drug-library screening in interactomics, and of the secretory behavior of single cells in the laboratory.

Comparison of free-solution and surface-immobilized molecular interactions using a single platform

While it is generally accepted that surface immobilization affects the binding properties of proteins, it has been difficult to quantify these effects due to the lack of technology capable of making affinity measurements with species tethered and in free solution on a single platform. Further, quantifying the interaction of binding pairs with widely differing masses has also been challenging, particularly when it is desirable to tether the high molecular weight protein. Here we describe the use of backscattering interferometry (BSI) to quantify the binding affinity of mannose and glucose to concanavalin A (ConA), a 106 KDa homotetramer protein, in free solution using picomoles of the protein. Using the same platform, BSI, we then studied the effect on the binding constants of the ConA-carbohydrate interactions upon chemically immobilizing ConA on the sensor surface. By varying the distances (0, 7.17, and 20.35 nm) of the ConA tether and comparing these results to the free-solution measurements, it has been possible to quantify the effect that protein immobilization has on binding. Our results indicate that the apparent binding affinity of the sugar-lectin pair increases as the distance between ConA and the surface decreases. These observations could lend insight as to why the affinity values reported in the literature sometimes vary significantly from one measurement technique to another.

Simultaneous measurements of absorption spectrum and refractive index in a microfluidic system

The characterization of dyes in various solvents requires determination of the absorption spectrum of the dye as well as the refractive index of the solvent. Typically, the refractive index of the solvent and the absorption spectrum of the solute are measured using separate experimental setups where significant liquid volumes are required. In this work the first optical measurement system that is able to do simultaneous measurements of the refractive index of the solvent and the spectral properties of the solute in a microscopic volume is presented. The laser dye Rhodamine 6G in glycerol is investigated, and the refractive index of the solution is monitored using the interference pattern of the light scattered off the channel, while its spectral properties is found by monitoring reflected light from the channel.

Rapid, multiplexed microfluidic phage display

The development of a method for high-throughput, automated proteomic screening could impact areas ranging from fundamental molecular interactions to the discovery of novel disease markers and therapeutic targets. Surface display techniques allow for efficient handling of large molecular libraries in small volumes. In particular, phage display has emerged as a powerful technology for selecting peptides and proteins with enhanced, target-specific binding affinities. Yet, the process becomes cumbersome and time-consuming when multiple targets are involved. Here we demonstrate for the first time a microfluidic chip capable of identifying high affinity phage-displayed peptides for multiple targets in just a single round and without the need for bacterial infection. The chip is shown to be able to yield well-established control consensus sequences while simultaneously identifying new sequences for clinically important targets. Indeed, the confined parameters of the device allow not only for highly controlled assay conditions but also introduce a significant time-reduction to the phage display process. We anticipate that this easily-fabricated, disposable device has the potential to impact areas ranging from fundamental studies of protein, peptide, and molecular interactions, to applications such as fully automated proteomic screening.

Evolution and protein packaging of small-molecule RNA aptamers

A high-affinity RNA aptamer (K(d) = 50 nM) was efficiently identified by SELEX against a heteroaryldihydropyrimidine structure, chosen as a representative drug-like molecule with no cross reactivity with mammalian or bacterial cells. This aptamer, its weaker-binding variants, and a known aptamer against theophylline were each embedded in a longer RNA sequence that was encapsidated inside a virus-like particle by a convenient expression technique. These nucleoprotein particles were shown by backscattering interferometry to bind to the small-molecule ligands with affinities similar to those of the free (nonencapsidated) aptamers. The system therefore comprises a general approach to the production and sequestration of functional RNA molecules, characterized by a convenient label-free analytical technique.

Label-free quantification of membrane-ligand interactions using backscattering interferometry

Although membrane proteins are ubiquitous within all living organisms and represent the majority of drug targets, a general method for direct, label-free measurement of ligand binding to native membranes has not been reported. Here we show that backscattering interferometry (BSI) can accurately quantify ligand-receptor binding affinities in a variety of membrane environments. By detecting minute changes in the refractive index of a solution, BSI allows binding interactions of proteins with their ligands to be measured at picomolar concentrations. Equilibrium binding constants in the micromolar to picomolar range were obtained for small- and large-molecule interactions in both synthetic and cell-derived membranes without the use of labels or supporting substrates. The simple and low-cost hardware, high sensitivity and label-free nature of BSI should make it readily applicable to the study of many membrane-associated proteins of biochemical and pharmacological interest.

Combining biophysical screening and X-ray crystallography for fragment-based drug discovery

Over the past decade, fragment-based drug discovery (FBDD) has gained importance for the generation of novel ideas to inspire synthetic chemistry. In order to identify small molecules that bind to a target protein, multiple approaches have been utilized by various groups in the pharmaceutical industry and by academic groups. The combination of fragment screening by biophysical methods and in particular with surface plasmon resonance technologies (SPR) together with the visualization of the binding properties by X-ray crystallography offers a number of benefits. Screening by SPR identifies ligands for a target protein as well as provides an assessment of the binding properties with respect to affinity, stoichiometry, and specificity of the interaction. Despite the huge technology advances of the past years, X-ray crystallography is still a resource-intensive technology, and SPR binding data provides excellent measures to prioritize X-ray experiments and consequently enable a better success rate in obtaining structural information. Information on the chemical structures of fragments binding to a protein can be used to perform similarity searches in compound libraries in order to establish structure-activity relationships as well as to explore particular scaffolds. At Roche we have applied this workflow for a number of targets and the experiences will be outlined in this review.

Protein-binding assays in biological liquids using microscale thermophoresis

Protein interactions inside the human body are expected to differ from the situation in vitro. This is crucial when investigating protein functions or developing new drugs. In this study, we present a sample-efficient, free-solution method, termed microscale thermophoresis, that is capable of analysing interactions of proteins or small molecules in biological liquids such as blood serum or cell lysate. The technique is based on the thermophoresis of molecules, which provides information about molecule size, charge and hydration shell. We validated the method using immunologically relevant systems including human interferon gamma and the interaction of calmodulin with calcium. The affinity of the small-molecule inhibitor quercetin to its kinase PKA was determined in buffer and human serum, revealing a 400-fold reduced affinity in serum. This information about the influence of the biological matrix may allow to make more reliable conclusions on protein functionality, and may facilitate more efficient drug development.

Label-free detection techniques for protein microarrays: prospects, merits and challenges

Protein microarrays, on which thousands of discrete proteins are printed, provide a valuable platform for functional analysis of the proteome. They have been widely used for biomarker discovery and to study protein–protein interactions. The accomplishments of DNA microarray technology, which had enabled massive parallel studies of gene expression, sparked great interest for the development of protein microarrays to achieve similar success at the protein level. Protein microarray detection techniques are often classified as being label‐based and label‐free. Most of the microarray applications have employed labelled detection such as fluorescent, chemiluminescent and radioactive labelling. These labelling strategies have synthetic challenges, multiple label issues and may exhibit interference with the binding site. Therefore, development of sensitive, reliable, high‐throughput, label‐free detection techniques are now attracting significant attention. Label‐free detection techniques monitor biomolecular interactions and simplify the bioassays by eliminating the need for secondary reactants. Moreover, they provide quantitative information for the binding kinetics. In this article, we will review several label‐free techniques, which offer promising applications for the protein microarrays, and discuss their prospects, merits and challenges.

Immunoassays in microfluidic systems

Immunoassays have greatly benefited from miniaturization in microfluidic systems. This review, which summarizes developments in microfluidics-based immunoassays since 2000, includes four sections, focusing on the configurations of immunoassays that have been implemented in microfluidics, the main fluid handling modalities that have been used for microfluidic immunoassays, multiplexed immunoassays in microfluidic platforms, and the emergence of label-free detection techniques. The field of microfluidic immunoassays is continuously improving and has great promise for the future.

Mobile magnetic particles as solid-supports for rapid surface-based bioanalysis in continuous flow

An extremely versatile microfluidic device is demonstrated in which multi-step (bio)chemical procedures can be performed in continuous flow. The system operates by generating several co-laminar flow streams, which contain reagents for specific (bio)reactions across a rectangular reaction chamber. Functionalized magnetic microparticles are employed as mobile solid-supports and are pulled from one side of the reaction chamber to the other by use of an external magnetic field. As the particles traverse the co-laminar reagent streams, binding and washing steps are performed on their surface in one operation in continuous flow. The applicability of the platform was first demonstrated by performing a proof-of-principle binding assay between streptavidin coated magnetic particles and biotin in free solution with a limit of detection of 20 ng mL(-1) of free biotin. The system was then applied to a mouse IgG sandwich immunoassay as a first example of a process involving two binding steps and two washing steps, all performed within 60 s, a fraction of the time required for conventional testing.

Measurement of monovalent and polyvalent carbohydrate-lectin binding by back-scattering interferometry

Carbohydrate-protein binding is important to many areas of biochemistry. Here, backscattering interferometry (BSI) has been shown to be a convenient and sensitive method for obtaining quantitative information about the strengths and selectivities of such interactions. The surfaces of glass microfluidic channels were covalently modified with extravidin, to which biotinylated lectins were subsequently attached by incubation and washing. The binding of unmodified carbohydrates to the resulting avidin-immobilized lectins was monitored by BSI. Dose-response curves that were generated within several minutes and were highly reproducible in multiple wash/measure cycles provided adsorption coefficients that showed mannose to bind to concanavalin A (conA) with 3.7 times greater affinity than glucose consistent with literature values. Galactose was observed to bind selectively and with similar affinity to the lectin BS-1. The avidities of polyvalent sugar-coated virus particles for immobilized conA were much higher than monovalent glycans, with increases of 60-200 fold per glycan when arrayed on the exterior surface of cowpea mosaic virus or bacteriophage Qbeta. Sugar-functionalized PAMAM dendrimers showed size-dependent adsorption, which was consistent with the expected density of lectins on the surface. The sensitivity of BSI matches or exceeds that of surface plasmon resonance and quartz crystal microbalance techniques, and is sensitive to the number of binding events, rather than changes in mass. The operational simplicity and generality of BSI, along with the near-native conditions under which the target binding proteins are immobilized, make BSI an attractive method for the quantitative characterization of the binding functions of lectins and other proteins.

Design of high-density antibody microarrays for disease proteomics: key technological issues

Antibody-based microarray is a novel proteomic technology setting a new standard for molecular profiling of non-fractionated complex proteomes. The first generation of antibody microarrays has already demonstrated its potential for generating detailed protein expression profiles, or protein atlases, of human body fluids in health and disease, paving the way for new discoveries within the field of disease proteomics. The process of designing highly miniaturized, high-density and high-performing antibody microarray set-ups have, however, proven to be challenging. In this mini-review we discuss key technological issues that must be addressed in a cross-disciplinary manner before true global proteome analysis can be performed using antibody microarrays.

Detecting protein-ligand binding on supported bilayers by local pH modulation

Herein, we describe a highly sensitive technique for detecting protein-ligand binding at the liquid/solid interface. The method is based upon modulation of the interfacial pH when the protein binds. This change is detected by ortho-Texas Red DHPE, which is doped into supported phospholipid bilayers and used as a pH-sensitive dye. The dye molecule fluoresces strongly at acidic pH values but not basic ones and has an apparent pK(A) of 7.8 in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine membranes containing 0.5 mol % biotin-cap-PE. This method was used to detect antibiotin/biotin binding interactions as well as the binding of cholera toxin B subunits to GM(1). Since these proteins are negatively charged under the conditions of the experiment the interface became slightly more acidic upon binding. In each case, the equilibrium dissociation constant was determined by following the rise in fluorescence as protein was introduced. This change is essentially linear with protein coverage under the conditions employed. For the biotin/antibiotin system it was determined that K(D) = 24 +/- 5 nM, which is in excellent agreement with classical measurements made by total internal reflection fluorescence microscopy involving fluorophore-conjugated antibody molecules. Moreover, the limit of detection was approximately 350 fM at the 99% confidence level. This corresponds to 1 part in 69,000 of the K(D) value. Such a finding compares favorably with surface plasmon resonance studies of similar systems and conditions. The assay could be run in imaging mode to obtain multiple simultaneous measurements using a CCD camera.

Phase sensitive interferometry for biosensing applications

A simple yet highly sensitive implementation of an interferometric technique for a label-free molecular biosensing application is described. The intereferometric detection method is based on the phase-sensitive detection of spectral interference fringes. The change in optical path length due to binding of biomolecules on functionalized optically clear substrates can be quantified by detecting the change in the phase of the spectral fringes. The common path interferometeric design permits measurement of sub-monolayer binding of biomolecules to the sensor surfaces.

Label-free and selective nonlinear fiber-optical biosensing

We demonstrate that the inherent nonlinearity of a microstructured optical fiber (MOF) may be used to achieve label-free selective biosensing, thereby eliminating the need for post-processing of the fiber. This first nonlinear biosensor utilizes a change in the modulational instability (MI) gain spectrum (a shift of the Stokes- or anti-Stokes wavelength) caused by the selective capture of biomolecules by a sensor layer immobilised on the walls of the holes in the fiber. We find that such changes in the MI gain spectrum can be made detectable, and that engineering of the dispersion is important for optimizing the sensitivity. The nonlinear sensor shows a sensitivity of around 10.4 nm/nm, defined as the shift in resonance wavelength per nm biolayer, which is a factor of 7.5 higher than the hitherto only demonstrated label-free MOF biosensor.

Innovations in optical microfluidic technologies for point-of-care diagnostics

Despite a growing focus from the academic community, the field of microfluidics has yet to produce many commercial devices for point-of-care (POC) diagnostics. One of the main reasons for this is the difficulty in producing low-cost, sensitive, and portable optical detection systems. Although electrochemical methods work well for certain applications, optical detection is generally regarded as superior and is the method most widely employed in laboratory clinical chemistry. Conventional optical systems, however, are costly, require careful alignment, and do not translate well to POC devices. Furthermore, many optical detection paradigms such as absorbance and fluorescence suffer at smaller geometries because the optical path length through the sample is shortened. This review examines the innovative techniques which have recently been developed to address these issues. We highlight microfluidic diagnostic systems which demonstrate practical integration of sample preparation, analyte enrichment, and optical detection. We also examine several emerging detection paradigms involving nanoengineered materials which do not suffer from the same miniaturization disadvantages as conventional measurements.

Multiplexing ligand-receptor binding measurements by chemically patterning microfluidic channels

A method has been designed for patterning supported phospholipid bilayers (SLBs) on planar substrates and inside microfluidic channels. To do this, bovine serum albumin (BSA) monolayers were formed via adsorption at the liquid/solid interface. Next, this interfacial protein film was selectively patterned by using deep UV lithography. Subsequently, SLBs could be deposited in the patterned locations by vesicle fusion. By cycling through this process several times, spatially addressed bilayer arrays could be formed with intervening protein molecules serving as two-dimensional corrals. By employing this method, phospholipid bilayers containing various concentrations of ganglioside GM1 were addressed along the length of individual microfluidic channels. Therefore, the binding of GM1 with pentameric cholera toxin B (CTB) subunits could be probed. A seven-channel microfluidic device was fabricated for this purpose. Each channel was simultaneously patterned with four chemically distinct SLBs containing 0, 0.2, 0.5, and 2.0 mol % GM1, respectively. Varying concentrations of CTB were then introduced into each of the channels. With the use of total internal reflection fluorescence microscopy, it was possible to simultaneously abstract multiple equilibrium dissociation constants as a function of ligand density for the CTB-GM1 system in a single shot.

Sensitive optical biosensors for unlabeled targets: A review

This article reviews the recent progress in optical biosensors that use the label-free detection protocol, in which biomolecules are unlabeled or unmodified, and are detected in their natural forms. In particular, it will focus on the optical biosensors that utilize the refractive index change as the sensing transduction signal. Various optical label-free biosensing platforms will be introduced, including, but not limited to, surface plasmon resonance, interferometers, waveguides, fiber gratings, ring resonators, and photonic crystals. Emphasis will be given to the description of optical structures and their respective sensing mechanisms. Examples of detecting various types of biomolecules will be presented. Wherever possible, the sensing performance of each optical structure will be evaluated and compared in terms of sensitivity and detection limit.

Suspended microchannel resonators for ultralow volume universal detection

Universal detectors that maintain high sensitivity as the detection volume is reduced to the subnanoliter scale can enhance the utility of miniaturized total analysis systems (mu-TAS). Here the unique scaling properties of the suspended microchannel resonator (SMR) are exploited to show universal detection in a 10 pL analysis volume with a density detection limit of approximately 1 microg/cm (3) (10 Hz bandwidth) and a dynamic range of 6 decades. Analytes with low UV extinction coefficients such as polyethylene glycol (PEG) 8 kDa, glucose, and glycine are measured with molar detection limits of 0.66, 13.5, and 31.6 microM, respectively. To demonstrate the potential for real-time monitoring, gel filtration chromatography was used to separate different molecular weights of PEG as the SMR acquired a chromatogram by measuring the eluate density. This work suggests that the SMR could offer a simple and sensitive universal detector for various separation systems from liquid chromatography to capillary electrophoresis. Moreover, since the SMR is itself a microfluidic channel, it can be directly integrated into mu-TAS without compromising overall performance.

Label-free optical detection of aptamer-protein interactions using gold-capped oxide nanostructures

Optical biosensors based on noble nanostructures currently receive attention due to their highly efficient, simultaneous analysis of a number of important biomolecules from proteomics to genomics. In this study, the combination of localized surface plasmon resonance (LSPR) with interferometry in the relative reflected intensity (RRI) spectrum of the gold-capped oxide nanostructure was thoroughly exploited for label-free detection of aptamer-protein interactions. The fabrication of gold-capped oxide nanostructure involved the deposition of gold on the surface of porous anodic alumina (PAA) layer chip. This novel nanomaterial enabled us to simultaneously monitor the changes in both LSPR and interferometric characteristics since the biomolecular interactions occur. After immobilizing the aptamer I on the chip surface, our sensor could be easily applied for specific detection of thrombin and aptamer II with a limit of detection of 1 nM thrombin in the sample. Our optical biosensing device connecting with the gold-capped oxide nanostructure has a high potential for highly sensitive monitoring of the other biomolecular interactions such as protein-protein interactions, DNA-protein interactions, DNA-DNA hybridizations, and ligand-receptor interactions with a massively parallel detection capability in a high-throughput system.

Novel dense CO2 technique for beta-galactosidase immobilization in polystyrene microchannels

In this study we design new fabrication techniques and demonstrate the potential of using dense CO2 for facilitating crucial steps in the fabrication of polymeric lab-on-a-chip microdevices by embedding biomolecules at temperatures well below the polymer's glass transition temperature (T(g)). These new techniques are environmentally friendly and done without the use of a clean room. Carbon dioxide at 40 degrees C and between 4.48 and 6.89 MPa was used to immobilize the biologically active molecule, beta-galactosidase (beta-gal), on the surface of polystyrene microchannels. To our knowledge, this is the first time dense CO2 has been used to directly immobilize an enzyme in a microchannel. beta-gal activity was maintained and shown via a fluorescent reaction product, after enzyme immobilization and microchannel capping by the designed fabrication steps at 40 degrees C and pressures up to 6.89 MPa.

In-situ synthesis of poly(dimethylsiloxane)-gold nanoparticles composite films and its application in microfluidic systems

We presented a simple approach for in-situ synthesis of poly(dimethylsiloxane) (PDMS)-gold nanoparticles composite film based on the special characteristics of PDMS itself. It is an environmentally safe synthesis method without the requirement of additional reducing/stabilizing agents. The region where the resulting gold nanoparticles distribute (in the matrix or on the surface of the polymer) and the size of the nanoparticles, as well as the colour of the free-standing films, can be simply controlled by adjusting the ratio of curing agent and the PDMS monomer. The chemical and optical properties of these composite films were studied. Using such a method, gold nanoparticle micropatterns on PDMS surfaces can be performed. And based on the gold nanoparticles micropattern, further modification with antibodies, antigens, enzymes and other biomolecules can be achieved. To verify this ability, an immobilized glucose oxidase (GOx) reactor in microchannels was built and its performance was studied. The experiments have shown that the resulting composite film may have a lot of potential merits in protein immobilization, immunoassays and other biochemical analysis on PDMS microchips.

Microsystems technology and biosensing

This review addresses the recent developments in miniaturized microsystems or lab-on-a-chip devices for biosensing of different biomolecules: DNA, proteins, small molecules, and cells, especially at the single-molecule and single-cell level. In order to sense these biomolecules with sensitivity we have fabricated chip devices with respect to the biomolecule to be analyzed. The details of the fabrication are also dealt with in this review. We mainly developed microarray and microfluidic chip devices for DNA, protein, and cell analyses. In addition, we have introduced the porous anodic alumina layer chip with nanometer scale and gold nanoparticles for label-free sensing of DNA and protein interactions. We also describe the use of microarray and microfluidic chip devices for cell-based assays and single-cell analysis in drug discovery research.

Free-Solution, Label-Free Molecular Interactions Studied by Back-Scattering Interferometry

Free-solution, label-free molecular interactions were investigated with back-scattering interferometry in a simple optical train composed of a helium-neon laser, a microfluidic channel, and a position sensor. Molecular binding interactions between proteins, ions and protein, and small molecules and protein, were determined with high dynamic range dissociation constants (Kd spanning six decades) and unmatched sensitivity (picomolar Kd's and detection limits of 10,000s of molecules). With this technique, equilibrium dissociation constants were quantified for protein A and immunoglobulin G, interleukin-2 with its monoclonal antibody, and calmodulin with calcium ion Ca2+, a small molecule inhibitor, the protein calcineurin, and the M13 peptide. The high sensitivity of back-scattering interferometry and small volumes of microfluidics allowed the entire calmodulin assay to be performed with 200 picomoles of solute.

Progress in miniaturization of protein arrays--a step closer to high-density nanoarrays

Protein microarrays is a technology with great promise for high-throughput proteomics. Designing high-performance protein microarrays for global proteome analysis has, however, turned out to be challenging. To this end, major efforts are under way to design novel array formats capable of harboring the tremendous range of probes required to target complex proteomes composed of more than 10000 analytes. By adopting nanotechnology, the first generation of miniaturized nanoarrays has recently emerged, which opens up new avenues for global proteome analysis and disease proteomics. This review describes the progress and key issues in designing miniaturized protein arrays.

Nanoparticle-enhanced diffraction gratings for ultrasensitive surface plasmon biosensing

Ultrasensitive surface bioaffinity sensors are created by the adsorption of gold nanoparticles onto gold diffraction gratings. An enhanced diffraction obtained in a surface plasmon resonance geometry is observed due to the optical coupling of the planar surface plasmons in the grating to the localized surface plasmons in the gold nanoparticles. As a first example, these nanoparticle grating biosensors are employed to detect unmodified DNA at a concentration of 10 fM.

Label-Free DNA Biosensor Based on Localized Surface Plasmon Resonance Coupled with Interferometry

In this report, we developed a new optical biosensor in connection with a gold-deposited porous anodic alumina (PAA) layer chip. In our sensor, we observed that the gold deposition onto the chip surface formed a "caplike" layer on the top of the oxide nanostructures in an orderly fashion, so we called this new surface formation a "gold-capped oxide nanostructure". As a result of its interferometric and localized surface plasmon resonance properties, the relative reflected intensity (RRI) at surface of the chip resulted in an optical pattern that was highly sensitive to the changes in the effective thickness of the biomolecular layer. We demonstrated the method on the detection of picomolar quantities of untagged oligonucleotides and the hybridization with synthetic and PCR-amplified DNA samples. The detection limit of our PAA layer chip was determined as 10 pM synthetic target DNA. The capability of observing both RRI increment and wavelength shift upon biomolecular interactions promises to make our chip widely applicable in various analytical tests.

Patterning microbeads inside poly(dimethylsiloxane) microfluidic channels and its application for immobilized microfluidic enzyme reactors

We propose a convenient and reliable approach for immobilizing microbeads on poly(dimethylsiloxane) (PDMS) microchips. It is built upon a simple fabrication procedure of PDMS chip through directly printing the master with an office laser printer which was described in our previous work (J. Chromatogr. A 2005, 1089, 270-275). On the printed toners used as the positive relief of the master, microbeads were immobilized by a thermal treatment and then transferred to the surface of the microchip by direct molding of the prepolymer on the master. With this approach, the region-selective immobilization of microbeads and the fabrication of PDMS microchips can be accomplished at the same time. Then, using these microbeads as supports, further modification with enzyme was achieved. Surface characteristics of the microbeads-modified PDMS microchannels were investigated with scanning electron microscope, atomic force microscope, and inverse fluorescence microscope. The electrokinetic properties of the native PDMS and the modified PDMS chips were also compared. Based on this approach, an immobilized glucose oxidase (GOD) reactor was constructed and the reaction using glucose as substrate was studied. All these experiments aim to show that the proposed approach may have a good potential in the study of biochemistry and other related areas.

Protein-sensing assay formats and devices

Proteins are used as biocatalysts, therapeutic or diagnostic agents, and as such they are biotechnological products. Moreover, they are biomarkers for health states, diseases or toxic or other adverse effects, and the intracellular protein network is essential for the adaptation of an organism to its environment. Thus, there is a strong need for analytical methods for protein determination, which allow not only to indicate the presence of a protein, but also its concentration, covalent modification and activity, and corresponding developments of new methods experienced strong support. Among those methods only those were considered here, which are based on affinity reactions between an immobilized capture agent, such as an antibody or a receptor, and the target protein. Immobilization methods range from adsorption on hydrophobic materials, in membranes or gels to covalent binding and bioaffinity reactions, such as the oriented immobilization of antibodies on protein A/G layers. The applicability of the various methods is dependent on physical and chemical properties of the immobilization substrate and of the capture agent, i.e. the presence of surface charges, hydrophobic areas or functional groups for chemical coupling. The choice of the immobilization substrate is influenced by the combination of the assay and detection principle, which meets best the practical requirements. Assay formats range from direct, label-free one-step detection of the affinity reaction between the capture agent and the target protein to multi-step procedures, such as an enzyme-tracer-based sandwich assays. Each approach has its particular advantages and disadvantages with respect to the complexity of the assay, i.e. number of required reagents and of incubation steps, the possible degree of automation, assay time, availability of suitable reagents, required sample volume, sensitivity and specificity, including the possibility to determine several proteins simultaneously. No general recommendation for the "best choice" was given in this contribution, but examples were chosen, which illustrate the potential of the different systems.