DNA and protein microarray printing on silicon nitride waveguide surfaces

Controlled Carboxylic Acid-Functionalized Silicon Nitride Surfaces through Supersonic Molecular Beam Deposition

The functionalization of inorganic surfaces by organic functional molecules is a viable and promising method towards the realization of novel classes of biosensing devices. The proper comprehension of the chemical properties of the interface, as well as of the number of active binding sites for bioreceptor molecules are characteristics that will determine the interaction of the sensor with the analyte, and thus its final efficiency. We present a new and reliable surface functionalization route based on supersonic molecular beam deposition (SuMBD) using 2,6-naphthalene dicarboxylic acid as a bi-functional molecular linker on the chemically inert silicon nitride surface to further allow for stable and homogeneous attachment of biomolecules. The kinetically activated binding of the molecular layer to silicon nitride and the growth as a function of deposition time was studied by X-ray photoelectron spectroscopy, and the properties of films with different thicknesses were investigated by optical and vibrational spectroscopies. After subsequent attachment of a biological probe, fluorescence analysis was used to estimate the molecular layer's surface density. The successful functionalization of silicon nitride surface via SuMBD and the detailed growth and interface analysis paves the way for reliably attaching bioreceptor molecules onto the silicon nitride surface.

Polymer Brushes on Silica Nanostructures Prepared by Aminopropylsilatrane Click Chemistry: Superior Antifouling and Biofunctionality

In nanobiotechnology, the importance of controlling interactions between biological molecules and surfaces is paramount. In recent years, many devices based on nanostructured silicon materials have been presented, such as nanopores and nanochannels. However, there is still a clear lack of simple, reliable, and efficient protocols for preventing and controlling biomolecule adsorption in such structures. In this work, we show a simple method for passivation or selective biofunctionalization of silica, without the need for polymerization reactions or vapor-phase deposition. The surface is simply exposed stepwise to three different chemicals over the course of ∼1 h. First, the use of aminopropylsilatrane is used to create a monolayer of amines, yielding more uniform layers than conventional silanization protocols. Second, a cross-linker layer and click chemistry are used to make the surface reactive toward thiols. In the third step, thick and dense poly(ethylene glycol) brushes are prepared by a grafting-to approach. The modified surfaces are shown to be superior to existing options for silica modification, exhibiting ultralow fouling (a few ng/cm2) after exposure to crude serum. In addition, by including a fraction of biotinylated polymer end groups, the surface can be functionalized further. We show that avidin can be detected label-free from a serum solution with a selectivity (compared to nonspecific binding) of more than 98% without the need for a reference channel. Furthermore, we show that our method can passivate the interior of 150 nm × 100 nm nanochannels in silica, showing complete elimination of adsorption of a sticky fluorescent protein. Additionally, our method is shown to be compatible with modifications of solid-state nanopores in 20 nm thin silicon nitride membranes and reduces the noise in the ion current. We consider these findings highly important for the broad field of nanobiotechnology, and we believe that our method will be very useful for a great variety of surface-based sensors and analytical devices.

Waveguide Enhanced Raman Spectroscopy for Biosensing: A Review

Waveguide enhanced Raman spectroscopy (WERS) utilizes simple, robust, high-index contrast dielectric waveguides to generate a strong evanescent field, through which laser light interacts with analytes residing on the surface of the waveguide. It offers a powerful tool for the direct identification and reproducible quantification of biochemical species and an alternative to surface enhanced Raman spectroscopy (SERS) without reliance on fragile noble metal nanostructures. The advent of low-cost laser diodes, compact spectrometers, and recent progress in material engineering, nanofabrication techniques, and software modeling tools have made realizing portable and cheap WERS Raman systems with high sensitivity a realistic possibility. This review highlights the latest progress in WERS technology and summarizes recent demonstrations and applications. Following an introduction to the fundamentals of WERS, the theoretical framework that underpins the WERS principles is presented. The main WERS design considerations are then discussed, and a review of the available approaches for the modification of waveguide surfaces for the attachment of different biorecognition elements is provided. The review concludes by discussing and contrasting the performance of recent WERS implementations, thereby providing a future roadmap of WERS technology where the key opportunities and challenges are highlighted.

Revealing the Kinetic Advantage of a Competitive Small-Molecule Immunoassay by Direct Detection

Small-molecule detection in an immunoassay format generally employs competition or labeling. A novel direct-detection label-free primary immunoassay utilizing second harmonic generation (SHG) has been developed and the utility of the method has been demonstrated for several small-molecule narcotics. Specifically, the binding of morphine, methadone, and cocaine to antimorphine, antimethadone, and anticocaine antibodies was measured by SHG, allowing binding affinities and rates of dissociation to be obtained. The SHG primary immunoassay has provided the first kinetic measurements of small-molecule hapten interactions with a receptor antibody. The kinetics reveal for the first time that competitive immunoassays achieve their selectivity by taking advantage of the kinetics of association and dissociation of the labeled and unlabeled target and nontarget small-molecule to the capture antibody. In particular, the induced fit of the target small-molecule to their antibody pairs prolongs their residence time, while the nontarget small-molecule dissociate rapidly in comparison.

Multifunctional biophotonic nanostructures inspired by the longtail glasswing butterfly for medical devices

Numerous living organisms possess biophotonic nanostructures that provide colouration and other diverse functions for survival. While such structures have been actively studied and replicated in the laboratory, it remains unclear whether they can be used for biomedical applications. Here, we show a transparent photonic nanostructure inspired by the longtail glasswing butterfly (Chorinea faunus) and demonstrate its use in intraocular pressure (IOP) sensors in vivo. We exploit the phase separation between two immiscible polymers (poly(methyl methacrylate) and polystyrene) to form nanostructured features on top of a Si3N4 substrate. The membrane thus formed shows good angle-independent white-light transmission, strong hydrophilicity and anti-biofouling properties, which prevent adhesion of proteins, bacteria and eukaryotic cells. We then developed a microscale implantable IOP sensor using our photonic membrane as an optomechanical sensing element. Finally, we performed in vivo testing on New Zealand white rabbits, which showed that our device reduces the mean IOP measurement variation compared with conventional rebound tonometry without signs of inflammation.

Electrospun polyethersolfone nanofibrous membrane as novel platform for protein immobilization in microfluidic systems

In the present study, the feasibility of electrospun polyethersolfone (PES) nanofibrous membrane as the solid substrate for microfluidic based immunoassays to enhance the density of immobilized antibody on the surface of membrane was assessed. Conversely, the efficacy of antibody immobilization was compared by two different strategies as 1-Ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC)/N-Hydroxysuccinimide (NHS) coupling chemistry and hydrophobic interaction. Compared to conventional immunoassays carried out in plates or gels, microfluidic based immunoassays grant a lot of advantages such as a consumption of little samples and reagents, shorter analysis time, and higher efficiency. Therefore, microfluidic immunoassays can be efficiently used as a point-of-care device in medical diagnosis. Surprisingly, we found the increase of specific surface areas of the microfluidic channels improve density of immobilized proteins and leads to higher signal strength. Anti-staphylococcus enterotoxin B (anti-SEB) was used as an analyte model to demonstrate the utility of our proposed platform. Fluorescent microscopy, Fourier transform infrared spectroscopic (FTIR), gas adsorption, contact angle, X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), Uv-Vis spectrophotometer and atomic force microscopy (AFM) techniques were used to assess the efficacy of antibody immobilization on the surface. To understand dominant mechanism of protein immobilization, zeta potential measurement was also carried out and it was found electrostatic attraction play significant role in antibody immobilization running into micro- channels containing through EDC/NHS. Moreover, incorporation of nanofibrous membrane causes significant improvement in the signal detection of microfluidic based immunoassay. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 106B: 1108-1120, 2018.

Using single nanoparticle tracking obtained by nanophotonic force microscopy to simultaneously characterize nanoparticle size distribution and nanoparticle-surface interactions

Comprehensive characterization of nanomaterials for medical applications is a challenging and complex task due to the multitude of parameters which need to be taken into consideration in a broad range of conditions. Routine methods such as dynamic light scattering or nanoparticle tracking analysis provide some insight into the physicochemical properties of particle dispersions. For nanomedicine applications the information they supply can be of limited use. For this reason, there is a need for new methodologies and instruments that can provide additional data on nanoparticle properties such as their interactions with surfaces. Nanophotonic force microscopy has been shown as a viable method for measuring the force between surfaces and individual particles in the nano-size range. Here we outline a further application of this technique to measure the size of single particles and based on these measurement build the distribution of a sample. We demonstrate its efficacy by comparing the size distribution obtained with nanophotonic force microscopy to established instruments, such as dynamic light scattering and differential centrifugal sedimentation. Our results were in good agreement to those observed with all other instruments. Furthermore, we demonstrate that the methodology developed in this work can be used to study complex particle mixtures and the surface alteration of materials. For all cases studied, we were able to obtain both the size and the interaction potential of the particles with a surface in a single measurement.

A portable optical waveguide resonance light-scattering scanner for microarray detection

In the present work, a portable and low-cost planar waveguide based resonance light scattering (RLS) scanner (termed as: PW-RLS scanner) has been developed for microarray detection. The PW-RLS scanner employs a 2 × 4 white light emitting diode array (WLEDA) as the excitation light source, a folded optical path with a complementary metal oxide semiconductor (CMOS) as the signal/image acquisition device and stepper motors with gear drives as the mechanical drive system. The biological binding/recognizing events on the microarray can be detected with an evanescent waveguide-directed illumination and light-scattering label (e.g., nanoparticles) while the microarray slide acts as an evanescent waveguide substrate. The performance of the as-developed PW-RLS scanner has been evaluated by analyzing type 2 diabetes mellitus (T2DM) risk genes. Highly selective and sensitive (less than 1% allele frequency at the attomole-level) T2DM risk gene detection is achieved using single-stranded DNA functionalized gold nanoparticles (ssDNA-GNPs) as detection probes. Additionally, the successful simultaneous analysis of 15 T2DM patient genotypes suggests that the device has great potential for the realization of a personalized diagnostic test for a given disease or patient follow-up.

Optimizing Pin-Printed and Hydrosilylated Microarray Spot Density on Porous Silicon Platforms

Microarrays of spatially isolated chemistries on planar surfaces are powerful tools. An important factor in microarray technology is the density of chemically unique spots that can be formed per unit area. In this paper, we use contact pin-printing and evaluate how to decrease contact pin-printed spot diameters on porous silicon (pSi) platforms. Using hydrosilylation chemistry to covalently attach chemistries to the pSi surface, the variables studied included pSi porosity and surface polarity, active agent viscosity, and pin diameter. The spot characteristics were assessed by Fourier transform infrared spectroscopy (FT-IR) microscopy and X-ray photoelectron spectroscopy (XPS). Spot size decreased as pSi porosity increased in accordance with molecular kinetic theory and Darcy's law of imbibition. Increasing active agent viscosity and pin diameter (volume of printed agent) led to larger spot diameters in accordance with molecular kinetic theory and Darcy's law. Oxidizing the pSi with H2O2 increased the surface polarity but had no detectable impact on the spot size. This is consistent with formation of an oxide layer atop an unoxidized pSi sublayer.

A critical comparison of protein microarray fabrication technologies

Of the diverse analytical tools used in proteomics, protein microarrays possess the greatest potential for providing fundamental information on protein, ligand, analyte, receptor, and antibody affinity-based interactions, binding partners and high-throughput analysis. Microarrays have been used to develop tools for drug screening, disease diagnosis, biochemical pathway mapping, protein-protein interaction analysis, vaccine development, enzyme-substrate profiling, and immuno-profiling. While the promise of the technology is intriguing, it is yet to be realized. Many challenges remain to be addressed to allow these methods to meet technical and research expectations, provide reliable assay answers, and to reliably diversify their capabilities. Critical issues include: (1) inconsistent printed microspot morphologies and uniformities, (2) low signal-to-noise ratios due to factors such as complex surface capture protocols, contamination, and static or no-flow mass transport conditions, (3) inconsistent quantification of captured signal due to spot uniformity issues, (4) non-optimal protocol conditions such as pH, temperature, drying that promote variability in assay kinetics, and lastly (5) poor protein (e.g., antibody) printing, storage, or shelf-life compatibility with common microarray assay fabrication methods, directly related to microarray protocols. Conventional printing approaches, including contact (e.g., quill and solid pin), non-contact (e.g., piezo and inkjet), microfluidics-based, microstamping, lithography, and cell-free protein expression microarrays, have all been used with varying degrees of success with figures of merit often defined arbitrarily without comparisons to standards, or analytical or fiduciary controls. Many microarray performance reports use bench top analyte preparations lacking real-world relevance, akin to "fishing in a barrel", for proof of concept and determinations of figures of merit. This review critiques current protein-based microarray preparation techniques commonly used for analytical and function-based proteomics and their effects on array-based assay performance.

An extremely simple method for fabricating 3D protein microarrays with an anti-fouling background and high protein capacity

Protein microarrays have become vital tools for various applications in biomedicine and bio-analysis during the past decade. The intense requirements for a lower detection limit and industrialization in this area have resulted in a persistent pursuit to fabricate protein microarrays with a low background and high signal intensity via simple methods. Here, we report on an extremely simple strategy to create three-dimensional (3D) protein microarrays with an anti-fouling background and a high protein capacity by photo-induced surface sequential controlled/living graft polymerization developed in our lab. According to this strategy, "dormant" groups of isopropyl thioxanthone semipinacol (ITXSP) were first introduced to a polymeric substrate through ultraviolet (UV)-induced surface abstraction of hydrogen, followed by a coupling reaction. Under visible light irradiation, the ITXSP groups were photolyzed to initiate surface living graft polymerization of poly(ethylene glycol) methyl methacrylate (PEGMMA), thus introducing PEG brushes to the substrate to generate a full anti-fouling background. Due to the living nature of this graft polymerization, there were still ITXSP groups on the chain ends of the PEG brushes. Therefore, by in situ secondary living graft cross-linking copolymerization of glycidyl methacrylate (GMA) and polyethylene glycol diacrylate (PEGDA), we could finally plant height-controllable cylinder microarrays of a 3D PEG network containing reactive epoxy groups onto the PEG brushes. Through a commonly used reaction of amine and epoxy groups, the proteins could readily be covalently immobilized onto the microarrays. This delicate design aims to overcome two universal limitations in protein microarrays: a full anti-fouling background can effectively eliminate noise caused by non-specific absorption and a 3D reactive network provides a larger protein-loading capacity to improve signal intensity. The results of non-specific protein absorption tests demonstrated that the introduction of PEG brushes greatly improved the anti-fouling properties of the pristine low-density polyethylene (LDPE), for which the absorption to bovine serum albumin was reduced by 83.3%. Moreover, the 3D protein microarrays exhibited a higher protein capacity than the controls to which were attached the same protein on PGMA brushes and monolayer epoxy functional groups. The 3D protein microarrays were used to test the immunoglobulin G (IgG) concentration in human serum, suggesting that they could be used for biomedical diagnosis, which indicates that more potential bio-applications could be developed for these protein microarrays in the future.

Effect of Sample Elevation in Radio Frequency Plasma Enhanced Chemical Vapor Deposition (RF PECVD) Reactor on Optical Properties and Deposition Rate of Silicon Nitride Thin Films

In this paper we investigate influence of radio frequency plasma enhanced chemical vapor deposition (RF PECVD) process parameters, which include gas flows, pressure and temperature, as well as a way of sample placement in the reactor, on optical properties and deposition rate of silicon nitride (SiN_x) thin films. The influence of the process parameters has been determined using Taguchi’s orthogonal tables approach. As a result of elevating samples above the electrode, it has been found that deposition rate strongly increases with distance between sample and the stage electrode, and reaches its maximum 7 mm above the electrode. Moreover, the refractive index of the films follows increase of the thickness. The effect can be observed when the thickness of the film is below 80 nm. It has been also found that when the deposition temperature is reduced down to 200 °C, as required for many temperature-sensitive substrate materials, the influence of the substrate material (Si or oxidized Si) can be neglected from the point of view of the properties of the films. We believe that the obtained results may help in designing novel complex in shape devices, where optical properties and thickness of thin plasma-deposited coatings need to be well defined.

Construction of DNA microarrays on cyclic olefin copolymer surfaces using confined photocatalytic oxidation

A novel strategy for DNA immobilization on cyclic olefin copolymer surfaces.

Biotinylation of silicon and nickel surfaces and detection of streptavidin as biosensor

The availability of metal mesh device sensors has been investigated using surface-modified nickel mesh. Biotin was immobilized on the sensor surfaces consisting of silicon and nickel via a thiol-ene click reaction, known as the Michael addition reaction. Biotinylation on the maleimidated surface was confirmed by X-ray photoelectron spectroscopy. The binding of streptavidin to the biotinylated surfaces was evaluated using a quartz crystal microbalance and a metal mesh device sensor, with both techniques providing similar binding constant value. The recognition ability of the biotin immobilized using the thiol-maleimide method for streptavidin was comparable to that of biotin immobilized via several other methods. The adsorption of a biotin conjugate onto the streptavidin-immobilized surface via the biotin-streptavidin-biotin sandwich method was evaluated using a fluorescent microarray, with the results demonstrating that the biological activity of the streptavidin remained.

Surface modification of siliceous materials using maleimidation and various functional polymers synthesized by reversible addition-fragmentation chain transfer polymerization

A novel surface modification method was investigated. The surface of siliceous materials was modified using polystyrene, poly(acrylic acid), poly(N-isopropylacrylamide), and poly(p-acrylamidophenyl-α-mannoside) synthesized by reversible addition-fragmentation chain transfer polymerization. Thiol-terminated polymers were obtained by reduction of the thiocarbonate group using sodium borohydride. The polymers were immobilized on the surface via the thiol-ene click reaction, known as the Michael addition reaction. Immobilization of the polymers on the maleimidated surface was confirmed by X-ray photoelectron spectroscopy, infrared spectroscopy, and contact angle measurements. The polymer-immobilized surfaces were observed by atomic force microscopy, and the thickness of the polymer layers was determined by ellipsometry. The thickness of the polymer immobilized by the maleimide-thiol reaction was less than that formed by spin coating, except for polystyrene. Moreover, the polymer-immobilized surfaces were relatively smooth with a roughness of less than 1 nm. The amounts of amine, maleimide, and polymer immobilized on the surface were determined by quartz crystal microbalance measurements. The area occupied by the amine-containing silane coupling reagent was significantly less than the theoretical value, suggesting that a multilayer of the silane coupling reagent was formed on the surface. The polymer with low molecular weight had the tendency to efficiently immobilize on the maleimidated surface. When poly(p-acrylamidophenyl-α-mannoside)-immobilized surfaces were used as a platform for protein microarrays, strong interactions were detected with the mannose-binding lectin concanavalin A. The specificity of poly(p-acrylamidophenyl-α-mannoside)-immobilized surfaces for concanavalin A was compared with poly-l-lysine-coated surfaces. The poly-l-lysine-coated surfaces nonspecifically adsorbed both concanavalin A and bovine serum albumin, while the poly(p-acrylamidophenyl-α-mannoside)-immobilized surface preferentially adsorbed concanavalin A. Moreover, the poly(p-acrylamidophenyl-α-mannoside)-immobilized surface was applied to micropatterning with photolithography. When the micropattern was formed on the poly(p-acrylamidophenyl-α-mannoside)-spin-coated surface by irradiation with ultraviolet light, the pattern of the masking design was not observed on the surface adsorbed with fluorophore-labeled concanavalin A using a fluorescent microscope because of elution of poly(p-acrylamidophenyl-α-mannoside) from the surface. In contrast, fluorophore-labeled concanavalin A was only adsorbed on the shaded region of the poly(p-acrylamidophenyl-α-mannoside)-immobilized surface, resulting in a distinctive fluorescent pattern. The surface modification method using maleimidation and reversible addition-fragmentation chain transfer polymerization can be used for preparing platforms for microarrays and micropatterning of proteins.

Copper-free click biofunctionalization of silicon nitride surfaces via strain-promoted alkyne-azide cycloaddition reactions

Cu-free "click" chemistry is explored on silicon nitride (Si(3)N(4)) surfaces as an effective way for oriented immobilization of biomolecules. An ω-unsaturated ester was grafted onto Si(3)N(4) using UV irradiation. Hydrolysis followed by carbodiimide-mediated activation yielded surface-bound active succinimidyl and pentafluorophenyl ester groups. These reactive surfaces were employed for the attachment of bicyclononyne with an amine spacer, which subsequently enabled room temperature strain-promoted azide-alkyne cycloaddition (SPAAC). This stepwise approach was characterized by means of static water contact angle, X-ray photoelectron spectroscopy, and fluorescence microscopy. The surface-bound SPAAC reaction was studied with both a fluorine-tagged azide and an azide-linked lactose, yielding hydrophobic and bioactive surfaces for which the presence of trace amounts of Cu ions would have been problematic. Additionally, patterning of the Si(3)N(4) surface using this metal-free click reaction with a fluorescent azide is shown. These results demonstrate the ability of the SPAAC as a generic tool for anchoring complex molecules onto a surface under extremely mild, namely ambient and metal-free, conditions in a clean and relatively fast manner.

Interfacial recognition of human prostate-specific antigen by immobilized monoclonal antibody: effects of solution conditions and surface chemistry

The specific recognition between monoclonal antibody (anti-human prostate-specific antigen, anti-hPSA) and its antigen (human prostate-specific antigen, hPSA) has promising applications in prostate cancer diagnostics and other biosensor applications. However, because of steric constraints associated with interfacial packing and molecular orientations, the binding efficiency is often very low. In this study, spectroscopic ellipsometry and neutron reflection have been used to investigate how solution pH, salt concentration and surface chemistry affect antibody adsorption and subsequent antigen binding. The adsorbed amount of antibody was found to vary with pH and the maximum adsorption occurred between pH 5 and 6, close to the isoelectric point of the antibody. By contrast, the highest antigen binding efficiency occurred close to the neutral pH. Increasing the ionic strength reduced antibody adsorbed amount at the silica-water interface but had little effect on antigen binding. Further studies of antibody adsorption on hydrophobic C8 (octyltrimethoxysilane) surface and chemical attachment of antibody on (3-mercaptopropyl)trimethoxysilane/4-maleimidobutyric acid N-hydroxysuccinimide ester-modified surface have also been undertaken. It was found that on all surfaces studied, the antibody predominantly adopted the 'flat on' orientation, and antigen-binding capabilities were comparable. The results indicate that antibody immobilization via appropriate physical adsorption can replace elaborate interfacial molecular engineering involving complex covalent attachments.

Mapping spatiotemporal molecular distributions using a microfluidic array

The spatial and temporal distributions of an extensive number of diffusible molecules drive a variety of complex functions. These molecular distributions often possess length scales on the order of a millimeter or less; therefore, microfluidic devices have become a powerful tool to study the effects of these molecular distributions in both chemical and biological systems. Although there exist a number of studies utilizing microdevices for the creation of molecular gradients, there are few, if any, studies focusing on the measurement of spatial and temporal distributions of molecular species created within the study system itself. Here we present a microfluidic device capable of sampling multiple chemical messengers in a spatiotemporally resolved manner. This device operates through spatial segregation of nanoliter-sized volumes of liquid from a primary sample reservoir into a series of analysis microchannels, where fluid pumping is accomplished via a system of passive microfluidic pumps. Subsequent chemical analysis within each microchannel, achieved via optical or bioanalytical methods, yields quantitative data on the spatial and temporal information for any analytes of interest existing within the sample reservoir. These techniques provide a simple, cost-effective route to measure the spatiotemporal distributions of molecular analytes, where the system can be tailored to study both chemical and biological systems.

Photochemical properties and sensor applications of modified yellow fluorescent protein (YFP) covalently attached to the surfaces of etched optical fibers (EOFs)

Fluorescent proteins have the inherent ability to act as sensing components which function both in vitro and inside living cells. We describe here a novel study on a covalent site-specific bonding of fluorescent proteins to form self-assembled monolayers (SAMs) on the surface of etched optical fibers (EOFs). Deposition of fluorescent proteins on EOFs gives the opportunity to increase the interaction of guided light with deposited molecules relative to plane glass surfaces. The EOF modification is carried out by surface activation using 3-aminopropylthrimethoxysilane (APTMS) and bifunctional crosslinker sulfosuccinimidyl 4-[N-maleimidomethyl]cyclohexane-1-carboxylate (sulfo-SMCC) which exposes sulfhydryl-reactive maleimide groups followed by covalent site-specific coupling of modified yellow fluorescent protein (YFP). Steady-state and fluorescence lifetime measurements confirm the formation of SAM. The sensor applications of YPF SAMs on EOF are demonstrated by the gradual increase of emission intensity upon addition of Ca(2+) ions in the concentration range from a few tens of micromolars up to a few tens of millimolars. The studies on the effect of pH, divalent cations, denaturing agents, and proteases reveal the stability of YFP on EOFs at normal physiological conditions. However, treatments with 0.5% SDS at pH 8.5 and protease trypsin are found to denaturate or cleave the YFP from fiber surfaces.

Effect of co-axially hybridized gene targets on hybridization efficiency of microarrayed DNA probes

The effect of relative size of two co-axially hybridized gene targets on the hybridization efficiency was studied for two DNA probe configurations and various probe concentrations. Each of two sets of microarrayed probes contained a pair of DNA probes and a pair of their complementary samples labeled with two distinct fluorescent dyes. The sequence of each probe is especially designed so that two targets are simultaneously complementary to two adjacent sections of the probe. The molecular steric effect on the hybridization efficiency is investigated by comparing the dye signals between configurations of one-target and two-target hybridization scenarios. The results show that a low probe concentration gives better hybridization efficiency and the first-hybridization conducted by a shorter-size DNA target improves the hybridization efficiency of the second target coupling onto the same probe.

Investigation of non-nucleophilic additives for the reduction of morphological anomalies in protein arrays

Uniform spot morphology is of critical importance in the fabrication and successful use of protein arrays, and solution additives are often needed to ensure good spot quality. Whereas hydroxyl-bearing molecules such as glycerol have found wide use, in our experience these reduce the efficiency of probe immobilization (particularly in the context of aldehyde-terminated surfaces). Here, we report a series of non-nucleophilic molecules that can be used as additives to improve spot homogeneity in protein arrays. Arrayed imaging reflectometry, a label-free optical biosensing technique, has been used along with spectroscopic ellipsometry to test the spot homogeneity, antibody immobilization efficiency, and activity of antihuman IgG arrays prepared with these non-nucleophilic additives on glutaraldehyde surfaces. It has been determined that 0.1% v/v 12-crown-4 performs optimally in MPBS buffer.

Diagnostic devices as biomaterials: a review of nucleic acid and protein microarray surface performance issues

This review of current DNA and protein microarray diagnostic and bio-analytical technologies focuses on the different surface chemistries used in these miniaturized surface-capture formats. Description of current strategies in bio-immobilization and coupling to create multiplexed affinity bioassays in micrometer-sized printed spots, problems with current formats and review of some detection methods are included. Recommendations for improving long-standing challenges in DNA- and protein-based arrays are forwarded. The biomaterials community can contribute relevant expertise to these formidable bio-interfacial problems that represent significant barriers to clinical implementation of microarray assays.

Influence of nanometric holes on the sensitivity of a waveguide-mode sensor: label-free nanosensor for the analysis of RNA aptamer-ligand interactions

Evanescent-field-coupled (EFC) waveguide-mode sensors can be used to detect nucleic acids or proteins from the changes in the local index of refraction upon adsorption of the target molecule on a waveguide surface. We recently described an EFC waveguide-mode sensor in which nanometric holes on a waveguide film resulted in an improved sensitivity in the analysis of the interactions of biomolecules. In the present study, we have shown that sensitivity depends upon the diameter of the holes, where increase in diameter of holes increases spectral shift resulting in an improved sensitivity. Using this improved EFC waveguide-mode sensor, we could detect interactions between RNA and a small ligand, cyanocobalamin (vitamin B 12), and between RNA and a protein (human coagulation factor IXa). These two interactions were monitored on surfaces modified with biotin-streptavidin-biotin and N-(2-trifluoroethanesulfonatoethyl)- N-(methyl)triethoxysilylpropyl-3-amine, respectively.

Quantitation of surface coverage of oligonucleotides bound to chip surfaces: a fluorescence-based approach using alkaline phosphatase digestion

Silanized chip surfaces provide a reliable substrate for immobilization of oligonucleotides. The ability for rapid and sensitive detection of oligonucleotide surface coverage on these chips is crucial for their wide and effective applications in biotechnology. In this paper, two different silanization procedures were used to covalently bind fluorescent-labeled single-stranded DNA onto silicon dioxide or nitride chip surfaces. Effects of surface functionalization techniques for different surfaces, and immobilization conditions, including buffers and solution ionic strength, on surface probe coverage were investigated, quantifying the endpoint probe density by fluorescent measurement upon digestion with alkaline phosphatase (ALP). Digestion of surface-immobilized oligonuleotides with ALP released the fluorophore-tagged probe fragments back into the solution. The detection of DNA was accomplished by laser-induced fluorescence detection of the solution containing those cleaved fragments. The probe surface density on gold thin film, determined by ALP-digestion, was found to coincide well with that measured using the conventional alkanethiol-based fluorescence-displacement technique for the same system. The developed method has important implications for evaluating the performance of different oligonucleotide immobilization strategies. Also, it has the potential to serve as a sample-thrifty, time saving, and therefore routine tool to realize more realistic, practical quantification of the surface coverage of oligonucleotides immobilized on any solid surfaces.

The incredible shrinking world of DNA microarrays

The efficacy of microarrays in examining gene expression, gene and genome structure, protein-DNA interactions, whole-genome similarities and differences, microRNA expression, methylation (and more) is no longer in question. It is a fast-developing, cutting edge technology that has grown up along with massive sequence databases and is likely to become part of everyday patient care. Many advances have recently expanded the power and utility of microarrays; among them is our development of a new array tiling technique that dramatically increases the scope of coverage of an oligonucleotide tiling array without substantially increasing its cost.

Enhancement of target-DNA hybridization efficiency by pre-hybridization on sequence-orientated micro-arrayed probes

The enhancement of hybridization efficiency of deoxyribonucleic acid (DNA) targets using oligonucleotide pre-hybridization is studied on two sequence-inversed micro-arrayed probes. The sequences for pre-hybridizing both oligo and target DNA are designed to be fully complementary with their shared DNA probe in a coaxial stacking configuration; i.e. they hybridize immediately alongside each other along the continuous complement probe strand. The pre-hybridizing oligo and target DNA are differentiated by being labeled with two distinct fluorescent dyes, and the cooperative effect on hybridization efficiency is investigated through the comparison of the stacking and individual hybridization configurations based on the detection signals of the labeling dyes. The results show that the pre-hybridization of a DNA oligo enhances the subsequent hybridization efficiency of the target-DNA coupling onto the same probe. The efficiency is enhanced if the hybridization position occurs at a site close to the substrate surface.

Competitive immunoassays for simultaneous detection of metabolites and proteins using micromosaic patterning

New high-throughput immunoassay methods for rapid point-of-care diagnostic applications represent an unmet need and current focus of numerous innovative methods. We report a new micromosaic competitive immunoassay developed for the analysis of the thyroid hormone thyroxine (T4), inflammation biomarker C-reactive protein (CRP), and the oxidative damage marker 3-nitrotyrosine (BSA-3NT) on a silicon nitride substrate. To demonstrate the versatility of the method, both direct and indirect format competitive immunoassays were developed and could be applied simultaneously for single samples. Signals from standard solutions were fit to a logistic equation, allowing simultaneous detection of T4 (7.7-257.2 nM), CRP (0.3-4.2 microg/mL), and BSA-3NT (0.03-22.3 microg/mL). Total assay time including sample introduction, washing, and fluorescence measurement was less than 45 min. Dissociation constants for affinity pairs in the system have been estimated using regression. This proof-of-concept experiment shows that both small and macromolecular biomarkers can be quantified from a single sample using the method and suggests that groups of clinically related analytes may be analyzed by competitive micromosaic immunoassay techniques.

Computer modeling in biotechnology: a partner in development

Computational modeling can be a useful partner in biotechnology, in particular, in nanodevice engineering. Such modeling guides development through nanoscale views of biomolecules and devices not available through experimental imaging methods. We illustrate the role of computational modeling, mainly of molecular dynamics, through four case studies: development of silicon bionanodevices for single molecule electrical recording, development of carbon nano-tube-biomolecular systems as in vivo sensors, development of lipoprotein nanodiscs for assays of single membrane proteins, and engineering of oxygen tolerance into the enzyme hydrogenase for photosynthetic hydrogen gas production. The four case studies show how molecular dynamics approaches were adapted to the specific technical uses through (i) multi-scale extensions, (ii) fast quantum chemical force field evaluation, (iii) coarse graining, and (iv) novel sampling methods. The adapted molecular dynamics simulations provided key information on device behavior and revealed development opportunities, arguing that the "computational microscope" is an indispensable nanoengineering tool.

Structure and DNA hybridization properties of mixed nucleic acid/maleimide-ethylene glycol monolayers

The surface structure and DNA hybridization performance of thiolated single-strand DNA (HS-ssDNA) covalently attached to a maleimide-ethylene glycol disulfide (MEG) monolayer on gold have been investigated. Monolayer immobilization chemistry and surface coverage of reactive ssDNA probes were studied by X-ray photoelectron spectroscopy and time-of-flight secondary ion mass spectrometry. Orientation of the ssDNA probes was determined by near-edge X-ray absorption fine structure (NEXAFS). Target DNA hybridization on the DNA-MEG probe surfaces was measured by surface plasmon resonance (SPR) to demonstrate the utility of these probe surfaces for detection of DNA targets from both purified target DNA samples and complex biological mixtures such as blood serum. Data from complementary techniques showed that immobilized ssDNA density is strongly dependent on the spotted bulk DNA concentration and buffer ionic strength. Variation of the immobilized ssDNA density had a profound influence on the DNA probe orientation at the surface and subsequent target hybridization efficiency. With increasing surface probe density, NEXAFS polarization dependence results (followed by monitoring the N 1s --> pi* transition) indicate that the immobilized ssDNA molecules reorient toward a more upright position on the MEG monolayer. SPR assays of DNA targets from buffer and serum showed that DNA hybridization efficiency increased with decreasing surface probe density. However, target detection in serum was better on the "high-density" probe surface than on the "high-efficiency" probe surface. The amounts of target detected for both ssDNA surfaces were several orders of magnitude poorer in serum than in purified DNA samples due to nonspecific serum protein adsorption onto the sensing surface.

Comparison of hydroxylated print additives on antibody microarray performance

Various hydroxylated additives were added to antibody print buffers at different concentrations to stabilize printed antibodies during normal array spot desiccation on commercial polymer-coated microarray slides. Polyvinyl alcohol addition to print buffers produced the most regular spot morphologies, homogeneous intra-spot antibody distribution, uniform fluorescence intensity, and improved analyte capture activity, maintained up to 1 month at 4 degrees C for capturing model analytes, anti-human IL-1beta, IL-4, and TNFalpha, on these microarraying slides.

Surface Modification for DNA and Protein Microarrays

Microarrays of biomolecules are emerging as powerful tools for genomics, proteomics, and clinical assays, since they make it possible to screen biologically important binding events in a parallel and high throughput fashion. Because the microarrays are fabricated on a solid support, coating of the surface and immobilization strategy of the biomolecules are major issues for successful microarray fabrication. This review deals with both DNA microarrays and protein microarrays, and focuses on the various modification approaches for the two-dimensional surface materials and three-dimensional ones. In addition, the immobilization strategies including adsorption, covalent attachment, physical entrapment, and affinity attachment of the biomolecules are summarized, and advantage and limitation of representative efforts are discussed.

A novel route for immobilization of oligonucleotides onto modified silica nanoparticles

A novel approach for immobilization of probe oligonucleotides that uses zirconium phosphate modified silica nanoparticles is proposed. The surface modification of nanoparticles was carried out in two stages. Initially binding of Zr4+ to the surface of silica nanoparticles and later treated with phosphoric acid for terminal phosphate groups. Oligonucleotide probes modified with amine group at 5'-end were strongly binds to the phosphate terminated silica nanoparticles with imidazole in presence of 0.1 mol L(-1) EDC [N-ethyl-N'-(3-dimethylaminopropyl) carbodiimide], as phosphate groups are more reactive towards amine group. Various studies, i.e., synthesis of silica nanoparticles, their surface modification, probe immobilization, measurement of hybridization and effect of bovine serum albumin (BSA) were carried out during optimization of reaction conditions. The significant reduction in the background signal was observed by treating the probe modified silica nanoparticles with bovine serum albumin prior to hybridization. The probe modified silica nanoparticles were retained their properties and the hybridization was induced by exposure of single-stranded DNA (ssDNA) containing silica nanoparticles to the complementary DNA in solution. The decrease in the fluorescence signal for one mismatch and three mismatch was observed upon hybridization of probe with target DNAs, while there was no response for the random target ssDNA under the same experimental conditions. The intensity of fluorescence signal was linear to the concentration of target DNA ranging from 3.9 x 10(-9) to 3.0 x 10(-6)mol L(-1). A detection limit of 1.22 x 10(-9) mol L(-1) of oligonucleotides can be estimated. The proposed hybridization assay is simple and possesses good analytical characteristics and it can provide an effective and efficient route in the development of DNA biosensors and biochips.