Submicron streptavidin patterns for protein assembly

New Aldehyde-Functional Methacrylic Water-Soluble Polymers

Aldehyde groups enable facile conjugation to proteins, enzymes, oligonucleotides or fluorescent dyes, yet there are no literature examples of water-soluble aldehyde-functional vinyl monomers. We report the synthesis of a new hydrophilic cis-diol-based methacrylic monomer (GEO5MA) by transesterification of isopropylideneglycerol penta(ethylene glycol) using methyl methacrylate followed by acetone deprotection via acid hydrolysis. The corresponding water-soluble aldehyde monomer, AGEO5MA, is prepared by aqueous periodate oxidation of GEO5MA at 22 °C. RAFT polymerization of GEO5MA yields the water-soluble homopolymer, PGEO5MA. Aqueous periodate oxidation of the terminal cis-diol units on PGEO5MA at 22 °C affords a water-soluble aldehyde-functional homopolymer (PAGEO5MA). Moreover, a library of hydrophilic statistical copolymers bearing cis-diol and aldehyde groups was prepared using sub-stoichiometric periodate/cis-diol molar ratios. The aldehyde groups on PAGEO5MA homopolymer were reacted in turn with three amino acids to demonstrate synthetic utility.

A Fast and Simple Contact Printing Approach to Generate 2D Protein Nanopatterns

Protein micropatterning has become an important tool for many biomedical applications as well as in academic research. Current techniques that allow to reduce the feature size of patterns below 1 μm are, however, often costly and require sophisticated equipment. We present here a straightforward and convenient method to generate highly condensed nanopatterns of proteins without the need for clean room facilities or expensive equipment. Our approach is based on nanocontact printing and allows for the fabrication of protein patterns with feature sizes of 80 nm and periodicities down to 140 nm. This was made possible by the use of the material X-poly(dimethylsiloxane) (X-PDMS) in a two-layer stamp layout for protein printing. In a proof of principle, different proteins at various scales were printed and the pattern quality was evaluated by atomic force microscopy (AFM) and super-resolution fluorescence microscopy.

Porous Silicon-Based Biosensors: Towards Real-Time Optical Detection of Target Bacteria in the Food Industry

Rapid detection of target bacteria is crucial to provide a safe food supply and to prevent foodborne diseases. Herein, we present an optical biosensor for identification and quantification of Escherichia coli (E. coli, used as a model indicator bacteria species) in complex food industry process water. The biosensor is based on a nanostructured, oxidized porous silicon (PSi) thin film which is functionalized with specific antibodies against E. coli. The biosensors were exposed to water samples collected directly from process lines of fresh-cut produce and their reflectivity spectra were collected in real time. Process water were characterized by complex natural micro-flora (microbial load of >10⁷ cell/mL), in addition to soil particles and plant cell debris. We show that process water spiked with culture-grown E. coli, induces robust and predictable changes in the thin-film optical interference spectrum of the biosensor. The latter is ascribed to highly specific capture of the target cells onto the biosensor surface, as confirmed by real-time polymerase chain reaction (PCR). The biosensors were capable of selectively identifying and quantifying the target cells, while the target cell concentration is orders of magnitude lower than that of other bacterial species, without any pre-enrichment or prior processing steps.

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.

High-yielding and photolabile approaches to the covalent attachment of biomolecules to surfaces via hydrazone chemistry

The development of strategies to couple biomolecules covalently to surfaces is necessary for constructing sensing arrays for biological and biomedical applications. One attractive conjugation reaction is hydrazone formation--the reaction of a hydrazine with an aldehyde or ketone--as both hydrazines and aldehydes/ketones are largely bioorthogonal, which makes this particular reaction suitable for conjugating biomolecules to a variety of substrates. We show that the mild reaction conditions afforded by hydrazone conjugation enable the conjugation of DNA and proteins to the substrate surface in significantly higher yields than can be achieved with traditional bioconjugation techniques, such as maleimide chemistry. Next, we designed and synthesized a photocaged aryl ketone that can be conjugated to a surface and photochemically activated to provide a suitable partner for subsequent hydrazone formation between the surface-anchored ketone and DNA- or protein-hydrazines. Finally, we exploit the latent functionality of the photocaged ketone and pattern multiple biomolecules on the same substrate, effectively demonstrating a strategy for designing substrates with well-defined domains of different biomolecules. We expect that this approach can be extended to the production of multiplexed assays by using an appropriate mask with sequential photoexposure and biomolecule conjugation steps.

A step closer to membrane protein multiplexed nanoarrays using biotin-doped polypyrrole

Whether for fundamental biological research or for diagnostic and drug discovery applications, protein micro- and nanoarrays are attractive technologies because of their low sample consumption, high-throughput, and multiplexing capabilities. However, the arraying platforms developed so far are still not able to handle membrane proteins, and specific methods to selectively immobilize these hydrophobic and fragile molecules are needed to understand their function and structural complexity. Here we integrate two technologies, electropolymerization and amphipols, to demonstrate the electrically addressable functionalization of micro- and nanosurfaces with membrane proteins. Gold surfaces are selectively modified by electrogeneration of a polymeric film in the presence of biotin, where avidin conjugates can then be selectively immobilized. The method is successfully applied to the preparation of protein-multiplexed arrays by sequential electropolymerization and biomolecular functionalization steps. The surface density of the proteins bound to the electrodes can be easily tuned by adjusting the amount of biotin deposited during electropolymerization. Amphipols are specially designed amphipathic polymers that provide a straightforward method to stabilize and add functionalities to membrane proteins. Exploiting the strong affinity of biotin for streptavidin, we anchor distinct membrane proteins onto different electrodes via a biotin-tagged amphipol. Antibody-recognition events demonstrate that the proteins are stably immobilized and that the electrodeposition of polypyrrole films bearing biotin units is compatible with the protein-binding activity. Since polypyrrole films show good conductivity properties, the platform described here is particularly well suited to prepare electronically transduced bionanosensors.

Effect of avidin-like proteins and biotin modification on mesenchymal stem cell adhesion

The avidin-biotin system is a highly specific reaction that has been used in a wide range of biomedical applications, including surface modification and cell patterning. We systematically examined a number of avidin derivatives as the basis for a simple and cost effective tissue culture polystyrene substrate surface modification for human stem cell culture. Non-specific adhesion between human mesenchymal stem cells and various avidin derivatives, media conditions, and subsequent biotinylation reactions was quantified. We observed significant non-specific cell adhesion to avidin and strepthavidin, indicating that previous observations using this system may be artifactual. Seeding of cells in serum free media, blocking with bovine serum albumin, and the use of the avidin derivative neutravidin were all necessary for elimination of background adhesion. Neutravidin conjugated with biotinylated bsp-RGD(15) peptide provided the most robust cell adhesion, as well as the greatest increase in cell adhesion over background levels.

Immobilization of proteins on carboxylic acid functionalized nanopatterns

The immobilization of proteins on nanopatterned surfaces was investigated using in situ atomic force microscopy (AFM) and ex situ infrared reflectance-absorption spectroscopy (IRAS). The AFM-based lithography technique of nanografting provided control of the size, geometry, and spatial placement of nanopatterns within self-assembled monolayers (SAMs). Square nanopatterns of carboxylate-terminated SAMs were inscribed within methyl-terminated octadecanethiolate SAMs and activated using carbodiimide/succinimide coupling chemistry. Staphylococcal protein A was immobilized on the activated nanopatterns before exposure to rabbit immunoglobulin G. In situ AFM was used to monitor changes in the topography and friction of the nanopatterns in solution upon protein immobilization. Complementary studies with ex situ IRAS confirmed the surface chemistry that occurred during the steps of SAM activation and subsequent protein immobilization on unpatterned samples. Since carbodiimide/succinimide coupling chemistry can be used for surface attachment of different biomolecules, this protocol shows promise for development of other aqueous-based studies for nanopatterned protein immobilization.

Direct biomolecule binding on nonfouling surfaces via newly discovered supramolecular self-assembly of lysozyme under physiological conditions

When lysozyme is dissolved in a neutral HEPES buffer solution (pH = 7.4) with 0.001-0.050 M TCEP added, a fast phase transition process occurs and the resulting novel fiber-like hierarchical supramolecular assemblies made by primary spherical-particle aggregation can function as a "superglue" that binds strongly and quickly onto non-fouling coatings. This binding is highly selective towards lysozyme, and excludes synthetic, chemical/physical activation/deactivation (blocking) steps. By using biotinylated lysozyme, such a phase transition quickly creates a perfect biotinylated surface on non-fouling surfaces for avidin binding, showing great potential for the development of low-cost and practical biochips.

Different EDC/NHS activation mechanisms between PAA and PMAA brushes and the following amidation reactions

Infrared spectroscopy was applied to investigate the well-known EDC/NHS (N-ethyl-N'-(3-(dimethylamino)propyl)carbodiimide/N-hydroxysuccinimide) activation details of poly(acrylic acid) (PAA) and poly(methacrylic acid) (PMAA) brushes grafted on porous silicon. Succinimidyl ester (NHS-ester) is generally believed to be the dominant intermediate product, conveniently used to immobilize biomolecules containing free primary amino groups via amide linkage. To our surprise, the infrared spectral details revealed that the EDC/NHS activation of PMAA generated anhydride (estimated at around 76% yield and 70% composition), but not NHS-ester (around 5% yield and 11% composition) under the well-documented reaction conditions, as the predominant intermediate product. In contrast, EDC/NHS activation of PAA still follows the general rule, i.e., the expected NHS-ester is the dominant intermediate product (around 45% yield and 57% composition), anhydride the side product (40% yield and 28% composition), under the optimum reaction conditions. The following amidation on PAA-based NHS-esters with a model amine-containing compound, L-leucine methyl ester, generated approximately 70% amides and 30% carboxylates. In contrast, amidation of PAA- or PMAA-based anhydrides with L-leucine methyl ester only produced less than 30% amides but more than 70% carboxylates. The above reaction yields and percentage compositions were estimated by fitting the carbonyl stretching region with 5 possible species, NHS-ester, anhydride, N-acylurea, unreacted acid, unhydrolyzed tert-butyl ester, and using the Beer-Lambert law. The different surface chemistry mechanisms will bring significant effects on the performance of surface chemistry-derived devices such as biochips, biosensors, and biomaterials.

Conductive AFM patterning on oligo(ethylene glycol)-terminated alkyl monolayers on silicon substrates: proposed mechanism and fabrication of avidin patterns

Micro- and nanopatterns of biomolecules on inert, ultrathin platforms on nonoxidized silicon are ideal interfaces between silicon-based microelectronics and biological systems. We report here the local oxidation nanolithography with conductive atomic force microscopy (cAFM) on highly protein-resistant, oligo(ethylene glycol) (OEG)-terminated alkyl monolayers on nonoxidized silicon substrates. We propose a mechanism for this process, suggesting that it is possible to oxidize only the top ethylene glycol units to generate carboxylic acid and aldehyde groups on the film surface. We show that avidin molecules can be attached selectively to the oxidized pattern and the density can be varied by altering the bias voltage during cAFM patterning. Biotinylated molecules and nanoparticles are selectively immobilized on the resultant avidin patterns. Since one of the most established methods for immobilization of biomolecules is based on avidin-biotin binding and a wide variety of biotinylated biomolecules are available, this approach represents a versatile means for prototyping any nanostructures presenting these biomolecules on silicon substrates.

Protein nanopatterns by oxime bond formation

Patterning proteins on the nanoscale is important for applications in biology and medicine. As feature sizes are reduced, it is critical that immobilization strategies provide site-specific attachment of the biomolecules. In this study, oxime chemistry was exploited to conjugate proteins onto nanometer-sized features. Poly(Boc-aminooxy tetra(ethylene glycol) methacrylate) was synthesized by free radical polymerization. The polymer was patterned onto silicon wafers using an electron beam writer. Trifluoroacetic acid removal of the Boc groups provided the desired aminooxy functionality. In this manner, patterns of concentric squares and contiguous bowtie shapes were fabricated with 150-170-nm wide features. Ubiquitin modified at the N-terminus with an α-ketoamide group and N(ε)-levulinyl lysine-modified bovine serum albumin were subsequently conjugated to the polymer nanopatterns. Protein immobilization was confirmed by fluorescence microscopy. Control studies on protected surfaces and using proteins presaturated with O-methoxyamine indicated that attachment occurred via oxime bond formation.

Spatially addressable chemoselective C-terminal ligation of an intein fusion protein from a complex mixture to a hydrazine-terminated surface

Protein immobilization on surfaces is useful in many areas of research, including biological characterization, antibody purification, and clinical diagnostics. A critical limitation in the development of protein microarrays and heterogeneous protein-based assays is the enormous amount of work and associated costs in the purification of proteins prior to their immobilization onto a surface. Methods to address this problem would simplify the development of interfacial diagnostics that use a protein as the recognition element. Herein, we describe an approach for the facile, site-specific immobilization of proteins on a surface without any preprocessing or sample purification steps that ligates an intein fusion protein at its C-terminus by reaction with a hydrazine group presented by a surface. Furthermore, we demonstrate that this methodology can directly immobilize a protein directly from cell lysate onto a protein-resistant surface. This methodology is also compatible with soft lithography and inkjet printing so that one or more proteins can be patterned on a surface without the need for purification.

Enzyme-assisted photolithography for spatial functionalization of hydrogels

The ability to form functional polymeric patterning structures has important implications for the studies of cell biology, tissue engineering, and medical diagnostics. We have developed a novel enzyme-assisted photolithography (EAPL) method for spatial functionalization of hydrogels via a high throughput fashion. A bisacrylated peptide crosslinker, containing a protease cleavable amino acid sequence and caged by a photolabile moiety, is used during hydrogel polymerization. A facile two-step process is employed, including UV exposure to decage the peptide crosslinker at a desired area and protease development to specifically digest gels at UV treated regions only. Importantly, proteolysis of the peptide bonds generates free nucleophilic amine groups at the patterned area that can be further functionalized. Using this strategy and caspase-3 as the enzyme developer, we demonstrate the simultaneous generation of topographical and functional patterns into poly(ethylene glycol) (PEG) hydrogels. We show that 20 microm-wide line arrays functionalized with arginine-glycine-aspartic acid (RGD)-containing peptides can be used to generate cell patterns with individual cell resolution. We also fabricated arrays 20 mum diameter cavities decorated with B lymphocyte specific anti-CD19, which was used to achieve a 600-fold enrichment of B-cells from a 0.1% starting B-cell mixture. The simple fabrication process, straightforward chemistry and an all-aqueous based biocompatible and environmentally friendly approach render EAPL a versatile platform to construct biologically responsive 2D patterns or 3D scaffolds for lab-on-a-chip systems and tissue engineering.

Pattern formation and molecular transport of histidine-tagged GFPs using supported lipid bilayers

We fabricated a heterogeneous supported lipid bilayer (SLB) by employing binary lipid mixtures comprising a saturated acyl chain DSPC and an unsaturated acyl chain nickel-chelating lipid. By using the specific adsorption properties of histidine-tagged proteins (His-tagged GFPs) in relation to nickel-chelating lipids, we demonstrated protein pattern formation on the SLB corresponding to the phase separation pattern of the SLB. In addition, by using a lipid mixture consisting of an unsaturated acyl chain DOPC and a nickel-chelating lipid, and His-tagged GFPs, we succeeded in transporting the proteins along a hydrophilic micropattern on a SiO(2) substrate. The protein transport is induced by the self-spreading behavior of a fluid SLB with a kinetic spreading coefficient beta = 10.4 microm(2) s(-1). This method provides a guide for strategically carrying various biomolecules to specific positions by using a soft biointerface on a solid surface. In addition, the results demonstrate the importance of using techniques that allow the controlled manipulation of biomolecules based on the static or dynamic properties of the SLB platform.

Functional immobilization and patterning of proteins by an enzymatic transfer reaction

Functional immobilization and lateral organization of proteins into micro- and nanopatterns is an important prerequisite for miniaturizing bioanalytical and biotechnological devices. Here, we report an approach for efficient site-specific protein immobilization based on enzymatic phosphopantetheinyl transfer (PPT) from coenzyme A (CoA)-functionalized glass-type surfaces to specific peptide tags. We devised a bottom-up surface modification approach for coupling CoA densely to a molecular poly(ethylene glycol) polymer brush. Site-specific enzymatic immobilization of proteins fused to different target peptides for the PPTase Sfp was confirmed by real-time label-free detection. Quantitative protein-protein interaction experiments confirmed that significantly more than 50% of the immobilized protein was fully active. The method was successfully applied with different proteins. However, different immobilization efficiencies of PPT-based immobilization were observed for different peptide tags being fused to the N- and C-termini of proteins. On the basis of this immobilization method, we established photolithographic patterning of proteins into functional binary microstructures.

A simple approach to patterned protein immobilization on silicon via electrografting from diazonium salt solutions

A highly versatile method utilizing diazonium salt chemistry has been developed for the fabrication of protein arrays. Conventional ultraviolet mask lithography was used to pattern micrometer sized regions into a commercial photoresist on a highly doped p-type silicon (100) substrate. These patterned regions were used as a template for the electrochemical grafting of the in situ generated p-aminobenzenediazonium cation to form patterns of aminophenyl film on silicon. Immobilization of biomolecules was demonstrated by coupling biotin to the aminophenyl regions followed by reaction with fluorescently labeled avidin and visualization with fluorescence microscopy. This simple patterning strategy is promising for future application in biosensor devices.

Controlled oxidation, biofunctionalization, and patterning of alkyl monolayers on silicon and silicon nitride surfaces using plasma treatment

A new method is presented for the fast and reproducible functionalization of silicon and silicon nitride surfaces coated with covalently attached alkyl monolayers. After formation of a methyl-terminated 1-hexadecyl monolayer on H-terminated Si(100) and Si(111) surfaces, short plasma treatments (1-3 s) are sufficient to create oxidized functionalities without damaging the underlying oxide-free silicon. The new functional groups can, e.g., be derivatized using the reaction of surface aldehyde groups with primary amines to form imine bonds. In this way, plasma-treated monolayers on silicon or silicon nitride surfaces were successfully coated with nanoparticles, or proteins such as avidin. In addition, we demonstrate the possibility of micropatterning, using a soft contact mask during the plasma treatment. Using water contact angle measurements, ellipsometry, XPS, IRRAS, AFM, and reflectometry, proof of principle is demonstrated of a yet unexplored way to form patterned alkyl monolayers on oxide-free silicon surfaces.

Synthesis of Aminooxy End-functionalized pNIPAAm by RAFT Polymerization for Protein and Polysaccharide Conjugation

A Boc-protected aminooxy end-functionalized poly(N-isopropylacrylamide) (pNIPAAm) was synthesized by reversible addition-fragmentation chain transfer (RAFT) polymerization. The monomer was polymerized in the presence of a Boc-protected aminooxy trithiocarbonate chain transfer agent (CTA) utilizing 2,2'-azobis(2-isobutyronitrile) (AIBN) as the initiator in DMF at 70 °C. The final polymer had a number-average molecular weight (M(n)) of 4,200 Da as determined by (1)H NMR spectroscopy and a narrow polydispersity index (1.14) by gel permeation chromatography (GPC). The Boc group was removed, and the polymer was then incubated with N(ε)-levulinyl lysine-modified bovine serum albumin (BSA). Gel electrophoresis confirmed that the conjugation was successful. The aminooxy end-functionalized pNIPAAm was also immobilized on a gold surface after reduction of the trithiocarbonate end-group. The pNIPAAm surface was then incubated with an aldehyde-modified heparin to yield the polysaccharide-functionalized surface. All surface modifications were monitored by FT-IR spectroscopy.

Fabrication of mixed self-assembled monolayers designed for avidin immobilization by irradiation promoted exchange reaction

An applicability of irradiation-promoted exchange reaction (IPER) to the fabrication of mixed self-assembled monolayers (SAMs) composed of the protein-repelling matrix and the moieties bearing binding sites for specific attachment of a target protein is demonstrated. As test systems, we took mixed films of oligoethylene glycol (OEG)-substituted alkanethiols (OEG-ATs) and biotin-substituted alkanethiols (BATs) on Au{111}. Such SAMs are suitable for the specific immobilization of avidin protein and its variants. The composition of the mixed OEG-AT/BAT SAMs could be precisely controlled by varying the irradiation dose, which is important prerequisite for the fabrication of the respective patterns by electron-beam lithography. While the general trend in the immobilization of avidin onto the mixed OEG-AT/BAT SAMs prepared by IPER was found to be consistent with the earlier reports regarding the analogous films fabricated by the coassembly method, the concentration of the BAT component in the mixed SAMs needed for the maximum surface coverage of the specific protein was found to be somewhat lower, and the maximum avidin coverage somewhat higher in the case of IPER as compared to the coassembly method. We ascribe these differences to the lack of phase segregation and better separation of the individual BAT species in the OEG-AT matrix in the case of IPER.

Serial DNA immobilization in micro- and extended nanospace channels

That focused arrays, even with a small set of ligands, provide more data than single point experiments is well established in the DNA microarray research field, but microarray technology has yet to be transferred to fused silica microchips. Fused silica microchips have several attractive features such as stability to pressure, solvents, acids and bases, and can be fabricated with minute dimensions, making them good candidates for nanofluidic research. However, due to harsh bonding conditions, DNA ligands must be immobilized after fabrication, thus preventing standard microarray spotting techniques from being used. In this paper, we provide tools for serial DNA immobilization in fused silica microchips using UV. We report the synthesis of a new UV-linker which was used to covalently couple functional DNA oligos to the inside of channels in fused silica microchips. With some simple modifications to our mask aligner, we were able to transfer OHP mask patterns, which allows the creation of basically any pattern in the channels. The functionality of the oligos was measured through the binding of fluorophore-labeled complementary target oligos. We examined parameters influencing DNA immobilization, and carry-over between spots after consecutive immobilizations inside the same channel. We also report the first successful multiple immobilizations of functional DNA oligos inside single channels of extended nanospace depth (460 nm).

Biotin-avidin binding kinetics measured by single-molecule imaging

The high affinity of avidin for biotin has made it useful for many bioanalytical applications involving the immobilization of proteins, vesicles, and other biomolecules to surfaces. To understand the formation and stability of the resulting biotin-avidin complex, it is useful to know the kinetics of the binding reaction, especially for situations where the complex is formed at a liquid-solid interface typically used in sensor or separation applications. In this work, a single-molecule fluorescence method is developed for measuring the kinetics and affinity constant for the binding of neutravidin, a deglycosylated variant of avidin, to surface-immobilized biotin. Biotin was immobilized using succinimidyl ester chemistry onto amine sites on glass surfaces. The surface density of biotin was controlled by the extreme dilution of 3-aminopropyltriethoxysilane into a monolayer of 2-cyanoethyltriethoxysilane. The resulting biotin binding sites are spaced apart by micrometer distances, and this avoids crowding effects and makes the resolution of single molecules possible. The binding and unbinding of individual tetramethylrhodamine-labeled neutravidin molecules is measured in situ by total-internal-reflection fluorescence (TIRF) microscopy imaging. Single-molecule detection and counting is readily achieved by this measurement, where quantitative control is established by determining the probabilities of false positive and negative events based on the intensity distributions of background and single-molecule spots and by comparing the bound molecule populations with the independently measured density of binding sites on the surface. The kinetics of binding and unbinding are evaluated by intermittent imaging and counting the number of bound neutravidin molecules versus time, following introduction of a neutravidin solution or its replacement by buffer over the low-density biotinylated surface. The neutravidin binding kinetics were found to be fast, essentially diffusion-controlled, while the stability of the complex and its dissociation rate appear to be influenced by the chemistry of biotin immobilization.

Phototocatalytic lithography of poly(propylene sulfide) block copolymers: toward high-throughput nanolithography for biomolecular arraying applications

Photocatalytic lithography (PCL) is an inexpensive, fast, and robust method of oxidizing surface chemical moieties to produce patterned substrates. This technique has utility in basic biological research as well as various biochip applications. We report on porphyrin-based PCL for patterning poly(propylene sulfide) block copolymer films on gold substrates on the micrometer and submicrometer scales. We confirm chemical patterning with imaging ToF-SIMS and low-voltage SEM. Biomolecular patterning on micrometer and submicrometer scales is demonstrated with proteins, protein-linked beads. and fluorescently labeled proteins.

Chemical strategies for generating protein biochips

Protein biochips are at the heart of many medical and bioanalytical applications. Increasing interest has been focused on surface activation and subsequent functionalization strategies for immobilizing these biomolecules. Different approaches using covalent and noncovalent chemistry are reviewed; particular emphasis is placed on the chemical specificity of protein attachment and on retention of protein function. Strategies for creating protein patterns (as opposed to protein arrays) are also outlined. An outlook on promising and challenging future directions for protein biochip research and applications is also offered.

Surface-anchored poly(2-vinyl-4,4-dimethyl azlactone) brushes as templates for enzyme immobilization

We explored surface-anchored poly(2-vinyl-4,4-dimethyl azlactone) (PVDMA) brushes as potential templates for protein immobilization. The brushes were grown using atom transfer radical polymerization from surface-anchored initiators and characterized by a combination of ellipsometry, atomic force microscopy, and X-ray photoelectron spectroscopy. RNase A was immobilized as a model enzyme through the nucleophilic attack of azlactone by the amine groups in the lysines located in the protein. The surface density of RNase A increased linearly from 5 to 50 nm. For 50 nm thick poly(2-vinyl-4,4-dimethyl azlactone) brushes, 7.5 microg/cm2 of RNase A was bound. The kinetics and thermodynamics of RNase A immobilization, the activity relative to surface density, and the pH and temperature dependence were examined. A Langmuir-like model for binding kinetics indicates that the kinetics are controlled by the rate of adsorption of RNase A and has an adsorption rate constant, k(ads), of 2.8 x 10(-8) microg(-1) s(-1) cm3. A maximum relative activity of approximately 0.95, which is near the activity of free RNase A, was reached at 1.2 microg/cm2 (approximately 3.0 monolayers) of immobilized RNase A. The immobilized RNase A had a similar temperature and pH dependence as free RNase A, indicating no significant change in conformation. The PVDMA template was extended to other biotechnologically relevant enzymes, such as deoxyribonuclease I, glucose oxidase, glucoamylase, and trypsin, with relative activities higher than or comparable to those of enzymes immobilized by other means. PVDMA brushes offer an efficient route to immobilize proteins via the ring opening of azlactone without the need for activation or pretreatment while retaining high relative activities of the bound enzymes.

Photolithographic Approaches for Fabricating Highly Ordered Nanopatterned Arrays

In this work, we report that large area metal nanowire and polymer nanotube arrays were successfully patterned by photolithographic approach using anodic aluminum oxide (AAO) templates. Nanowires were produced by electrochemical deposition, and nanotubes by solution-wetting. The highly ordered patterns of nanowire and nanotube arrays were observed using scanning electron microscopy (SEM) and found to stand free on the substrate. The method is expected to play an important role in the application of microdevices in the future.

Simultaneous investigation of the influence of topography and charge on protein adsorption using artificial nanopatterns

The combined influence of surface topography and charge of a polymer surface on the adsorption of the protein avidin has been investigated. Atomic force microscopy contact mode imaging and charge writing were used to create defined topographical roughness and electrostatic charge patterns on the surface of polystyrene. Increased avidin adsorption was found on nanometer-size topographical patterns, but the adsorption remained unaffected by electrostatic patterns.

Polymeric brushes as functional templates for immobilizing ribonuclease A: study of binding kinetics and activity

The ability to immobilize proteins with high binding capacities on surfaces while maintaining their activity is critical for protein microarrays and other biotechnological applications. We employed poly(acrylic acid) (PAA) brushes as templates to immobilize ribonuclease A (RNase A), which is commonly used to remove RNA from plasmid DNA preparations. The brushes are grown by surface-anchored atom-transfer radical polymerization (ATRP) initiators. RNase A was immobilized by both covalent esterification and a high binding capacity metal-ion complexation method to PAA brushes. The polymer brushes immobilized 30 times more enzyme compared to self-assembled monolayers. As the thickness of the brush increases, the surface density of the RNase A increases monotonically. The immobilization was investigated by ellipsometry, X-ray photoelectron spectroscopy (XPS), thermogravimetric analysis (TGA), and near-edge X-ray absorption fine structure spectroscopy (NEXAFS). The activity of the immobilized RNase A was determined using UV absorbance. As much as 11.0 microg/cm(2) of RNase A was bound to PAA brushes by metal-ion complexation compared to 5.8 microg/cm(2) by covalent immobilization which is 30 and 16 times the estimated mass bound in a monolayer. The calculated diffusion coefficient D was 0.63 x 10(-14) cm(2)/s for metal-ion complexation and 0.71 x 10(-14) cm(2)/s for covalent immobilization. Similar values of D indicate that the binding kinetics is similar, but the thermodynamic equilibrium coverage varies with the binding chemistry. Immobilization kinetics and thermodynamics were characterized by ellipsometry for both methods. A maximum relative activity of 0.70-0.80 was reached between five and nine monolayers of the immobilized enzyme. However, the relative activity for covalent immobilization was greater than that of metal-ion complexation. Covalent esterification resulted in similar temperature dependence as free enzyme, whereas metal-ion complexation showed no temperature dependence indicating a significant change in conformation.