A novel glass slide-based peptide array support with high functionality resisting non-specific protein adsorption

Acid-Modulated Peptide Synthesis for Application on Oxide Biosensor Interfaces

In this paper we report an acid-modulated strategy for novel peptide microarray production on biosensor interfaces. We initially selected a controlled pore glass (CPG) as a support for solid-phase peptide synthesis (SPPS) to implement a chemistry that can be performed at the interface of multiple field effect transistor (FET) sensors, eventually to generate label-free peptide microarrays for protein screening. Our chemistry uses a temporary protection of the N-terminal amino function of each amino acid building block with a tert-butyloxycarbonyl (Boc) group that can be removed after each SPPS cycle, in combination with semi-permanent protection of the side chains of trifunctional amino acid residues. Such a protection scheme with a well-proven record of application in conventional, batchwise SPPS has been fine-tuned for optimal performance on CPG and, from there, translated to SPR chips that allow layer-by-layer monitoring of amino acid coupling. Our results validate this acid-modulated synthesis as a feasible approach for producing peptides in high yields and purity on flat glass surfaces, such as those in bio-FETs.

Massively-multiplexed epitope mapping techniques for viral antigen discovery

Following viral infection, viral antigens bind specifically to receptors on the surface of lymphocytes thereby activating adaptive immunity in the host. An epitope, the smallest structural and functional unit of an antigen, binds specifically to an antibody or antigen receptor, to serve as key sites for the activation of adaptive immunity. The complexity and diverse range of epitopes are essential to study and map for the diagnosis of disease, the design of vaccines and for immunotherapy. Mapping the location of these specific epitopes has become a hot topic in immunology and immune therapy. Recently, epitope mapping techniques have evolved to become multiplexed, with the advent of high-throughput sequencing and techniques such as bacteriophage-display libraries and deep mutational scanning. Here, we briefly introduce the principles, advantages, and disadvantages of the latest epitope mapping techniques with examples for viral antigen discovery.

Pesticides monitoring in biological fluids: Mapping the gaps in analytical strategies

Pesticides play a key-role in the development of the agrifood sector allowing controlling pest growth and, thus, improving the production rates. Pesticides chemical stability is responsible of their persistency in environmental matrices leading to bioaccumulation in animal tissues and hazardous several effects on living organisms. The studies regarding long-term effects of pesticides exposure and their toxicity are still limited to few studies focusing on over-exposed populations, but no extensive dataset is currently available. Pesticides biomonitoring relies mainly on chromatographic techniques coupled with mass spectrometry, whose large-scale application is often limited by feasibility constraints (costs, time, etc.). On the contrary, chemical sensors allow rapid, in-situ screening. Several sensors were designed for the detection of pesticides in environmental matrices, but their application in biological fluids needs to be further explored. Aiming at contributing to the implementation of pesticides biomonitoring methods, we mapped the main gaps between screening and chromatographic methods. Our overview focuses on the recent advances (2016-2021) in analytical methods for the determination of commercial pesticides in human biological fluids and provides guidelines for their application.

Selective C-Terminal Conjugation of Protease-Derived Native Peptides for Proteomic Measurements

Bottom-up proteomic experiments often require selective conjugation or labeling of the N- and/or C-termini of peptides resulting from proteolytic digestion. For example, techniques based on surface fluorescence imaging are emerging as a promising route to high-throughput protein sequencing but require the generation of peptide surface arrays immobilized through single C-terminal point attachment while leaving the N-terminus free. While several robust approaches are available for selective N-terminal conjugation, it has proven to be much more challenging to implement methods for selective labeling or conjugation of the C-termini that can discriminate between the C-terminal carboxyl group and other carboxyl groups on aspartate and glutamate residues. Further, many approaches based on conjugation through amide bond formation require protection of the N-terminus to avoid unwanted cross-linking reactions. To overcome these challenges, herein, we describe a new strategy for single-point selective immobilization of peptides generated by protease digestion via the C-terminus. The method involves immobilization of peptides via lysine amino acids which are found naturally at the C-terminal end of cleaved peptides from digestions of certain serine endoproteinases, like LysC. This lysine and the N-terminus, the sole two primary amines in the peptide fragments, are chemically reacted with a custom phenyl isothiocyanate (EPITC) that contains an alkyne handle. Subsequent exposure of the double-modified peptides to acid selectively cleaves the N-terminal amino acid, while the modified C-terminus lysine remains unchanged. The alkyne-modified peptides with free N-termini can then be immobilized on an azide surface through standard click chemistry. Using this general approach, surface functionalization is demonstrated using a combination of X-ray photoelectron spectroscopy (XPS), ellipsometry, and atomic force microscopy (AFM).

Peptide Affinity Chromatography Applied to Therapeutic Antibodies Purification

The interest in therapeutic monoclonal antibodies (mAbs) has significantly grown in the pharmaceutical industry, exceeding 100 FDA mAbs approved. Although the upstream processing of their industrial production has been significantly improved in the last years, the downstream processing still depends on immobilized protein A affinity chromatography. The high cost, low capacity and short half-life of immobilized protein A chromatography matrices, encouraged the design of alternative short-peptide ligands for mAb purification. Most of these peptides have been obtained by screening combinatorial peptide libraries. These low-cost ligands can be easily produced by solid-phase peptide synthesis and can be immobilized on chromatographic supports, thus obtaining matrices with high capacity and selectivity. Furthermore, matrices with immobilized peptide ligands have longer half-life than those with protein A due to the higher stability of the peptides. In this review the design and synthesis of peptide ligands, their immobilization on chromatographic supports and the evaluation of the affinity supports for their application in mAb purification is described.

The impact of antifouling layers in fabricating bioactive surfaces

Bioactive surfaces modified with functional peptides are critical for both fundamental research and practical application of implant materials and tissue repair. However, when bioactive molecules are tethered on biomaterial surfaces, their functions can be compromised due to unwanted fouling (mainly nonspecific protein adsorption and cell adhesion). In recent years, researchers have continuously studied antifouling strategies to obtain low background noise and effectively present the function of bioactive molecules. In this review, we describe several commonly used antifouling strategies and analyzed their advantages and drawbacks. Among these strategies, antifouling molecules are widely used to construct the antifouling layer of various bioactive surfaces. Subsequently, we summarize various structures of antifouling molecules and their surface grafting methods and characteristics. Application of these functionalized surfaces in microarray, biosensors, and implants are also introduced. Finally, we discuss the primary challenges associated with antifouling layers in fabricating bioactive surfaces and provide prospects for the future development of this field. STATEMENT OF SIGNIFICANCE: The nonspecific protein adsorption and cell adhesion will cause unwanted background "noise" on the surface of biological materials and detecting devices and compromise the performance of functional molecules and, therefore, impair the performance of materials and the sensitivity of devices. In addition, the selection of antifouling surfaces with proper chain length and high grafting density is also of great importance and requires further studies. Otherwise, the surface-tethered bioactive molecules may not function in their optimal status or even fail to display their functions. Based on these two critical issues, we summarize antifouling molecules with different structures, variable grafting methods, and diverse applications in biomaterials and biomedical devices reported in literature. Overall, we expect to shed some light on choosing the appropriate antifouling molecules in fabricating bioactive surfaces.

Peptide array functionalization via the Ugi four-component reaction

The Ugi four-component reaction was investigated as a tool for the functionalization of peptide arrays via post-synthetic side-chain modification, mimicking post-translational processes. Additionally, as a proof of concept for the synthesis of peptidomimetics on arrays, the integration of an Ugi unit into a growing peptide chain was demonstrated.

Efficient near infrared fluorescence detection of elastase enzyme using peptide-bound unsymmetrical squaraine dye

Extended wavelength analyte-responsive fluorescent probes are highly desired for the imaging applications owing to their deep tissue penetration, and minimum interference from autofluorescence by biomolecules. Near infra-red (NIR) sensitive and self-quenching fluorescent probe based on the dye-peptide conjugate (SQ 1 PC) was designed and synthesized by facile and efficient one-pot synthetic route for the detection of Elastase activity. In the phosphate buffer solution, there was an efficient quenching of fluorescence of SQ 1 PC (86%) assisted by pronounced dye-dye interaction due to H-aggregate formation. Efficient and fast recovery of this quenched fluorescence of SQ 1 PC (> 50% in 30s) was observed on hydrolysis of this peptide-dye conjugate by elastase enzyme. Presently designed NIR sensitive self-quenching substrate offers the potential application for the detection of diseases related to proteases by efficient and fast detection of their activities.

Printing Peptide arrays with a complementary metal oxide semiconductor chip

: In this chapter, we discuss the state-of-the-art peptide array technologies, comparing the spot technique, lithographical methods, and microelectronic chip-based approaches. Based on this analysis, we describe a novel peptide array synthesis method with a microelectronic chip printer. By means of a complementary metal oxide semiconductor chip, charged bioparticles can be patterned on its surface. The bioparticles serve as vehicles to transfer molecule monomers to specific synthesis spots. Our chip offers 16,384 pixel electrodes on its surface with a spot-to-spot pitch of 100 μm. By switching the voltage of each pixel between 0 and 100 V separately, it is possible to generate arbitrary particle patterns for combinatorial molecule synthesis. Afterwards, the patterned chip surface serves as a printing head to transfer the particle pattern from its surface to a synthesis substrate. We conducted a series of proof-of-principle experiments to synthesize high-density peptide arrays. Our solid phase synthesis approach is based on the 9-fluorenylmethoxycarbonyl protection group strategy. After melting the particles, embedded monomers diffuse to the surface and participate in the coupling reaction to the surface. The method demonstrated herein can be easily extended to the synthesis of more complicated artificial molecules by using bioparticles with artificial molecular building blocks. The possibility of synthesizing artificial peptides was also shown in an experiment in which we patterned biotin particles in a high-density array format. These results open the road to the development of peptide-based functional modules for diverse applications in biotechnology.

Stiff chains inhibit and flexible chains promote protein adsorption to polyelectrolyte multilayers

We tested the hypothesis that the level of protein adsorption onto polyelectrolyte multilayers (PEMs) is influenced by the chain stiffness of the polymers forming the multilayer. The implication being that by altering the chain stiffness, PEMs can be formed that promote or inhibit protein adsorption. Protein adsorption to PEMs consisting of flexible and semi-flexible polyelectrolytes was investigated. The flexible polyelectrolytes were poly(sodium 4-styrene sulfonate) (PSS) and poly(diallyldimethylammonium chloride) (PDDA) and the semi-flexible polyelectrolytes were sulfated chitosan (SC) and cationic guar gum (CGG). Polyelectrolytes were used in pairs to produce four types of polyelectrolyte multilayer films. Moreover, each of these films could be terminated with either of the polyelectrolytes resulting in protein adsorption being studied on 8 systems. Protein adsorption was investigated by optical reflectometry and quartz crystal microbalance with dissipation using bovine serum albumin as the test protein. We found that when a pair of semi-flexible polyelectrolytes was used very little protein adsorption took place, irrespective of which polyelectrolyte was used to terminate the film. When the film was formed by flexible polyelectrolytes, significant protein adsorption took place and the degree of adsorption depended strongly on which polyelectrolyte was used to terminate the film. We explain these observations by considering the conformation of the polyelectrolyte in the outermost region of the film and relate this to the flexibility of the polyelectrolyte chains employed to produce the polyelectrolyte multilayer.

Improving stability and biocompatibility of alginate/chitosan microcapsule by fabricating bi-functional membrane

Cell encapsulation technology holds promise for the cell-based therapy. But poor mechanical strength and biocompatibility of microcapsule membrane are still obstacles for the clinical applications. A novel strategy is presented to prepare AC₁ C₂ A microcapsules with bi-functional membrane (that is, both desirable biocompatibility and membrane stability) by sequentially complexing chitosans with higher deacetylation degree (C₁) and lower deacetylation degree (C₂) on alginate (A) gel beads. Both in vitro and in vivo evaluation of AC₁C₂ A microcapsules demonstrate higher membrane stability and less cell adhesion, because the introduction of C₂ increases membrane strength and decreases surface roughness. Moreover, diffusion test of AC₁C₂ A microcapsules displays no inward permeation of IgG protein suggesting good immunoisolation function. The results demonstrate that AC₁C₂ A microcapsules with bi-functional membrane could be a promising candidate for microencapsulated cell implantation with cost effective usage of naturally biocompatible polysaccharides.

A method for controlling the aggregation of gold nanoparticles: tuning of optical and spectroscopic properties

Gold nanoparticles (AuNPs) have many interesting optical properties, which are derived from their surface plasmon resonance (SPR). However, the SPR of single AuNPs occurs around 520 nm, which is a limitation for biomedical imaging applications, because the maximum falls outside the tissue transparency window (∼650-1000 nm). Here the aggregation of AuNPs is mediated by balancing aggregation and steric stabilization processes. This is achieved by varying the relative amounts of hydrophobic small molecules, which act as aggregating agents, and end functional hydrophilic polymers that serve as steric stabilizing agents. This approach allows the position of the SPR shifted into the tissue transparency window, while maintaining colloidal stability. Importantly, increased depolarized scattering and surface enhanced Raman scattering (SERS) cross sections in this region are achieved compared to the single nanoparticles. By varying the structure of the aggregating agent slightly, the SERS spectra exhibit significant changes, thus demonstrating the potential to encode different aggregates. The aggregates have potential applications in biomedical imaging, as an encoding strategy for combinatorial chemistry, and for use in flow cytometry applications.

Purification of high-complexity peptide microarrays by spatially resolved array transfer to gold-coated membranes

A method for the one-step purification of high-complexity peptide microarrays is presented. The entire peptide library is transferred from the synthesis support to a gold coated polyvinylidenfluoride (PVDF) membrane, whereby only full-length peptides covalently couple to the receptor membrane via an N-terminally added cysteine. Highly resolved peptide transfer and purification of up to 10 000 features per cm(2) is demonstrated.

Optimised 'on demand' protein arraying from DNA by cell free expression with the 'DNA to Protein Array' (DAPA) technology

We have previously described a protein arraying process based on cell free expression from DNA template arrays (DNA Array to Protein Array, DAPA). Here, we have investigated the influence of different array support coatings (Ni-NTA, Epoxy, 3D-Epoxy and Polyethylene glycol methacrylate (PEGMA)). Their optimal combination yields an increased amount of detected protein and an optimised spot morphology on the resulting protein array compared to the previously published protocol. The specificity of protein capture was improved using a tag-specific capture antibody on a protein repellent surface coating. The conditions for protein expression were optimised to yield the maximum amount of protein or the best detection results using specific monoclonal antibodies or a scaffold binder against the expressed targets. The optimised DAPA system was able to increase by threefold the expression of a representative model protein while conserving recognition by a specific antibody. The amount of expressed protein in DAPA was comparable to those of classically spotted protein arrays. Reaction conditions can be tailored to suit the application of interest.

BIOLOGICAL SIGNIFICANCE

DAPA represents a cost effective, easy and convenient way of producing protein arrays on demand. The reported work is expected to facilitate the application of DAPA for personalized medicine and screening purposes.

Poly(acrylic acid)-poly(ethylene glycol) layers on positively charged surface coatings: molecular structure, protein resistance, and application to single protein deposition

A new copolymer (PAA-PEG2000) has been designed, consisting of a negatively charged poly(acrylic acid) (PAA) backbone to which poly(ethylene glycol) (PEG) side chains with a molecular weight of about 2 kDa were grafted in a molecular ratio of 3:10. It readily adsorbs to positively charged surfaces and may be considered to be the anionic counterpart of PEG-grafted poly(l-lysine) (PLL-PEG), which was first described by Kenausis et al. and is widely used to render negatively charged surfaces protein-resistant. The synthesis of PAA-PEG2000 can be carried out in aqueous solution at room temperature and does not require any sophisticated techniques such as handling in an inert gas atmosphere. Using ellipsometry and infrared reflection absorption spectroscopy (IRRAS), the film structure has been carefully analyzed for copolymer adsorption onto three different positively charged surfaces, namely, thin layers of poly(allylamine) (PAH), poly(ethyleneimine) (PEI) and (3-aminopropyl)triethoxysilane (APTES). Besides the film thickness, the conformation of the PEG chains and their orientation with respect to the surface normal appear to be important parameters for the protein resistance of the films. Although PAA-PEG2000 adsorbed to PAH and PEI renders the surfaces inert, only partial protein resistance has been observed if the copolymer is deposited on APTES. In a model application, we have generated heterogeneous surfaces composed of isolated small Au nanoparticles (AuNP's) embedded in a protein-resistant layer of PAA-PEG2000 and demonstrated that the AuNP's can serve as adsorption sites for single protein species. In the future, these nanopatterned surfaces may be used for the investigation of isolated proteins.

Deciphering enzyme function using peptide arrays

Enzymes are key molecules in signal-transduction pathways. However, only a small fraction of more than 500 human kinases, 300 human proteases and 200 human phosphatases is characterised so far. Peptide microarray based technologies for extremely efficient profiling of enzyme substrate specificity emerged in the last years. This technology reduces set-up time for HTS assays and allows the identification of downstream targets. Moreover, peptide microarrays enable optimisation of enzyme substrates. Focus of this review is on assay principles for measuring activities of kinases, phosphatases or proteases and on substrate identification/optimisation for kinases. Additionally, several examples for reliable identification of substrates for lysine methyl-transferases, histone deacetylases and SUMO-transferases are given. Finally, use of high-density peptide microarrays for the simultaneous profiling of kinase activities in complex biological samples like cell lysates or lysates of complete organisms is described. All published examples of peptide arrays used for enzyme profiling are summarised comprehensively.

Peptide Arrays

Despite the concern over the potential loss of structural information as a result of the use of peptides as opposed to proteins as molecular probes, peptide arrays have been implemented in a broad range of applications including antibody screening and epitope mapping, characterization of molecular interactions, and enzymatic activity profiling, and they have become a valuable tool for proteomics research. In this chapter, we first (Sect. 7.1) recapitulate the development of these arrays and highlight a couple of key improvements in the array production and the application in proteomics research. For clinical and biomarker development applications, it is important to measure entities that are directly related to physiological function (and dysfunction). In this respect, the assessment of enzymatic activities is obviously preferable to genotyping, expression profiling, or even measurement of protein amounts. In Sect. 7.2, an original technology based on peptides arrayed onto a porous support allows detailed profiling of kinase activities in a biological sample. The applications described range from kinase characterization to inhibition profiles, detection of off-target effects, and drug response prediction in a clinical setting, allowing rational choice of the drug to be used. Such directly functional approaches will have an important role in the transition to more personalized medicine. Finally, in Sect. 7.3, a recently developed method for “laser printing” of peptide arrays that will make these approaches much more practical is presented.

Regenerable immuno-biochip for screening ochratoxin A in green coffee extract using an automated microarray chip reader with chemiluminescence detection

Ochratoxin A (OTA) can contaminate foodstuffs in the ppb to ppm range and once formed, it is difficult to remove. Because of its toxicity and potential risks to human health, the need exists for rapid, efficient detection methods that comply with legal maximum residual limits. In this work we have synthesized an OTA conjugate functionalized with a water-soluble peptide for covalent immobilization on a glass biochip by means of contact spotting. The chip was used for OTA determination with an indirect competitive immunoassay format with flow-through reagent addition and chemiluminescence detection, carried out with the stand-alone automated Munich Chip Reader 3 (MCR 3) platform. A buffer model and real green coffee extracts were used for this purpose. At the present, covalent conjugate immobilization allowed for at least 20 assay-regeneration cycles of the biochip surface. The total analysis time for a single sample, including measurement and surface regeneration, was 12 min and the LOQ of OTA in green coffee extract was 0.3 μg L(-1) which corresponds to 7 μg kg(-1).

Chitosan-g-MPEG-modified alginate/chitosan hydrogel microcapsules: a quantitative study of the effect of polymer architecture on the resistance to protein adsorption

The chemical modification of the alginate/chitosan/alginate (ACA) hydrogel microcapsule with methoxy poly(ethylene glycol) (MPEG) was investigated to reduce nonspecific protein adsorption and improve biocompatibility in vivo. The graft copolymer chitosan-g-MPEG (CS-g-MPEG) was synthesized, and then alginate/chitosan/alginate/CS-g-MPEG (ACAC(PEG)) multilayer hydrogel microcapsules were fabricated by the layer-by-layer (LBL) polyelectrolyte self-assembly method. A quantitative study of the modification was carried out by the gel permeation chromatography (GPC) technique, and protein adsorption on the modified microcapsules was also investigated. The results showed that the apparent graft density of the MPEG side chain on the microcapsules decreased with increases in the degree of substitution (DS) and the MPEG chain length. During the binding process, the apparent graft density of CS-g-MPEG showed rapid growth-plateau-rapid growth behavior. CS-g-MPEG was not only bound to the surface but also penetrated a certain depth into the microcapsule membranes. The copolymers that penetrated the microcapsules made a smaller contribution to protein repulsion than did the copolymers on the surfaces of the microcapsules. The protein repulsion ability decreased with the increase in DS from 7 to 29% with the same chain length of MPEG 2K. CS-g-MPEG with MPEG 2K was more effective at protein repulsion than CS-g-MPEG with MPEG 550, having a similar DS below 20%. In this study, the microcapsules modified with CS-g-MPEG2K-DS7% had the lowest IgG adsorption of 3.0 ± 0.6 μg/cm(2), a reduction of 61% compared to that on the chitosan surface.

Orthogonal functionalization of silicon substrates using self-assembled monolayers

A fabrication process for multifunctional surfaces is designed leading to five different functional moieties (amine, thiol, carboxylic acid, fluoro, and methyl) being present on a single structured surface. The multifunctional surface is created by combining UV-ozone patterning, electro-oxidative lithography, the local deposition of self-assembled monolayers (SAMs), and surface modification schemes. Besides the characterization with conventional surface-sensitive techniques, the nature of the locally functionalized regions is demonstrated by self-assembly of three different probe nanomaterials (Si nanoparticles, Au nanoparticles, and hydroxyl functionalized micelles). A versatile fabrication approach for complex surfaces with addressable functionalities can be created, and it was possible to integrate five different functionalized areas on one substrate.

Peptide arrays with a chip

Today, lithographic methods enable combinatorial synthesis of >50,000 oligonucleotides per cm(2), an advance that has revolutionized the whole field of genomics. A similar development is expected for the field of proteomics, provided that affordable, very high-density peptide arrays are available. However, peptide arrays lag behind oligonucleotide arrays. This is mainly due to the monomer-by-monomer repeated consecutive coupling of 20 different amino acids associated with lithography, which adds up to an excessive number of coupling cycles. A combinatorial synthesis based on electrically charged solid amino acid particles resolves this problem. A computer chip consecutively addresses the different charged particles to a solid support, where, when completed, the whole layer of solid amino acid particles is melted at once. This frees hitherto immobilized amino acids to couple all 20 different amino acids in one single coupling reaction to the support. The method should allow for the translation of entire genomes into a set of overlapping peptides to be used in proteome research.

Surface Engineered Polymeric Biomaterials with Improved Biocontact Properties

We present many examples of surface engineered polymeric biomaterials with nanosize modified layers, controlled protein adsorption, and cellular interactions potentially applicable for tissue and/or blood contacting devices, scaffolds for cell culture and tissue engineering, biosensors, biological microchips as well as approaches to their preparation.

Combinatorial peptide synthesis on a microchip

Microchips are used in the combinatorial synthesis of peptide arrays by means of amino acid microparticle deposition. The surface of custom-built microchips can be equipped with an amino-modified poly(ethylene glycol)methacrylate (PEGMA) graft polymer coating, which permits high loading of functional groups and resists nonspecific protein adsorption. Specific microparticles that are addressed to the polymer-coated microchip surface in a well defined pattern release preactivated amino acids upon melting, and thus allow combinatorial synthesis of high-complexity peptide arrays directly on the chip surface. Currently, arrays with densities of up to 40,000 peptide spots/cm(2) can be generated in this way, with a minimum of coupling cycles required for full combinatorial synthesis. Without using any additional blocking agent, specific peptide recognition has been verified by background-free immunostaining on the chip-based array. This unit describes microchip surface modification, combinatorial peptide array synthesis on the chip, and a typical immunoassay employing the resulting high-density peptide arrays.

Enzyme-activated RGD ligands on functionalized poly(ethylene glycol) monolayers: surface analysis and cellular response

We report on the design, stepwise synthesis, and surface analysis of enzyme-responsive surfaces that present cell adhesive RGD sequences on-demand, that is, by enzymatic hydrolysis of inactive RGD containing precursors that carry cleavable steric blocking groups. These surfaces, incorporating poly(ethylene glycol) (PEG) monolayers coupled via epoxy silanes to glass, are functionalized via stepwise solid phase synthesis, presenting a versatile and straightforward approach to preparation of peptide surfaces. Successive amino acid coupling and deprotection steps using fluorenylmethoxycarbonyl (Fmoc) chemistry are verified using surface analysis with time-of-flight secondary-ion mass spectrometry (ToF-SIMS) and X-ray photoelectron spectroscopy (XPS). Exposure of surfaces to elastase results in activation of cell binding ligands as demonstrated using osteoblast cells. These surfaces may have applications in spatiotemporally controlled attachment of cells as relevant for three-dimensional tissue engineering scaffolds and cell-based biosensors.

Label-free DNA biosensors based on functionalized carbon nanotube field effect transistors

A carbon nanotube transistor array was used to detect DNA hybridization. A new approach to ensure specific adsorption of DNA to the nanotubes was developed. The polymer poly (methylmethacrylate(0.6)-co-poly(ethyleneglycol)methacrylate(0.15)-co-N-succinimidyl methacrylate(0.25)) was synthesized and bonded noncovalently to the nanotube. Aminated single-strand DNA was then attached covalently to the polymer. After hybridization, statistically significant changes were observed in key transistor parameters. Hybridized DNA traps both electrons and holes, possibly caused by the charge-trapping nature of the base pairs.

A novel combinatorial approach to high-density peptide arrays

Combinatorial synthesis of peptides on solid supports (1), either as spots on cellulose membranes (2) or with split-pool-libraries on polymer beads (3), substantially forwarded research in the field of peptide-protein interactions. Admittedly, these concepts have specific limitations, on one hand the number of synthesizable peptide sequences per area, on the other hand elaborate decoding/encoding strategies, false-positive results and sequence limitations. We recently established a method to produce high-density peptide arrays on microelectronic chips (4). Solid amino acid microparticles were charged by friction and transferred to defined pixel electrodes onto the chip's surface, where they couple to a functional polymer coating simply upon melting (Fig. 16.1 A-D,F). By applying standard Fmoc chemistry according to Merrifield, peptide array densities of up to 40,000 spots per square centimetre were achieved (Fig. 16.1G). The term "Merrifield synthesis" describes the consecutive linear coupling and deprotecting of L-amino acids modified with base-labile fluorenylmethoxy (Fmoc) groups at the N-terminus and different acid-sensitive protecting groups at their side chains. Removing side chain protecting groups takes place only once at the very end of each synthesis and generates the natural peptide sequence thereby.

Peptide arrays for enzyme profiling

Enzymes are key molecules in signal transduction pathways. However, only a small fraction of more than 500 predicted human kinases, 250 proteases and 250 phosphatases is characterized so far. Peptide microarray-based technologies for extremely efficient profiling of enzyme substrate specificity emerged in the last years. Additionally, patterns of enzymatic activities could be used to fingerprint the status of cells or organisms. This technology reduces set-up time for HTS assays and allows the identification of downstream targets. Moreover, peptide microarrays enable optimization of enzyme substrates. A comprehensive overview regarding enzyme profiling using peptide microarrays is presented with special focus on assay principles.

Self-assembly of brush-like poly[poly(ethylene glycol) methyl ether methacrylate] synthesized via aqueous atom transfer radical polymerization

Self-assembly of brush-like well-defined poly[poly(ethylene glycol) methyl ether methacrylate] homopolymers, abbreviated as P(PEGMA-475) and P(PEGMA-1100) is investigated in aqueous solution by employing dynamic/static light scattering (DLS/SLS) and transmission electron microscopy (TEM), whereas 475 and 1100 is molar mass of the respective PEGMA macromonomer. The mentioned brush-like homopolymers are synthesized by aqueous ATRP at room temperature. The critical association concentration (CAC) of the synthesized polymers in water depends on the length of the PEG side chains but not on the overall molar mass of the polymer. Thus, approximately the same CAC of approximately 0.35 mg/mL is estimated for various P(PEGMA-1100) samples, and approximately 0.7 mg/mL is estimated for P(PEGMA-475) series. All the investigated P(PEGMA-1100) samples form multimolecular micelles in aqueous solution, where the hydrodynamic size (Rh) and the aggregation number (Nagg) of micelles decreases as the molecular weight of P(PEGMA-1100) increases. This can be attributed to the increased steric hindrances between the PEG side chains in corona of micelles formed by higher molar mass P(PEGMA-1100). The tendency of micelle formation by samples of P(PEGMA-475) series is significantly lower than that of P(PEGMA-1100) series, as demonstrated by their significantly higher CAC and micelles of lower Nagg. The Rh of micelles does not depend strongly on polymer concentration, which suggests that these micelles are formed via the closed association model. Micelles formed by P(PEGMA-1100) series slightly shrink with increase in temperature from 25 to 60 degrees C, while those of P(PEGMA-475) series are found to be insensitive to the same temperature variation. Finally, TEM is carried out to visualize the formed micelles after transferring the aqueous solution to carbon film.

PEGMA/MMA copolymer graftings: generation, protein resistance, and a hydrophobic domain

We synthesized various graft copolymer films of poly(ethylene glycol) methacrylate (PEGMA) and methyl methacrylate (MMA) on silicon to examine the dependency of protein-surface interactions on grafting composition. We optimized atom transfer radical polymerizations to achieve film thicknesses from 25 to 100 nm depending on the monomer mole fractions, and analyzed the resulting surfaces by X-ray photoelectron spectroscopy (XPS), ellipsometry, contact angle measurements, and atomic force microscopy (AFM). As determined by XPS, the stoichiometric ratios of copolymer graftings correlated with the concentrations of provided monomer solutions. However, we found an unexpected and pronounced hydrophobic domain on copolymer films with a molar amount of 10-40% PEGMA, as indicated by advancing contact angles of up to 90 degrees . Nevertheless, a breakdown of the protein-repelling character was only observed for a fraction of 15% PEGMA and lower, far in the hydrophobic domain. Investigation of the structural basis of this exceptional wettability by high-resolution AFM demonstrated the independence of this property from morphological features.

Surface modification of plastic, glass and titanium by photoimmobilization of polyethylene glycol for antibiofouling

Photoreactive poly(ethylene glycol) (PEG) was prepared and the polymer was photoimmobilized on organic, inorganic and metal surfaces to reduce their interaction with proteins and cells. The photoreactive PEG was synthesized by co-polymerization of methacrylate-PEG and acryloyl 4-azidobenzene. Surface modification was carried in the presence and the absence of a micropatterned photomask. It was then straightforward to confirm the immobilization using the micropatterning. Using the micropatterning method, immobilization of the photoreactive PEG on plastic (Thermanox), glass and titanium was confirmed by time-of-flight secondary ion mass spectroscopy and atomic force microscopy observations. The contact angle on an unpatterned surface was measured. Although the original surfaces have different contact angles, the contact angle on PEG-immobilized surfaces was the same on all surfaces. This result demonstrated that the surface was completely covered with PEG by the photoimmobilization. To assess non-specific protein adsorption on the micropatterned surface, horseradish peroxidase (HRP)-conjugated proteins were adsorbed. Reduced protein adsorption was confirmed by vanishingly small staining of HRP substrates on the immobilized regions. COS-7 cells were cultured on the micropatterned surface. The cells did not adhere to the PEG-coated regions. In conclusion, photoreactive PEG was immobilized on various surfaces and tended to reduce interactions with proteins and cells.

Functional peptide arrays for high-throughput chemical biology based applications

Constant advancements in printing technology, informatics, surface modification strategies and peptide chemistries mean that peptide arrays have, like DNA arrays, become even more miniaturised and complex in terms of not only the numbers of peptides immobilised but also their lengths. As a result peptide-based arrays have become a powerful tool in the interrogation, examination and perturbation of a host of biological systems.

Multifunctional CMOS microchip coatings for protein and peptide arrays

Complementary metal oxide semiconductor (CMOS) microelectronic chips fulfill important functions in the field of biomedical research, ranging from the generation of high complexity DNA and protein arrays to the detection of specific interactions thereupon. Nevertheless, the issue of merging pure CMOS technology with a chemically stable surface modification which further resists interfering nonspecific protein adsorption has not been addressed yet. We present a novel surface coating for CMOS microchips based on poly(ethylene glycol)methacrylate graft polymer films, which in addition provides high loadings of functional groups for the linkage of probe molecules. The coated microchips were compatible with the harshest conditions emerging in microarray generating methods, thoroughly retaining structural integrity and microelectronic functionality. Nonspecific adsorption of proteins on the chip's surface was completely obviated even with complex serum protein mixtures. We could demonstrate the background-free antibody staining of immobilized probe molecules without using any blocking agents, encouraging further integration of CMOS technology in proteome research.

Optically responsive nanoparticle layers for the label-free analysis of biospecific interactions in array formats

A novel nanocomposite surface is prepared by coating surface-adsorbed dielectric colloidal particles with a contiguous layer of gold nanoparticles. The resulting surface shows pronounced optical extinction in reflection with the extinction peaks located in the UV-Vis and NIR region of the electromagnetic spectrum. The peak positions of these maxima change very sensitively with the adsorption of organic molecules onto the surface. For the adsorption of a monolayer of octadecanethiol, we observe a peak shift of 55 nm on average, which is about five times that of established label-free sensing methods based on propagating and localized surface plasmons. In a first proof-of-principle experiment, the interaction of peptides with specific antibodies has been detected without labeling by means of a fiber-optical set-up with microscopic lateral resolution. To avoid crosstalk in high-density arrays, the optically responsive surface areas can be locally separated on a micro- or even nanometer scale. Accordingly, the newly developed optically responsive surfaces are well suited for integration into high-density peptide or DNA arrays as demanded in genomics, proteomics, and biomedical research in general.