Chemically programmed supramolecular assembly of hemoprotein and streptavidin with alternating alignment

Alternating: a cofactor dyad consisting of a heme group (red in picture) and a bis(biotin) unit (blue) was synthesized and shown to specifically bind to both apomyoglobin and streptavidin. In the presence of the dyad, the 1:1 association of a disulfide-bridged myoglobin dimer (green) with streptavidin (gray) afforded a submicrometer-sized fibrous alternating copolymer.     

Colorimetric and electrochemical detection of ligase through ligation reaction-induced streptavidin assembly

We propose a concept for ligase detection by conversion of aggregation-based homogeneous analysis into surface-tethered electrochemical assay through streptavidin（SA）-biotin interaction. Sortase A（Srt A）served as the model analyte and two biotinylated peptides（bio-LPETGG and GGGK-bio） were used as the substrates. Srt A-catalyzed ligation of the peptide substrates led to the generation of bio-LPETGGGKbio. The ligation product（bio-LPETGGGK-bio） induced the aggregation and color change of SA-modifi...     

Templated protein assembly on micro-contact-printed surface patterns. Use of the SNAP-tag protein functionality

Micro contact printing (microCP) has been established as a simple technique for high-resolution protein patterning for micro- and nanoarrays. However, as biochemical assays based on immobilized protein arrays progress from immunoassays to more delicate functional assays, the demand for methods of miniaturized, gentle, and oriented immobilization, which are applicable to many different target proteins, becomes larger. In this study, we present a novel microCP templated assembly approach, based on a recombinant SNAP-FLAG-HIS 10 (SFH) immobilization vehicle, which exploits the recently developed SNAP-tag protein. The SNAP-tag is derived from the human DNA repair protein hAGT, which covalently transfers the alkyl group of benzyl guanine (BG) substrates onto itself. We have designed a model SFH cassette carrying three tags (SNAP-tag, FLAG-tag, and HIS-tag), each of which can be used for fluorescence labeling or surface immobilization. When patterns of streptavidin modified with BG-biotin (streptavidin-BG) are stamped onto a surface, the SFH can subsequently assemble on the ligand pattern from solution, functioning as a general immobilization vehicle for high-resolution patterning of any protein expressed in the SFH cassette, in a gentle and oriented manner. Alternatively, the SFH can be site-selectively biotinylated using BG-biotin and, subsequently, assemble on stamped streptavidin. We exploit several ways to biotinylate the SFH protein via the SNAP-tag, promoting its templated assembly on micropatterns of streptavidin in four complementary formats. Quantitative analysis of the obtained patterns, revealed by immunostaining, indicates that all four approaches resulted in proper SFH immobilization and antibody recognition, demonstrating the versatility of the SFH cassette and the potential for high resolution patterning applications. Also, our data confirm that streptavidin can be stamped directly on surfaces, without loss of activity. While three strategies resulted in similar patterning efficiencies, one particular approach--namely templated assembly of SFH directly on streptavidin-BG patterns--resulted in an order of magnitude increase in patterning efficiency.     

A native, affinity-based protein blot for the analysis of streptavidin heterogeneity: consequences for the specificity of streptavidin mediated binding assays

Commercial preparations of streptavidin, a bacterial biotin-binding protein, were analyzed by isoelectric focusing combined with an affinity-based protein blot using biotinylated, protein-saturated nitrocellulose. The colorimetrical detection of streptavidin with biotinylated alkaline phosphatase allows the selective visualization of streptavidin molecules with at least two active biotin-binding sites. Dependent on the preparation, seven to sixteen streptavidin forms were found with isoelectric points ranging from 5 to 8. Molecular weight analysis of the subunits of streptavidin showed that the observed heterogeneity was mainly due to limited proteolysis, which does not destroy the biotin-binding activity. The preparations differed also in the nonspecific reactivity of streptavidin with single-stranded DNA, bovine serum albumin and Tween 20. No relationship was observed between heterogeneity and non-specific binding activity. Data obtained from protein blots onto nitrocellulose saturated with single-stranded DNA showed that it cannot be excluded that streptavidin with only a single active biotin-binding site is mainly responsible for the nonspecific reactivity of some streptavidin preparations.     

DNA-directed protein immobilization on mixed self-assembled monolayers via a streptavidin bridge

The simultaneous detection of multiple analytes is an important consideration for the advancement of biosensor technology. Currently, few sensor systems possess the capability to accurately and precisely detect multiple antigens. This work presents a simple approach for the functionalization of sensor surfaces suitable for multichannel detection. This approach utilizes self-assembled monolayer (SAM) chemistry to create a nonfouling, functional sensor platform based on biotinylated single-stranded DNA immobilized via a streptavidin bridge to a mixed SAM of biotinylated alkanethiol and oligo(ethylene glycol). Nonspecific binding is minimized with the nonfouling background of the sensor surface. A usable protein chip is generated by applying protein-DNA conjugates which are directed to specific sites on the sensor chip surface by utilizing the specificity of DNA hybridization. The described platform is demonstrated in a custom-built surface plasmon resonance biosensor. The detection capabilities of a sensor using this protein array have been characterized using human chorionic gonadotropin (hCG). The platform shows a higher sensitivity in detection of hCG than that observed using biotinylated antibodies. Results also show excellent specificity in protein immobilization to the proper locations in the array. The vast number of possible DNA sequences combine with the selectivity of base-pairing makes this platform an excellent candidate for a sensor capable of multichannel protein detection.     

Chitosan biotinylation and electrodeposition for selective protein assembly

An alternative route to protein assembly at surfaces based on using the unique capabilities of biological materials for the spatially selective assembly of proteins is described. Specifically, the stimuli-responsive properties of aminopolysaccharide chitosan are combined with the molecular-recognition capabilities of biotin-streptavidin binding. Biotinylated chitosan retains its stimuli-responsive properties and is capable of electrodepositing at specific electrode addresses. Once deposited, it is capable of binding streptavidin, which can mediate the subsequent assembly of biotinylated proteins. Spatially selective protein assembly using biotinylated Protein A and fluorescently-labeled antibodies is demonstrated.     

Engineering of a redox protein for DNA-directed assembly

Engineered enzyme conjugate of the small laccase enzyme from Streptomyces coelicolor and zinc finger DNA binding domain from Zif268 is demonstrated to bind double stranded DNA in a site specific manner while retaining enzymatic activity.     

Protein-directed assembly of binary monolayers at the interface and surface patterns of protein on the monolayers

Ferritin-directed assembly of binary monolayers of zwitterionic dipalmitoylphosphatidylcholine and cationic dioctadecyldimethylammonium bromide (DOMA) at the interface and surface patterns of ferritin on the monolayers have been investigated using a combination of infrared reflection absorption spectroscopy, surface plasmon resonance, and atomic force microscopy. Ferritin binding to the binary monolayers at the air-water interface at the surface pressure 30 mN/m, primarily driven by the electrostatic interaction, gives rise to a change in tilt angle of hydrocarbon chains from 15 degrees +/- 1 degrees to 10 degrees +/- 1 degrees with respect to the normal of the monolayer at the mole fraction of DOMA (XDOMA) of 0.1. The chains at XDOMA = 0.3 are oriented vertical to the water surface before and after protein binding. A new mechanism for protein binding to the binary monolayers is proposed. The secondary structures of the adsorbed ferritin are prevented from changing to some extent due to the existence of the monolayers. The amounts of the bound protein on the monolayers at the air-water interface are increased in comparison with those on the pre-immobilized monolayers at low XDOMA. The increased amounts and different patterns of the adsorbed protein at the monolayers are mostly attributed to the formation of multiple binding sites available for ferritin, which is due to the lateral reorganization of the lipid components in the monolayers induced by the protein in the subphase. The created multiple binding sites on the monolayer surfaces through the protein-directed assembly can be preserved for subsequent protein binding.     

Evolutionary method for the assembly of rigid protein fragments

Genetic algorithms constitute a powerful optimization method that has already been used in the study of the protein folding problem. However, they often suffer from a lack of convergence in a reasonably short time for complex fitness functions. Here, we propose an evolutionary strategy that can reproducibly find structures close to the minimum of a potential function for a simplified protein model in an efficient way. The model reduces the number of degrees of freedom of the system by treating the protein structure as composed of rigid fragments. The search incorporates a double encoding procedure and a merging operation from subpopulations that evolve independently of one another, both contributing to the good performance of the full algorithm. We have tested it with protein structures of different degrees of complexity, and present our conclusions related to its possible application as an efficient tool for the analysis of folding potentials.     

Prototype protein assembly as scaffold for time-resolved fluoroimmuno assays

Turnip yellow mosaic virus (TYMV) is an icosahedral plant virus with an average diameter of 28 nm and can be isolated in gram quantities from turnip or Chinese cabbage inexpensively. In this study, it was selected as a prototype bionanoparticle for time-resolved fluoroimmuno assay (TRFIA). Two types of reactive amino acid residues were employed to anchor luminescent terbium complexes and biotin groups based on orthogonal chemical reactions. While terbium complexes were used as luminescent signaling groups, biotin motifs acted as a model ligand for protein binding. The bioconjugation results were confirmed by MS and Western blot analysis. Steady-state and time-resolved luminescence study of the dual-modified viruses demonstrated that the spectroscopic properties of the Tb complex are unperturbed by the labeling procedure. The dual-modified particle was probed by fluorescence resonance energy transfer (FRET) experiments using avidin labeled with an Alexa488 fluorophore, which bound to the biotin on the surface of the particle, as an energy acceptor, and terbium complexes as an energy donor. The emission and excitation spectra of the dual-labeled TYMV particle displayed residual virus fluorescence and Tb luminescence upon ligand-centered excitation. The Tb luminescence lifetime was 1.62 ms and could be effectively fitted with a single-exponential behavior. In the TRFIA, an efficient transfer of 66% was observed, and the calculation using the F?rster radius of 41 A allowed for an estimation of the average donor-acceptor distance of 36 A. Our studies show that the two reactive sites can communicate with each other on the surface of a nanoscale biological assembly. In particular, the ligand-receptor binding (biotin and avidin in this paper) was not interfered with when anchored to the surface of TYMV. Therefore, as a prototype of polyvalent bionanoparticles, TYMV can be used as scaffold for sensor development with TRFIA.     

Divalent ligand for intramolecular complex formation to streptavidin

Monovalent ligand and divalent ligand have been synthesized, and their thermodynamic parameters of complexation to avidin and streptavidin have been analyzed in terms of multivalent binding.     

Spatially addressable protein array: ssDNA-directed assembly for antibody microarray

Protein microarray offers a means for high-throughput profiling of cellular proteins to provide insights into the mechanisms of biological processes. This study describes the design and fabrication of a robust platform, spatially addressable protein array (SAPA), by exploring the specificity of ssDNA hybridization for self-assembly of semi-synthetic ssDNA-antibody conjugates which capture antigens from complex biological samples. This approach does not involve the direct immobilization of antibodies nor antigen, but instead captures the target antigens in the solution phase followed by self-directed assembly of the complex onto the surface. In an effort to optimize the platform, the effects of surface chemistry, nonspecific protein adsorption, facile preparation, and purification of ssDNA-conjugated antibody and capture of the antigen from a complex biological sample such as cell lysate were examined. This platform allowed antigen detection in cell lysate with high sensitivity (1 pM). The method described herein can be extended to the high-throughput detection of other interacting molecules in solution phase and their subsequent assembly onto any substrate.     

Artificial metalloenzyme for enantioselective sulfoxidation based on vanadyl-loaded streptavidin

Nature's catalysts are specifically evolved to carry out efficient and selective reactions. Recent developments in biotechnology have allowed the rapid optimization of existing enzymes for enantioselective processes. However, the ex nihilo creation of catalytic activity from a noncatalytic protein scaffold remains very challenging. Herein, we describe the creation of an artificial enzyme upon incorporation of a vanadyl ion into the biotin-binding pocket of streptavidin, a protein devoid of catalytic activity. The resulting artificial metalloenzyme catalyzes the enantioselective oxidation of prochiral sulfides with good enantioselectivities both for dialkyl and alkyl-aryl substrates (up to 93% enantiomeric excess). Electron paragmagnetic resonance spectroscopy, chemical modification, and mutagenesis studies suggest that the vanadyl ion is located within the biotin-binding pocket and interacts only via second coordination sphere contacts with streptavidin.     

Surface modification of polystyrene biochip for biotin‐labelled protein/streptavidin or neutravidin coupling used in fluorescence assay

A polystyrene biosensing chip to be used as a medical diagnostic tool has been developed. Its surface functionalization is optimized to bind the bioanalytes with high efficiency. Coatings of allyldextran monolayers were carried out on polystyrene chips activated with γ‐irradiation. The effect of the concentration of allyldextran solution on the coating efficiency was studied by surface‐sensitive x‐ray photoelectron spectroscopy (XPS) and contact‐angle measurements. In a second step, sodium periodate chemistry was applied to functionalize the dextran layer, followed by coupling with streptavidin or neutravidin. Copyright © 2004 John Wiley & Sons, Ltd.     

Controlled assembly of bacteria on chemical patterns using soft lithography

Highly ordered arrays of single living bacteria were obtained by selective adsorption of bacteria onto chemical patterns with micrometric resolution. The chemically engineered template surfaces were prepared with the combination of microcontact printing process and a simple incubation technique. This methodology can be used for fundamental studies of bacterium's inner mechanisms and sub-cellular organization as well as for interfacing living bacteria with artificial microsystems.     

Controlled protein assembly on a switchable surface

The strategy presented in this work supplies a general method of controlling protein assembly on a switchable low-density SAM, which may open a new way to design functional biocomposite films for biosensors or protein chips.     

Immobilized streptavidin gradients as bioconjugation platforms

Surface density gradients of streptavidin (SAV) were created on solid surfaces and demonstrated functionality as a bioconjugation platform. The surface density of immobilized streptavidin steadily increased in one dimension from 0 to 235 ng cm(-2) over a distance of 10 mm. The density of coupled protein was controlled by its immobilization onto a polymer surface bearing a gradient of aldehyde group density, onto which SAV was covalently linked using spontaneous imine bond formation between surface aldehyde functional groups and primary amine groups on the protein. As a control, human serum albumin was immobilized in the same manner. The gradient density of aldehyde groups was created using a method of simultaneous plasma copolymerization of ethanol and propionaldehyde. Control over the surface density of aldehyde groups was achieved by manipulating the flow rates of these vapors while moving a mask across substrates during plasma discharge. Immobilized SAV was able to bind biotinylated probes, indicating that the protein retained its functionality after being immobilized. This plasma polymerization technique conveniently allows virtually any substrate to be equipped with tunable protein gradients and provides a widely applicable method for bioconjugation to study effects arising from controllable surface densities of proteins.     

Reactive and Highly Submicron Magnetic Latexes for Bionanotechnology Applications

Summary: Colloidal particles are largely used in biomedical applications as a solid support, as a carrier, as nanoreactors and as labels for target molecule detection. With the recent development of bionanotechnology, more appropriate colloidal particles should be elaborated. In this direction, new specification are listed in order to develop reactive nanoparticles to be use in microsystems, microfluids and all combined systems in which we can conduct sample preparation, specific capture, purification, concentration and detection in small volume (generally less than 100 µl). Then the aim of this short review is to give to the readers some recent orientations of reactive magnetic latex particles for in vitro bionanotechnology applications.