Fabrication of Oligomeric Avidin Scaffolds for Valency‐Controlled Surface Display of Functional Ligands

Multivalent surface display of biomolecules is crucial to study and utilize multivalent biological interactions. However, precise valency control of surface‐displayed ligands remains extremely difficult. Now a series of new oligomeric avidin proteins were fabricated that allow facile control of surface multivalency of biotinylated ligands. Naturally dimeric rhizavidin (RA) was engineered to form a mixture of oligomeric avidin assemblies, and discrete RA oligomers from the dimer to octamer of RA, were homogeneously prepared. These oligomeric avidins are in polygonal forms with expected numbers of stable biotin binding sites. Upon immobilization on low‐density biotin‐coated gold surfaces, RA dimer, trimer, and tetramer scaffolds provided accurate mean residual valencies of 2, 3, and 4, respectively, for biotinylated proteins. Valency‐controlled display of antibody binding protein G on these RA surfaces showed clear valency‐dependent enhancement of antibody capturing stability.     

Quantitative FT-IRRAS spectroscopic studies of the interaction of avidin with biotin on functionalized quartz surfaces

The interaction of avidin with biotin was studied on functionalized quartz surfaces terminated with 3-aminopropyltrimethoxysilane (3-APTMS), 2,2'-(ethylenedioxy)bis(ethylenediamine) (DADOO), and fourth-generation amine-terminated polyamidoamine (G4-NH2 PAMAM) dendrimers with the use of Fourier transform infrared reflection-absorption spectroscopy (FT-IRRAS). In particular, the molecular recognition ability of these surfaces was quantified through FT-IRRAS in combination with the use of an alkyne dicobalt hexacarbonyl probe coupled with avidin. The degree of nonspecific adsorption of avidin was determined by exposure of the amine-terminated and/or biotinylated surfaces to solutions of biotin-saturated avidin. The results indicate that the biotinylated 3-APTMS layer exhibits a very low specific binding capacity for avidin (on the order of 0.15 pmol of avidin/cm2) and substantial nonspecific adsorption. Both the binding capacity and the specificity were greatly improved when the 3-APTMS layer on quartz was modified through serial chemisorption of glutaraldehyde (GA), DADOO, and/or G4-NH2 PAMAM dendrimer layers. Among these layers, the biotinylated G4-NH2 PAMAM dendrimer layer exhibited the highest capacity for avidin binding (2.02 pmol of avidin/cm2) with a specificity of approximately 90%. This effect can be attributed to the efficient packing/ordering of the binding dendrimer layer, leading to a more dense and better organized layer of biotin headgroups on the subsequent biotinylated surface.     

A Rhizavidin Monomer with Nearly Multimeric Avidin‐Like Binding Stability Against Biotin Conjugates

Developing a monomeric form of an avidin‐like protein with highly stable biotin binding properties has been a major challenge in biotin‐avidin linking technology. Here we report a monomeric avidin‐like protein—enhanced monoavidin—with off‐rates almost comparable to those of multimeric avidin proteins against various biotin conjugates. Enhanced monoavidin (eMA) was developed from naturally dimeric rhizavidin by optimally maintaining protein rigidity during monomerization and additionally shielding the bound biotin by diverse engineering of the surface residues. eMA allowed the monovalent and nonperturbing labeling of head‐group‐biotinylated lipids in bilayer membranes. In addition, we fabricated an unprecedented 24‐meric avidin probe by fusing eMA to a multimeric cage protein. The 24‐meric avidin and eMA were utilized to demonstrate how artificial clustering of cell‐surface proteins greatly enhances the internalization rates of assembled proteins on live cells.     

A rapid and simple separation and direct detection of glutathione by gold nanoparticles and graphene‐based MALDI–TOF‐MS

In this study, we present a rapid and simple method for the separation and direct detection of glutathione by combining gold nanoparticles and MALDI–TOF‐MS with graphene as matrix. Gold nanoparticles enable the selective capture of thiol‐containing compounds. Gold nanoparticles bound with analytes can be mixed with graphene matrix for direct analysis by MALDI–TOF‐MS, which can avoid sample loss and contamination during transfer process. Compared with a conventional matrix, α‐cyano‐4‐hydroxycinnamic acid, graphene exhibits an excellent desorption/ionization efficiency, thermal and mechanical properties. The use of graphene as matrix avoids the fragmentation of analytes. Stable analysis was achieved with less background interference even at the concentration of 0.625 ng/μL. To further confirm its efficiency, the optimized approach was applied to the separation and detection of glutathione in mouse liver extraction. This result showed the great potential of detection of biologically important thiols in biochemical and biomedical research.     

On‐chip solid‐phase extraction pre‐concentration/focusing substrates coupled to atmospheric pressure matrix‐assisted laser desorption/ionization ion trap mass spectrometry for high sensitivity biomolecule analysis

Atmospheric pressure matrix‐assisted laser desorption/ionization (AP‐MALDI) has proven a convenient and rapid method for ion production in the mass spectrometric (MS) analysis of biomolecules. AP‐MALDI and electrospray ionization (ESI) sources are easily interchangeable in most mass spectrometers. However, AP‐MALDI suffers from less‐than‐optimal sensitivity due to ion losses during transport from the atmosphere into the vacuum of the mass spectrometer. Here, we study the signal‐to‐noise ratio (S/N) gains observed when an on‐chip dynamic pre‐concentration/focusing approach is coupled to AP‐MALDI for the MS analysis of neuropeptides and protein digests. It was found that, in comparison with conventional AP‐MALDI targets, focusing targets showed (1) a sensitivity enhancement of approximately two orders of magnitude with S/N gains of 200–900 for hydrophobic substrates, and 150–400 for weak cation‐exchange (WCX) substrates; (2) improved detection limits as low as 5 fmol/µL for standard peptides; (3) significantly reduced matrix background; and (4) higher inter‐day reproducibility. The improved sensitivity allowed successful tandem mass spectrometric (MS/MS) sequencing of dilute solutions of a derivatized tryptic digest of a protein standard, and enabled the first reported AP‐MALDI MS detection of neuropeptides from Aedes aegypti mosquito heads. Copyright © 2009 John Wiley & Sons, Ltd.     

Aptasensor for Thrombin Based on Carbon Nanotubes‐Methylene Blue Composites

The amperometric and EQCM aptasensors based on DNA aptamers immobilized by avidin‐biotin method or by electrostatic adsorption onto multiwalled carbon nanotube layer contained methylene blue (MB) have been developed and examined for thrombin detection in buffer and in spiked blood serum. The presence of MB increases the binding capacity of the surface layer and enhances the range of thrombin concentrations to be determined. This results in significant improvement of analytical characteristics of thrombin detection. The EQCM aptasensors allowed us to detect 0.3–100 nM and amperometric aptasensors 10–1000 nM of thrombin.     

Fragmentation of biotinylated cyclic peptides

Electrospray ionization coupled with tandem mass spectrometry (MS/MS) was used to determine the preferred binding site(s) of biotin NHS ester with a series of cyclic peptides with antibiotic properties. The peptides investigated are polymyxins, cyclic peptides produced by Bacillus polymyxa. In spite of the 1:1 stoichiometry used in the labeling reaction, multiple biotin molecules were incorporated into intact polymyxin peptides. Given the amine specificity of the activated biotin and the large number of amino acids with primary amines in the polymyxins, it was not clear by inspection which binding sites were more reactive than others. MS/MS was used to characterize the structure of the biotinylated peptides. MS/MS spectra of cyclic peptides often lead to ambiguous structure determinations due to the potential for multiple ring openings which result in the generation of multiple ion series. The MS/MS spectra of polymyxin peptides are especially difficult to characterize due to the lack of variety in their amino acids; however, the added complexity of the biotin aided the elucidation of the fragmentation pathways. MS/MS spectra of the species with biotin additions were used to rationalize the preferential binding sites of these molecules.     

Comparison by QCM and photometric enzymatic test of the biotin-avidin recognition on a biotinylated polypyrrole

By gravimetric measurements using a quartz cristal microbalance (QCM), we have studied the immobilization of biotinylated glucose oxidase enzymes (B-GOx) bound through on an intermediate avidin layer to a biotinylated polypyrrole film. The aim is to assess the amount of B-GOx specifically anchored on the biotinylated polypyrrole/avidin assembly thank to the biotin/avidin interaction between avidin and B-GOx. Indeed the estimated amount from the QCM measurement corresponds to the specific recognition of avidin/B-GOx added to a non-specific recognition (adsorption) of B-GOx. In order to discriminate these two phenomena, we have carried out a study by QCM of the anchoring of B-GOx on an avidin layer linked by adsorption to a polypyrrole free from biotin units. From QCM measurements we have deduced for the biotinylated polypyrrole/avidin assembly that the amount of B-GOx bound via the biotin/avidin interaction and those due to the avidin adsorption process correspond to 3.9 pmol cm(-2) (1.3 equivalent of B-Gox monolayer) and 1.4 pmol cm(-2) (0.46 equivalent of B-GOx monolayer) respectively. These values have been corroborated by measurements of the enzymatic activity of GOx.     

Chemically selective sensing through layer-by-layer incorporation of biorecognition into thin film substrates for surface-enhanced resonance Raman scattering

In this work, the fabrication, characterization, and application of avidin/Ag nanoparticle layer-by-layer (LbL) films as chemically selective substrates for surface-enhanced resonance Raman scattering (SERRS) is demonstrated. The biospecific interaction between avidin and the small molecule biotin, one of the strongest known to exist in nature, is exploited to preferentially capture biotinylated species from solution. This highly favored adsorption is shown to yield SERRS concentration enhancements and improved detection sensitivities of ca. 102 for commercially available and in situ prepared biotinylated species over their nontagged counterparts.     

Self‐assembled supramolecular microgels: Fractal structure and aggregation mechanism

Multifunctional molecules were designed to produce microgels with specific structures. Both static light scattering and dynamic light scattering were employed to determine the fractal dimension of the microgels. The protein, avidin, was strongly bound to four biotin moieties. Biotin was attached covalently to specifically engineered peptide nucleic acid (PNA) oligomers. Three designed DNA oligomers self‐assembled to produce a trifunctional three‐way junction (TWJ) with single‐stranded ends that were complementary to the PNA sequence. The sizes of the supramolecular aggregates were characterized by dynamic light scattering. The fractal dimension was obtained from the angular dependence of the scattered intensity when the microgels were large enough. When the microgels were formed via cooling from a temperature above the melting point of the PNA–DNA helices, reversible structures with a fractal dimension of approximately 1.86 were formed, which is consistent with a cluster–cluster aggregation mechanism. When the microgels were formed by the slow addition of biotinylated PNA bound to the TWJ to a solution of avidin at room temperature, the observed fractal dimension approached 2.6, which is consistent with a point–cluster aggregation mechanism. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 3037–3046, 2003     

Determination of the bioavailability of biotin conjugated onto shell cross-linked (SCK) nanoparticles

Shell cross-linked nanoparticles (SCKs) presenting surface- and bioavailable biotin functional groups were synthesized via a mixed micelle methodology, whereby co-micellization of chain terminal biotinylated poly(acrylic acid)-b-poly(methyl acrylate) (PAA-b-PMA) and nonbiotinylated PAA-b-PMA were cross-linked in an intramicellar fashion within the shell layer of the mixed micelles, between the carboxylic acid groups of PAA and the amine functionalities of 2,2'-(ethylenedioxy)diethylamine. The hydrodynamic diameters (D(h)) of the micelles and the SCKs with different biotinylated block copolymer contents were determined by dynamic light scattering (DLS), and the dimensions of the SCKs were characterized with tapping-mode atomic force microscopy (AFM) and transmission electron microscopy (TEM). The amount of surface-available biotin was tuned by varying the stoichiometric ratio of the biotinylated PAA-b-PMA versus the nonbiotinylated PAA-b-PMA, as demonstrated with solution-state, binding interaction analyses, an avidin/HABA (avidin/4'-hydroxyazobenzene-2-carboxylic acid) competitive binding assay, and fluorescence correlation spectroscopy (FCS). The avidin/HABA assay found the amount of available biotin at the surface of the biotinylated SCK nanoparticles to increase with increasing biotin-terminated block copolymer incorporation, but to be less than 25% of the theoretical value. FCS measurements showed the same trend.     

MALDI‐MS detection of noncovalent interactions of single stranded DNA with Escherichia coli single‐stranded DNA‐binding protein

The Escherichia coli single‐stranded DNA binding protein (SSB) selectively binds single‐stranded (ss) DNA and participates in the process of DNA replication, recombination and repair. Different binding modes have previously been observed in SSB?ssDNA complexes, due to the four potential binding sites of SSB. Here, chemical cross‐linking, combined with high‐mass matrix‐assisted laser desorption/ionization (MALDI) mass spectrometry (MS), is used to determine the stoichiometry of the SSB?ssDNA complex. SSB forms a stable homotetramer in solution, but only the monomeric species (m/z 19 100) can be detected with standard MALDI‐MS. With chemical cross‐linking, the quaternary structure of SSB is conserved, and the tetramer (m/z 79 500) was observed. We found that ssDNA also functions as a stabilizer to conserve the quaternary structure of SSB, as evidenced by the detection of a SSB?ssDNA complex at m/z 94 200 even in the absence of chemical cross‐linking. The stability of the SSB?ssDNA complex with MALDI strongly depends on the length and strand of oligonucleotides and the stoichiometry of the SSB?ssDNA complex, which could be attributed to electrostatic interactions that are enhanced in the gas phase. The key factor affecting the stoichiometry of the SSB?ssDNA complex is how ssDNA binds to SSB, rather than the protein‐to‐DNA ratio. This further suggests that detection of the complex by MALDI is a result of specific binding, and not due to non‐specific aggregation in the MALDI plume. Copyright © 2012 John Wiley & Sons, Ltd.     

Enhanced electrochemical activity of redox-labels in multi-layered protein films on indium tin oxide nanoparticle-based electrode

Facile electrical communication between redox-active labeling molecules and electrode is essential in the electrochemical detection of bio-affinity reactions. In this report, nanometer-sized indium tin oxide (ITO) particles were employed in the fabrication of porous thick film electrodes to enhance the otherwise impeded electrochemical activity of redox labels in multi-layered protein films, and to enable quantitative detection of avidin/biotin binding interaction. To carry out the affinity reaction, avidin immobilized on an ITO electrode was reacted with mouse IgG labeled with both biotin and ruthenium Tris-(2,2′-bipyridine) (Ru-bipy). The binding reaction between avidin and biotin was detected by the catalytic voltammetry of Ru-bipy in an oxalate-containing electrolyte. On sputtered ITO thin film electrode, although a single layer of Ru-bipy labeled avidin exhibited substantial anodic current, attaching the label to the outer IgG layer of the avidin/biotin-IgG binding pair resulted in almost complete loss of the signal. However, electrochemical current was recovered on ITO film electrodes prepared from nanometer-sized particles. The surface of the nanoparticle structured electrode was found by scanning electron microscopy to be very porous, and had twice as much surface binding capacity for avidin as the sputtered electrode. The results were rationalized by the assumption of different packing density of avidin inner layer on the two surfaces, and consequently different electron transfer distance between the electrode and Ru-bipy on the IgG outer layer. A linear relationship between electrochemical current and IgG concentration was obtained in the range of 40-4000 nmol L⁻¹ on the nanoparticle-based electrode. The approach can be employed in the electrochemical detection of immunoassays using non-enzymatic redox labels.     

Small Noncytotoxic Carbon Nano‐Onions: First Covalent Functionalization with Biomolecules

Small carbon nano‐onions (CNOs, 6–8 shells) were prepared in high yield and functionalized with carboxylic groups by chemical oxidation. After functionalization these nanostructures were soluble in aqueous solutions. 3‐(4,5‐dimethylthiazol‐2‐yl)‐5‐(3‐carboxymethoxyphenyl)‐2‐(4‐sulfophenyl)‐2 tetrazolium (MTS) tests showed excellent cytocompatibility of all CNOs analyzed at 30 and 300 μg mL^?1, so these carbon nanostructures can be safely used for biological applications. The first covalent functionalization of oxidized CNOs (ox‐CNOs) with biomolecules, by using biotin–avidin interactions is reported here. Multilayers were prepared on a gold surface by layer‐by‐layer assembly and the process was monitored by surface plasmon resonance (SPR) spectroscopy and atomic force microscopy (AFM). Covalent binding of molecules to the short amine‐terminated organosulfur monolayers was assessed by Fourier transform infrared spectroscopy using total attenuated reflactance mode (FT‐IR/HATR).     

Half‐Sandwich Ruthenium(II) Biotin Conjugates as Biological Vectors to Cancer Cells

Ruthenium(II)–arene complexes with biotin‐containing ligands were prepared so that a novel drug delivery system based on tumor‐specific vitamin‐receptor mediated endocytosis could be developed. The complexes were characterized by spectroscopic methods and their in vitro anticancer activity in cancer cell lines with various levels of major biotin receptor (COLO205, HCT116 and SW620 cells) was tested in comparison with the ligands. In all cases, coordination of ruthenium resulted in significantly enhanced cytotoxicity. The affinity of Ru^II–biotin complexes to avidin was investigated and was lower than that of unmodified biotin. Hill coefficients in the range 2.012–2.851 suggest strong positive cooperation between the complexes and avidin. To estimate the likelihood of binding to the biotin receptor/transporter, docking studies with avidin and streptavidin were conducted. These explain, to some extent, the in vitro anticancer activity results and support the conclusion that these novel half‐sandwich ruthenium(II)–biotin conjugates may act as biological vectors to cancer cells, although no clear relationship between the cellular Ru content, the cytotoxicity, and the presence of the biotin moiety was observed.     

Composite Assembly of Silver Nanoparticles with Avidin and Biotinylated AChE on Gold for the Pesticidal Electrochemical Sensing

An amperometric pesticide biosensor has been devised by the composite assembly of silver nanoparticles with avidin and biotinylated acetylcholinesterase (AChE) on gold electrodes modified with a biotin‐terminated self assembly monolayer (SAM). This composite assembly strategy takes use of the biospecific recognition avidin with the biotin from the SAM‐terminals and biotinylated AChE, as well as the electrostatic interaction between silver nanoparticles with negatively charged citrate shell and avidin with encounter charge at pH 7.2. The construction process of the composite interface on gold was monitored by surface plasmon resonance (SPR), and its structure was characterized by attenuated total reflection Fourier‐transform infrared spectra, atomic force microscopy and UV‐vis spectra. The composite interface shows excellent electron transfer ability, as characterized by cyclic voltammetry and electrochemical impedance spectroscopy. Under the optimum conditions a quantitative measurement of organophosphate pesticide dimethoate was achieved with the linear range of 0.05 μM to10 μM and the detection limit 0.01 μM, taken as the concentration equivalent to a 10% decrease in signal. Silver nanoparticles conjugated biotin‐avidin system represents a simple and functional approach to the integration of electrode sensing interface with improved biocompatibility and electron transfer ability, which may provide an analytical access to a large group of enzymes for bioelectrochemical application.     

MALDI‐TOF‐Massenspektrometrie: Risikoanalyse im Flug

The high accuracy, molecular resolution and sensitivity of matrix‐assisted laser desorption/ionisation time‐of‐flight mass spectrometry (MALDI‐TOF‐MS) make it an efficient method for analysing all kinds of biomolecules including nucleic acids, proteins/peptides, carbohydrates and lipids. MALDI‐TOF‐MS based high‐throughput genotyping of genetic heterogeneities possesses the potential of becoming a routine method. MAL‐DI‐TOF‐MS can be used for the identification of proteins and posttranslational modifications. Taken together, MALDI‐TOF‐MS represents a integrated platform technology in bioanalytics and molecular medicine.     

Chromatography of functionalized liposomes and their components

The antitumour drug 1-beta-D-arabinofuranosylcytosine (ara C) was acylated by means of oleic acid anhydride, resulting in the prodrug N4-oleoyl-ara C. Together with a lipophilic biotin derivative, this lipophilic prodrug was incorporated into the bilayer membrane of unilamellar liposomes prepared by means of the detergent dialysis method. On addition of these biotinylated prodrug-liposomes to an excess of avidin, biotin residues were complexed with avidin. The unreacted avidin was removed by chromatography on the Ultrogel AcA-22 column. The prodrug-liposome-avidin complex was coupled to biotinylated monoclonal antibodies through the free binding sites of the immobilized avidin. Unreacted antibodies were removed by chromatography on an Ultrogel AcA-22 column. In vitro, the liposome-antibody complexes selectively bound to cells which were recognized by the monoclonal antibodies linked to the liposomes. For this reason, a promising strategy towards a specific chemotherapy of cancer is expected.     

Unbinding Molecular Recognition Force Maps of Localized Single Receptor Molecules by Atomic Force Microscopy

Atomic force microscopy is a technique capable to study biological recognition processes at the single‐molecule level. In this work we operate the AFM in a force‐scan based mode, the jumping mode, where simultaneous topographic and tip–sample adhesion maps are acquired. This approach obtains the unbinding force between a well‐defined receptor molecule and a ligand attached to the AFM tip. The method is applied to the avidin–biotin system. In contrast with previous data, we obtain laterally resolved adhesion maps of avidin–biotin unbinding forces highly correlated with single avidin molecules in the corresponding topographic map. The scanning rate 250 pixel s^?1 (2 min for a 128×128 image) is limited by the hydrodynamic drag force. We are able to build a rupture‐force distribution histogram that corresponds to a single defined molecule. Furthermore, we find that due to the motility of the polymer used as spacer to anchor the ligand to the tip, its direction at rupture does not generally coincide with the normal to the tip–sample, this introduces an appreciable error in the measured force.     

A two‐step strategy to visually identify molecularly imprinted polymers for tagged proteins

A practical and relatively simple method to identify molecularly imprinted polymers capable of binding proteins via the molecular tagging (epitope‐like) approach has been developed. In our two‐step method, we first challenge a previously obtained anti‐tag molecularly imprinted polymer with a small molecule including the said tag of choice (a biotin derivative as shown here or other) connected to a linker bound to a second biotin moiety. An avidin molecule partially decorated with fluorescent labels is then allowed to bind the available biotin derivative associated with the polymer matrix. At the end of this simple process, and after washing off all the low‐affinity binding molecules from the polymer matrix, only suitable molecularly imprinted polymers binding avidin through its previously acquired small molecule tag (or epitope‐like probe, in a general case) will remain fluorescent. For confirmation, we tested the selective performance of the anti‐biotin molecularly imprinted polymer binding it to biotinylated alkaline phosphatase. Residual chemical activity of the enzyme on the molecularly imprinted polymer solid support was observed. In all cases, the corresponding nonimprinted polymer controls were inactive.