Detection of DNA and Protein Molecules Using an FET‐Type Biosensor with Gold as a Gate Metal

In this study, a field effect transistor (FET)‐type biosensor based on 0.5 μm standard complementary metal oxide semiconductor (CMOS) technology is proposed and its feasibility for detecting deoxyribonucleic acid (DNA) and protein molecules is investigated. Au, which has a chemical affinity with thiol by forming a self‐assembled monolayer (SAM), was used as the gate metal in order to immobilize DNA and protein molecules. A Pt pseudo‐reference electrode was employed for the detection of biomolecules. The sensor was fabricated as a p‐channel (P)MOSFET‐type because PMOSFET with positive surface potential is useful for detecting negatively charged biomolecules from the view point of its high sensitivity and fast response time. DNA and protein molecules were detected by measuring the variation of the drain current due to the variation of biomolecular charge and capacitance. DNA and protein molecules used in the experiment were 15mer–oligonucleotide probe and streptavidin‐biotin protein complexes, respectively. DNA was detected by both in situ and ex situ measurements. Additionally, to verify the interactions among SAM, streptavidin, and biotin, surface plasmon resonance (SPR) measurement was performed.     

A Cofactor‐Substrate‐Based Supramolecular Fluorescent Probe for the Ultrafast Detection of Nitroreductase under Hypoxic Conditions

Identifying the location and expression levels of enzymes under hypoxic conditions in cancer cells is vital in early‐stage cancer diagnosis and monitoring. By encapsulating a fluorescent substrate, L‐NO₂ , within the NADH mimic‐containing metal–organic capsule Zn‐ MPB , we developed a cofactor‐substrate‐based supramolecular luminescent probe for ultrafast detection of hypoxia‐related enzymes in solution in vitro and in vivo. The host–guest structure fuses the coenzyme and substrate into one supramolecular probe to avoid control by NADH, switching the catalytic process of nitroreductase from a double‐substrate mechanism to a single‐substrate one. This probe promotes enzyme efficiency by altering the substrate catalytic process and enhances the electron transfer efficiency through an intra‐molecular pathway with increased activity. The enzyme content and fluorescence intensity showed a linear relationship and equilibrium was obtained in seconds, showing potential for early tumor diagnosis, biomimetic catalysis, and prodrug activation.     

Flexibility of a biotinylated ligand in artificial metalloenzymes based on streptavidin—an insight from molecular dynamics simulations with classical and ab initio force fields

In the field of enzymatic catalysis, creating activity from a non catalytic scaffold is a daunting task. Introduction of a catalytically active moiety within a protein scaffold offers an attractive means for the creation of artificial metalloenzymes. With this goal in mind, introduction of a biotinylated d⁶-piano-stool complex within streptavidin (SAV) affords enantioselective artificial transfer-hydrogenases for the reduction of prochiral ketones. Based on an X-ray crystal structure of a highly selective hybrid catalyst, displaying significant disorder around the biotinylated catalyst [η⁶-(p-cymene)Ru(Biot-p-L)Cl], we report on molecular dynamics simulations to shed light on the protein–cofactor interactions and contacts. The results of these simulations with classical force field indicate that the SAV-biotin and SAV-catalyst complexes are more stable than ligand-free SAV. The point mutations introduced did not affect significantly the overall behavior of SAV and, unexpectedly, the P64G substitution did not provide additional flexibility to the protein scaffold. The metal-cofactor proved to be conformationally flexible, and the S112K or P64G mutants proved to enhance this effect in the most pronounced way. The network of intermolecular hydrogen bonds is efficient at stabilizing the position of biotin, but much less at fixing the conformation of an extended biotinylated ligand. This leads to a relative conformational freedom of the metal-cofactor, and a poorly localized catalytic metal moiety. MD calculations with ab initio potential function suggest that the hydrogen bonds alone are not sufficient factors for full stabilization of the biotin. The hydrophobic biotin-binding pocket (and generally protein scaffold) maintains the hydrogen bonds between biotin and protein.     

The manganese ion of the heterodinuclear Mn/Fe cofactor in Chlamydia trachomatis ribonucleotide reductase R2c is located at metal position 1

The essential catalytic radical of Class-I ribonucleotide reductase is generated and delivered by protein R2, carrying a dinuclear metal cofactor. A new R2 subclass, R2c, prototyped by the Chlamydia trachomatis protein was recently discovered. This protein carries an oxygen-activating heterodinuclear Mn(II)/Fe(II) metal cofactor and generates a radical-equivalent Mn(IV)/Fe(III) oxidation state of the metal site, as opposed to the tyrosyl radical generated by other R2 subclasses. The metal arrangement of the heterodinuclear cofactor remains unknown. Is the metal positioning specific, and if so, where is which ion located? Here we use X-ray crystallography with anomalous scattering to show that the metal arrangement of this cofactor is specific with the manganese ion occupying metal position 1. This is the position proximal to the tyrosyl radical site in other R2 proteins and consistent with the assumption that the high-valent Mn(IV) species functions as a direct substitute for the tyrosyl radical.     

Evaluation of Binding Between Electroactive Biotin Derivative and Streptavidin Immobilized on Chitin Film

Evaluation of the streptavidin‐biotin binding at the surface of chitin film was carried out with voltammetry. Immobilization of streptavidin was attempted to the protonated chitin film, based on an electrostatic interaction that hardly causes any change in the protein structure. The streptavidin‐biotin binding was estimated from changes in the electrode response of biotin labeled with an electroactive compound. Although the response of daunomycin as an electroactive compound did not change at an electrode covered with streptavidin/chitin film, the response of the labeled biotin decreased. This observation shows that streptavidin is immobilized on the chitin film and the biotin binds with immobilized streptavidin. Consequently, it was clear that the chitin film is useful as a reaction field for protein‐ligand binding. Generally, a binding event between protein and its ligand in the living body occurs on the cell surface. The electrochemical evaluation of protein‐ligand binding on a natural polysaccharide like chitin membrane surface is important.     

Encapsulation of a Quinhydrone Cofactor in the Inner Pocket of Cobalt Triangular Prisms: Combined Light‐Driven Reduction of Protons and Hydrogenation of Nitrobenzene

The design of artificial systems that mimic highly evolved and finely tuned natural photosynthetic systems has attracted intensive research interest. A new system was formulated that encapsulates a quinhydrone (QHQ) cofactor in metal–organic hosts based on inspiration from the redox relays of photosystem II. The M₆L₃ triangular prism hosts provided a special redox‐modulated environment for the cofactor localized within the pocket, and the proximity effects of the host–guest interactions facilitated the formation of charge‐transfer complexes that are typically very difficult to form in normal homogeneous systems. Extensive electron delocalization and well‐controlled redox potential were induced to decrease the overpotential of the metal sites for proton reduction. The excellent activity and stability of the supramolecular systems allow the tandem reductions being combined to efficiently reduce nitrobenzene using active H‐sources from the light activation of water.     

Single‐Walled Carbon Nanotubes as Scaffolds to Concentrate DNA for the Study of DNA–Protein Interactions

Genomic DNA in bacteria exists in a condensed state, which exhibits different biochemical and biophysical properties from a dilute solution. DNA was concentrated on streptavidin‐covered single‐walled carbon nanotubes (Strep ? SWNTs) through biotin–streptavidin interactions. We reasoned that confining DNA within a defined space through mechanical constraints, rather than by manipulating buffer conditions, would more closely resemble physiological conditions. By ensuring a high streptavidin loading on SWNTs of about 1 streptavidin tetramer per 4 nm of SWNT, we were able to achieve dense DNA binding. DNA is bound to Strep ? SWNTs at a tunable density and up to as high as 0.5 mg mL^?1 in solution and 29 mg mL^?1 on a 2D surface. This platform allows us to observe the aggregation behavior of DNA at high concentrations and the counteracting effects of HU protein (a histone‐like protein from Escherichia coli strain U93) on the DNA aggregates. This provides an in vitro model for studying DNA–DNA and DNA–protein interactions at a high DNA concentration.     

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.     

Enantiocomplementary Epoxidation Reactions Catalyzed by an Engineered Cofactor‐Independent Non‐natural Peroxygenase

Peroxygenases are heme‐dependent enzymes that use peroxide‐borne oxygen to catalyze a wide range of oxyfunctionalization reactions. Herein, we report the engineering of an unusual cofactor‐independent peroxygenase based on a promiscuous tautomerase that accepts different hydroperoxides (t‐BuOOH and H₂O₂) to accomplish enantiocomplementary epoxidations of various α,β‐unsaturated aldehydes (citral and substituted cinnamaldehydes), providing access to both enantiomers of the corresponding α,β‐epoxy‐aldehydes. High conversions (up to 98 %), high enantioselectivity (up to 98 % ee), and good product yields (50–80 %) were achieved. The reactions likely proceed via a reactive enzyme‐bound iminium ion intermediate, allowing tweaking of the enzyme's activity and selectivity by protein engineering. Our results underscore the potential of catalytic promiscuity for the engineering of new cofactor‐independent oxidative enzymes.     

Comparative Study of HRP,a Peroxidase‐Mimicking DNAzyme,and ALP as Enzyme Labels in Developing Electrochemical Genosensors for Pathogenic Bacteria

A comparative evaluation of an electrochemical sandwich genoassay for pathogenic bacteria based on immobilized hairpin DNA probes and three different enzyme labels (horseradish peroxidase, alkaline phosphatase and a biomimetic peroxidase‐like DNAzyme) is reported. The natural enzymes were used as streptavidin conjugates, coupled to the surface duplex by using a biotin‐labeled signaling probe, whereas the DNAzyme was directly incorporated to the sequence of the signaling probe. HRP provides enhanced sensitivity although the choice of a catalytic reporter DNA sequence could simplify the assay.     

The Fe–V Cofactor of Vanadium Nitrogenase Contains an Interstitial Carbon Atom

The first direct evidence is provided for the presence of an interstitial carbide in the Fe? V cofactor of Azotobacter vinelandii vanadium nitrogenase. As for our identification of the central carbide in the Fe? Mo cofactor, we employed Fe Kβ valence‐to‐core X‐ray emission spectroscopy and density functional theory calculations, and herein report the highly similar spectra of both variants of the cofactor‐containing protein. The identification of an analogous carbide, and thus an atomically homologous active site in vanadium nitrogenase, highlights the importance and influence of both the interstitial carbide and the identity of the heteroatom on the electronic structure and catalytic activity of the enzyme.     

Highly Mesoporous Metal‐Organic Frameworks as Synergistic Multimodal Catalytic Platforms for Divergent Cascade Reactions

Rational engineering and assimilation of diverse chemo‐ and biocatalytic functionalities in a single nanostructure is highly desired for efficient multistep chemical reactions but has so far remained elusive. Here, we design and synthesize multimodal catalytic nanoreactors (MCNRs) based on a mesoporous metal‐organic framework (MOF). The MCNRs consist of customizable metal nanocrystals and stably anchored enzymes in the mesopores, as well as coordinatively unsaturated cationic metal MOF nodes, all within a single nanoreactor space. The highly intimate and diverse catalytic mesoporous microenvironments and facile accessibility to the active site in the MCNR enables the cooperative and synergistic participation from different chemo‐ and biocatalytic components. This was shown by one‐pot multistep cascade reactions involving a heterogeneous catalytic nitroaldol reaction followed by a [Pd/lipase]‐catalyzed chemoenzymatic dynamic kinetic resolution to yield optically pure (>99 % ee) nitroalcohol derivatives in quantitative yields.     

“Metal‐Free” Catalytic Oxygen Reduction Reaction on Heteroatom‐Doped Graphene is Caused by Trace Metal Impurities

The oxygen reduction reaction (ORR) is of high industrial importance. There is a large body of literature showing that metal‐based catalytic nanoparticles (e.g. Co, Mn, Fe or hybrid Mn/Co‐based nanoparticles) supported on graphene act as efficient catalysts for the ORR. A significant research effort is also directed to the so‐called “metal‐free” oxygen reduction reaction on heteroatom‐doped graphene surfaces. While such studies of the ORR on nonmetallic heteroatom‐doped graphene are advertised as “metal‐free” there is typically no sufficient effort to characterize the doped materials to verify that they are indeed free of any trace metal. Here we argue that the claimed “metal‐free” electrocatalysis of the oxygen reduction reaction on heteroatom‐doped graphene is caused by metallic impurities present within the graphene materials.     

A Novel Streptavidin–luciferase Fusion Protein: Preparation,Properties and Application in Hybridization Analysis of DNA

A streptavidin–luciferase fusion protein comprising the thermostable mutant form of firefly luciferase Luciola mingrelica and minimal core streptavidin was constructed. The streptavidin–luciferase fusion was mainly produced in a tetrameric form with high luciferase and biotin‐binding activities. It was shown that fusion has the same K_m values for ATP and luciferin and the bioluminescence spectra as initial luciferase. The linear dependence of the bioluminescence signal on the content of the fusion was observed within the range of 10^?18–10^?13 mol per well. Successful application of obtained fusion in a biospecific bioluminescence assay based on biotin–streptavidin interactions was demonstrated by the example of a specific DNA hybridization analysis. A DNA hybridization analysis for Escherichia coli cells identification was developed using unique for these cells gadB fragment encoding glutamate decarboxylase. The amplified biotinylated GadB fragments were hybridized with the immobilized oligonucleotide probes; then, the biotin in the DNA duplexes was detected using the streptavidin–luciferase fusion protein. To reach the high sensitivity of the assay, we optimized the conditions of the assay. It was shown that the use of Pluronic for plate modification resulted in a significant reduction in the DNA detection limit which finally was 0.4 ng per well.     

Designing Light‐Activated Charge‐Separating Proteins with a Naphthoquinone Amino Acid

The first principles design of manmade redox‐protein maquettes is used to clarify the physical/chemical engineering supporting the mechanisms of natural enzymes with a view to recapitulate and surpass natural performance. Herein, we use intein‐based protein semisynthesis to pair a synthetic naphthoquinone amino acid (Naq) with histidine‐ligated photoactive metal–tetrapyrrole cofactors, creating a 100 μs photochemical charge separation unit akin to photosynthetic reaction centers. By using propargyl groups to protect the redox‐active para‐quinone during synthesis and assembly while permitting selective activation, we gain the ability to employ the quinone amino acid redox cofactor with the full set of natural amino acids in protein design. Direct anchoring of quinone to the protein backbone permits secure and adaptable control of intraprotein electron‐tunneling distances and rates.     

Photo‐Driven Hydrogen Evolution by an Artificial Hydrogenase Utilizing the Biotin‐Streptavidin Technology

Photocatalytic hydrogen evolution by an artificial hydrogenase based on the biotin‐streptavidin technology is reported. A biotinylated cobalt pentapyridyl‐based hydrogen evolution catalyst (HEC) was incorporated into different mutants of streptavidin. Catalysis with [Ru(bpy)₃]Cl₂ as a photosensitizer (PS) and ascorbate as sacrificial electron donor (SED) at different pH values highlighted the impact of close lying amino acids that may act as a proton relay under the reaction conditions (Asp, Arg, Lys). In the presence of a close‐lying lysine residue, both, the rates were improved, and the reaction was initiated much faster. The X‐ray crystal structure of the artificial hydrogenase reveals a distance of 8.8 Å between the closest lying Co‐moieties. We thus suggest that the hydrogen evolution mechanism proceeds via a single Co centre. Our findings highlight that streptavidin is a versatile host protein for the assembly of artificial hydrogenases and their activity can be fine‐tuned via mutagenesis.     

Catalytic Water Oxidation by Iridium‐Modified Carbonic Anhydrase

Carbonic anhydrase (CA) is a ubiquitous metalloenzyme with a Zn cofactor coordinated to trigonal histidine imidazole moieties in a tetrahedral geometry. Removal of the Zn cofactor in CA and subsequent binding of Ir afforded CA[Ir]. Under mild and neutral conditions (30 °C, pH 7), CA[Ir] exhibited water‐oxidizing activity with a turnover frequency (TOF) of 39.8 min^?1, which is comparable to those of other Ir‐based molecular catalysts. Coordination of Ir to the apoprotein of CA is thermodynamically preferred and is associated with an exothermic energy change (ΔH) of ?10.8 kcal mol^?1, which implies that the CA apoprotein is stabilized by Ir binding. The catalytic oxygen‐evolving activity of CA[Ir] is displayed only if Ir is bound to CA, which functions as an effective biological scaffold that activates the Ir center for catalysis. The results of this study indicate that the histidine imidazoles at the CA active site could be exploited as beneficial biological ligands to provide unforeseen biochemical activity by coordination to a variety of transition‐metal ions.     

Coupling Proteins to Amine-terminated Magnetic Particles Activated with 1,4-Phenylene Diisothiocyanate

The homobifunctional crosslinker 1,4‐phenylene diisothiocyanate (PDC) was coupled to amine‐terminated magnetic particles, and human IgG, streptavidin, protein G and protein A were immobilized on the activated magnetic particles. The coupling of PDC to the amine‐terminated magnetic particles was completed in 10 min, and 1 mg of activated magnetic particles was able to immobilize 95 (g of protein G, 120 µg of protein A, 160 µg of streptavidin and 280 µg of IgG. Ultraviolet‐visible spectroscopy, FTIR spectroscopy and electron micrography were used to characterize the functional particles. The results indicated that PDC was successfully coupled to the surface of the amine‐terminated magnetic particles, and the proteins were effectively immobilized on their surface. The activity of protein G immobilized on the activated magnetic particles was confirmed by its ability to purify IgG from plasma.     

RAFT‐mediated synthesis of poly[(oligoethylene glycol) methyl ether acrylate] brushes for biological functions

The synthesis of poly[(oligoethylene glycol) methyl ether acrylate] [poly(OEGA)] brushes was achieved via reversible addition‐fragmentation chain transfer (RAFT) polymerization and used to selectively immobilize streptavidin proteins. Initially, gold surfaces were modified with a trithiocarbonate‐based RAFT chain transfer agent (CTA) by using an ester reaction involving a gold substrate modified with 11‐mercapto‐1‐undecanol and bis(2‐butyric acid)trithiocarbonate. poly(OEGA) brushes were then prepared via RAFT‐mediated polymerization from the surface‐immobilized CTA. The immobilization of CTA on the gold surface and the subsequent polymer formation were followed by ellipsometry, X‐ray photoelectron spectroscopy, grazing angle‐Fourier transform infrared spectroscopy, atomic force microscopy, and water contact‐angle measurements. RAFT‐mediated polymerization method gave CTA groups to grafted poly(OEGA) termini, which can be converted to various biofunctional groups. The terminal carboxylic acid groups of poly(OEGA) chains were functionalized with amine‐functionalized biotin units to provide selective attachment points for streptavidin proteins. Fluorescence microscopy measurements confirmed the successful immobilization of streptavidin molecules on the polymer brushes. It is demonstrated that this fabrication method may be successfully applied for specific protein recognition and immobilization. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012     

Enhanced Photocatalytic Hydrogen Production by Hybrid Streptavidin-Diiron Catalysts

Hybrid protein–organometallic catalysts are being explored for selective catalysis of a number of reactions, because they utilize the complementary strengths of proteins and of organometallic complex. Herein, we present an artificial hydrogenase, StrepH2, built by incorporating a biotinylated [Fe–Fe] hydrogenase organometallic mimic within streptavidin. This strategy takes advantage of the remarkable strength and specificity of biotin-streptavidin recognition, which drives quantitative incorporation of the biotinylated diironhexacarbonyl center into streptavidin, as confirmed by UV/Vis spectroscopy and X-ray crystallography. FTIR spectra of StrepH2 show characteristic peaks at shift values indicative of interactions between the catalyst and the protein scaffold. StrepH2 catalyzes proton reduction to hydrogen in aqueous media during photo- and electrocatalysis. Under photocatalytic conditions, the protein-embedded catalyst shows enhanced efficiency and prolonged activity compared to the isolated catalyst. Transient absorption spectroscopy data suggest a mechanism for the observed increase in activity underpinned by an observed longer lifetime for the catalytic species Fe^IFe⁰ when incorporated within streptavidin compared to the biotinylated catalyst in solution.