Theory and practice of enzyme bioaffinity electrodes. Chemical, enzymatic, and electrochemical amplification of in situ product detection

The two articles in this series are dedicated to bioaffinity electrodes with in situ detection of the product of the enzyme label after recognition by its conjugate immobilized on the electrode. Part 1 was devoted to direct electrochemical detection, whereas the present contribution deals with homogeneous chemical and enzymatic amplification of the primary electrochemical signal. The theoretical relationships that are established for these modes of amplification are applied to the avidin-biotin recognition in a system that involves alkaline phosphatase as enzyme label and 4-amino-2,6-dichloro-phenyl phosphate as substrate, generating 2,6-dichloro-4-aminophenol as electrochemically active product. Chemical amplification then results from the addition of NADH, which reduces the 2,6-dichloro-quinonimine resulting from the electrochemical oxidation of 2,6-dichloro-4-aminophenol. An increased amplification is obtained when the reduction of 2,6-dichloro-quinonimine involves diaphorase in solution with NADH as substrate. The excellent agreement between theoretical predictions and experimental data required a detailed theoretical analysis and the independent determination of the key kinetic parameters of the system. The theoretical analysis was extended to monolayer and multilayered films of auxiliary enzyme as well as to electrochemical amplification by means of closely spaced dual electrodes so as to offer a rational comparative panorama of the amplification capabilities of the various possible strategies. Confinement of the profile of the product, and/or its oxidized form, in the vicinity the electrode surface appears as a key parameter of amplification.     

Signal transduction and amplification through enzyme-triggered ligand release and accelerated catalysis

Signal transduction and signal amplification are both important mechanisms used within biological signalling pathways. Inspired by this process, we have developed a signal amplification methodology that utilises the selectivity and high activity of enzymes in combination with the robustness and generality of an organometallic catalyst, achieving a hybrid biological and synthetic catalyst cascade. A proligand enzyme substrate was designed to selectively self-immolate in the presence of the enzyme to release a ligand that can bind to a metal pre-catalyst and accelerate the rate of a transfer hydrogenation reaction. Enzyme-triggered catalytic signal amplification was then applied to a range of catalyst substrates demonstrating that signal amplification and signal transduction can both be achieved through this methodology.     

Selective enzyme amplification of NAD/NADH using coimmobilized glycerol dehydrogenase and diaphorase with amperometric detection

A flow system for substrate recycling of NAD⁺/NADH was set up with an enzyme reactor containing coimmobilized glycerol dehydrogenase (GDH) and diaphorase. The product from the diaphorase catalysis, hexacyanoferrate(II), aws detected amperometrically at a glassy carbon electrode. The amplification factor was 150 for a reactor volume of 100 μ l at a flow-rate of 0.5 ml/min. With a stopped flow of four minutes, the signal increased another 88 times, resulting in a signal amplification of 13 300 times. Equations are derived for the amplification factor and used for a discussion of the optimization of amplification systems. The K_m for GDH with glycerol as a substrate was found to be 5 × 10⁻³ M at pH 8.0. GDH from Cellulomonas sp. was purified on a gel filtration column and the purified enzyme showed a specificity toward NAD⁺, compared to NADP⁺, that was higher than 99.9%. Due to the NAD⁺ specificity of the purified GDH, the enzyme amplification system reported here could be used in detection systems for enzyme immunoassays when using alkaline phosphatase as a label and NADP⁺ as a substrate. The stability of immobilized GDH and diaphorase is several orders of magnitude better than that of alcohol dehydrogenase, which is the enzyme commonly used for NAD⁺-specific detection in these applications.     

Theoretical Assessment of Binding and Mass‐Transport Effects in Electrochemical Affinity Biosensors That Utilize Nanoparticle Labels for Signal Amplification

This paper presents a theoretical study of electrochemical affinity biosensors for the detection of DNA/protein that utilize nanoparticle labels for signal amplification. This study analyzes the effects of binding and mass transport of the analytes on biosensor performance by using numerical simulations. Four cases were considered: 1) nanoparticles used to increase the loading of an electroactive species, or used as catalysts under pseudo‐first‐order conditions; 2) nanoparticles used as ultramicroelectrode arrays for the electrolysis of large concentrations of substrate; 3) nanoparticles used as seeds to deposit electrochemically detectable species; and 4) nanoparticles used to mediate the deposition of electrocatalysts. By using nanoparticle labels, high sensitivity is possible under all conditions considered. However, theoretical findings suggested that nonspecific adsorption could be more problematic in cases 2–4 due to the mismatch between the chemistry of surface binding and the principle of signal amplification that originates from the effect of mass transport. Under these conditions, any given signal would plateau at a much lower analyte concentration, well before the analyte binding had actually reached a plateau. Views on possible solutions to the above limitations are also presented.     

Solid-supported single- and multi-enzyme amplified assays for clostridiopeptidase A

A rapid and sensitive spectrophotometric assay for Clostridium histolyticum clostridiopeptidase A (collagenase) was accomplished by measuring the activity of an alkaline phosphatase indicator enzyme released into solution from insoluble, covalently linked alkaline phosphatase indicator enzyme released into solution from activity of the alkaline phosphatase was monitored spectrophotometrically using either p-nitrophenyl phosphate as substrate or more sensitively by a signal amplification system consisting of NAD⁺, alcohol dehydrogenase, diaphorase and INT-Violet. Under the reaction conditions the amount of indicator enzyme produced is directly proportional to the concentration of collagenase. With p-nitrophenyl phosphate as substrate the magnitude of the signal was 0.003 abs. min^?1 per 100 ng ml^?1 collagenase whereas with the multienzyme amplification system it was 0.035 abs. min^?1, i.e. approximately as 12-fold increase. The method consists in first incubating the substrate with the bacterial collagenase for 20 min, then up to 96 samples of the released alkaline phosphatase can be analysed in 2 min using a microtitre plate reader run in the kinetic mode.     

Biochemical analysis with microfluidic systems

Microfluidic systems are capillary networks of varying complexity fabricated originally in silicon, but nowadays in glass and polymeric substrates. Flow of liquid is mainly controlled by use of electroosmotic effects, i.e. application of electric fields, in addition to pressurized flow, i.e. application of pressure or vacuum. Because electroosmotic flow rates depend on the charge densities on the walls of capillaries, they are influenced by substrate material, fabrication processes, surface pretreatment procedures, and buffer additives. Microfluidic systems combine the properties of capillary electrophoretic systems and flow-through analytical systems, and thus biochemical analytical assays have been developed utilizing and integrating both aspects. Proteins, peptides, and nucleic acids can be separated because of their different electrophoretic mobility; detection is achieved with fluorescence detectors. For protein analysis, in particular, interfaces between microfluidic chips and mass spectrometers were developed. Further levels of integration of required sample-treatment steps were achieved by integration of protein digestion by immobilized trypsin and amplification of nucleic acids by the polymerase chain reaction. Kinetic constants of enzyme reactions were determined by adjusting different degrees of dilution of enzyme substrates or inhibitors within a single chip utilizing mainly the properties of controlled dosing and mixing liquids within a chip. For analysis of kinase reactions, however, a combination of a reaction step (enzyme with substrate and inhibitor) and a separation step (enzyme substrate and reaction product) was required. Microfluidic chips also enable separation of analytes from sample matrix constituents, which can interfere with quantitative determination, if they have different electrophoretic mobilities. In addition to analysis of nucleic acids and enzymes, immunoassays are the third group of analytical assays performed in microfluidic chips. They utilize either affinity capillary electrophoresis as a homogeneous assay format, or immobilized antigens or antibodies in heterogeneous assays with serial supply of reagents and washing solutions.     

Theory and practice of enzyme bioaffinity electrodes. Direct electrochemical product detection

The use of enzyme labeling techniques to convert biorecognition events into high sensitivity electrochemical signals may follow two different strategies. One, in which the current is the electrocatalytic response of a redox couple serving as cosubstrate to a redox enzyme label and another that consists in the detection of an electrochemically active product of the enzyme label. The theoretical relationships that link, in the latter case, the electrochemical current response to the amount of recognized labeled target analyte are established for steady-state diffusion-convection chronoamperometric regimes. Two governing parameters thus emerge. One measures the Michaelis-Menten competition in the enzyme kinetics. The other characterizes the competition between the enzymatic kinetics and the diffusion of the substrate. The electrochemical response is finally related to the labeled target analyte concentration in solution through the recognition isotherm. The direct electrochemical product detection thus provides a route to the characteristics of the recognition isotherm, which serves as a calibration curve in analytical applications. The establishment of further theoretical relationships allows one to surmise the increase in sensitivity that may be obtained by using cyclic voltammetry instead of steady-state chronoamperometry in standard electrochemical cells or by accumulation of the enzyme-product in cells of small volume/surface ratios. The theoretical predictions are tested with the example of the avidin-biotin recognition process in a system that involves alkaline phosphatase as enzyme label and 4-amino-2,6-dichlorophenyl phosphate as substrate, generating 4-amino-2,6-dichlorophenol as electrochemically active product. The advantages of the dichloro-substitution are discussed. The theoretical analysis is a requisite for a rational and realistic discussion of the analytical performances of the steady-state chronoamperometric and cyclic voltammetric approaches. These are shown to compare favorably with the best heterogeneous bioaffinity assays so far reported.     

Enzyme Electrode for Amplification of NAD+/NADH Using Glycerol Dehydrogenase and Diaphorase with Amperometric Detection

Abstract

An enzyme electrode is made from a glassy carbon electrode covered with a gelatin membrane containing entrapped glycerol dehydrogenase (GDH) and diaphorase, and protected with a dialysis membrane. Based on amplification by the recycling reaction catalyzed by the two-enzyme systems, NAD⁺ and NADH can be determined with 800–1200 times higher sensitivity than for the same electrode in a substrate sensing mode when the flow rate was 0.08 ml/min. The detection limit was about 0.03 μM for NADH. The amplification factors were around 1000 for 0.08 ml/min, with quite large variations between electrodes. They had decreased to about 70% of the original value after 7 days. The biosensor is intended for detection in immunoassays with alkaline phosphatase as a marker.     

Ultrasensitive SERS Detection of Lysozyme by a Target‐Triggering Multiple Cycle Amplification Strategy Based on a Gold Substrate

An ultrasensitive surface enhanced Raman scattering (SERS) method has been designed to selectively and sensitively detect lysozyme. The gold chip as the detection substrate, the aptamer‐based target‐triggering cascade multiple cycle amplification, and gold nanoparticles (AuNPs) bio‐barcode Raman probe enhancement on the gold substrate are employed to enhance the SERS signals. The cascade amplification process consists of the nicking enzyme signaling amplification (NESA), the strand displacement amplification (SDA), and the circular‐hairpin‐assisted exponential amplification reaction (HA‐EXPAR). With the involvement of an aptamer‐based probe, two amplification reaction templates, and a Raman probe, the whole circle amplification process is triggered by the target recognition of lysozyme. The products of the upstream cycle (NESA) could act as the “DNA trigger” of the downstream cycle (SDA and circular HA‐EXPAR) to generate further signal amplification, resulting in the immobility of abundant AuNPs Raman probes on the gold substrate. “Hot spots” are produced between the Raman probe and the gold film, leading to significant SERS enhancement. This detection method exhibits excellent specificity and sensitivity towards lysozyme with a detection limit of 1.0×10^?15 M . Moreover, the practical determination of lysozyme in human serum demonstrates the feasibility of this SERS approach in the analysis of a variety of biological specimens.     

A designed synthetic analogue of 4-OT is specific for a non-natural substrate

The substrate specificity of 4-oxalocrotonate tautomerase (4-OT) is characterized by electrostatic interactions between positively charged arginine (Arg) side chains on the enzyme and the dianionic substrate, 4-oxalocrotonate. To generate specific hydrogen-bonding interactions with a monoanionic substrate analogue, we have introduced a urea functional group into the active site by replacing arginine side chains with isosteric citrulline (Cit) residues. This design was based on the complementarity between the urea functionality of citrulline and the uncharged amide function of the substrate, as opposed to the guanidinium-carboxylate electrostatic interaction between the wild-type enzyme and the natural substrate. Indeed, the synthetic (Arg39Cit)4-OT analogue catalyzed the tautomerization of the non-natural monoamide-monoacid substrate while it was a poor catalyst for the natural diacid substrate. The specificity of (Arg39Cit)4-OT for the monoamide-monoacid substrate relative to that of the diacid substrate was found to be 740-fold greater than that of the wild-type enzyme for tautomerization of the non-natural substrate as compared with the natural one. The role of electrostatic interactions in the tautomerization of the monoamide-monoacid substrate was probed in detail with several other Arg to Cit analogues of this enzyme. This study has demonstrated that chemical manipulation of the functional groups within the active site of an enzyme can modify its catalytic activity and substrate specificity in a predictable way, suggesting that the incorporation of noncoded amino acids into proteins has great promise for the development of new enzymatic mechanisms and new binding interactions.     

Nanomolar Level Amperometric Determination of ATP Through Substrate Recycling in an Enzyme Reactor in a FIA System

Abstract

ATP, adenosine-5′-triphosphate, was determined by recycling in an enzyme reactor with co-immobilized pyruvate kinase and hexokinase in the presence of glucose, NAD⁺, and phosphoenolpyruvate, PEP. Recycling produces glucose-6-phosphate which is converted to an equivalent amount of NADH by glucose-6-phosphate dehydrogenase. The NADH is detected at a graphite flow-through electrode modified with an adsorbed 3,3′-bis(benzo[a]phenoxazin-7-ium, 5-amino-9-(diethylamino))1,4,N,N′-diamidobenzene, BPT. Oxidation of NADH takes place at 0 mM vs Ag/AgCl due to the adsorbed phenoxazine. The amplification factor is directly proportional to the residence time in the reactor and it is increased as the flow rate decreases; it becomes350 at a flow rate of 0.07 ml/min. The amplification factor can be increased further by a controlled stop-time recycling; it became 1200 at a stop-time of 12 min. A theoretical expression for the amplification factor was derived and it shows that the amplification depends o n the residence time and the pseudo-first order rate coefficients of the recycling enzyme systems. The response was linear over more than three decades, from 1 nM to 5 μM ATP. The detection limit, 1 nM ATP was set by cofactor impurities in the reagent rather than by system sensitivity or noise.     

DNA detection and signal amplification via an engineered allosteric enzyme

Rapid, sensitive, and sequence-specific DNA detection can be achieved in one step using an engineered intrasterically regulated enzyme. The semi-synthetic inhibitor-DNA-enzyme (IDE) construct (left) rests in the inactive state but upon exposure to a complementary DNA sequence undergoes a DNA hybridization-triggered allosteric enzyme activation (right). The ensuing rapid substrate turnover provides the built-in signal amplification mechanism for detecting approximately 10 fmol DNA in less than 3 min under physiological conditions.     

Structure and Properties of Polymer Biocomposite Materials

Results of studying the structure and properties of biocomposite materials are summarized. The materials in question include an enzyme (laccase, peroxidase), an ion- or electron-conducting polymer (Nafion, polymethylpyrrole), and a carbon substrate (compact, disperse). It is shown that the orientation of a large number of enzyme molecules in an enzyme/Nafion composite material on the substrate surface favors direct bioelectrocatalysis. During co-immobilization of an enzyme and polymethylpyrrole, conditions are realized under which the polymer takes part in the electron transfer between the active center of the enzyme and the surface of the electroconducting substrate. A fresh approach to constructing a biocomposite material is developed. The material is based on an extremely finely divided carbon material (colloidal graphite), which ensures a high specific activity of laccase immobilized on it. The size of colloidal-graphite particles is commensurate with that of the laccase molecule, owing to which the enzyme macromolecule is surrounded by carbon particles. As a result, practically all adsorbed enzyme molecules are electrochemically active and participate in direct bioelectrocatalysis.     

Integration of microfabricated needle-type glucose sensor devices with a novel thin-film Ag/AgCl electrode and plasma-polymerized thin film: mass production techniques

We developed an integrated array of needle-type biosensors employing a novel process of fabrication, comprising conventional semiconductor fabrication and micromachining technology. Amperometric sensing electrodes with plasma-polymerized films and a thin-film Ag/AgCl reference electrode were directly integrated on a glass substrate with thin-film process, e.g., sputtering. An enzyme was immobilized on the electrode via the plasma-polymerized film, which was deposited directly on the substrate using a dry process. The novel thin-film Ag/AgCl reference electrode showed stable potentials in concentrated chloride solutions for a long period. The plasma-polymerized film is considered to play an important role as an interfacial design between the sensing electrode and the immobilized enzyme considering that the film is extremely thin, adheres well to the substrate (electrode) and has a highly cross-linked network structure and functional groups, such as amino groups. The results showed increments of the sensor signal, probably because the plasma-polymerized film allowed a large amount of enzyme to be immobilized. The greatest advantage is that the process can permit the mass production of high-quality biosensors at a low cost.     

Quantitative assessment of the enzymatic degradation of amorphous cellulose by using a quartz crystal microbalance with dissipation monitoring

The systematic evaluation of the degradation of an amorphous cellulose film by a monocomponent endoglucanase (EG I) by using a quartz crystal microbalance with dissipation monitoring (QCM-D) identified several important aspects relevant to the study the kinetics of cellulose degradation by enzymes. It was demonstrated that, to properly evaluate the mechanism of action, steady state conditions in the experimental set up need to be reached. Rinsing or diluting the enzyme, as well as concentration of the enzyme, can have a pronounced effect on the hydrolysis. Quantification of the actual hydrolysis was carried out by measuring the film thickness reduction by atomic force microscopy after the enzymatic treatment. The values correlated well with the frequency data obtained by QCM-D measurement for corresponding films. This demonstrated that the evaluation of hydrolysis by QCM-D can be done quantitatively. Tuning of the initial thickness of films enabled variation of the volume of substrate available for hydrolysis which was then utilized in establishing a correlation between substrate volume and hydrolytic activity of EG I as measured by QCM-D. It was shown that, although the amount of substrate affects the absolute rate of hydrolysis, the relative rate of hydrolysis does not depend on the initial amount of substrate in steady state system. With this experimental setup it was also possible to demonstrate the impact of concentration on crowding of enzyme and subsequent hydrolysis efficiency. This effort also shows the action of EG I on a fully amorphous substrate as observed by QCM-D. The enzyme was shown to work uniformly within the whole volume of swollen film, however being unable to fully degrade the amorphous film.     

水溶性香豆素荧光底物的制备及在液滴数字式检测中的应用

4-甲基伞形酮磷酸酯(4-MUP)是一类重要的荧光底物, 由于具有较高的疏水性, 荧光信号易在液滴间扩散而限制了其在液滴微流控芯片领域中的应用. 本文首先通过修饰7-羟基香豆素-4-乙酸, 制备了具有较高水溶性的新型底物分子7-二羟基磷酸酯香豆素-4-乙酸甲酯; 进而以7-二羟基磷酸酯香豆素-4-乙酸甲酯为底物, 以球刷酶(荷载大量碱性磷酸酶的聚电解质纳米颗粒, SP-AKP)为模式酶, 建立了基于液滴微流控的单SP-AKP数字式检测体系. 结果表明, 该水溶性香豆素荧光底物具有与传统4-MUP底物相似的荧光光谱和酶催化性能. 传统4-MUP酶促荧光产物5 min即在液滴中发生明显扩散, 而该水溶性香豆素荧光底物酶催化后产生的荧光产物7-羟基香豆素-4-乙酸甲酯在24 h后仍未观察到明显扩散现象, 具有优异的抑制荧光扩散性能. 在基于液滴微流控芯片的单SP-AKP数字式检测中, 对SP-AKP的检测限可达29.9 amol/L, 同时有效提升了检测时间的可操作性与数字式信号读取的准确性. 新型水溶性香豆素荧光底物有望替代4-MUP应用于以基于液滴数字式超敏生物检测为代表, 在液滴分区实现酶促反应进行超灵敏检测的众多检测领域中.     

In‐capillary reactant mixing for monitoring glycerol kinase kinetics by CE

CE was used for the first time to study the two‐substrate enzyme glycerol kinase. The capillary was used as a nanoreactor in which the enzyme and its two substrates glycerol and adenosine‐5′‐triphosphate were in‐capillary mixed to realize the enzymatic assay. For kinetic parameters determination, reactants were injected (50 mbar × 5 s) as follows: (i) incubation buffer; (ii) adenosine‐5′‐triphosphate; (iii) enzyme, and (iv) glycerol. Enzymatic reaction was then initiated by mixing the reactants using electrophoretically mediated microanalysis (+20 kV for 6 s) followed by a zero‐potential amplification step of 3 min. Finally, electrophoretic separation was performed; the product adenosine‐5′‐diphosphate was detected at 254 nm and quantified. For enzyme inhibition, an allosteric inhibitor fructose‐1,6‐bisphosphate plug was injected before the first substrate plug and +20 kV for 8 s was applied for reactant mixing. A simple, economic, and robust CE method was developed for monitoring glycerol kinase activity and inhibition. Only a few tens of nanoliters of reactants were used. The results compared well with those reported in literature. This study indicates, for the first time, that at least four reactant plugs can be in‐capillary mixed using an electrophoretically mediated microanalysis approach.     

Effect of substrate inhibition and cooperativity on the electrochemical responses of glucose dehydrogenase. Kinetic characterization of wild and mutant types

Thanks to its insensitivity to dioxygen and to its good catalytic reactivity, and in spite of its poor substrate selectivity, quinoprotein glucose dehydrogenase (PQQ-GDH) plays a prominent role among the redox enzymes that can be used for analytical purposes, such as glucose detection, enzyme-based bioaffinity assays, and the design of biofuel cells. A detailed kinetic analysis of the electrochemical catalytic responses, leading to an unambiguous characterization of each individual steps, seems a priori intractable in view of the interference, on top of the usual ping-pong mechanism, of substrate inhibition and of cooperativity effects between the two identical subunits of the enzyme. Based on simplifications suggested by extended knowledge previously acquired by standard homogeneous kinetics, it is shown that analysis of the catalytic responses obtained by means of electrochemical nondestructive techniques, such as cyclic voltammetry, with ferrocene methanol as a mediator, does allow a full characterization of all individual steps of the catalytic reaction, including substrate inhibition and cooperativity and, thus, allows to decipher the reason that makes the enzyme more efficient when the neighboring subunit is filled with a glucose molecule. As a first practical illustration of this electrochemical approach, comparison of the native enzyme responses with those of a mutant (in which the asparagine amino acid in position 428 has been replaced by a cysteine residue) allowed identification of the elementary steps that makes the mutant type more efficient than the wild type when cooperativity between the two subunits takes place, which is observed at large mediator and substrate concentrations. A route is thus opened to structure-reactivity relationships and therefore to mutagenesis strategies aiming at better performances in terms of catalytic responses and/or substrate selectivity.     

Hybridization detection of enzyme-labeled DNA at electrically heated electrodes

In this report we describe an electrochemical DNA hybridization sensor approach, in which signal amplification is achieved using heated electrodes together with an enzyme as DNA-label. On the surface of the heatable low temperature co-fired ceramic (LTCC) gold electrode, an immobilized thiolated capture probe was hybridized with a biotinylated target using alkaline phosphatase (SA-ALP) as reporter molecule. The enzyme label converted the redox-inactive substrate 1-naphthyl phosphate (NAP) into the redox-active 1-naphthol voltammetrically determined at the modified gold LTCC electrode. During the measurement only the electrode was heated leaving the bulk solution at ambient temperature. Elevated temperature during detection led to increased enzyme activity and enhanced analytical signals for DNA hybridization detection. The limit of detection at 53 °C electrode temperature was 1.2 nmol/L.     

Ribonucleotide activation by enzyme ribonucleotide reductase: understanding the role of the enzyme

This article focuses on the first step of the catalytic mechanism for the reduction of ribonucleotides catalyzed by the enzyme Ribonucleotide Reductase (RNR). This corresponds to the activation of the substrate. In this work a large model of the active site region involving 130 atoms was used instead of the minimal gas phase models used in previous works. The ONIOM method was employed to deal with such a large system. The results gave additional information, which previous small models could not provide, allowing a much clearer evaluation of the role of the enzyme in this step. Enzyme-substrate interaction energies, specific transition state stabilization, and substrate steric strain energies were obtained. It was concluded that the transition state is stabilized in 4.0 kcal/mol by specific enzyme-substrate interactions. However, this stabilization is cancelled by the cost in conformational energy for the enzyme to adopt the transition state geometry; the overall result is that the enzyme machinery does not lead to a rate enhancement in this step. It was also found that the substrate binds to the active site with almost no steric strain, emphasizing the complementarity and specificity of the RNR active site for nucleotide binding. The main role of the enzyme at the very beginning of the catalytic cycle was concluded to be to impose stereospecifity upon substrate activation and to protect the enzyme radical from the solvent, rather than to be an reaction rate enhancement.