Real-time Reaction Monitoring Research Articles

Real-Time Electrochemical Monitoring of the Polymerase Chain Reaction by Mediated Redox Catalysis

We described the proof-of-principle of a nonoptical real-time PCR that uses cyclic voltammetry for indirectly monitoring the amplified DNA product generated in the PCR reaction solution after each PCR cycle. To enable indirect measurement of the amplicon produced throughout PCR, we monitor electrochemically the progressive consumption (i.e., the decrease of concentration) of free electroactive deoxynucleoside triphosphates (dNTPs) used for DNA synthesis. This is accomplished by exploiting the fast catalytic oxidation of native deoxyguanosine triphosphate (dGTP) or its unnatural analogue 7-deaza-dGTP by the one-electron redox catalysts Ru(bpy)(3)(3+) (with bpy = 2,2'-bipyridine) or Os(bpy)(3)(3+) generated at an electrode. To demonstrate the feasibility of the method, a disposable array of eight miniaturized self-contained electrochemical cells (working volume of 50 microL) has been developed and implemented in a classical programmable thermal cycler and then tested with the PCR amplification of two illustrated examples of real-world biological target DNA sequences (i.e., a relatively long 2300-bp sequence from the bacterial genome of multidrug-resistant Achromobacter xylosoxidans and a shorter 283-bp target from the human cytomegalovirus). Although the method works with both mediator/base couples, the catalytic peak current responses recorded with the Ru(bpy)(3)(3+)/dGTP couple under real-time PCR conditions are significantly affected by a continuous current drift and interference with the background solvent discharge, thus leading to poorly reproducible data. Much more reproducible and reliable results are finally obtained with the Os(bpy)(3)(3+)/7-deaza-dGTP, a result that is attributed to the much lower anodic potential at which the catalytic oxidation of 7-deaza-dGTP by Os(bpy)(3)(3+) is detected. Under these conditions, an exponential decrease of the catalytic signal as a function of the number of PCR cycles is obtained, allowing definition of a cycle threshold value (C(t)) that correlates inversely with the initial amount of target DNA. A semilogarithmic plot of C(t) with the initial copy number of target DNA gives a standard linear curve similar to that obtained with fluorescent-based real-time PCR. Although the detection limit (10(3) molecules of target DNA in 50 microL) and sensitivity of the electrochemical method is not as high as conventional optical-based real-time PCR, the methodology described here offers many of the advantages of real-time PCR, such as a high dynamic range (over 8-log(10)) and speed, high amplification efficiency (close to 2), and the elimination of post-PCR processing. The method also has the advantage of being very simple, just requiring the use of low-cost single-use electrodes and the addition of a minute amount of redox catalyst into the PCR mixture. Moreover, compared to the other recently developed electrochemical real-time PCR based on solid-phase amplification, the present approach does not require electrode functionalization by a DNA probe. Finally, on account of the relative insensitivity of electrochemical methods to downscaling, the detection scheme is quite promising for use in miniaturized devices and in the development of point-of-care diagnosis applications.

Substrate-Selective Supramolecular Tandem Assays: Monitoring Enzyme Inhibition of Arginase and Diamine Oxidase by Fluorescent Dye Displacement from Calixarene and Cucurbituril Macrocycles

A combination of moderately selective host-guest binding with the impressive specificity of enzymatic transformations allows the real-time monitoring of enzymatic reactions in a homogeneous solution. The resulting enzyme assays ("supramolecular tandem assays") exploit the dynamic binding of a fluorescent dye with a macrocyclic host in competition with the binding of the substrate and product. Two examples of enzymatic reactions were investigated: the hydrolysis of arginine to ornithine catalyzed by arginase and the oxidation of cadaverine to 5-aminopentanal by diamine oxidase, in which the substrates have a higher affinity to the macrocycle than the products ("substrate-selective assays"). The depletion of the substrate allows the fluorescent dye to enter the macrocycle in the course of the enzymatic reaction, which leads to the desired fluorescence response. For arginase, p-sulfonatocalix[4]arene was used as the macrocycle, which displayed binding constants of 6400 M(-1) with arginine, 550 M(-1) with ornithine, and 60,000 M(-1) with the selected fluorescent dye (1-aminomethyl-2,3-diazabicyclo[2.2.2]oct-2-ene); the dye shows a weaker fluorescence in its complexed state, which leads to a switch-off fluorescence response in the course of the enzymatic reaction. For diamine oxidase, cucurbit[7]uril (CB7) was used as the macrocycle, which showed binding constants of 4.5 x 10(6) M(-1) with cadaverine, 1.1 x 10(5) M(-1) with 1-aminopentane (as a model for the thermally unstable 1-aminopentanal), and 2.9 x 10(5) M(-1) with the selected fluorescent dye (acridine orange, AO); AO shows a stronger fluorescence in its complexed state, which leads to a switch-on fluorescence response upon enzymatic oxidation. It is demonstrated that tandem assays can be successfully used to probe the inhibition of enzymes. Inhibition constants were estimated for the addition of known inhibitors, i.e., S-(2-boronoethyl)-L-cysteine and 2(S)-amino-6-boronohexanoic acid for arginase and potassium cyanide for diamine oxidase. Through the sequential coupling of a "product-selective" with a "substrate-selective" assay it was furthermore possible to monitor a multistep biochemical pathway, namely the decarboxylation of lysine to cadaverine by lysine decarboxylase followed by the oxidation of cadaverine by diamine oxidase. This "domino tandem assay" was performed in the same solution with a single reporter pair (CB7/AO).

Real-time monitoring of odorant-induced cellular reactions using surface plasmon resonance

Surface plasmon resonance (SPR) is a powerful technique for measuring molecular interaction in real-time. SPR can be used to detect molecule to cell interactions as well as molecule to molecule interactions. In this study, the SPR-based biosensing technique was applied to real-time monitoring of odorant-induced cellular reactions. An olfactory receptor, OR I7, was fused with a rho-tag import sequence at the N-terminus of OR I7, and expressed on the surface of human embryonic kidney (HEK)-293 cells. These cells were then immobilized on a SPR sensor chip. The intensity of the SPR response was linearly dependent on the amount of injected odorant. Among all the aldehyde containing odorants tested, the SPR response was specifically high for octanal, which is the known cognate odorant for the OR I7. This SPR response is believed to have resulted from intracellular signaling triggered by the binding of odorant molecules to the olfactory receptors expressed on the cell surface. This SPR system combined with olfactory receptor-expressed cells provides a new olfactory biosensor system for selective and quantitative detection of volatile compounds.

Real-time label-free detection of complement activation products in human serum by white light reflectance spectroscopy

We present a label-free, real-time sensor based on white light reflectance spectroscopy for quantitating the complement activation product C3b and its metabolites as a biomarker in human serum. Our novel sensor allows real-time monitoring of biomolecular reactions (in this case, antigen–antibody reactions) taking place on a reflective surface within a flow cell. Detection was based on monitoring the increase in film thickness caused by its immunoreaction with a specific antibody; this reaction was seen as a shift in the wavelength at which constructive interference was observed . Quantitation of C3b was achieved by immobilizing a specific mouse monoclonal antibody onto the refractive surface and monitoring the rate of the signal changes occurring during the first 60 s of the immunoreaction between the antibody and known concentrations of purified C3b or dilutions of complement-activated human serum. The lowest detectable concentration of purified C3b was 20 ng/mL, and complement activation products in human serum samples could be detected at dilutions as high as 6000-fold. The advantages of the method include its relatively low cost, short analysis time, and high assay sensitivity and reliability. Thus, this novel assay method can be used to monitor serum C3b produced as a result of complement activation in a variety of normal and pathologic conditions.

Structure, interaction and real-time monitoring of the enzymatic reaction of wild-type APOBEC3G

Human APOBEC3G exhibits anti-human immunodeficiency virus-1 (HIV-1) activity by deaminating cytidines of the minus strand of HIV-1. Here, we report a solution structure of the C-terminal deaminase domain of wild-type APOBEC3G. The interaction with DNA was examined. Many differences in the interaction were found between the wild type and recently studied mutant APOBEC3Gs. The position of the substrate cytidine, together with that of a DNA chain, in the complex, was deduced. Interestingly, the deamination reaction of APOBEC3G was successfully monitored using NMR signals in real time. Real-time monitoring has revealed that the third cytidine of the d(CCCA) segment is deaminated at an early stage and that then the second one is deaminated at a late stage, the first one not being deaminated at all. This indicates that the deamination is carried out in a strict 3' --> 5' order. Virus infectivity factor (Vif) of HIV-1 counteracts the anti-HIV-1 activity of APOBEC3G. The structure of the N-terminal domain of APOBEC3G, with which Vif interacts, was constructed with homology modelling. The structure implies the mechanism of species-specific sensitivity of APOBEC3G to Vif action.

Real-time monitoring of chemical reactions by mass spectrometry utilizing a low-temperature plasma probe

Real-time and in-situ monitoring of ongoing chemical reactions by mass spectrometry was achieved by simply directing the low-temperature plasma (LTP) to the surface of the reaction system for analyte desorption and ionization without any sample pretreatment.

Mechanism-Based Probing, Characterization, and Inhibitor Design of Glycosidases and Glycosyltransferases

Recent structural and kinetic studies indicated that enzymes shift their peripheral structures of the catalytic sites dynamically to modify the substrate structures. Molecules which disturb such mechanism of specific enzymes may become potent candidates for therapeutic reagent. This article describes a versatile strategy to synthesize new class of mechanism-based inhibitors for glycosyltransferases and glycoside hydrolases. Combination of irreversible tagging and proteomic analysis of crucial amino acid residues using MALDI-TOF/TOF mass spectrometry allowed a promising method to probe such invisible transitional state in the enzymatic reactions. Feasibility of the fluorescence energy resonance transfer (FRET) is also documented as novel protocol for the real-time and continuous monitoring of glycosyltransferase catalyzed reactions. It was demonstrated that FRET method greatly facilitates discovery research of selective inhibitors in combination with click chemistry.

Electrochemical assay of plasmin activity and its kinetic analysis

A sensitive and convenient electrochemical assay of plasmin activity and its kinetic analysis are described. Thus, a ferrocenyl peptide substrate (FcPS) having a plasmin-specific substrate sequence, Lys-Thr-Phe-Lys, and a Cys residue was prepared and immobilized on a gold electrode through the sulfur–gold linkage. The obtained electrode showed a redox signal based on the ferrocene moiety, suggesting the immobilization of FcPS on the electrode. After treatment of this electrode with plasmin, its electrochemical signal was decreased in proportion to an increase of the amount of plasmin. The detection limit for plasmin in this assay system was as low as 50 ng/ml or 0.15 mU/ml. Real-time monitoring of plasmin reaction on the electrode could also be achieved, and the kinetic parameters of this enzymatic reaction could be determined; for example, the k cat/ K m value was 0.063 μM −1 s −1. Furthermore, a quantitative assay for streptokinase as a plasminogen activator was also demonstrated by using this system.

Real‐time, on‐line monitoring of organic chemical reactions using extractive electrospray ionization tandem mass spectrometry

Extractive electrospray ionization mass spectrometry (EESI-MS) for real-time monitoring of organic chemical reactions was demonstrated for a well-established pharmaceutical process reaction and a widely used acetylation reaction in the presence of a nucleophilic catalyst, 4-dimethylaminopyridine (4-DMAP). EESI-MS provides real-time information that allows us to determine the optimum time for terminating the reaction based on the relative intensities of the precursors and products. In addition, tandem mass spectrometric (MS/MS) analysis via EESI-MS permits on-line validation of proposed reaction intermediates. The simplicity and rapid response of EESI-MS make it a valuable technique for on-line characterization and full control of chemical and pharmaceutical reactions, resulting in maximized product yield and minimized environmental costs.

Organic Synthesis in Soft Wall-Free Microreactors: Real-Time Monitoring of Fluorogenic Reactions

A new approach of "laboratory on a chip" (LOC) devoted to organic synthesis based on electrically operated ionic liquid microdroplets used as air-stable "soft" microreactors was recently introduced. A number of challenging issues have yet to be addressed to allow standard macroscale organic chemistry to be directly transposed in these nonclassical microreactors. In particular, since standard (i.e., magnetical or mechanical) stirring methods are prohibited in such wall-free microreactors, effective alternatives have to be developed to circumvent mass-transfer limitations. With this aim in mind, a fluorogenic version of a click chemistry reaction was developed to evaluate the efficiency of alternative mixing methods on the reaction kinetics. We demonstrate that the combination of chaotic advection created by surface acoustic waves combined with a temperature increase (Marangoni effect) leads to the same kinetics regime as in standard macroscale conditions. This opens the route for application of the new generation of LOC to efficient organic synthesis in microscale.

Real-Time Polymerase Chain Reaction Monitoring of Recombinant DNA Entry into Soil from Decomposing Roundup Ready Leaf Biomass

Glyphosate-tolerant, Roundup Ready (RR) soybeans account for about 57% of all genetically modified (GM) crops grown worldwide. The entry of recombinant DNA into soil from GM crops has been identified as an environmental concern due to the possibility of their horizontal transfer to soil microorganisms. RR soybeans contain recombinant gene sequences that can be differentiated from wild-type plant and microbial genes in soil by using a sequence-specific molecular beacon and real-time polymerase chain reaction (PCR). A molecular beacon-based real-time PCR system to quantify a wild-type soybean lectin ( le1) gene was designed to compare amounts of endogenous soybean genes to recombinant DNA in soil. Microcosm studies were carried out to develop methodologies for the detection of recombinant DNA from RR soybeans in soil. RR soybean leaf litterbags were imbedded in the soil under controlled environmental conditions (60% water holding capacity, 10/15 degrees C, and 8/16 h day/night) for 30 days. The soybean biomass decomposition was described using a single-phase exponential equation, and the DNA concentration in planta and in soil was quantified using real-time PCR using sequence-specific molecular beacons for the recombinant cp4 epsps and endogenous soybean lectin ( le1) genes. The biomass of RR soybean leaves was 8.6% less than nontransgenic (NT) soybean leaves after 30 days. The pooled half-disappearance time for cp4 epsps and le1 in RR and of le1 in NT soybean leaves was 1.4 days. All genes from leaves were detected in soil after 30 days. This study provides a methodology for monitoring the entry of RR and NT soybean DNA into soil from decomposing plant residues.

Blood-stage Challenge for Malaria Vaccine Efficacy Trials: A Pilot Study with Discussion of Safety and Potential Value

There is increasing interest in malaria vaccines targeting the asexual blood stage of Plasmodium falciparum. Without accepted immunologic correlates of clinical protection, challenge studies are useful for assessing the efficacy of candidate vaccines in vivo in healthy volunteers. We report a pilot study of a safe and robust challenge protocol using a blood-stage inoculum. We have applied well-validated trial endpoints and twice daily real-time quantitative polymerase chain reaction monitoring of parasitemia to blood-stage challenge, which enabled direct comparison with sporozoite challenge. We found that greater accuracy in quantification of blood-stage growth rates can be achieved with blood-stage challenge. This finding may provide greater power to detect partial efficacy of many blood-stage candidate vaccines. We discuss the potential utility of blood-stage challenge studies in accelerating malaria vaccine development.

Label-Free and Real-Time Monitoring of Phosphatase Reactions Using a Phosphate-Specific and Fluorescent Probe

A phosphate-specific and fluorescent probe was prepared for label-free phosphatase assays based on fluorescence polarization. By using the probe, dephosphorylation reactions of DNA and protein substrates by calf intestinal alkaline phosphatase (CIP) could effectively be monitored in real-time. Since this assay method does not require additional materials such as labeled substrates and phosphospecific antibodies to obtain fluorescence polarization signals, it is simple, cost-effective, and expected to be useful not only for measuring activity of phosphatases but also for high-throughput screening of phosphatase inhibitors.

Preparation of Ruthenium and Osmium Carbonyl Complexes Using Microwave Heating: Demonstrating the Use of a Gas-Loading Accessory and Real-Time Reaction Monitoring by Means of a Digital Camera

By using a gas-loading accessory, we show that it is possible to perform reactions involving gases and prepare organometallic complexes easily in good yields using microwave heating. The complexes Ru3(CO)12, H4Ru4(CO)12, and H2Os3(CO)10 are prepared. Ligand substitution reactions of Ru3(CO)12 are also studied and, in the case of the reaction with triphenylphosphine, the reaction is monitored in real time by means of a digital camera interfaced with the microwave unit.

Development of an NMR Interface Microchip “MICCS” for Direct Detection of Reaction Products and Intermediates of Micro-syntheses Using a “MICCS-NMR”

The development of an NMR interface microchip and its applications to the real-time monitoring of chemical reactions are described. The microchip device was named "MICCS" (MIcro Channeled Cell for Synthesis monitoring), and the method using it was named "MICCS-NMR". MICCS was inserted into a 5 mm Phi NMR sample tube. Thus standard solution NMR probes without any modifications can be used in MICCS-NMR measurements. A gap between MICCS and the sample tube was filled with a deuterated solvent for an NMR lock. The reaction temperature and reaction time in MICCS can be easily changed by adjusting the temperature of the NMR probe and changing the flow rates, respectively. The effectiveness of the MICCS-NMR was verified in the real-time monitoring of the Wittig reaction. Preliminary data on the direct detection of intermediates of the Grignard reaction is also reported. Besides real-time monitoring of chemical reactions, MICCS-NMR would be useful as a qualitative detection method for microchip-based synthesis.

Immobilization of Ligands with Precise Control of Density to Electroactive Surfaces

We report a broadly applicable surface chemistry methodology to immobilize ligands, proteins, and cells to an electroactive substrate with precise control of ligand density. This strategy is based on the coupling of soluble aminooxy terminated ligands with an electroactive quinone terminated monolayer. The surface chemistry product oxime is also redox active but at a different potential and therefore allows for real-time monitoring of the immobilization reaction. Only the quinone form of the immobilized redox pair is reactive with soluble aminooxy groups, which allows for the determination of the yield of reaction, the ability to immobilize multiple ligands at controlled densities, and the in-situ modulation of ligand activity. We demonstrate this methodology by using cyclic voltammetry to characterize the kinetics of a model interfacial reaction with aminooxy acetic acid. We also demonstrate the synthetic flexibility and utility of this method for biospecific interactions by installing aminooxy terminated FLAG peptides and characterizing their binding to soluble anti-FLAG with surface plasmon resonance spectroscopy. We further show this methodology is compatible with microarray technology by printing rhodamine-oxyamine in various size spots and characterizing the yield within the spots by cyclic voltammetry. We also show this methodology is compatible with cell culture conditions and fluorescent microscopy technology for cell biological studies. Arraying RGD-oxyamine peptides on these substrates allows for bio-specific adhesion of Swiss 3T3 Fibroblasts.

Real-Time Quantitative Polymerase Chain Reaction (RQ-PCR) Monitoring of Minimal Residual Disease (MRD) in Core Binding Factor Acute Myeloid Leukaemia (CBF AML).

Background: CBF AML, with t(8;21)(q22;q22), inv(16)(p13q22) or t(16;16)(p13;q22) and the associated fusion proteins AML1/ETO or CBFβ/MYH11, has a favourable clinical prognosis although significant numbers of patients still relapse. We examined the prognostic utility of MRD monitoring by RQ-PCR and propose a simple model for prediction of impending haematological relapse.Methods: Patients with CBF AML had samples collected at diagnosis, after induction and consolidation chemotherapy and at routine regular intervals thereafter. RQ-PCR, using the Applied Biosystems 7700 Sequence Detection System, was performed in triplicate and the final result was calculated by averaging 3 values, expressed relative to PGK levels. Stratified Cox regression was used to assess the impact of predictor variables (diagnostic, post-induction, post-consolidation RQ-PCR levels and presence of a 1 log10 increase in sequential RQ-PCR levels) on leukaemia-free survival (LFS).Results: Of 46 patients identified with CBF AML, 29 had diagnostic, regular longitudinal samples and clinical follow up allowing further evaluation; 12 AML1-ETO and 17 CBFβ-MYH11. The median age was 39 years (range 7–68) with 52% male. Median follow up was 34 months (range 1–106) and median sample number was 6 (2–15). Twelve relapses occurred at a median of 11 months (range 4–17) from diagnosis. There were significant differences between transcript levels at diagnosis (median 1.9), post-induction (8.96*10−04), post-consolidation (5.01*10−05), in remission (1*10−06) or relapse (0.15) (p=0.01). Diagnostic, post-induction and post-consolidation RQ-PCR levels did not predict outcome. A log10 rise in a remission bone marrow sample correlated with adverse LFS and imminent risk of haematological relapse (HR 8.6). Relapses occurred a median of 60 days (range 45–272) after a log10 rise.RQ-PCR levelsHazard Ratio (HR) LFS95% CIP-valueDiagnosis0.220.02–2.90.25Post-induction1.30.8–2.10.36Post-consolidation0.80.5–1.20.271 log10 increase8.61.8–420.008Conclusions: A 1 log10 rise in transcript levels was a highly significant predictor of haematological relapse. Transcript levels at early post-treatment time points did not predict long term outcome, cautioning against de-escalation protocols based on these results. Prospective identification of high risk patients will enable clinical trials to address the efficacy of treatment initiated at molecular progression.

Treatment of solid organ transplant recipients with autologous Epstein Barr virus–specific cytotoxic T lymphocytes (CTLs)

AbstractWe have investigated the in vivo safety, efficacy, and persistence of autologous Epstein Barr virus (EBV)–specific cytotoxic T lymphocytes (CTLs) for the treatment of solid organ transplant (SOT) recipients at high risk for EBV-associated posttransplantation lymphoproliferative disease (PTLD). EBV-CTLs generated from 35 patients expanded with normal kinetics contained both CD8 and CD4 lymphocytes and produced significant specific killing of autologous EBV-transformed B lymphoblastoid cell lines (LCLs). Twelve SOT recipients at high risk for PTLD, or with active disease, received autologous CTL infusions without toxicity. Real-time polymerase chain reaction (PCR) monitoring of EBV-DNA showed a transient increase in plasma EBV-DNA suggestive of lysis of EBV-infected cells, although there was no consistent decrease in virus load in peripheral-blood mononuclear cells. Interferon-γ enzyme-linked immunospot (ELISPOT) assay and tetramer analysis showed an increase in the frequency of EBV-responsive T cells, which returned to preinfusion levels after 2 to 6 months. None of the treated patients developed PTLD. One patient with liver PTLD showed a complete response, and one with ocular disease has had a partial response stable for over one year. These data are consistent with an expansion and persistence of adoptively transferred EBV-CTLs that is limited in the presence of continued immunosuppression but that nonetheless produces clinically useful antiviral activity.

Real-Time Monitoring of Microwave-Promoted Suzuki Coupling Reactions Using in Situ Raman Spectroscopy

The progress of microwave-promoted Suzuki reactions has been monitored using an in situ Raman spectroscopy apparatus assembled from commercially available components. It was possible to see if any reaction occurred and, if so, when it reached completion. In addition, the monitoring technique has given us an insight into the reaction, confirming that, when run in aqueous media, the coupling is in competition with the rapid deboronation of the boronic acid.

Effects of ozone pretreatment on the performance of Au/TiO 2 catalyst for CO oxidation reaction

O 3-pretreated O 3-Au/TiO 2 catalyst exhibited better catalyst dispersion and stability compared with O 2-pretreated O 2-Au/TiO 2. Ozone effectively removed the carbonaceous byproducts of catalyst preparation that oxygen was unable to completely decompose. This resulted in the poor catalyst dispersion and a bimodal gold particle size distribution of O 2-Au/TiO 2. The catalyst performance was tested for the CO oxidation reaction and compared with the gold reference catalyst (GRC). The reaction was carried out in an in situ DRIFTS apparatus that provides real-time monitoring of surface reaction and simultaneous collection of reaction conversion data. Both Au/TiO 2 catalysts displayed higher conversion rates for CO oxidation reaction compared with GRC. Gold sintering was evident for the O 2-Au/TiO 2 and GRC after the CO oxidation reaction at 473 K, and both catalysts suffered a loss in activity. The formation of oxidic gold observed in O 3-Au/TiO 2 is expected to afford a stronger metal–support interaction and may be the reason for the excellent stability of this catalyst against sintering.