Antibody-Mediated Small Molecule Detection Using Programmable DNA-Switches.

The development of rapid, cost-effective, and single-step methods for the detection of small molecules is crucial for improving the quality and efficiency of many applications ranging from life science to environmental analysis. Unfortunately, current methodologies still require multiple complex, time-consuming washing and incubation steps, which limit their applicability. In this work we present a competitive DNA-based platform that makes use of both programmable DNA-switches and antibodies to detect small target molecules. The strategy exploits both the advantages of proximity-based methods and structure-switching DNA-probes. The platform is modular and versatile and it can potentially be applied for the detection of any small target molecule that can be conjugated to a nucleic acid sequence. Here the rational design of programmable DNA-switches is discussed, and the sensitive, rapid, and single-step detection of different environmentally relevant small target molecules is demonstrated.

Electrochemical Biosensors for Rapid Detection of Foodborne Salmonella: A Critical Overview.

Abstract:Salmonella has represented the most common and primary cause of food poisoning in many countries for at least over 100 years. Its detection is still primarily based on traditional microbiological culture methods which are labor-intensive, extremely time consuming, and not suitable for testing a large number of samples. Accordingly, great efforts to develop rapid, sensitive and specific methods, easy to use, and suitable for multi-sample analysis, have been made and continue. Biosensor-based technology has all the potentialities to meet these requirements. In this paper, we review the features of the electrochemical immunosensors, genosensors, aptasensors and phagosensors developed in the last five years for Salmonella detection, focusing on the critical aspects of their application in food analysis.

Screen-printed electrode modified with carbon black and chitosan: a novel platform for acetylcholinesterase biosensor development.

We report a screen-printed electrode (SPE) modified with a dispersion of carbon black (CB) and chitosan by drop casting. A cyclic voltammetry technique towards ferricyanide, caffeic acid, hydroquinone, and thiocholine was performed and an improvement of the electrochemical response with respect to bare SPE as well as SPE modified only with chitosan was observed. The possibility to detect thiocholine at a low applied potential with high sensitivity was exploited and an acetylcholinesterase (AChE) biosensor was developed. A dispersion of CB, chitosan, and AChE was used to fabricate this biosensor in one step by drop casting. The enzymatic activity of the immobilized AChE was determined measuring the enzymatic product thiocholine at +300 mV. Owing to the capability of organophosphorus pesticides to inhibit AChE, this biosensor was used to detect these pollutants, and paraoxon was taken as model compound. The enzyme inhibition was linearly related to the concentration of paraoxon up to 0.5 µg L(-1), and a low detection limit equal to 0.05 µg L(-1) (calculated as 10% of inhibition) was achieved. This biosensor was challenged for paraoxon detection in drinking waters with satisfactory recovery values. The use of AChE embedded in a dispersion of CB and chitosan allowed an easy and fast production of a sensitive biosensor suitable for paraoxon detection in drinking waters at legal limit levels. Graphical Abstract Biosensors based on screen-printed electrodes modified with Acetylcholinesterase, Carbon Black, and Chitosan for organophosphorus pesticide detection.

Phosphate Detection through a Cost-Effective Carbon Black Nanoparticle-Modified Screen-Printed Electrode Embedded in a Continuous Flow System.

An automatable flow system for the continuous and long-term monitoring of the phosphate level has been developed using an amperometric detection method based on the use of a miniaturized sensor. This method is based on the monitoring of an electroactive complex obtained by the reaction between phosphate and molybdate that is consequently reduced at the electrode surface. The use of a screen-printed electrode modified with carbon black nanoparticles (CBNPs) leads to the quantification of the complex at low potential, because CBNPs are capable of electrocatalitically enhancing the phosphomolybdate complex reduction at +125 mV versus Ag/AgCl without fouling problems. The developed system also incorporates reagents and waste storage and is connected to a portable potentiostat for rapid detection and quantification of phosphate. Main analytical parameters, such as working potential, reagent concentration, type of cell, and flow rate, were evaluated and optimized. This system was characterized by a low detection limit (6 µM). Interference studies were carried out. Good recovery percentages comprised between 89 and 131.5% were achieved in different water sources, highlighting its suitability for field measurements.

Methodological strategies to assess the degree of bone preservation for ancient DNA studies.

BACKGROUND: Archaeological bones contain only small amounts of DNA due to post-mortem DNA degradation and the changes endogenous DNA is subjected to during diagenesis. An important step before undertaking such time-consuming and costly analyses as ancient DNA investigation is to predict the presence of DNA in ancient samples. To date, the leading screening method has been amino acid racemization; however, other analytical techniques can also be used to assess the degree of bone preservation. AIM: The aim of the present study was to relate the presence of DNA with bone preservation in order to select samples potentially suitable for ancient DNA analysis. SUBJECTS AND METHODS: Bones collected from several archaeological sites, different locations (cave, rockshelter or sub divo) and diachronic periods were selected for analytical and spectroscopic analysis in order to correlate bone tissue preservation with the presence of DNA. Different techniques were combined to assess the degree of preservation of organic and inorganic components. RESULTS: As determined by different analytical methods, preservation of the inorganic component was best associated with the presence of DNA. CONCLUSION: Evaluation of the bone preservation state may be an efficient step to predict the presence of DNA in ancient samples prior to aDNA analysis.

A choline oxidase amperometric bioassay for the detection of mustard agents based on screen-printed electrodes modified with Prussian Blue nanoparticles.

In this work a novel bioassay for mustard agent detection was proposed. The bioassay is based on the capability of these compounds to inhibit the enzyme choline oxidase. The enzymatic activity, which is correlated to the mustard agents, was electrochemically monitored measuring the enzymatic product, hydrogen peroxide, by means of a screen-printed electrode modified with Prussian Blue nanoparticles. Prussian Blue nanoparticles are able to electrocatalyse the hydrogen peroxide concentration reduction at low applied potential (-50 mV vs. Ag/AgCl), thus allowing the detection of the mustard agents with no electrochemical interferences. The suitability of this novel bioassay was tested with the nitrogen mustard simulant bis(2-chloroethyl)amine and the sulfur mustard simulants 2-chloroethyl ethyl sulfide and 2-chloroethyl phenyl sulfide. The bioassay proposed in this work allowed the detection of mustard agent simulants with good sensitivity and fast response, which are excellent premises for the development of a miniaturised sensor well suited for an alarm system in case of terrorist attacks.

Development of a hydrogen peroxide sensor based on screen-printed electrodes modified with inkjet-printed Prussian blue nanoparticles.

A sensor for the simple and sensitive measurement of hydrogen peroxide has been developed which is based on screen printed electrodes (SPEs) modified with Prussian blue nanoparticles (PBNPs) deposited using piezoelectric inkjet printing. PBNP-modified SPEs were characterized using physical and electrochemical techniques to optimize the PBNP layer thickness and electroanalytical conditions for optimum measurement of hydrogen peroxide. Sensor optimization resulted in a limit of detection of 2 × 10(-7) M, a linear range from 0 to 4.5 mM and a sensitivity of 762 µA ∙ mM(-1) ∙ cm(-2) which was achieved using 20 layers of printed PBNPs. Sensors also demonstrated excellent reproducibility (<5% rsd).

Determinants of the detection limit and specificity of surface-based biosensors.

Here, we employ a model electrochemical DNA sensor to demonstrate that the detection limit and specificity of surface-based sensors often are not dependent on the true affinity of the probe for its target but are simply dependent on the effective probe concentration. Under these circumstances, the observed affinity (and thus the sensor's detection limit and specificity) will depend on the density with which the probes are packed on the surface of the sensor, the surface area, and even the volume of sample employed.

Development of a competitive immunoassay for the determination of cortisol in human saliva.

Two new protein conjugates were prepared and studied to develop and compare two (direct and indirect) competitive enzyme-linked immunosorbent assay (ELISA) formats for the determination of cortisol in human saliva. Toward this goal, ovalbumin was conjugated to cortisol and used for developing an indirect competitive ELISA, while alkaline phosphatase was coupled with the same analyte for a direct competitive assay. The yield of the conjugation reactions was evaluated. The results obtained show that the indirect and direct ELISA formats developed for cortisol had working ranges of 0.5-70 and 2-330 ng/ml and detection limits of 0.5 and 1.2 ng/ml, respectively. Artificial and real saliva samples were spiked with cortisol to study the matrix effect of saliva. The suitability of the assays for quantification of cortisol in saliva was also studied.

Electrochemical investigation of the interaction between lysozyme-shelled microbubbles and vitamin C.

We report loading of vitamin C (ascorbic acid) on to lysozyme-shelled microbubbles. The interaction between lysozyme-shelled microbubbles and vitamin C was studied by use of cyclic and differential pulse voltammetry, zeta potential measurements, and scanning electron microscopy. The effect of microbubbles on electrochemical measurement of ascorbic acid was evaluated. The linear range for ascorbic acid obtained for differential pulse measurement in the presence of 1 mg mL(-1) microbubbles was 1-50 µmol L(-1) (y = 0.067x + 0.130, r(2) = 0.995), with a detection limit of 0.5 µmol L(-1). The experimental conditions, i.e., pH and ionic strength, were optimized to improve the interaction between ascorbic acid and lysozyme-shelled microbubbles. The results were satisfactory when the interaction was performed for 1 h in aqueous solution at pH 6. The amount of vitamin C loaded on the microbubbles (90% of the analyte added, RSD(inter-expt.) = 3%, n = 6) and the stability of microbubbles-ascorbic acid complex (until 72 h at 25 °C) were also evaluated by use of differential pulse voltammetry and zeta potential measurements.

Employing the metabolic "branch point effect" to generate an all-or-none, digital-like response in enzymatic outputs and enzyme-based sensors.

Here, we demonstrate a strategy to convert the graded Michaelis-Menten response typical of unregulated enzymes into a sharp, effectively all-or-none response. We do so using an approach analogous to the "branch point effect", a mechanism observed in naturally occurring metabolic networks in which two or more enzymes compete for the same substrate. As a model system, we used the enzymatic reaction of glucose oxidase (GOx) and coupled it to a second, nonsignaling reaction catalyzed by the higher affinity enzyme hexokinase (HK) such that, at low substrate concentrations, the second enzyme outcompetes the first, turning off the latter's response. Above an arbitrarily selected "threshold" substrate concentration, the nonsignaling HK enzyme saturates leading to a "sudden" activation of the first signaling GOx enzyme and a far steeper dose-response curve than that observed for simple Michaelis-Menten kinetics. Using the well-known GOx-based amperometric glucose sensor to validate our strategy, we have steepen the normally graded response of this enzymatic sensor into a discrete yes/no output similar to that of a multimeric cooperative enzyme with a Hill coefficient above 13. We have also shown that, by controlling the HK reaction we can precisely tune the threshold target concentration at which we observe the enzyme output. Finally, we demonstrate the utility of this strategy for achieving effective noise attenuation in enzyme logic gates. In addition to supporting the development of biosensors with digital-like output, we envisage that the use of all-or-none enzymatic responses will also improve our ability to engineer efficient enzyme-based catalysis reactions in synthetic biology applications.

Combining a hydrogel and an electrochemical biosensor to determine the extent of degradation of paper artworks.

Paper-based artworks are among the most valuable assets for transmission of knowledge. Historical paper is composed of different polysaccharides (e.g. cellulose), binders, and glues. During aging all of these components undergo several degradation processes, as a result of external and intrinsic causes, and these can compromise the state of conservation of the document. In this work, application of a new biotechnological strategy for paper artefact preservation is reported. By making use of innovative and non-invasive materials, for example appropriate hydrogels, in combination with selective electrochemical biosensors, it is possible to simultaneously verify the degradation condition of the paper artwork and then to efficiently clean it, while monitoring the process of removal of both pollution and degradation products. In this paper, we focus on specific examples in which such techniques have been applied to paper artworks and that illustrate the advantages and potential of this biotechnology compared with the traditional paper-cleaning methods currently in use.

Probe accessibility effects on the performance of electrochemical biosensors employing DNA monolayers.

Surface-confined DNA probes are increasingly used as recognition elements (or presentation scaffolds) for detection of proteins, enzymes, and other macromolecules. Here we demonstrate that the density of the DNA probe monolayer on the gold electrode is a crucial determinant of the final signalling of such devices. We do so using redox modified single-stranded and double-stranded DNA probes attached to the surface of a gold electrode and measuring the rate of digestion in the presence of a non-specific nuclease enzyme. We demonstrate that accessibility of DNA probes for binding to their macromolecular target is, as expected, improved at lower probe densities. However, with double-stranded DNA probes, even at the lowest densities investigated, a significant fraction of the immobilized probe is inaccessible to nuclease digestion. These results stress the importance of the accessibility issue and of probe density effects when DNA-based sensors are used for detection of macromolecular targets.

An ELIME assay for hepatitis A virus detection.

An Enzyme Linked ImmunoMagnetic Electrochemical assay (ELIME) was developed for the detection of the hepatitis A virus (HAV). This system is based on the use of new polydopamine-modified magnetic nanobeads as solid support for the immunochemical chain, and an array of 8 screen-printed electrodes as a sensing platform. Enzymatic-by-product is quickly measured by differential pulse voltammetry. For this purpose, all analytical parameters were optimized; in particular, different blocking reagents were evaluated in order to minimize the nonspecific interaction of bioreagents. Using the ELIME assays, a quantitative determination of HAV can be achieved with a detection limit of 1·10-11 IU mL-1 and a working range between 10-10 - 5 × 10-7 IU mL-1. The cross-reactivity of the commercial monoclonal antibodies against HAV used in ELIME assays was tested for Coxsackie B4, resulting very low. The sensitivity was also investigated and compared with spectrophotometric sandwich ELISA. The average relative standard deviation (RSD) of the ELIME method was less than 5% for the assays performed on the same day, and 7% for the measurements made on different days. The proposed system was applied to the cell culture of HAV, which title was quantified by Real-Time Quantitative Reverse Transcription PCR (RT¬qPCR). To compare the results, a correlation between the units used in ELIME (IU mL-1) and those used in RT¬qPCR (genome mL-1) was established using a HAV-positive sample, resulting in 1 IU mL-1-10-4 gen mL-1 (R2 = 0.978). The ELIME tool exhibits good stability and high biological selectivity for HAV antigen detection and was successfully applied for the determination of HAV in tap water.

Using triplex-forming oligonucleotide probes for the reagentless, electrochemical detection of double-stranded DNA.

We report a reagentless, electrochemical sensor for the detection of double-stranded DNA targets that employs triplex-forming oligonucleotides (TFOs) as its recognition element. These sensors are based on redox-tagged TFO probes strongly chemisorbed onto an interrogating gold electrode. Upon the addition of the relevant double-stranded DNA target, the probe forms a rigid triplex structure via reverse Hoogsteen base pairing in the major groove. The formation of the triplex impedes contact between the probe's redox moiety and the interrogating electrode, thus signaling the presence of the target. We first demonstrated the proof of principle of this approach by using a well-characterized 22-base polypurine TFO sequence that readily detects a synthetic, double-stranded DNA target. We then confirmed the generalizability of our platform with a second probe, a 19-base polypyrimidine TFO sequence that targets a polypurine tract (PPT) sequence conserved in all HIV-1 strains. Both sensors rapidly and specifically detect their double-stranded DNA targets at concentrations as low as ~10 nM and are selective enough to be employed directly in complex sample matrices such as blood serum. Moreover, to demonstrate real-world applicability of this new sensor platform, we have successfully detected unpurified, double-stranded PCR amplicons containing the relevant conserved HIV-1 sequence.

Carbon black nanoparticles to sense algae oxygen evolution for herbicides detection: Atrazine as a case study.

A novel amperometric algae-based biosensor was developed for the detection of photosynthetic herbicides in river water. The green photosynthetic algae Chlamydomonas reinhardtii was immobilized on carbon black modified screen-printed electrodes, exploiting carbon black as smart nanomaterial to monitor changes in algae oxygen evolution during the photosynthetic process. The decrease of oxygen evolution, occurring in the presence of herbicides, results in a decrease of current signals by means of amperometric measurements, in an analyte concentration dependent manner. Atrazine as case study herbicide was detected in a concentration range of 0.1 and 50 µM, with a linear range from 0.1 to 5 µM and a detection limit of 1 nM. No interference was observed in presence of 100 ppb arsenic, 20 ppb copper, 5 ppb cadmium, 10 ppb lead, 10 ppb bisphenol A, and 1 ppb paraoxon, tested as safety limits. A ~25% matrix effect and satisfactory recovery values of 107 ± 10% and 96 ± 8% were obtained in river water for 3 and 5 µM of atrazine, respectively. Stability studies were also performed obtaining a high working stability up to 10 h and repeatability with an RSD of 1.1% (n = 12), as well as a good storage stability up to 3 weeks.

An eco-designed paper-based algal biosensor for nanoformulated herbicide optical detection.

In this study we reported the development of a paper-based algal biosensor for the optical detection of nanoencapsulated-atrazine, a forefront nanoformulated herbicide with a high effective post-emergence herbicidal activity. In particular, the unicellular green photosynthetic algae Chlamydomonas reinhardtii was immobilised on a paper substrate soaked with an agar thin film and placed in a glass optical measurement cell, obtaining a totally environmental-friendly device. Nanoencapsulated-atrazine was detected by following the variable fluorescence (1-VJ) parameter, which decreased inversely proportional to the herbicide concentrations, in a range between 0.5 and 200 nM, indicating a linear relationship in the measured dose-response curves and a detection limit of 4 pM. Interference studies resulted in a very slight interference in presence of 2 ppm copper and 10 ppb arsenic at safety limits, as well as a slight matrix effect and a satisfactory recovery value of 96 ± 5% for 75 nM nanoencapsulated-atrazine in tap water. Stability studies were also performed obtaining a good storage stability up to 3 weeks. Results demonstrated the suitability of the proposed paper-based optical biosensor as a valid support in smart agriculture for on site, environmental friendly, cost effective and sensitive nanoencapsulated-atrazine analysis.

Iridium oxide (IV) nanoparticle-based electrocatalytic detection of PBDE.

Polybrominated diphenyl ethers (PBDEs) are a type of flame retardants which are currently banned in EU and USA due their hazardousness for humans and mammals. However, these compounds were highly used during more than 30 years and still persist in the environment since they are resistant to degradation. Herein we present a biosensor for the detection of PBDEs using screen printed carbon electrodes (SPCEs) based on the electrochemical monitoring of water oxidation reaction (WOR) catalyzed by iridium oxide (IV) nanoparticles (IrO2 NPs). Our assay shows a limit of detection of 21.5 ppb of PBDE in distilled water. We believe that such an IrO2 NPs-based electrocatalytic sensing system can lead to a rapid, sensitive, low cost and miniaturizable device for the detection of PBDEs.

A label-free impedimetric aptasensor for the detection of Bacillus anthracis spore simulant.

Herein, we report an impedimetric DNA-based aptamer sensor for a single-step detection of B. anthracis spore simulant (B. cereus spore). Specifically, we designed a miniaturized label-free aptasensor for B. cereus spores based on a gold screen-printed electrode functionalized with B. cereus spores-binding aptamer (BAS-6R). Several parameters were optimized to fabricate the aptasensor such as the concentration of DNA aptamer solution (0.5 µM), the time (48 h), the temperature (4 °C), and the pH (7.5) for aptamer immobilization on the working electrode surface. Once the aptasensor was developed, it was tested against B. cereus spores 14579 evaluating the effect of incubation time and MgCl2 concentration. Under the optimized conditions (incubation time equal to 3 h and absence of MgCl2), B. cereus spores 14579 were detected with a linear range between 104 CFU/ml and 5 × 106 CFU/ml and a detection limit of 3 × 103 CFU/ml. Furthermore, the study of selectivity toward B. cereus 11778, B. subtilis, Legionella pneumophila, and Salmonella Typhimurium has demonstrated the capability of this sensor to detect B. cereus spores, proving the suitability of the DNA-based sensing element combined with a portable instrument for a label-free measurement on site of B. anthracis spore simulant.

How to extend range linearity in enzyme inhibition-based biosensing assays.

Bioassays based on enzyme inhibition are analytical tools widely employed for inhibitor analysis. Beside the conventional analytical techniques such as chromatography and mass spectrometry, these bioassays are cost-effective, easy to use, and suitable for in situ measurement but they are often characterised by a quite narrow linear range. Herein, we report a novel graphical method based on integrated Michaelis-Menten equation, valid for all types of reversible inhibition, which provides an extended linear range. The suitability of this innovative approach was demonstrated in the case of fluoride quantification using a colorimetric bioassay based on acetylcholinesterase inhibition. The "half time reaction", estimated by the progress curve of cholinesterase inhibition, was plotted versus the fluoride inhibitor concentration, observing an extended linear range up to 5 mM, instead of 0.6 mM using initial rate measurements. The applicability of this new concept was further demonstrated in the case of catalase enzyme inhibited by cyanide. Furthermore, it was demonstrated that fixed substrate conversion at level of 10-50% allows determination of inhibitor concentration in a wide linear range with high precision and in short time of analysis. This novel theoretical and practical approach allows for the extension of the linear range without any further experiments, with several advantages including low reagent consumption, reduced waste generation and time of measurement.