Detection of the Carcinogenic Water Pollutant Benzo[a]pyrene with an Electro-Switchable Biosurface

A portable spectroscopic instrument for multiplexed monitoring of acute water toxicity: Design, testing, and evaluation

The deteriorating water environment worldwide, mainly due to population explosion and uncontrolled direct disposal of harmful industrial and farming wastes, earnestly demands new approaches and accurate technologies to monitor water quality before consumption overcoming the shortcomings of the current methodologies. A spectroscopic water quality monitoring and early-warning instrument for evaluating acute water toxicity are the need of the hour. In this study, we have developed a prototype capable of the quantification of dissolved organic matter, dissolved chemicals, and suspended particulate matter in trace amounts dissolved in the water. The prototype estimates the water quality of the samples by measuring the absorbance, fluorescence, and scattering of the impurities simultaneously. The performance of the instrument was evaluated by detecting common water pollutants such as Benzopyrene, Crystal Violet, and Titanium di-oxide. The limit of detection values was found to be 0.50, 23.9, and 23.2 ppb (0.29 µM), respectively.

Application of the SwitchSense Technique for the Study of Small Molecules’ (Ethidium Bromide and Selected Sulfonamide Derivatives) Affinity to DNA in Real Time

The discovery and introduction of the switchSense technique in the chemical laboratory have drawn well-deserved interest owing to its wide range of applications. Namely, it can be used to determine the diameter of proteins, alterations in their tertiary structures (folding), and many other conformational changes that are important from a biological point of view. The essence of this technique is based on its ability to study of the interactions between an analyte and a ligand in real time (in a buffer flow). Its simplicity, on the other hand, is based on the use of a signaling system that provides information about the ongoing interactions based on the changes in the fluorescence intensity. This technique can be extremely advantageous in the study of new pharmaceuticals. The design of compounds with biological activity, as well as the determination of their molecular targets and modes of interactions, is crucial in the search for new drugs and the fight against drug resistance. This article presents another possible application of the switchSense technique for the study of the binding kinetics of small model molecules such as ethidium bromide (EB) and selected sulfonamide derivatives with DNA in the static and dynamic modes at three different temperatures (15, 25, and 37 °C) each. The experimental results remain in very good agreement with the molecular dynamics docking ones. These physicochemical insights and applications obtained from the switchSense technique allow for the design of an effective strategy for molecular interaction assessments of small but pharmaceutically important molecules with DNA.

Controlling amphipathic peptide adsorption by smart switchable germanium interfaces

The in situ control of reversible protein adsorption to a surface is a critical step towards biofouling prevention and finds utilisation in bioanalytical applications. In this work, adsorption of peptides is controlled by employing the electrode potential induced, reversible change of germanium (100) surface termination between a hydrophobic, hydrogen terminated and a hydrophilic, hydroxyl terminated surface. This simple but effective 'smart' interface is used to direct adsorption of two peptides models, representing the naturally highly abundant structural motifs of amphipathic helices and coiled-coils. Their structural similarity coincides with their opposite overall charge and hence allows the examination of the influence of charge and hydrophobicity on adsorption. Polarized attenuated total reflection infrared (ATR-IR) spectroscopy at controlled electrode potential has been used to follow the adsorption process at physiological pH in deuterated buffer. The delicate balance of hydrophobic and electrostatic peptide/surface interactions leads to two different processes upon switching that are both observed in situ: reversible adsorption and reversible reorientation. Negatively charged peptide adsorption can be fully controlled by switching to the hydrophobic interface, while the same switch causes the positively charged, helical peptide to tilt down. This principle can be used for 'smart' adsorption control of a wider variety of proteins and peptides and hence find application, as e.g. a bioanalytical tool or functional biosensor.

Recent Progress in Rapid Determination of Mycotoxins Based on Emerging Biorecognition Molecules: A Review

Mycotoxins are secondary metabolites produced by fungal species, which pose significant risk to humans and livestock. The mycotoxins which are produced from Aspergillus, Penicillium, and Fusarium are considered most important and therefore regulated in food- and feedstuffs. Analyses are predominantly performed by official laboratory methods in centralized labs by expert technicians. There is an urgent demand for new low-cost, easy-to-use, and portable analytical devices for rapid on-site determination. Most significant advances were realized in the field bioanalytical techniques based on molecular recognition. This review aims to discuss recent progress in the generation of native biomolecules and new bioinspired materials towards mycotoxins for the development of reliable bioreceptor-based analytical methods. After brief presentation of basic knowledge regarding characteristics of most important mycotoxins, the generation, benefits, and limitations of present and emerging biorecognition molecules, such as polyclonal (pAb), monoclonal (mAb), recombinant antibodies (rAb), aptamers, short peptides, and molecularly imprinted polymers (MIPs), are discussed. Hereinafter, the use of binders in different areas of application, including sample preparation, microplate- and tube-based assays, lateral flow devices, and biosensors, is highlighted. Special focus, on a global scale, is placed on commercial availability of single receptor molecules, test-kits, and biosensor platforms using multiplexed bead-based suspension assays and planar biochip arrays. Future outlook is given with special emphasis on new challenges, such as increasing use of rAb based on synthetic and naïve antibody libraries to renounce animal immunization, multiple-analyte test-kits and high-throughput multiplexing, and determination of masked mycotoxins, including stereoisomeric degradation products.

Standard operation procedure for switchSENSE DRX systems

There is currently a large panel of technologies available to address molecular interactions in vitro. Each technology presents individual advantages and drawbacks, and it becomes challenging to choose which technology will be best suited for a molecular interaction of interest. Approaches can be broadly categorized as either microfluidic surface-bound methods (such as Surface Plasmon Resonance (SPR) or switchSENSE) or in-solution methods (such as Isothermal Titration Calorimetry (ITC) or MicroScale Thermophoresis (MST)). In-solution methods are advantageous in terms of sample preparation and ease of use as none of the binding partners are subjected to immobilization. On the other hand, surface-based techniques require only small amounts of immobilized interaction partner and provide off-rate characterization as unbound analytes can be removed from the surface to observe analyte dissociation. Here, a standard operating procedure (SOP) for the switchSENSE method is presented, which aims to guide new users through the process of a switchSENSE measurement, covering sample preparation, instrument and biochip handling as well as data acquisition and analysis. This guide will help researchers decide whether switchSENSE is the right method for their application as well as supporting novice users to get the most information out of a switchSENSE measurement. switchSENSE technology offers the unique advantage of a controlled DNA-based ligand surface within a microfluidic channel which allows the user to distribute specifically up to two different ligand molecules on the surface at a customized density and ratio. The technology offers multi-parameter characterization of binding kinetics, affinity, enzymatic activity, and changes in protein conformation.

Future Trends for In Situ Monitoring of Polycyclic Aromatic Hydrocarbons in Water Sources: The Role of Immunosensing Techniques

Polycyclic aromatic hydrocarbons (PAHs) are hazardous environmental pollutants found in water, soil, and air. Exposure to this family of chemicals presents a danger to human health, and as a result, it is imperative to design methods that are able to detect PAHs in the environment, thus improving the quality of drinking water and agricultural soils. This review presents emerging immunoassay techniques used for in situ detection of PAH in water samples and how they compare to common-place techniques. It will discuss their advantages and disadvantages and why it is required to find new solutions to analyze water samples. These techniques are effective in reducing detection times and complexity of measurements. Immunoassay methods presented here are able to provide in situ analysis of PAH concentrations in a water sample, which can be a great complement to existing laboratory techniques due to their real-time screening and portability for immunoassay techniques. The discussion shows in detail the most relevant state-of-the-art surface functionalization techniques used in the field of immunosensors, with the aim to improve PAH detection capabilities. Specifically, three surface functionalization techniques are key approaches to improve the detection of PAHs, namely, substrate surface reaction, layer-by-layer technique, and redox-active probes. These techniques have shown promising improvements in the detection of PAHs in water samples, since they show a wider linear range and high level of sensitivity compared to traditional PAH detection techniques. This review explores the various methods used in the detection of PAH in water environments. It provides extra knowledge to scientists on the possible solutions that can be used to save time and resources. The combination of the solutions presented here shows great promise in the development of portable solutions that will be able to analyze a sample in a matter of minutes on the field.

Assembly and Characterization of a Slingshot DNA Nanostructure for the Analysis of Bivalent and Bispecific Analytes with Biosensors

The characterization of novel therapeutic antibodies with multivalent or multispecific binding sites requires new measurement modalities for biosensors, to discriminate the engagement of antigens via one, two, or even more binding moieties. The presentation of antigens on a sensor surface in a well-controlled spatial arrangement is a prerequisite for the successful interpretation of binding kinetics measurements of multivalent analytes, but the adjustment of defined distances between immobilized ligands is difficult to achieve in state-of-the-art biosensor systems. Here, we introduce a simple DNA nanostructure resembling a slingshot, which can be configured with two identical or two different antigens (bivalent or bispecific), which are spaced at a defined distance. We characterize the slingshot structure with a chip-based biosensor using electrically switchable DNA nanolevers and demonstrate that bivalent and monovalent antibodies selectively interact with slingshots that have been functionalized with two identical or two different antigens, respectively. The dissociation kinetics are quantified in real-time measurements and we show that the slingshot structure enables a clear differentiation between affinity and avidity effects.

Rapid fluorescence immunoassay of benzo[a]pyrene in mainstream cigarette smoke based on a dual-functional antibody–DNA conjugate

Benzo[a]pyrene (BaP) is considered as one of the most carcinogenic pollutants in cigarette smoke. The development of simple and sensitive BaP screening methods can help assess the risk of cigarette exposure to the human body rapidly. In this report, a rapid fluorescence immunoassay (RFIA) method for the detection of BaP is proposed, the core of which is the synthesis of bifunctional covalent antibody–DNA conjugates for target recognition and signal amplification. Based on the optimization of the SYBR Green I and PAH–BSA concentrations, as well as DNA–antibody immune complex's dilution in the RFIA system, a serial dilution of BaP was tested with this method. The results showed that the linear working range of the RFIA for BaP is 0.46 to 333 ng mL⁻¹, which is much wider than traditional ELISA. The detection limit was 0.32 ng mL⁻¹, which was more sensitive than other methods such as the redox-labeled electrochemical immunoassay method and the competitive piezoelectric biosensor. Then the cross-reactions (CR) of other PAHs in cigarette smoke were evaluated using this RFIA and found that the cross-reactions of naphthalene, anthracene, and pyrene were very low (<1%). The cross-reaction in this RFIA system can be reduced by improving the specificity of the antibody. To the best of our knowledge, this is the first time that the BaP in mainstream cigarette smoke was tested; the RFIA demonstrates fast and simple experimental manipulations and better working curves and sensitivity.

Benzo[a]pyrene (BaP) is considered as one of the most carcinogenic pollutants in cigarette smoke.

Tight Molecular Recognition of Benzo[a]pyrene by a High-Affinity Antibody

Benzo[a]pyrene, which is produced during the incomplete combustion of organic material, is an abundant noxious pollutant because of its carcinogenic metabolic degradation products. The high-affinity (K_D ≈3 nm) monoclonal antibody 22F12 allows facile bioanalytical quantification of benzo[a]pyrene even in complex matrices. We report the functional and X-ray crystallographic analysis of 22F12 in complex with 3-hydroxybenzo[a]pyrene after cloning of the V-genes and production as a recombinant Fab fragment. The polycyclic aromatic hydrocarbon is bound in a deep pocket between the light and heavy chains, surrounded mainly by aromatic and aliphatic amino acid side chains. Interestingly, the hapten-antibody interface is less densely packed than expected and reveals polar, H-bond-like interactions with the polycyclic aromatic π-electron system, which may allow the antibody to maintain a large, predominantly hydrophobic binding site in an aqueous environment while providing sufficient complementarity to its ligand.

Nanoporous Gold Films Prepared by a Combination of Sputtering and Dealloying for Trace Detection of Benzo[a]pyrene Based on Surface Plasmon Resonance Spectroscopy

A wavelength-interrogated surface plasmon resonance (SPR) sensor based on a nanoporous gold (NPG) film has been fabricated for the sensitive detection of trace quantities of benzo[a]pyrene (BaP) in water. The large-area uniform NPG film was prepared by a two-step process that includes sputtering deposition of a 60-nm-thick AuAg alloy film on a glass substrate and chemical dealloying of the alloy film in nitric acid. For SPR sensor applications, the NPG film plays the dual roles of analyte enrichment and supporting surface plasmon waves, which leads to sensitivity enhancement. In this work, the as-prepared NPG film was first modified with 1-dodecanethiol molecules to make the film hydrophobic so as to improve BaP enrichment from water via hydrophobic interactions. The SPR sensor with the hydrophobic NPG film enables one to detect BaP at concentrations as low as 1 nmol·L^-1. In response to this concentration of BaP the sensor produced a resonance-wavelength shift of Δλ_R = 2.22 nm. After the NPG film was functionalized with mouse monoclonal IgG1 that is the antibody against BaP, the sensor's sensitivity was further improved and the BaP detection limit decreased further down to 5 pmol·L^-1 (the corresponding Δλ_R = 1.77 nm). In contrast, the conventional SPR sensor with an antibody-functionalized dense gold film can give a response of merely Δλ_R = 0.9 nm for 100 pmol·L^-1 BaP.

switchSENSE: A new technology to study protein-RNA interactions

Characterization of RNA-binding protein interactions with RNA became inevitable to properly understand the cellular mechanisms involved in gene expression regulation. Structural investigations bring information at the atomic level on these interactions and complementary methods such as Isothermal Titration Calorimetry (ITC) and Surface Plasmon Resonance (SPR) are commonly used to quantify the affinity of these RNA-protein complexes and evaluate the effect of mutations affecting these interactions. The switchSENSE technology has recently been developed and already successfully used to investigate protein interactions with different types of binding partners (DNA, protein/peptide or even small molecules). In this study, we show that this method is also well suited to study RNA binding proteins (RBPs). We could successfully investigate the binding to RNA of three different RBPs (Fox-1, SRSF1 and Tra2-β1) and obtained K_D values very close to the ones determined previously by SPR or ITC for these complexes. These results show that the switchSENSE technology can be used as an alternative method to study protein-RNA interactions with K_D values in the low micromolar (10^-6) to nanomolar (10^-7-10^-9) and probably picomolar (10^-10-10^-12) range. The absence of labelling requirement for the analyte molecules and the use of very low amounts of protein and RNA molecules make the switchSENSE approach very attractive compared to other methods. Finally, we discuss about the potential of this approach in obtaining more sophisticated information such as structural conformational changes upon RBP binding to RNA.

Determination of benzo[a]pyrene in cigarette mainstream smoke by using mid-infrared spectroscopy associated with a novel chemometric algorithm

Determination of benzo[a]pyrene (BaP) in cigarette smoke can be very important for the tobacco quality control and the assessment of its harm to human health. In this study, mid-infrared spectroscopy (MIR) coupled to chemometric algorithm (DPSO-WPT-PLS), which was based on the wavelet packet transform (WPT), discrete particle swarm optimization algorithm (DPSO) and partial least squares regression (PLS), was used to quantify harmful ingredient benzo[a]pyrene in the cigarette mainstream smoke with promising result. Furthermore, the proposed method provided better performance compared to several other chemometric models, i.e., PLS, radial basis function-based PLS (RBF-PLS), PLS with stepwise regression variable selection (Stepwise-PLS) as well as WPT-PLS with informative wavelet coefficients selected by correlation coefficient test (rtest-WPT-PLS). It can be expected that the proposed strategy could become a new effective, rapid quantitative analysis technique in analyzing the harmful ingredient BaP in cigarette mainstream smoke.

Exonuclease III-based target recycling for ultrasensitive homogeneous monitoring of HIV DNA using Ag(+)-coordinated hairpin probe

A new homogeneous electrochemical sensing strategy based on exonuclease III-assisted target recycling amplification was utilized for simple, rapid and highly sensitive detection of human immunodeficiency virus (HIV) DNA on an immobilization-free Ag(I)-assisted hairpin DNA through the cytosine-Ag(+)-cytosine coordination chemistry. The assay involved target-induced strand-displacement reaction accompanying dissociation of the chelated Ag(+) in the hairpins and exonuclease III-triggered target recycling. Initially, the added target DNA hybridized with hairpin DNA to disrupt the Ag(I)-coordinated hairpin probe and releases the coordinated Ag(+) ion. Then, the newly formed DNA double-stranded DNA could be cleaved by exonuclease III, and released target HIV DNA, which retriggered the strand-displacement reaction with the hairpin for target recycling, thereby resulting in formation of numerous free Ag(+) ions in the detection cell. The released Ag(+) ions can be readily captured by the negatively charged electrode, and subsequent anodic-stripping voltammetric detection of the captured Ag(+) ions are conducted to form the anodic current for the production of the electronic signal within the applied potential. Under optimal conditions, the exonuclease III-based sensing system exhibited good electrochemical responses for the detection of HIV DNA at a concentration as low as 23 fM.