Enzyme-modulated cleavage of dsDNA for supramolecular design of biosensors

Evolution of Supramolecular Systems Towards Next-Generation Biosensors

Supramolecular materials, which rely on dynamic non-covalent interactions, present a promising approach to advance the capabilities of currently available biosensors. The weak interactions between supramolecular monomers allow for adaptivity and responsiveness of supramolecular or self-assembling systems to external stimuli. In many cases, these characteristics improve the performance of recognition units, reporters, or signal transducers of biosensors. The facile methods for preparing supramolecular materials also allow for straightforward ways to combine them with other functional materials and create multicomponent sensors. To date, biosensors with supramolecular components are capable of not only detecting target analytes based on known ligand affinity or specific host-guest interactions, but can also be used for more complex structural detection such as chiral sensing. In this Review, we discuss the advancements in the area of biosensors, with a particular highlight on the designs of supramolecular materials employed in analytical applications over the years. We will first describe how different types of supramolecular components are currently used as recognition or reporter units for biosensors. The working mechanisms of detection and signal transduction by supramolecular systems will be presented, as well as the important hierarchical characteristics from the monomers to assemblies that contribute to selectivity and sensitivity. We will then examine how supramolecular materials are currently integrated in different types of biosensing platforms. Emerging trends and perspectives will be outlined, specifically for exploring new design and platforms that may bring supramolecular sensors a step closer towards practical use for multiplexed or differential sensing, higher throughput operations, real-time monitoring, reporting of biological function, as well as for environmental studies.

Triple-signaling amplification strategy based electrochemical sensor design: boosting synergistic catalysis in metal-metalloporphyrin-covalent organic frameworks for sensitive bisphenol A detection

A covalent organic framework (COF) is a promising type of porous material with customizable surface characteristics. Confining multiple catalytic units within a mesoporous COF can generate abundant active sites and improve the catalytic performance. In this work, a COF with both metalloporphyrin and a metal nanoparticle complex denoted as hemin/TAPB-DMTP-COF/AuNPs (TAPB: 1,3,5-tris(4-amino-phenyl)benzene, DMTP: 2,5-dimethoxyterephaldehyde, AuNPs: Au nanoparticles) has been successfully fabricated through a hierarchical encapsulation method. The as-synthesized composite was then employed to construct an electrochemical sensing platform for the efficient detection of bisphenol A (BPA). Under the optimal conditions, the hemin/TAPB-DMTP-COF/AuNP sensor presented a linear range of 0.01-3 μmol L^-1 and a low detection limit of 3.5 nmol L^-1. The satisfactory signal amplification is based on a triple-signaling amplification strategy due to the abundant Fe³⁺ sites of Fe-porphyrin, high conductivity of AuNPs and a large specific surface area of the TAPB-DMTP-COF. The proposed method was used to measure the content of BPA in different water samples with a satisfactory recovery from 95.5 to 104.0%, suggesting the great potential of the sensor in practical applications.

Viruses Masquerading as Antibodies in Biosensors: The Development of the Virus BioResistor

The 2018 Nobel Prize in Chemistry recognized in vitro evolution, including the development by George Smith and Gregory Winter of phage display, a technology for engineering the functional capabilities of antibodies into viruses. Such bacteriophages solve inherent problems with antibodies, including their high cost, thermal lability, and propensity to aggregate. While phage display accelerated the discovery of peptide and protein motifs for recognition and binding to proteins in a variety of applications, the development of biosensors using intact phage particles was largely unexplored in the early 2000s. Virus particles, 16.5 MDa in size and assembled from thousands of proteins, could not simply be substituted for antibodies in any existing biosensor architectures.Incorporating viruses into biosensors required us to answer several questions: What process will allow the incorporation of viruses into a functional bioaffinity layer? How can the binding of a protein disease marker to a virus particle be electrically transduced to produce a signal? Will the variable salt concentration of a bodily fluid interfere with electrical transduction? A completely new biosensor architecture and a new scheme for electrical transduction of the binding of molecules to viruses were required.This Account describes the highlights of a research program launched in 2006 that answered these questions. These efforts culminated in 2018 in the invention of a biosensor specifically designed to interface with virus particles: the Virus BioResistor (VBR). The VBR is a resistor consisting of a conductive polymer matrix in which M13 virus particles are entrained. The electrical impedance of this resistor, measured across 4 orders of magnitude in frequency, simultaneously measures the concentration of a target protein and the ionic conductivity of the medium in which the resistor is immersed. Large signal amplitudes coupled with the inherent simplicity of the VBR sensor design result in high signal-to-noise ratio (S/N > 100) and excellent sensor-to-sensor reproducibility. Using this new device, we have measured the urinary bladder cancer biomarker nucleic acid deglycase (DJ-1) in urine samples. This optimized VBR is characterized by extremely low sensor-to-sensor coefficients of variation in the range of 3-7% across the DJ-1 binding curve down to a limit of quantitation of 30 pM, encompassing 4 orders of magnitude in concentration.

Impedance Biosensors: Applications to Sustainability and Remaining Technical Challenges

Due to their all-electrical nature, impedance biosensors have significant potential for use as simple and portable sensors for environmental studies and environmental monitoring. Detection of two endocrine-disrupting chemicals (EDC), norfluoxetine and BDE-47, is reported here by impedance biosensing, with a detection limit of 8.5 and 1.3 ng/mL for norfluoxetine and BDE-47, respectively. Although impedance biosensors have been widely studied in the academic literature, commercial applications have been hindered by several technical limitations, including possible limitations to small analytes, the complexity of impedance detection, susceptibility to nonspecific adsorption, and stability of biomolecule immobilization. Recent research into methods to overcome these obstacles is briefly reviewed. New results demonstrating antibody regeneration atop degenerate (highly doped) Si are also reported. Using 0.2 M KSCN and 10 mM HF for antibody regeneration, peanut protein Ara h 1 is detected daily during a 30 day trial.

Sensitivity and selectivity determination of BPA in real water samples using PAMAM dendrimer and CoTe quantum dots modified glassy carbon electrode

Bisphenol A (BPA) is an environmental pollutant to disrupt endocrine system or cause cancer, thus the detection of BPA is very important. Herein, an amperometric sensor was fabricated based on immobilized CoTe quantum dots (CoTe QDs) and PAMAM dendrimer (PAMAM) onto glassy carbon electrode (GCE) surface. The cyclic voltammogram of BPA on the sensor exhibited a well-defined anodic peak at 0.490V in 0.1M pH 8.0 PBS. The determination conditions were optimized and the kinetic parameters were calculated. The linear range was 1.3 x 10(-8) to 9.89 x 10(-6)M with the correlation coefficient of 0.9999. The limit of detection was estimated to be 1 x 10(-9)M. The current reached the steady-state current within about 5s. Furthermore, the fabricated sensor was successfully applied to determine BPA in real water samples.

Amperometric biosensor based on tyrosinase immobilized onto multiwalled carbon nanotubes-cobalt phthalocyanine-silk fibroin film and its application to determine bisphenol A

An amperometric bisphenol A (BPA) biosensor was fabricated by immobilizing tyrosinase on multiwalled carbon nanotubes (MWNTs)-cobalt phthalocyanine (CoPc)-silk fibroin (SF) composite modified glassy carbon electrode (GCE). In MWNTs-CoPc-SF composite film, SF provided a biocompatible microenvironment for the tyrosinase to retain its bioactivity, MWNTs possessed excellent inherent conductivity to enhance the electron transfer rate and CoPc showed good electrocatalytic activity to electrooxidation of BPA. The cyclic voltammogram of BPA at this biosensor exhibited a well defined anodic peak at 0.625 V. Compared with bare GCE, the oxidation signal of BPA significantly increased; therefore, this oxidation signal was used to determine BPA. The effect factors were optimized and the electrochemical parameters were calculated. The possible oxidation mechanism was also discussed. Under optimum conditions, the oxidation current was proportional to BPA concentration in the range from 5.0 x 10(-8) to 3.0 x 10(-6) M with correlation coefficient of 0.9979 and detection limit of 3.0 x 10(-8) M (S/N=3). The proposed method was successfully applied to determine BPA in plastic products and the recovery was in the range from 95.36% to 104.39%.

Direct electrical transduction of antibody binding to a covalent virus layer using electrochemical impedance

Electrochemical impedance spectroscopy is used to detect the binding of a 148.2 kDa antibody to a "covalent virus layer" (CVL) immobilized on a gold electrode. The CVL consisted of M13 phage particles covalently anchored to a 3 mm diameter gold disk electrode. The ability of the CVL to distinguish this antibody ("p-Ab") from a second, nonbinding antibody ("n-Ab") was evaluated as a function of the frequency and phase of the measured current relative to the applied voltage. The binding of p-Ab to the CVL was correlated with a change in the resistance, reducing it at low frequency (1-40 Hz) while increasing it at high frequency (2-140 kHz). The capacitance of the CVL was virtually uncorrelated with p-Ab binding. At both low and high frequency, the electrode resistance was linearly dependent on the p-Ab concentration from 20 to 266 nM but noise compromised the reproducibility of the p-Ab measurement at frequencies below 40 Hz. A "signal-to-noise" ratio for antibody detection was computed based upon the ratio between the measured resistance change upon p-Ab binding and the standard deviation of this change obtained from multiple measurements. In spite of the fact that the impedance change upon p-Ab binding in the low frequency domain was more than 100 times larger than that measured at high frequency, the S/N ratio at high frequency was higher and virtually independent of frequency from 4 to 140 kHz. Attempts to release p-Ab from the CVL using 0.05 M HCl, as previously described for mass-based detection, caused a loss of sensitivity that may be associated with a transition of these phage particles within the CVL from a linear to a coiled conformation at low pH.

The use of electrochemical impedance spectroscopy for biosensing

This review introduces the basic concepts and terms associated with impedance and techniques of measuring impedance. The focus of this review is on the application of this transduction method for sensing purposes. Examples of its use in combination with enzymes, antibodies, DNA and with cells will be described. Important fields of application include immune and nucleic acid analysis. Special attention is devoted to the various electrode design and amplification schemes developed for sensitivity enhancement. Electrolyte insulator semiconductor (EIS) structures will be treated separately.

Impedance spectroscopy and biosensing

This chapter introduces the basic terms of impedance and the technique of impedance measurements. Furthermore, an overview of the application of this transduction method for analytical purposes will be given. Examples for combination with enzymes, antibodies, DNA but also for the analysis of living cells will be described. Special attention is devoted to the different electrode design and amplification schemes developed for sensitivity enhancement. Finally, the last two sections will show examples from the label-free determination of DNA and the sensorial detection of autoantibodies involved in celiac disease.

Metal-enhanced biosensor for genetic mismatch detection

DNA biosensors are increasingly used in hybridization reactions, mutation detection, genomic sequencing, and identification of pathogens. However, the inability to monitor the recognition signals without resorting to the use of labels or electroactive mediators has led to DNA devices with inadequate sensitivity. Moreover, some electroactive species require high redox potentials that often destroy the DNA complementarity. This article presents the concept of metal-enhanced detection (MED) for the determination of DNA-DNA reactions and presents the application of this concept for mismatch detection. The MED concept relies on the idea that metallic films deposited as a continuous layer or monolayer onto a solid electrode, or even electrostatically held, could greatly enhance the rate of electron transfer by reducing the distance between the donor and acceptor species and could lead to label-free assays during DNA hybridization reactions. The MED concept has been tested for voltammetric detection of gene sequence of Microcystis spp. The resulting biosensor involved the immobilization of a 17-mer DNA probe that is complementary to a specific gene sequence of Microcystis spp. on a gold electrode via avidin-biotin chemistry. Electrochemical reduction and oxidation of DNA-captured Ag(+) ions provided the detection signals for the target gene sequence in solution. A linear response of silver cathodic peak current with concentration of the target oligonucleotide sequence was observed with a detection limit of 7 x 10(-9)M. This label-free approach was successfully applied to detecting two-base-pair mismatches in the gene sequence of Microcystis spp.

Electrochemical biosensors for monitoring the recognition of glycoprotein–lectin interactions

Despite the wide applicability and specificity of lectins to carbohydrate moieties, there are few lectin specific biosensors. This is attributed to the difficulty in defining the relevant experimental parameters to measure for sensing. We hereby describe the development of direct and indirect electrochemical sensors to determine the exact trace amounts of probarley lectin (ProBL) and its conversion product wheat germ agglutinin (WGA). In addition to WGA, the antigens (ProBL) employed in this study were over expressed in bacteria, isolated from protein bodies, and purified using immobilized N-acetylglusamine in order to obtain correctly folded active lectins. The amperometric immunosensor uses cell lines producing monoclonal antibody (mAB) to the pro-region of ProBL over expressed from Escherichia coli. The efficacy and sensing characteristics of the lectin were optimized using monoclonal antibody to WGA and the resulting sensor was found to detect only ProBL in the linear range 10(-3)-10(2) microg mL(-1) and a detection limit of 10(-3) microg mL(-1).

A survey of the 2001 to 2005 quartz crystal microbalance biosensor literature: applications of acoustic physics to the analysis of biomolecular interactions

The widespread exploitation of biosensors in the analysis of molecular recognition has its origins in the mid-1990s following the release of commercial systems based on surface plasmon resonance (SPR). More recently, platforms based on piezoelectric acoustic sensors (principally 'bulk acoustic wave' (BAW), 'thickness shear mode' (TSM) sensors or 'quartz crystal microbalances' (QCM)), have been released that are driving the publication of a large number of papers analysing binding specificities, affinities, kinetics and conformational changes associated with a molecular recognition event. This article highlights salient theoretical and practical aspects of the technologies that underpin acoustic analysis, then reviews exemplary papers in key application areas involving small molecular weight ligands, carbohydrates, proteins, nucleic acids, viruses, bacteria, cells and lipidic and polymeric interfaces. Key differentiators between optical and acoustic sensing modalities are also reviewed.

Advanced electrochemical sensors for cell cancer monitoring

The possibility of using minimally invasive analytical instruments to monitor cancerous cells and their interactions with analytes provide great advances in cancer research and toxicology. The real success in the development of a reliable sensor for cell monitoring depends on the ability to design powerful instrumentation that will facilitate efficient signal transduction from the biological process that occurs in the cellular environment. The resulting sensor should not affect cell viability and must function as well as adapt the system to the specific conditions imposed by the cell culture. Due to their performance, electrochemical biosensors could be used as an effective instrument in cell cancer research for studying biochemical processes, cancer development and progression as well as toxicity monitoring. Current research in this direction is conducted through high-throughput, compact, portable, and easy to use sensors that enable measurement of cells' activity in their optimum environment. This paper discusses the potential of a high-throughput electrochemical multisensor system, so-called the DOX system for monitoring cancerous cells and their interaction with chemical toxins. We describe the methodology, experiments, and the operation principle of this device, and we focus on the challenges encountered in optimizing and adapting the system to the specific cell-culture conditions. The DOX system is also compared with conventional cell-culture techniques.

Nanostructured polyamic acid membranes as novel electrode materials

This paper describes a new approach for the preparation of polyamic acid (PAA) composites containing Ag and Au nanoparticles. The composite film of PAA and metal particles were obtained upon electrodeposition of a PAA solution containing gold or silver salts with subsequent thermal treatment, while imidization to polyimide is prevented. The structural characterization of the films is provided by 1H NMR and Fourier transform infrared spectroscopy (FTIR), while the presence of metallic nanoparticles within the polymeric matrix was confirmed by scanning electron microscopy (SEM), cyclic voltammetry (CV), energy-dispersive X-ray analysis (EDX), X-ray diffraction (XRD), and X-ray photoelectron spectroscopy (XPS). This approach utilizes the unique reactivity of PAA by preventing the cyclization of the reactive soluble intermediate into polyimides at low temperature to design polymer-assisted nanostructured materials. The ability to prevent the cyclization process should enable the design of a new class of electrode materials by use of thermal reduction and/or electrodeposition.

Enzyme-based impedimetric detection of PCR products using oligonucleotide-modified screen-printed gold electrodes

This paper describes the optimisation and the analytical performances of an enzyme-based electrochemical genosensor, developed using disposable oligonucleotide-modified screen-printed gold electrodes. The immobilisation of a thiol-tethered probe was qualitatively investigated by means of faradic impedance spectroscopy. Impedance spectra confirmed that the thiol moiety unambiguously drives the immobilisation of the oligonucleotide probe. Furthermore, both probe surface densities and hybridisation efficiencies were quantified through chronocoulometric measurements. Electrochemical transduction of the hybridisation process was also performed by means of faradic impedance spectroscopy, after coupling of a streptavidin-alkaline phosphatase conjugate and bio-catalysed precipitation of an insoluble and insulating product onto the sensing interface. Chronocoulometric results allowed discussion of the magnitude of hybridisation signals in terms of probe surface densities and their corresponding hybridisation efficiency. The genosensor response varied linearly (r2 = 0.9998) with the oligonucleotide target concentration over three orders of magnitude, between 12 pmol/L and 12 nmol/L. The estimated detection limit was 1.2 pmol/L (i.e., 7.2 x 10(6) target molecules in 10 microL of sample solution). The analytical usefulness of the impedimetric genosensor was finally demonstrated analysing amplified samples obtained from the pBI121 plasmid and soy and maize powders containing 1 and 5% of genetically modified product. Sensing of such unmodified amplicons was achieved via sandwich hybridisation with a biotinylated signaling probe. The electrochemical enzyme-amplified assay allowed unambiguous identification of all genetically modified samples, while no significant non-specific signal was detected in the case of all negative controls.

AC impedance spectroscopy of native DNA and M-DNA

Monolayers of thiol-labeled DNA duplexes of 15, 20, and 30 basepairs were assembled on gold electrodes. Electron transfer was investigated by electrochemical impedance spectroscopy with Fe(CN)(6)(3-/4-) as a redox probe. The spectra, in the form of Nyquist plots, were analyzed with a modified Randles circuit which included an additional component in parallel, R(x), for the resistance through the DNA. For native B-DNA R(x) and R(ct), the charge transfer resistance, both increase with increasing length. M-DNA was formed by the addition of Zn(2+) at pH 8.6 and gave rise to characteristic changes in the Nyquist plots which were not observed upon addition of Mg(2+) or at pH 7.0. R(x) and R(ct) also increased with increasing duplex length for M-DNA but both were significantly lower compared to B-DNA. Therefore, electron transfer via the metal DNA film is faster than that of the native DNA film and certain metal ions can modulate the electrochemical properties of DNA monolayers. The results are consistent with an ion-assisted long-range polaron hopping mechanism for electron transfer.

Differential impedance spectroscopy for monitoring protein immobilization and antibody-antigen reactions

This work describes the theoretical and experimental approaches for monitoring the interfacial biomolecular reaction between immobilized antibody and the antigen binding partner using novel differential impedance spectroscopy. The prerequisite of any biosensor is the immobilization of macromolecules onto the surface of a transducer. It is clear that the function of most macromolecules changes from what is observed in solution once immobilization has occurred. In the worst case, molecules entirely lose their binding activity almost immediately after immobilization. Certain conditions (e.g., denaturation, interfacial effects based on ionic strength, surface charge, dielectric constants, etc.) at interfaces are responsible for alterations of binding activity; it is not clear whether a combination of such processes is understood. However, these processes in combination must be reliably modeled in order to predict the outcome for most macromolecules. This work presents the theoretical and practical means for elucidating the surface reactivity of biomolecular reagents using ion displacement model with antibody-antigen (Ab-Ag) reaction as the test case. The Ab-Ag reaction was directly monitored using a dual-channeled, impedance analyzer capable of 1 measurement/s using covalent immobilization chemistry and polymer-modified electrodes in the absence of a redox probe. The evidence of Ab-Ag binding was revealed through the evolution of differential admittance. The surface loading obtained using the covalent immobilization chemistry was 9.0 x 10(16)/cm2, whereas with polymer-modified electrodes, the surface loading was 9.0 x 10(15)/cm2, representing a 10 times increase in surface reactivity. The proposed approach may be applicable to monitoring other surface interfacial reactions such as DNA-DNA interactions, DNA-protein interactions, and DNA-small molecule interactions.