Coenzyme A-aptamer-facilitated label-free electrochemical stripping strategy for sensitive detection of histone acetyltransferase activity

Highly selective DNA aptamer sensor for intracellular detection of coenzyme A

Detecting Coenzyme A (CoA) in cells is vital for understanding its role in metabolism. DNA aptamers, though widely used for monitoring many other molecules, have not been effective for CoA detection, as previous attempts at obtaining DNA aptamers for CoA using SELEX resulted in aptamers that only recognize the adenine moiety of CoA. This "tyranny" of adenine dominating in SELEX has, therefore, hampered the SELEX of aptamers specific for CoA. To meet this challenge, we employed a capture SELEX method by incorporating rigorous counter selections against adenine, adenosine, ATP, pantetheine, and pantothenic acid, resulting in a highly specific DNA aptamer for CoA over adenosine, ATP and other related metabolites such as NADH, with a dissociation constant of 48.9 μM. This aptamer was then converted to a fluorescent sensor for CoA across pH 6.4-8.0. Confocal microscopy showed its ability to visualize CoA in living cells, with fluorescence changes observed upon manipulating CoA levels. This method broadens SELEX's application and presents a promising approach for studying and understanding CoA dynamics.

Advances in precise synthesis of metal nanoclusters and their applications in electrochemical biosensing of disease biomarkers

Metal nanoclusters (NCs), comprising tens to hundreds of metal atoms, are condensed matter with concrete molecular structures and discrete energy levels. Compared to metal atoms and nanoparticles, metal NCs exhibit unique physicochemical properties, especially fascinating electrocatalytic activities. This review focuses on recent progress in the precise synthesis of metal NCs and their applications in electrochemical analysis of various disease biomarkers. First, we provide a brief overview of current nanotechnology-enabled electrochemical biosensors. Subsequently, we highlight the precise synthesis of metal NCs protected by various ligands such as peptides, proteins and nucleic acids. Next, we summarize the design and construction of electrochemical biosensors that utilize metal NCs as electrode materials to detect electrochemically active and inactive disease-associated biomarkers, including small biomolecules (glucose, reactive oxygen species, cholesterol, neurotransmitters and amino acids) and biomacromolecules (proteins, enzymes, and nucleic acids). Due to unique electrocatalytic properties, high specific surface areas, and atomically modulated structures, metal NCs promote electron exchange or act as a redox medium in these electrochemical sensing platforms. Finally, we conclude with present challenges and propose future research directions, with the aim to enhance the specificity, sensitivity, and durability of customized metal NC-based electrochemical biosensors for precise disease diagnostics.

Extension characteristics of TdT and its application in biosensors

The advantages of rapid amplification of nucleic acid without a template based on terminal deoxyribonucleotidyl transferase (TdT) have been widely used in the field of biosensors. However, the catalytic efficiency of TdT is affected by extension conditions. The sensitivity of TdT- mediated biosensors can be improved only under appropriate conditions. Therefore, in this review, we provide a comprehensive overview of TdT extension characteristics and its applications in biosensors. We focus on the relationship between TdT extension conditions and extension efficiency. Furthermore, the construction strategy of TdT-mediated biosensors according to five different recognition types and their applications in targets are discussed and, finally, several current challenges and prospects in the field are taken into consideration.

Rational design of supramolecular self-assembly sensor for living cell imaging of HDAC1 and its application in high-throughput screening

Supramolecular chemistry offers new insights in bioimaging, but specific tracking of enzyme in living cells via supramolecular host-guest reporter pair remains challenging, largely due to the interference caused by the complex cellular environment on the binding between analytes and hosts. Here, by exploiting the principle of supramolecular tandem assay (STA) and the classic host-guest reporter pair (p-sulfonatocalix[4]arene (SC4A) and lucigenin (LCG)) and rationally designing artificial peptide library to screen sequence with high affinity of the target enzyme, we developed a "turn-on" fluorescent sensing system for intracellular imaging of histone deacetylase 1 (HDAC1), which is a potential therapeutic target for various diseases, including cancer, neurological, and cardiovascular diseases. Based on computational simulations and experimental validations, we verified that the deacetylated peptide by HDAC1 competed LCG, freeing it from the SC4A causing fluorescence increase. Enzyme kinetics experiments were further conducted to prove that this assay could detect HDAC1 specifically with high sensitivity (the LOD value is 0.015 μg/mL, ten times lower than the published method). This system was further applied for high-throughput screening of HDAC1 inhibitors over a natural compound library containing 147 compounds, resulting in the identification of a novel HDAC1 down-regulator (Ginsenoside RK3). Our results demonstrated the sensitivity and robustness of the assay system towards HDAC1. It should serve as a valuable tool for biochemical studies and drug screening.

Recent progress in optical and electrochemical aptasensor technologies for detection of aflatoxin B1

AFB1 (Aflatoxin B1) contamination is becoming a global concern issue due to its extraordinary occurrence, severe toxicity, as well as the great influence on the economic losses, food safety and environment. Therefore, it is desirable to develop novel analytical techniques for simple, rapid, accurate, and even point-of-care testing of AFB1. Fortunately, aptamer, considered as a new generation bioreceptor and even superior to classic antibody and enzyme, has been emerged remarkable application in food hazards detection. Correspondingly, aptasensors have been well-established toward AFB1 determination with outstanding performance. In this article, we first discuss and summarize the recent progress in optical and electrochemical aptasensors to monitor AFB1 over the past three years. In particular, the embedding of advanced nanomaterials for their improved analytical performance is highlighted. Furthermore, the critical analysis on various signal transduction strategies for aptasensors construction is discussed. Finally, we reveal the challenges and provide our opinion in future opportunities for aptasensor development.

Exonuclease-based aptasensors: Promising for food safety and diagnostic aims

As of today's requirement, developing cost-effective smart sensing tools with ultrahigh sensitivity for food safety insurance is of special importance. For this purpose, aptamer-based biosensors (aptasensors) powered by the superiorities of the recycling signal amplification strategies have been expanded especially. Target recycling supported by enzymes is an appealing approach for implementing signal amplification. As the supreme biocatalyst enzymes, exonucleases can inaugurate signal improvement by involving a single target in a process would result in appreciable repeating cycles of the cleavage of the phosphodiester bonds between the building blocks of the nucleic acid strands, and also, their terminals. Although there are diverse substances for catalyzing amplification strategies, including nanoparticles, carbon-based nanocomposites, and quantum dots (QDs), exonucleases are of superiority over them by simplifying the amplification process with no need for the complicated pre-treatment processes. The outstanding selectivity and great sensitivity of the aptasensors tuned by amplification potency of exonucleases nominate them as the promising sensing tools for label-free, ease-of-use, cost-effective, and real-time diagnosis of diverse targets. Here, we summarize the achievements and perspectives in the scientific branch of aptasensor design for the qualitative monitoring of diverse targets by cooperation of exonucleases with the conspicuous potential for the signal amplification. Finally, some results are expressed to provide a comprehensive viewpoint for developing novel nuclease-based aptasensors in the future.

A switchable Cas12a enabling CRISPR-based direct histone deacetylase activity detection

The efficient and robust signal reporting ability of CRISPR-Cas system exhibits huge value in biosensing, but its applicability for non-nucleic acid analyte detection relies on the coupling of additional recognition modules. To address this limitation, we described a switchable Cas12a and exploited it for CRISPR-based direct analysis of histone deacetylase (HDAC) activity. Starting from the acetylation-mediated inactivation of Cas12a by anti-CRISPR protein AcrVA5, we demonstrated that the acetyl-inactivated Cas12a could be reversibly activated by HDAC-mediated deacetylation based on computational simulations (e.g., deep learning and protein-protein docking analysis) and experimental verifications. By leveraging this switchable Cas12a for both target sensing and signal amplification, we established a sensitive one-pot assay capable of detecting deacetylase sirtuin-1 with sub-nanomolar sensitivity, which is 50 times lower than the standard two-step peptide-based assay. The versability of this assay was validated by the sensitive assessment of cellular HDAC activities in different cell lines with good accuracy, making it a valuable tool for biochemical studies and clinical diagnostics.

Tailored Biosensors for Drug Screening, Efficacy Assessment, and Toxicity Evaluation

Biosensors have been flourishing in the field of drug discovery with pronounced developments in the past few years. They facilitate the screening and discovery of innovative drugs. However, there is still a lack of critical reviews that compare the merits and shortcomings of these biosensors from a pharmaceutical point of view. This contribution presents a critical and up-to-date overview on the recent progress of tailored biosensors, including surface plasmon resonance, fluorescent, photoelectrochemical, and electrochemical systems with emphasis on their mechanisms and applications in drug screening, efficacy assessment, and toxicity evaluation. Multiple functional nanomaterials have also been incorporated into the biosensors. Representative examples of each type of biosensors are discussed in terms of design strategy, response mechanism, and potential applications. In the end, we also compare the results and summarize the major insights gained from the works, demonstrating the challenges and prospects of biosensors-assisted drug discovery.

Measurement of Neuropeptide Y Using Aptamer-Modified Microelectrodes by Electrochemical Impedance Spectroscopy

Aptamer-modified microelectrodes for Neuropeptide Y measurement by electrochemical impedance spectroscopy was described here. The advantages of using carbon fiber or platinum microelectrodes are because they are promising materials with high electrical conductivity, chemical stability, and high surface area that can be easily modified on their surface. The immobilization and biofouling were studied and compared using EIS. Moreover, the adsorption of NPY to the aptamer-modified microelectrodes was also demonstrated by EIS. Changes of -ω*Zimag, an impedance factor that gives information of the capacitance, is directly correlated with concentrations. A widely linear range was obtained from 10 to 1000 ng/mL of NPY. This method was able to detect NPY without performing a redox reaction by adsorption at the surface of the microelectrodes, with the specificity provided by aptamer functionalization of the microelectrode surface.

Limitation-induced fluorescence enhancement of carbon nanoparticles and their application for glucose detection

Rational design of detection strategy is the key to high-performance fluorescence analysis. In this article, we found that the glucose-induced limitations can greatly enhance the fluorescence of functionalized carbon nanoparticles (CNPs), which are synthesized through one-step thermal pyrolysis method using phenylboronic acid derivative as the precursors. The glucose can assembly onto the surface of the CNPs to form a "shell", limiting the surfaces' intramolecular rotation and reducing non-radiative decay, which hence resulted in enhanced fluorescence of the CNPs. Under optimal conditions, the fluorescence intensity of the CNPs is nearly 70-fold enhanced, and the method has low detection limit (10 μM) and linear response in the concentration range from 50 μM to 2000 μM. Based on this interesting "target-triggered limitation-induced fluorescence enhancement" phenomenon, a simple and effective non-enzymatic fluorescence enhancement method was developed and successfully applied to the determination of glucose in spiked serum samples. This work provides new insight into the design of fluorescence-enhanced detection strategies based on the limitation-induced property.

Electrochemical detection of β-lactoglobulin based on a highly selective DNA aptamer and flower-like Au@BiVO4 microspheres

Beta-lactoglobulin is a natural milk protein and the main cause of infant milk allergy. In this work, a sensitive, selective and inexpensive electrochemical biosensor for the detection of β-lactoglobulin was developed. In this sensor, a DNA aptamer was used instead of an expensive antibody as the recognition group highly selective for β-lactoglobulin. The flower-like BiVO₄ microspheres were firstly found to have peroxidase mimic catalytic activity and used to amplify the electrochemical signal. The aptamer can bind β-lactoglobulin and fall off from the working electrode, after which the DNA2/Au/BiVO₄ probe can be fixed to the DNA1/AuNPs/ITO working electrode by the hybridization of DNA2 with DNA1. Therefore, a higher concentration of β-lactoglobulin leads to increased fabrication of the DNA2/Au/BiVO₄ probe on the surface of the working electrode, and thereby increases the electrochemical signal. This electrochemical biosensor exhibited a wide detection range from 0.01 to 1000 ng mL^-1, with a limit of detection (LOD) of 0.007 ng mL^-1, which indicates a good potential application in the field of food analysis.