Optical aptasensors for quantitative detection of small biomolecules: a review

Electrochemical/Electrochemiluminescence Sensors Based on Vertically-Ordered Mesoporous Silica Films for Biomedical Analytical Applications

Vertically-ordered mesoporous silica films (VMSF, also named as silica isoporous membranes) have shown tremendous potential in the field of electroanalytical sensors due to their unique features in terms of controllable and ultrasmall nanopores, high molecular selectivity and permeability, and mechanical stability. This review will present the recent progress on the biomedical analytical applications of VMSF, focusing on the small biomolecules, diseases-related biomarkers, drugs and cancer cells. Finally, conclusions with recent developments and future perspective of VMSF in the relevant fields will be envisioned.

A turn-on fluorescent aptasensor for Pb2+ detection based on rhodamine B dye leakage from the internal cavity of hollow gold nanoparticles

In this project, a sensitive fluorescent aptasensor was fabricated to detect lead ions (Pb2+) by applying hollow gold nanoparticles (HGNPs) as a nano-carrier and rhodamine B (RDB) fluorescent dye as the signal agent. In the aptasensor that was created, the specific attachment of the aptamers to Pb2+ ions led to the release of aptamer from the chitosan (CTS) coated-HGNPs loaded with RDB, causing an increase in fluorescence intensity due to the leakage of RDB. The method demonstrated specific detection of the target analyte, achieving a detection limit (LOD) of 1 ppb and a broad linear dynamic range spanning from 2 to 1000 ppb. The aptasensor was able to accurately measure the concentration of Pb2+ in human serum, low-fat milk, and mineral water samples. The suggested biosensor, which offers the benefits of simplicity, user-friendliness, affordability, and high sensitivity, is well-suited for use with complex samples such as environmental and clinical samples.

Bridged Pt-OH-Mn Mediator in N-coordinated Mn Single Atoms and Pt Nanoparticles for Electrochemical Biomolecule Oxidation and Discrimination

The rational design of efficient catalysts for uric acid (UA) electrooxidation, as well as the establishment of structure-activity relationships, remains a critical bottleneck in the field of electrochemical sensing. To address these challenges, herein, a hybrid catalyst that integrates carbon-supported Pt nanoparticles and nitrogen-coordinated Mn single atoms (PtNPs/MnNC) is developed. The metal-metal interaction during annealing affords the construction of metallic-bonded Pt-Mn pairs between PtNPs and Mn single atoms, facilitating the electron transfer from PtNPs to the support and thereby optimizing the electronic structure of catalysts. More importantly, experiments and theoretical calculations provide visual proof for the 'incipient hydrous oxide adatom mediator' mechanism for UA oxidation. The Pt-Mn pairs first adsorb OH* to construct the bridged Pt-OH-Mn mediators to serve as a highly active intermediate for N-H bond dissociation and proton transfer. Benefiting from the unique electronic and geometric structure of the catalytic center and reactive intermediates, PtNPs/MnNC exhibits superior electrooxidation performance. The electrochemical sensor based on PtNPs/MnNC enables sensitive detection and discrimination of UA and dopamine in serum samples. This work offers new insights into the construction of novel electrocatalysts for sensitive sensing platforms.

Advances in Aptamer-Based Conjugate Recognition Techniques for the Detection of Small Molecules in Food

Small molecules are significant risk factors for causing food safety issues, posing serious threats to human health. Sensitive screening for hazards is beneficial for enhancing public security. However, traditional detection methods are unable to meet the requirements for the field screening of small molecules. Therefore, it is necessary to develop applicable methods with high levels of sensitivity and specificity to identify the small molecules. Aptamers are short-chain nucleic acids that can specifically bind to small molecules. By utilizing aptamers to enhance the performance of recognition technology, it is possible to achieve high selectivity and sensitivity levels when detecting small molecules. There have been several varieties of aptamer target recognition techniques developed to improve the ability to detect small molecules in recent years. This review focuses on the principles of detection platforms, classifies the conjugating methods between small molecules and aptamers, summarizes advancements in aptamer-based conjugate recognition techniques for the detection of small molecules in food, and seeks to provide emerging powerful tools in the field of point-of-care diagnostics.

Emerging biosensor probes for glycated hemoglobin (HbA1c) detection

Glycated hemoglobin (HbA1c), originating from the non-enzymatic glycosylation of βVal1 residues in hemoglobin (Hb), is an essential biomarker indicating average blood glucose levels over a period of 2 to 3 months without external environmental disturbances, thereby serving as the gold standard in the management of diabetes instead of blood glucose testing. The emergence of HbA1c biosensors presents affordable, readily available options for glycemic monitoring, offering significant benefits to small-scale laboratories and clinics. Utilizing nanomaterials coupled with high-specificity probes as integral components for recognition, labeling, and signal transduction, these sensors demonstrate exceptional sensitivity and selectivity in HbA1c detection. This review mainly focuses on the emerging probes and strategies integral to HbA1c sensor development. We discussed the advantages and limitations of various probes in sensor construction as well as recent advances in diverse sensing strategies for HbA1c measurement and their potential clinical applications, highlighting the critical gaps in current technologies and future needs in this evolving field.

Sandwich-type aptamer-based biosensors for thrombin detection

Thrombin, a proteolytic enzyme, plays an essential role in catalyzing many blood clotting reactions. Thrombin can act as a marker for some blood-related diseases, such as leukemia, thrombosis, Alzheimer's disease and liver disease. Therefore, its diagnosis is of great importance in the fields of biological and medical research. Biosensors containing sandwich-type structures have attracted much consideration owing to their superior features such as reproducible and stable responses with easy improvement in the sensitivity of detection. Sandwich-type platforms can be designed using a pair of receptors that are able to bind to diverse locations of the same target. Herein, we investigate recent advances in the progress and applications of thrombin aptasensors containing a sandwich-type structure, in which two thrombin-binding aptamers (TBAs) identify different parts of the thrombin molecule, leading to the formation of a sandwich structure and ultimately signal detection. We also discuss the pros and cons of these approaches and outline the most logical approach in each section.

Dual-mode colorimetric and photothermal aptasensor for detection of kanamycin using flocculent platinum nanoparticles

Chitosan (CS)-stabilized platinum nanoparticles (CS/PtNPs) were employed to develop a novel aptamer-based dual-mode colorimetric and photothermal biosensor for selective detection of kanamycin (KAN). As a peroxidase-like catalyst, the CS/PtNPs showed outstanding catalytic activity for the oxidation of 3,3',5,5'-tetramethylbenzidine (TMB) in the presence of hydrogen peroxide (H2O2). As a stabilizing agent, CS excelled at fixing the KAN binding aptamer on the surface of the CS/PtNPs, amplifying their catalytic activity and enhancing colloidal dispersion and stability. The oxidized TMB (TMBox) functioned as a signal for the colorimetric, photothermal aptasensor because of its observable absorbance of light in the visible and near-infrared (NIR) regions. When light from a NIR laser was absorbed by the TMBox in the reaction solution, heat was generated in inverse proportion to the KAN concentration. The developed colorimetric and photothermal modes of the aptasensor showed a linear detection range of 0.1-50 and 0.5-50 μM, with a limit of detection (LOD) of 0.04 and 0.41 μM, respectively. Moreover, the aptasensor successfully determined KAN concentrations in spiked milk samples, verifying the reliability and reproducibility in practical applications. The dual-mode aptasensor based on CS/PtNPs for KAN detection, utilizing both color change and heat generation signals through a single probe (TMBox), demonstrates rapid response, simplicity in operation, cost-effectiveness, and high sensitivity. In addition, unlike typical immunoassays, this aptamer-based peroxidase-like nanozyme activation and inhibition strategy required no washing process, which was very effective in terms of reducing the time required for an assay and sustaining a high sensitivity.

Biosensor for ATP detection via aptamer-modified PDA@POSS nanoparticles synthesized in a microfluidic reactor

This study introduces aptamer-functionalized polyhedral oligomeric silsesquioxane (POSS) nanoparticles for adenosine triphosphate (ATP) detection where the POSS nanoparticles were synthesized in a one-step, continuous flow microfluidic reactor utilizing thermal polymerization. A microemulsion containing POSS monomers was generated in the microfluidic reactor which was designed to prevent clogging by using a continuous oil flow around the emulsion during thermal polymerization. Surfaces of POSS nanoparticles were biomimetically modified by polydopamine. The aptamer sequence for ATP was successfully attached to POSS nanoparticles. The aptamer-modified POSS nanoparticles were tested for affinity-based biosensor applications using ATP as a model molecule. The nanoparticles were able to capture ATP molecules successfully with an affinity constant of 46.5 [Formula: see text]M. Based on this result, it was shown, for the first time, that microfluidic synthesis of POSS nanoparticles can be utilized in designing aptamer-functionalized nanosystems for biosensor applications. The integration of POSS in biosensing technologies not only exemplifies the versatility and efficacy of these nanoparticles but also marks a significant contribution to the field of biorecognition and sample preparation.

Novel CoOOH-based fluorescent aptasensor for rapid and sensitive detection of sulfamethazine in environmental samples

Sulfamethazine (SMZ) has been widely used in animal husbandry and exposed to water and soil environments, posing potential threat to human health and ecological environment. Hence, we designed a CoOOH-based aptasensor, the fluorescence resonance energy transfer between FAM-labeled aptamer and CoOOH was used to sensitively and selectively detect SMZ in water and soil environments. Molecular docking and molecular dynamics simulations were used to predict binding mechanisms of SMZ and aptamer. Under optimized conditions, the aptasensor exhibited high sensitivity and selectivity with a linear range of 5-40 ng/mL and a limit of detection of 2.43 ng/mL. The recoveries of the aptasensor were 84.6-115.8% in water and soil samples with relative standard deviations below 9%, and the detection results were highly consistent with high-performance liquid chromatography. Therefore, this developed aptasensor was a reliable tool and could be applied to monitoring of SMZ in environmental samples.

Nanoparticles-assisted aptamer biosensing for the detection of environmental pathogens

Given the importance of public health, it is crucial to develop quick, targeted, highly sensitive, and accurate technologies to monitor pathogenic microbes in response to the growing concerns of food and environmental safety. Although conventional approaches for microbiological detection are available, they are laborious, and often skill demanding. Therefore, such approaches are incompetent in the on-site or high-throughput assessment of pathogenic microbes. Numerous efforts have been made to develop biosensors that use nucleic acid aptamer as the biorecognition element, which would avoid the abovementioned limitations. Incorporating nanomaterials (NMs) into aptamer-based biosensors (aptasensors) improves their sensitivity and specificity, opening exciting possibilities for various applications, such as bioanalysis of food and environmental samples. Over the last decade, nanomaterial-conjugated aptasensors have seen a steadily rising demand. To this end, the main goal of this study is to demonstrate the novelty in the design of nanomaterial-conjugated aptasensors and how they can be used to detect different pathogenic microbes in water and food. The intent of this paper is to evaluate the cutting-edge techniques that have appeared in nano-aptasensors throughout the past few years, such as manufacturing procedures, analytical credibility, and sensing mechanisms. Additionally, the fundamental performance parameters of aptasensing techniques (such as detection limits, and sensing ranges response) were also used to evaluate their practical applicability. Finally, it is anticipated that this study will inspire innovative ideas and techniques for the construction and use of aptasensors for monitoring pathogenic microorganisms in food, drinks, recreational water, and wastewater.

Label-free colorimetric sensor for Pb2+ determination using catalytic activity of MnO2 nanoflowers and elongated aptamer

In this study, a label-free aptasensor utilizing colorimetric properties was developed to detect Pb2+ with high sensitivity. The approach involved applying modified aptamer which enhanced the oxidase-mimicking activity of MnO2 nanoflowers. This innovative method provides an efficient means for monitoring Pb2+ ions without requiring any labeling techniques. The fundamental principle of this aptasensor is based on the adsorption of a modified aptamer onto MnO2 nanoflowers' surface, which in turn increases their affinity for chromogenic substrates and enhances their catalytic activity. The proposed aptasensor exploits the high sensitivity due to the extension of the aptamer sequence length by terminal deoxynucleotidyl transferase (TdT). Under optimum experimental conditions, the developed colorimetric aptasensor indicated a linear detection range from 4 to 80 nM with a limit of detection (LOD) of 1.4 nM. Moreover, the aptasensor successfully monitored Pb2+ in the drinking water, milk and human serum samples. Henceforth, the colorimetric aptasensor exhibited in this study possesses several benefits such as uncomplicated operation, cost-effectiveness, label-free detection and remarkable sensitivity. Thus rendering it a suitable option for analyzing intricate samples.

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.

Apta-sensor for selective determination of dopamine using chitosan-stabilized Prussian blue nanoparticles

Chitosan-stabilized Prussian blue nanoparticles (CS/PBNPs) were fabricated by a simple synthetic method and used to develop a novel aptamer-based colorimetric assay for selective determination of dopamine (DA). Scanning electron microscopy (SEM) images exhibited a uniform shape of the CS/PBNPs with an average diameter of 37.0 ± 3.2 nm. The CS/PBNPs exhibited strong peroxidase-like activity that catalyzed the reaction between 3,3',5,5'-tetramethylbenzidine (TMB) and hydrogen peroxide (H₂O₂). Chitosan was used for stabilization of the PBNPs and fixation of the DA aptamer on the surface of the CS/PBNPs. The catalytic mechanism of the CS/PBNPs was confirmed to involve first the decomposition of H₂O₂ into a hydroxyl radical (˙OH) and then oxidation of TMB by the ˙OH to produce a blue color. An aptamer-based colorimetric assay was made with the CS/PBNPs to detect DA at concentrations of 0.25-100 μM with a limit of detection (LOD) of 0.16 μM. For comparison, a gold nanoparticle (AuNP)-based apta-sensor detected DA in concentrations of 1-25 μM with a LOD of 0.55 μM. The recovery results of DA concentrations (0.25, 0.5, and 1 μM) from spiked human serum were 92.6%, 102.1%, and 103.9%, verifying the reliability and reproducibility of the CS/PBNP-based apta-sensor for determination of DA level in clinical applications. Moreover, compared to traditional immunoassay, this aptamer-based nanozyme activation/inhibition system needs no washing step, which is very useful to shorten the assay time and maintain high sensitivity.

Simultaneous screening of multiple diarrhetic shellfish poisons with group-specific split aptamers and silver nanocluster beacon

Poisoning events concerning diarrhetic shellfish poisons (DSPs) are increasing continually. It is extremely necessary to develop simple analysis methods for screening simultaneously different types of DSPs from food-related samples. Okadaic acid (OA) and its analogues, i.e., dinophysistoxin-1 (DTX-1) and dinophysistoxin-2 (DTX-2), are the prevalent DSPs. Herein, a facile and label-free fluorescent aptasensor targeting the three DSPs was constructed with a pair of group-specific split aptamers and silver nanocluster beacon. In presence of the targets, the DNA templates attached at the ends of the split aptamers would be dragged close to trigger enhanced fluorescence signals from silver nanoclusters. The aptasensor offered high sensitivity and good selectivity, with limit of detection of 2.282 nmolL^-1, 19.38 nmolL^-1, and 13.61 nmolL^-1 for OA, DTX-1, and DTX-2, respectively. Moreover, the applicability of aptasensor was well verified with shellfish and seawater samples. This study provides good reference for further exploration on analysis methods for food-related molecules.

A simple tag-free fluorometric aptasensing assay for sensitive detection of kanamycin

A novel label-free and enzyme-free fluorescence aptasensing assay that uses Sybr Green I (SGI) as the signal indicator for the kanamycin determination was designed. An aptamer-complementary strand (Apt/CP) conjugate was formed, which provided the intercalation sites for SGI and, therefore, a considerable fluorescent signal. The introduction of the target led to the separation of Apt from CP due to the high affinity of Apt toward kanamycin. Hence, the suitable intercalation gaps reduced, which resulted in a decrease in the generated fluorescent signal. Under optimized conditions, a broad linear concentration range from 0.05 μM to 20 μM and a limit of detection of 11.76 nM were obtained, confirming the ability of the fabricated aptasensor for sensitive and specific kanamycin detection in real samples such as milk and human serum. The aptasensing method has the potential to be extensively employed in the food industry and veterinary science due to its simplicity, sensitivity, user-friendly, and capability of on-site detection of kanamycin.

Aptamers Targeting Membrane Proteins for Sensor and Diagnostic Applications

Many biological processes (physiological or pathological) are relevant to membrane proteins (MPs), which account for almost 30% of the total of human proteins. As such, MPs can serve as predictive molecular biomarkers for disease diagnosis and prognosis. Indeed, cell surface MPs are an important class of attractive targets of the currently prescribed therapeutic drugs and diagnostic molecules used in disease detection. The oligonucleotides known as aptamers can be selected against a particular target with high affinity and selectivity by iterative rounds of in vitro library evolution, known as Systematic Evolution of Ligands by EXponential Enrichment (SELEX). As an alternative to antibodies, aptamers offer unique features like thermal stability, low-cost, reuse, ease of chemical modification, and compatibility with various detection techniques. Particularly, immobilized-aptamer sensing platforms have been under investigation for diagnostics and have demonstrated significant value compared to other analytical techniques. These "aptasensors" can be classified into several types based on their working principle, which are commonly electrochemical, optical, or mass-sensitive. In this review, we review the studies on aptamer-based MP-sensing technologies for diagnostic applications and have included new methodological variations undertaken in recent years.

Recent advances in optical aptasensors for biomarkers in early diagnosis and prognosis monitoring of hepatocellular carcinoma

Hepatocellular carcinoma (HCC) accounts for approximately 90% of all primary liver cancers and is one of the main malignant tumor types globally. It is essential to develop rapid, ultrasensitive, and accurate strategies for the diagnosis and surveillance of HCC. In recent years, aptasensors have attracted particular attention owing to their high sensitivity, excellent selectivity, and low production costs. Optical analysis, as a potential analytical tool, offers the advantages of a wide range of targets, rapid response, and simple instrumentation. In this review, recent progress in several types of optical aptasensors for biomarkers in early diagnosis and prognosis monitoring of HCC is summarized. Furthermore, we evaluate the strengths and limitations of these sensors and discuss the challenges and future perspectives for their use in HCC diagnosis and surveillance.

Aptamer-based rapid diagnosis for point-of-care application

Aptasensors have attracted considerable interest and widespread application in point-of-care testing worldwide. One of the biggest challenges of a point-of-care (POC) is the reduction of treatment time compared to central facilities that diagnose and monitor the applications. Over the past decades, biosensors have been introduced that offer more reliable, cost-effective, and accurate detection methods. Aptamer-based biosensors have unprecedented advantages over biosensors that use natural receptors such as antibodies and enzymes. In the current epidemic, point-of-care testing (POCT) is advantageous because it is easy to use, more accessible, faster to detect, and has high accuracy and sensitivity, reducing the burden of testing on healthcare systems. POCT is beneficial for daily epidemic control as well as early detection and treatment. This review provides detailed information on the various design strategies and virus detection methods using aptamer-based sensors. In addition, we discussed the importance of different aptamers and their detection principles. Aptasensors with higher sensitivity, specificity, and flexibility are critically discussed to establish simple, cost-effective, and rapid detection methods. POC-based aptasensors' diagnostic applications are classified and summarised based on infectious and infectious diseases. Finally, the design factors to be considered are outlined to meet the future of rapid POC-based sensors.

Recent advances in gold nanoparticle-based colorimetric aptasensors for chemical and biological analyses

Aptasensors are amazing among many currently formed procedures due to their excellent particularity, selectivity and responsiveness. These biosensors get more popular in combination with gold nanoparticles (AuNPs) to detect chemical and biological molecules. The response of AuNPs by changing color provides a simple explanation of outcomes. The authors review the recent developments in AuNP-based colorimetric aptasensors designed to sense different chemical and biological molecules. They summarize the procedure of AuNP-based detection and the ordinary instances of currently formed AuNP-based colorimetric procedures. Furthermore, their uses for detecting different analytes based on analyte types are given and the present challenges, overview, and positive views for forming new aptasensors are also regarded.

Aptamer-based biosensors for virus protein detection

Virus threatens life health seriously. The accurate early diagnosis of the virus is vital for clinical control and treatment of virus infection. Aptamers are small single-stranded oligonucleotides (DNAs or RNAs). In this review, we summarized aptasensors for virus detection in recent years according to the classification of the viral target protein, and illustrated common detection mechanisms in the aptasensors (colorimetry, fluorescence assay, surface plasmon resonance (SPR), surface-enhanced raman spectroscopy (SERS), electrochemical detection, and field-effect transistor (FET)). Furthermore, aptamers against different target proteins of viruses were summarized. The relationships between the different biomarkers of the viruses and the detection methods, and their performances were revealed. In addition, the challenges and future directions of aptasensors were discussed. This review will provide valuable references for constructing on-site aptasensors for detecting viruses, especially the SARS-CoV-2.

A Review on Aptamers Selection and Application in Heart Diseases Diagnosis

Biomarkers detection and quantification in biological fluids play a key role in the screening, diagnosing and treating several diseases. Recently, a large number of aptamers have been selected and applied for the sensing of different biomarkers. Combined with different transducers, aptamers provide simple and rapid tools that allow highly sensitive and selective detection. Cardiology requires an accurate assessment of cardiac biomarkers for a complete diagnosis of cardiovascular diseases. The analysis is generally performed by immunoassays using antibodies as biorecognition elements. This review paper focuses on using aptamers as a promising alternative for antibodies in cardiac biomarkers biosensing. First, the different aptamers specific to the most important cardiac biomarkers are Troponin I, the peptide of B-type natriuretic peptide and myoglobin. Then, in the second part, we overview the electrochemical aptasensors principle and characteristics reported in the literature in the last five years.

Aptamers for SARS-CoV-2: Isolation, Characterization, and Diagnostic and Therapeutic Developments

The SARS-CoV-2 virus and COVID-19 pandemic continue to demand effective diagnostic and therapeutic solutions. Finding these solutions requires highly functional molecular recognition elements. Nucleic acid aptamers represent a possible solution. Characterized by their high affinity and specificity, aptamers can be rapidly identified from random-sequence nucleic acid libraries. Over the past two years, many labs around the world have rushed to create diverse aptamers that target two important structural proteins of SARS-CoV-2: the spike (S) protein and nucleocapsid (N) protein. These have led to the identification of many aptamers that show real promise for the development of diagnostic tests and therapeutic agents for SARS-CoV-2. Herein we review all these developments, with a special focus on the development of diverse aptasensors for detecting SARS-CoV-2. These include electrochemical and optical sensors, lateral flow devices, and aptamer-linked immobilized sorbent assays.

The Recent Progress in DNAzymes-Based Aptasensors for Thrombin Detection

Thrombin (TB) is classified among human blood coagulation proteins with key functions in hemostasis of blood vessels, wound healing, atherosclerosis, tissue adhesion, etc. Moreover, TB is involved as the main enzyme in the conversion of the fibrinogen to fibrin. Given the importance of TB detection in the clinical area, the development of innovative methods can considerably improve TB detection. Newly, aptasensors or aptamer-based biosensors have received special attention for sensitive and facile TB detection. In addition, the aptamer/nanomaterial conjugates have presented new prospects in accurate TB detection as nanoaptasensors. DNA-based enzymes or DNAzymes, as new biocatalysts, have many advantages over protein enzymes and can be used in analytical tools. This article reviews a brief overview of significant progresses regarding the various types of DNAzymes-based aptasensors and nano aptasensors developed for thrombin detection. In the following, challenges and prospects of TB detection by DNAzymes-based aptasensors are discussed.

A Simple Structure-Switch Aptasensor Using Label-Free Aptamer for Fluorescence Detection of Aflatoxin B1

Aflatoxin B1 (AFB1) is one of the mycotoxins produced by Aspergillus flavus and Aspergillus parasiticus, and it causes contamination in foods and great risk to human health. Simple sensitive detection of AFB1 is important and demanded for food safety and quality control. Aptamers can specifically bind to targets with high affinity, showing advantages in affinity assays and biosensors. We reported an aptamer structure-switch for fluorescent detection of aflatoxin B1 (AFB1), using a label-free aptamer, a fluorescein (FAM)-labeled complementary strand (FDNA), and a quencher (BHQ1)-labeled complementary strand (QDNA). When AFB1 is absent, these three strands assemble into a duplex DNA structure through DNA hybridization, making FAM close to BHQ1, and fluorescence quenching occurs. In the presence of AFB1, the aptamer binds with AFB1, instead of hybridizing with QDNA. Thus, FAM is apart from BHQ1, and fluorescence increases with the addition of AFB1. This assay allowed detection of AFB1 with a detection limit of 61 pM AFB1 and a dynamic concentration range of 61 pM to 4 μM. This aptamer-based method enabled detection of AFB1 in complex sample matrix (e.g., beer and corn flour samples).

Dual DNAzyme-catalytic assembly of G-quadruplexes for inducing the aggregation of gold nanoparticles and developing a novel antibiotic assay method

By utilizing a target biorecognition reaction to induce the self-assembly of G-quadruplexes and the aggregation of gold nanoparticles (Au NPs), this work develops a novel colorimetric biosensing method for kanamycin (Kana) antibiotic detection. The compact G-quadruplex structure was assembled from its two half-split sequences which were designed in two hairpin substrates of the Mg²⁺-dependent DNAzyme (MNAzyme). Besides hybridizing with the aptamer strand, the MNAzyme sequence was also split into two half fragments to be designed in the two substrates. Upon the aptamer-recognition reaction toward Kana, the MNAzyme strand could be quantitatively released to cause the exposure of the split G-quadruplex-sequences on two hairpin substrate-modified Au NPs and simultaneous release of two half fragments of the MNAzyme-sequence. Thus, the K⁺-assisted self-folding of G-quadruplexes causes the cross-linking of the two Au NPs to realize the Au NP aggregation-based colorimetric signal output (measured at the largest absorption peak near 520 nm). Meanwhile, the self-assembled formation of the second MNAzyme drastically amplified the signal response. Under the optimal conditions, a wide linear range from 0.1 pg mL^-1 to 10 ng mL^-1 and an ultrahigh sensitivity with the detection limit of 76 fg mL^-1 were obtained. The dose-recovery experiments in real samples showed satisfactory results with recoveries from 98.4 to 105.4% and relative errors compared with the ELISA method less than 4.1%. Due to the high selectivity, excellent repeatability and stability, and simple manipulation, this method indicates a promising potential for practical applications. A novel homogeneous biosensing method was developed for the convenient detection of the kanamycin antibiotic. The target biorecognition-induced and dual DNAzyme-catalytic assembly of G-quadruplexes enabled the amplified aggregation of gold nanoparticles for the simple, cheap, stable, and ultrasensitive colorimetric signal transduction of the method.

Aptamers against Pathogenic Bacteria: Selection Strategies and Apta-assay/Aptasensor Application for Food Safety

Pathogenic bacteria are primarily kinds of detrimental agents that cause mankind illness via contaminated food with traits of multiple types, universality, and low content. In view of the detection demands for rapidity, aptamer recognition factors emerged as a substitution for antibodies, which are short single strands of nucleic acid selected via in vitro. They display certain superiorities over antibodies, such as preferable stability, liable modification, and cost-efficiency. Taking advantage of the situation, numerous aptamers against pathogenic bacteria have been successfully selected and applied, yet there are still restrictions on commercial availability. In this review, the strategies/approaches to key sections in pathogen aptamers SELEX and post-SELEX are summarized and sorted out. Recently, optical, electrochemical, and piezoelectric aptamer-based assays or sensors dedicated to pathogen detection have been critically reviewed. Ultimately, the existing challenges and future trends in this field are proposed to further promote development prospects.

A Review of Apta-POF-Sensors: The Successful Coupling between Aptamers and Plastic Optical Fibers for Biosensing Applications

Aptamers represent the next frontier as biorecognition elements in biosensors thanks to a smaller size and lower molecular weight with respect to antibodies, more structural flexibility with the possibility to be regenerated, reduced batch-to-batch variation, and a potentially lower cost. Their high specificity and small size are particularly interesting for their application in optical biosensors since the perturbation of the evanescent field are low. Apart from the conventional plasmonic optical sensors, platforms based on silica and plastic optical fibers represent an interesting class of devices for point-of-care testing (POCT) in different applications. The first example of the coupling between aptamers and silica optical fibers was reported by Pollet in 2009 for the detection of IgE molecules. Six years later, the first example was published using a plastic optical fiber (POF) for the detection of Vascular Endothelial Growth Factor (VEGF). The excellent flexibility, great numerical aperture, and the large diameter make POFs extremely promising to be coupled to aptamers for the development of a sensitive platform easily integrable in portable, small-size, and simple devices. Starting from silica fiber-based surface plasmon resonance devices, here, a focus on significant biological applications based on aptamers, combined with plasmonic-POF probes, is reported.

Effect of DNA Aptamer Concentration on the Conductivity of a Water-Gated Al:ZnO Thin-Film Transistor-Based Biosensor

Field-effect transistor-based biosensors (bio-FETs) are promising candidates for the rapid high-sensitivity and high-selectivity sensing of various analytes in healthcare, clinical diagnostics, and the food industry. However, bio-FETs still have several unresolved problems that hinder their technological transfer, such as electrical stability. Therefore, it is important to develop reliable, efficient devices and establish facile electrochemical characterization methods. In this work, we have fabricated a flexible biosensor based on an Al:ZnO thin-film transistor (TFT) gated through an aqueous electrolyte on a polyimide substrate. In addition, we demonstrated techniques for establishing the operating range of such devices. The Al:ZnO-based devices with a channel length/width ratio of 12.35 and a channel thickness of 50 nm were produced at room temperature via magnetron sputtering. These Al:ZnO-based devices exhibited high field-effect mobility (μ = 6.85 cm2/Vs) and threshold voltage (Vth = 654 mV), thus showing promise for application on temperature-sensitive substrates. X-ray photoelectron spectroscopy was used to verify the chemical composition of the deposited films, while the morphological aspects of the films were assessed using scanning electron and atomic force microscopies. The gate-channel electric capacitance of 40 nF/cm2 was determined using electrochemical impedance spectroscopy, while the electrochemical window of the gate-channel system was determined as 1.8 V (from -0.6 V to +1.2 V) using cyclic voltammetry. A deionized water solution of 10 mer (CCC AAG GTC C) DNA aptamer (molar weight -2972.9 g/mol) in a concentration ranging from 1-1000 pM/μL was used as an analyte. An increase in aptamer concentration caused a proportional decrease in the TFT channel conductivity. The techniques demonstrated in this work can be applied to optimize the operating parameters of various semiconductor materials in order to create a universal detection platform for biosensing applications, such as multi-element FET sensor arrays based on various composition nanostructured films, which use advanced neural network signal processing.

A 1.8 V Low-Power Low-Noise High Tunable Gain TIA for CMOS Integrated Optoelectronic Biomedical Applications

This paper reports on a novel solution for a transimpedance amplifier (TIA) specifically designed as an analog conditioning circuit for low-voltage, low-power, wearable, portable and implantable optoelectronic integrated sensor systems in biomedical applications. The growing use of sensors in all fields of industry, biomedicine, agriculture, environment analysis, workplace security and safety, needs the development of small sensors with a reduced number of electronic components to be easily integrated in the standard CMOS technology. Especially in biomedicine applications, reduced size sensor systems with small power consumption are of paramount importance to make them non-invasive, comfortable tools for patients to be continuously monitored even with personalized therapeutics and/or that can find autonomous level of life using prosthetics. The proposed new TIA architecture has been designed at transistor level in TSMC 0.18 μm standard CMOS technology with the aim to operate with nanoampere input pulsed currents that can be generated, for example, by Si photodiodes in optical sensor systems. The designed solution operates at 1.8 V single supply voltage with a maximum power consumption of about 36.1 μW and provides a high variable gain up to about 124 dBΩ (with fine- and coarse-tuning capabilities) showing wide bandwidth up to about 1.15 MHz and low-noise characteristics with a minimum noise floor level down to about 0.39 pA/Hz. The overall circuit is described in detail, and its main characteristics and performances have been analyzed by performing accurate post-layout simulations.

Nanoarchitectonics for Abused-Drug Biosensors

Rapid, accessible, and highly accurate biosensors for the detection of addictive and abused drugs are needed to reduce the adverse personal and societal impacts of addiction. Modern sensors that utilize next-generation technologies, e.g., nanobiotechnology and nanoarchitectonics, have triggered revolutionary progress in the field as they allow accurate detection and tracking of trace levels of major classes of drugs. This paper reviews advances in the field of biosensors for the detection of commonly abused drugs, both prescribed such as codeine and morphine, and illegal narcotics like cocaine.

A novel aptasensor for colorimetric monitoring of tobramycin: Strategy of enzyme-like activity of AuNPs controlled by three-way junction DNA pockets

In this study, a novel colorimetric sensor was introduced to detect tobramycin (TOB) based on controlling the catalytic activity of gold nanoparticles (AuNPs) by the three-way junction aptamer pockets. In the absence of TOB, the surfaces of AuNPs were masked by the three-way junction pockets that prevented their catalytic activation for the reduction of 4-Nitrophenol in the presence of NaBH₄. While the formation of the pockets was prevented in the presence of TOB that facilitated the 4-Nitrophenol access to AuNPs. Hence, the catalytic reduction of 4-Nitrophenol induced a color change of the solution from yellow to colorless, highlighting the presence of the target. The aptasensing assay provided good target specificity with a detection limit (LOD) of 1.16 µM and a linear dynamic range over 4-32 µM. The aptasensor was successfully applied to quantitatively monitor TOB in the human serum and milk samples with the LODs of 1.38 and 1.42 µM and recovery values of 94.87-105.75% and 93.75-105.31%, respectively.

A genetically encoded fluorescent biosensor for monitoring ATP in living cells with heterobifunctional aptamers

Visualizing the dynamics of ATP in living cells is key to understanding cellular energy metabolism and related diseases. However, the live-cell applications of current methods are still limited due to challenges in biological compatibility and sensitivity to pH. Herein, a novel label-free fluorescent " turn-on " biosensor for monitoring ATP in living bacterias and mammalian cells was developed. This biosensor (Broc-ATP) employed heterobifunctional aptamers to detect ATP with high sensitivity in vitro. In our system, a very useful tandem method was established by combining four Broc-ATPs with 3 × F30 three-way junction scaffold to construct an intracellular biosensor that achieves sufficient fluorescence to respond to intracellular ATP. This intracellular biosensor can be used for sensitive and specific dynamic imaging of ATP in mammalian cells. Hence, this genetically encoded biosensor provides a robust and efficient tool for the detection of intracellular ATP dynamics and 3 × F30 tandem method expands the application of heterobifunctional aptamers in mammalian cells.

Selection and characterization of DNA aptamers for highly selective recognition of the major allergen of olive pollen Ole e 1

In this study, single-stranded DNA aptamers with binding affinity to Ole e 1, the major allergen of olive pollen, were selected using systematic evolution of ligands by exponential enrichment (SELEX) method. Binding of the aptamers was firstly established by enzyme-linked oligonucleotide assay (ELONA) and aptaprecipitation assays. Additionally, aptamer-modified monolithic capillary chromatography was used in order to evaluate the recognition of this allergenic protein against other non-target proteins. The results indicated that AptOle1#6 was the aptamer that provided the highest affinity for Ole e 1. The selected aptamer showed good selective recognition of this protein, being not able to retain other non-target proteins (HSA, cyt c, and other pollen protein such as Ole e 9). The feasibility of the affinity monolithic column was demonstrated by selective recognition of Ole e 1 in an allergy skin test. The stability and reproducibility of this monolithic column was suitable, with relative standard deviations (RSDs) in retention times and peak area values of 7.8 and 9.3%, respectively (column-to-column reproducibility). This is the first study that describes the design of an efficient DNA aptamer for this relevant allergen.

Ultrasensitive Aptasensors for the Detection of Viruses Based on Opto-Electrochemical Readout Systems

Viral infections are becoming the foremost driver of morbidity, mortality and economic loss all around the world. Treatment for diseases associated to some deadly viruses are challenging tasks, due to lack of infrastructure, finance and availability of rapid, accurate and easy-to-use detection methods or devices. The emergence of biosensors has proven to be a success in the field of diagnosis to overcome the challenges associated with traditional methods. Furthermore, the incorporation of aptamers as bio-recognition elements in the design of biosensors has paved a way towards rapid, cost-effective, and specific detection devices which are insensitive to changes in the environment. In the last decade, aptamers have emerged to be suitable and efficient biorecognition elements for the detection of different kinds of analytes, such as metal ions, small and macro molecules, and even cells. The signal generation in the detection process depends on different parameters; one such parameter is whether the labelled molecule is incorporated or not for monitoring the sensing process. Based on the labelling, biosensors are classified as label or label-free; both have their significant advantages and disadvantages. Here, we have primarily reviewed the advantages for using aptamers in the transduction system of sensing devices. Furthermore, the labelled and label-free opto-electrochemical aptasensors for the detection of various kinds of viruses have been discussed. Moreover, numerous globally developed aptasensors for the sensing of different types of viruses have been illustrated and explained in tabulated form.

An entropy driven catalytic reaction powered DNA motor for simultaneous detection of ochratoxin A and chloramphenicol in food

An entropy driven catalytic reaction powered DNA motor was proposed for simultaneous detection of ochratoxin A (OTA) and chloramphenicol (CAP) in food. The dumbbell hairpin structure was formed by the two aptamers of OTA and CAP. The dumbbell hairpin can be opened by the interaction of OTA and CAP with their aptamers. The tails of the end of dumbbell hairpin sequence can induce the entropy driven catalytic reactions on the AuNPs, causing the sustained releasing of the fluorophore labeled DNA sequences. The recovery of fluorescent intensities can be used for quantitative detection of OTA and CAP. The limit of detection reached 2 pM for OTA and 6 pM for CAP respectively, which was great improved by entropy driven amplification of the self-powdered DNA motor. This strategy is simple and sensitive and only needs one-step operation. It exhibits promising potentiality in food quality control and food security supervision.

Ultrasensitive and practical chemiluminescence sensing pesticide residue acetamiprid in agricultural products and environment: Combination of synergistically coupled co-amplifying signal and smart interface engineering

Practical detection of single-component pesticide residue at ultra-low concentrations in agricultural products and environment is very important for assessment of environmental risks and protection of human health. Herein, a practical and highly sensitive chemiluminescence (CL) sensing acetamiprid in agricultural products and environmental media was constructed based on the synergistic co-catalysis of graphene oxide (GO)/gold nanoparticles (AuNPs) nanocomposites for luminol CL reaction and the smart interface engineering. ss-DNA could inhibit co-catalysis of GO/AuNPs for luminol CL reaction. Once acetamiprid was added, aptamer conformation changed in dimension and synergistically catalytic amplification signal of GO/AuNPs was restored significantly. The limit of detection was 8.9 pM. High sensitivity could be due to strong signal amplification from synergistic catalysis of GO/AuNPs for CL reaction and perfect regulation of composite interface by DNA dimension. Moreover, the used GO/AuNPs could be stably stored for six months, which was superior to previously reported AuNPs (only half a month). The analysis exhibited excellent selectivity for acetamiprid. The detection results for real samples confirmed reliability in practical application. This analysis is an extremely useful method for monitoring pesticide residues in environment and agricultural products. Synergetic co-catalysis of GO/AuNPs and ingenious interface engineering provide important ideas for other biosensors.

Aptamer-based biosensors and their implications in COVID-19 diagnosis

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a novel infectious member of the coronavirus family, has caused millions of cases of infection and deaths all over the world, and been declared a pandemic by the World Health Organization. Conventional laboratory-based diagnostic testing has faced extreme difficulties in meeting the overwhelming demand for testing worldwide, and this has brought about a pressing need for cost-effective rapid diagnosis. There has been a surge in the number of prototypes of diagnostic kits developed, although many of these have been found to be lacking in terms of their accuracy and sensitivity. One type of chip-based diagnostic platform is the aptamer-based biosensor. Aptamers are artificially synthesized oligonucleotides that are capable of specifically binding to a target antigen. As of now, some aptamers have been reported for SARS-CoV-2. Although many ultrasensitive aptasensors have been developed for viruses, few have been successfully adapted for SARS-CoV-2 detection. Our review discusses the recent developments in the domain of SARS-CoV-2 specific aptamer isolation, the design of electrochemical and optical aptasensors, and the implications of aptasensor-based COVID-19 diagnosis.

Self-Assembling Nucleic Acid Nanostructures Functionalized with Aptamers

Researchers have worked for many decades to master the rules of biomolecular design that would allow artificial biopolymer complexes to self-assemble and function similarly to the diverse biochemical constructs displayed in natural biological systems. The rules of nucleic acid assembly (dominated by Watson-Crick base-pairing) have been less difficult to understand and manipulate than the more complicated rules of protein folding. Therefore, nucleic acid nanotechnology has advanced more quickly than de novo protein design, and recent years have seen amazing progress in DNA and RNA design. By combining structural motifs with aptamers that act as affinity handles and add powerful molecular recognition capabilities, nucleic acid-based self-assemblies represent a diverse toolbox for use by bioengineers to create molecules with potentially revolutionary biological activities. In this review, we focus on the development of self-assembling nucleic acid nanostructures that are functionalized with nucleic acid aptamers and their great potential in wide ranging application areas.

Nano optical and electrochemical sensors and biosensors for detection of narrow therapeutic index drugs

For the first time, a comprehensive review is presented on the quantitative determination of narrow therapeutic index drugs (NTIDs) by nano optical and electrochemical sensors and biosensors. NTIDs have a narrow index between their effective doses and those at which they produce adverse toxic effects. Therefore, accurate determination of these drugs is very important for clinicians to provide a clear judgment about drug therapy for patients. Routine analytical techniques have limitations such as being expensive, laborious, and time-consuming, and need a skilled user and therefore  the nano/(bio)sensing technology leads to high interest.

Graphene oxide-regulated low-background aptasensor for the "turn on" detection of tetracycline

Tetracyclines (TC) are a common antibiotic for using in livestock breeding and healthcare; however, due to the inappropriate application of TCs, more than 75% of TCs are excreted and released into the environment in an active form through human and animal urine and feces, which results in high levels of TCs in the ecological system, causing adverse effects on the food safety and human health. Thus, the high-performance monitoring of TC pollution is necessary. In this work, a highly sensitive fluorescent aptasensor was developed that was based on graphene oxide (GO) regulation of low background signal and target-induced fluorescence restoration. In the absence of analyte, the DNA probe (TC aptamer) was adsorbed completely by GO and failed to enhance the fluorescence of SYBR gold (SG), thereby resulting in a low background signal. When the TC-included samples were added, the DNA probe formed an aptamer-TC complex, thereby separating from the surface of the GO and inducing the fluorescence of SG. Under optimal conditions, the proposed strategy could detect TC concentrations of less than 6.2 × 10^-3 ng mL^-1, which is four orders of magnitude better than the detection limit of the "turn off" mode (53.9511 ng mL^-1). Moreover, this aptasensor has been used to detect TC from milk samples and wastewater samples, and its satisfactory performances demonstrate that the proposed strategy can be applied in practice for TC monitor in food safety and environmental protection. Therefore, we believe that this work is meaningful in pollution monitoring, environment restoration and emergency treatment.

Application of the catalytic activity of gold nanoparticles for development of optical aptasensors

Biosensor technology is considered to be a great alternative in analytical techniques over the conventional methods. Among many recently developed techniques and devices, aptasensors are interesting because of their high specificity, selectivity and sensitivity. Combining aptamer as a biological recognition element with gold nanoparticles (AuNPs) as probe, are becoming more general owing to their beneficial properties, including low cost and ability to analyze specific targets on-site and using naked eye. Hydrogen bonds, nucleic acid hybridization, aptamer-target and antigen-antibody binding, Raman signature, enzyme inhibition, and enzyme-mimicking activity are main different sensing strategies exploited in AuNPs-based optical aptasensors. In this review article, we discussed the recent advances in optical aptasensors with a special emphasis on the catalytic activity property of AuNPs.

Recent progress in developing fluorescent probes for imaging cell metabolites

Cellular metabolites play a crucial role in promoting and regulating cellular activities, but it has been difficult to monitor these cellular metabolites in living cells and in real time. Over the past decades, iterative development and improvements of fluorescent probes have been made, resulting in the effective monitoring of metabolites. In this review, we highlight recent progress in the use of fluorescent probes for tracking some key metabolites, such as adenosine triphosphate, cyclic adenosine monophosphate, cyclic guanosine 5'-monophosphate, Nicotinamide adenine dinucleotide (NADH), reactive oxygen species, sugar, carbon monoxide, and nitric oxide for both whole cell and subcellular imaging.

Aptamer-based strategies for recognizing adenine, adenosine, ATP and related compounds

Adenine is a key nucleobase, adenosine is an endogenous regulator of the immune system, while adenosine triphosphate (ATP) is the energy source of many biological reactions. Selective detection of these molecules is useful for understanding biological processes, biochemical reactions and signaling. Since 1993, various aptamers have been reported to bind to adenine and its derivatives. In addition, the adenine riboswitch was later discovered. This review summarizes the efforts for the selection of RNA and DNA aptamers for adenine derivatives, and we pay particular attention to the specificity of binding. In addition, other molecular recognition strategies based on rational sequence design are also introduced. Most of the work in the field was performed on the classic DNA aptamer for adenosine and ATP reported by the Szostak group. Based on this aptamer, some representative applications such as the design of fluorescent, colorimetric and electrochemical biosensors, intracellular imaging, and ATP-responsive materials are also described. In addition, we critically review the limit of the reported aptamers and also important problems in the field, which can give future research opportunities.