Advances in aptamer screening and aptasensors' detection of heavy metal ions

Recent advancements in aptamers as promising nanotool for therapeutic and diagnostic applications

Aptamers are single-strand oligonucleotide molecules having certain structural interactions which allow them to bind to specific targets. Modified nucleotides are added during or after a selection procedure like Systematic Evolution of Ligands by Exponential Enrichment i.e., SELEX to enhance the characteristics and functionality of aptamers. Aptamers are extensible molecular tools with several uses such as in drug administration, biosensing, bioimaging, drug therapies and diagnostics. The ability to detect is improved by using aptamer-based sensors in conjunction with biological molecules among other sensing techniques. Chemical modification, and strong resistance to denaturation, aptamers are appropriate biological recognizing agents for developing sensitive and repeatable aptasensors. This review discusses the most current developments in the aptamers, SELEX method, applications of aptamers as innovative diagnostic, therapeutic & theragnostic tool along with major limitations & prospective directions in the future.

From traditional to modern: Nanotechnology-driven innovation in mycotoxin sensing for Chinese herbal medicines

Mycotoxin contamination in Chinese herbal medicines (CHMs) is a pressing concern that jeopardizes their quality and safety, despite their widespread therapeutic use. Conventional detection methods are often limited by complexity, cost, and sensitivity, particularly in resource-limited settings. This gap in effective and efficient mycotoxin detection necessitates a comprehensive review that explores innovative solutions to enhance the safety and efficacy of CHMs. Advancements in nanomaterials and related advanced sensing techniques have emerged as a beacon of hope. Therefore, this review aims to fill the knowledge gap by providing a comprehensive overview of the latest developments in mycotoxin detection in CHMs, spotlighting the transformative role of nanomaterials and advanced sensing techniques. This review stands out for its in-depth exploration of functional nanomaterials across dimensions and their innovative applications in mycotoxin detection. Its innovation stems from a holistic approach that not only surveys current technologies but also charts a forward-looking path, emphasizing novel nanomaterial development, refined pretreatment, and advanced biosensing for on-site detection. It delves into the integration of nanomaterials with advanced sensing technologies, discussing the advantages and limitations of these approaches. A significant innovation of this review lies in the nuanced integration of nanomaterials with machine learning and artificial intelligence, revealing untapped potential for accuracy enhancement. Through this synthesis of knowledge, we hope to inspire further research and development in this critical area, ensuring the continued safe use of CHMs in traditional medicine practices.

A novel self-autocatalytic DNAzyme and catalytic hairpin assembly molecular circuit for highly sensitive and non-label fluorescence aptamer glypican-3 assay

Glypican-3 (GPC-3) is universally regarded as an early diagnostic biomarker and plays a crucial role in the sensitive detection and treatment efficacy evaluation of hepatocellular carcinoma (HCC). Here, a novel self-autocatalytic DNAzyme reaction and catalytic hairpin assembly (CHA)-integrated molecular circuit amplification strategy is developed for realizing an aptamer-based, enzyme- and non-label fluorescence assay of GPC-3. The sensing protocol involves GPC-3 analyte binding to the aptamer in aptamer/ssDNA to trigger the liberation of ssDNA for the initiation of CHA formation of duplexes containing both active DNAzyme and G-quadruplex fragments. The DNAzymes further cleave another G-quadruplex- and DNAzyme-caged signal hairpin to free these sequences to trigger the self-autocatalytic circuit process, which leads to the cyclic cutting of signal hairpins to yield large amounts of G-quadruplexes. Subsequent binding of thioflavin T dye to formed G-quadruplexes thus generates significantly intensified fluorescence signals for detecting GPC-3, with a 0.16 pM detection limit between 1 pM and 100 nM. Moreover, the ability of this method to distinguish GPC-3 from non-target proteins and its success in detecting GPC-3 at low levels in diluted human serum is examined, underscoring its promising potential for monitoring disease-specific biomarkers at trace concentrations for early disease diagnosis.

Interactions of metal-based nanozymes with aptamers, from the design of nanozyme to its application in aptasensor: Advances and perspectives

Nanozymes, characterized by enzyme-like activity, have been extensively used in quantitative analysis and rapid detection due to their small size, batch fabrication, and ease of modification. Researchers have combined aptamers, an emerging molecular probe, with nanozymes for biosensing to address the limited reaction specificity of nanozymes. Nanozyme aptasensors are currently experiencing significant growth, offering a promising solution to the lack of rapid detection methods across various fields. Unlike traditional nanozyme research, the development of nanozyme aptasensors is challenging as it requires the design of highly active nanozymes as well as the establishment of efficient and agile interactions between aptamers and nanozymes. Therefore, this review summarizes the active species and catalytic mechanisms of various nanozymes along with classical design options, discussing the future development of nanozyme aptasensors. It is anticipated that this review will inspire researchers in this domain, leading to the design of more enzymatically active nanozymes and advanced nanozyme aptasensors.

Nanomaterials-Integrated CRISPR/Cas Systems: Expanding the Toolbox for Optical Detection

Nanomaterials-integrated CRISPR/Cas systems have rapidly emerged as powerful next-generation platforms for optical biosensing. These integrated platforms harness the precision of CRISPR/Cas-mediated nucleic acid detection while leveraging the unique properties of nanomaterials to achieve enhanced sensitivity and expanded analytical capabilities, thereby broadening their diagnostic potential. By incorporating a diverse range of nanomaterials, these systems effectively expand the analytical toolbox for optical detection, offering adaptable solutions tailored to various diagnostic challenges. This review provides a comprehensive overview of the nanomaterials successfully integrated into CRISPR/Cas-based optical sensing systems. It examines multiple optical detection modalities, including fluorescence, electrochemiluminescence, colorimetry, and surface-enhanced Raman spectroscopy, highlighting how nanomaterials facilitate signal amplification, enable multiplexing, and support the development of point-of-care applications. Additionally, practical applications of these integrated systems in critical fields such as healthcare diagnostics and environmental monitoring are showcased. While these platforms offer considerable advantages, several real-world challenges such as the complexity of assay workflows, environmental impact of nanomaterials, cost, and regulatory hurdles must be addressed before widespread implementation can be achieved. By identifying these critical obstacles and proposing strategic solutions, we aim to pave the way for the continued advancement and adoption of nanomaterial-integrated CRISPR/Cas optical biosensing technologies.

[Research advances in non-immobilized aptamer screening techniques for small-molecule targets]

Aptamers obtained through systematic evolution of ligands by exponential enrichment (SELEX) techniques are single stranded deoxyribonucleic acid (ssDNA) or RNA molecules capable of specifically recognizing target molecules. Such aptamers are easily chemically synthesized and modified, highly thermally stable, and are low toxicity and low immunogenicity. Aptamers that target small molecules have broad applications prospects for the development of new drugs, treating tumors, diagnosing diseases, monitoring environmental pollution, detecting drugs, and in ultrafast and sensitive detection applications. However, the simple structures and low molecular masses of small molecules, along with the limited number of binding groups available for interacting with nucleic acids lead to unstable aptamer-small molecule binding, which poses significant challenges for aptamer screening and sensor development. Efficient screening techniques are crucial for identifying aptamers with excellent performance characteristics. At present, the aptamer screening techniques suitable for small-molecule targets are mainly divided into three categories: target-immobilized-based screening technique, nucleic acid library-immobilized-based screening technique, and target-non-immobilized screening technique. Among them, target-non-immobilized screening technique require fewer screening rounds and result in aptamers with superior (typically nmol/L level) affinities. This paper summarized non-immobilized aptamer screening techniques for small-molecule targets, including principle, advantages, disadvantages and application progress associated with graphene oxide (GO)-SELEX, capillary electrophoresis (CE)-SELEX, and gold nanoparticle-assisted (GNP)-SELEX techniques. In addition, strategies for selecting control targets in aptamer-specific evaluation were summarized.

Construction and mechanism analysis of an ultra-sensitive GCN/Pb2+/PPy heterojunction electrochemiluminescent sensor for detecting Cu(II)

A highly stable electrochemiluminescent (ECL) sensor based on graphitic carbon nitride (GCN)/Pb2+/polypyrrole (PPy) was developed to detect trace copper ions. The hydrochloric acid immersion technique was applied to rearrange PPy chains for the first time. Under optimal experimental conditions, the ECL intensity increased linearly with the increase of Cu2+ concentration in solution from 10-12 M to 10-6 M (1 pM to 1 μM), with a super low limit of detection (LOD) of 10-12 M (1 pM) (S/N = 3). Additionally, the impact of detection on the localized states of the composite nanomaterial was revealed by applying Vienna ab initio Simulation Package (VASP) and Gaussian 16.

Construction of a microfluidic SELEX platform for efficient screening of advanced glycation end products aptamer

Aptamers, as a kind of recognition molecules with stable nature and excellent binding ability, are usually obtained by systematic evolution of ligands by exponential enrichment (SELEX). However, the traditional SELEX suffers from the problems of low screening efficiency as well as excessive number of screening rounds, making the screening a cumbersome process, which greatly restricts the application and development of aptamers. Here, a microfluidic SELEX platform based on capture SELEX was designed and developed to make the screening more integrated and convenient. Nε-carboxymethyl lysine (CML) and Nε-carboxyethyl lysine (CEL), were selected as targets for screening, and candidate aptamers were identified after eight rounds of screening using the microfluidic SELEX platform. Following isothermal titration calorimetry (ITC) and SYBR GREEN I (SGI) analysis, aptamer S2 was identified with the highest affinity and specificity. Aptamer S2 was further optimized based on the binding sites explored by molecular docking. Eventually, the truncated aptamer S2-40 was obtained, which was superior to S2 in terms of affinity and specificity with dissociation constant (Kd) of 6.65 ± 3.07 μM (ITC) and 42.1 ± 9.34 nM (SGI), respectively. This indicated that the microfluidic SELEX platform offers a more integrated and convenient approach to aptamer screening.

DNA aptamer-based sensitive electrochemical biosensor for NAD(H) detection

Nicotinamide-adenine dinucleotide (NAD(H)) plays a critical role in cellular metabolism, and its accurate measurement is essential for elucidating biological mechanisms and disease progression. However, specific recognition probes and sensitive biosensors for NAD(H) remains a significant challenge. Here, we screen an aptamer (NAD3-1a) that exhibits specific binding to NAD(H) with micromolar affinity. By incorporating this aptamer with tetrahedral DNA nanostructure, we develop a highly selective and sensitive electrochemical biosensor for the detection of NAD(H). This biosensor enables precise detection of NAD(H) within a linear range of 10-12 ∼ 10-7 M, offering remarkable stability and reproducibility. Utilizing this biosensor, we observed significant variations in the NAD(H) levels between normal and tumor cells, as well as a notable reduction in NAD(H) in the skeletal muscle tissues of aged mice. These results highlight the potential of this aptamer-based biosensor to advance our understanding of metabolic variations in both health and disease contexts.

A colorimetric biosensor composed of split aptamers and mannan oligosaccharide nanozyme to monitor synthetic His-tagged food biomolecules

Food synthetic biology is garnering increasing attention for its potential to generate bioactive components. His-tag is one of the most popular tags used in food synthetic biology. Herein, His-tag, His-tagged proteins, and His-tagged peptides were adopted as the model targets, and a commonly used biosensor was developed to monitor His-tagged food biomolecules, using split aptamers as specific recognition probes and nanozyme as the transduction element. A strategy to generate high-affinity split aptamers was proposed, obtaining a pair of split aptamers for His-tag (Kd = 132 nM). AuNPs-mannan oligosaccharide nanozyme was fabricated and combined with the split aptamers to develop the biosensor. The functional mechanism of the probes and the nanozyme was revealed. The biosensor demonstrated good sensitivity, selectivity, and practicability when analyzing synthetic His-tagged proteins and peptides in real-world samples, with a limit of detection of 12.44 nM. The strategies provide robust reference for developing analytical methods for synthetic biomolecules.

Aptamer-based tri-mode sensing for detecting oxytetracycline mediated by SYBR Green I and functionalized Au nanoparticles

Exploiting multi-mode aptamer sensing approaches for target pollutants is urgently required to meet the multi-scene detection requirements and improve the accuracy of detection. Herein, we developed a novel aptamer-based tri-mode sensing for detecting oxytetracycline (OTC). First, OTC can induce the conformational changes of the aptamer, which can promote the formation of duplex structures of the aptamer. Then SYBR Green I (SGI) can embed into the duplex structures of the aptamer to enhance the fluorescence signal. Meanwhile, it can also induce the aggregation of functionalized Au nanoparticles (AuNPs-4MBA) based on the charge neutralization strategy, producing stable colorimetric and Raman signals. Furthermore, we evaluated for the first time the advantage of SGI over salt induced nanoparticles from the perspective of Raman detection. The detection limit for the fluorescence, colorimetric, and Raman mode was 0.074, 5.019, and 0.036 nM, respectively. Moreover, the tri-mode sensing could provide broad detection range with five orders of magnitude (0.1-10000 nM). It also exhibited excellent analytical performance for tap water and honey samples with recoveries of 90.11-119.75% (n = 3). The false-positive results could be effectively avoided through the cross-validation. We expect that aptamer-based tri-mode sensing will provide a potential application for the different application scenarios.

Trends in Aptasensing and the Enhancement of Diagnostic Efficiency and Accuracy

The field of healthcare diagnostics is navigating complex challenges driven by evolving patient demographics and the rapid advancement of new technologies worldwide. In response to these challenges, these biosensors offer distinctive advantages over traditional diagnostic methods, such as cost-effectiveness, enhanced specificity, and adaptability, making their integration with point-of-care (POC) platforms more feasible. In recent years, aptasensors have significantly evolved in diagnostic capabilities through the integration of emerging technologies such as microfluidics, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) systems, wearable devices, and machine learning (ML), driving progress in precision medicine and global healthcare solutions. Moreover, these advancements not only improve diagnostic accuracy but also hold the potential to revolutionize early detection, reduce healthcare costs, and improve patient outcomes, especially in resource-limited settings. This Account examines key advancements, focusing on how scientific breakthroughs, including artificial intelligence (AI), have improved sensitivity and precision. Additionally, the integration of aptasensors with these technologies has enabled real-time monitoring and data analysis, fostering advances in personalized healthcare. Furthermore, the potential commercialization of aptasensor technologies could increase their availability in clinical settings and support their use as widespread solutions for global health challenges. Hence, this review discusses technological improvements, practical uses, and prospects while also focusing on the challenges surrounding standardization, clinical validation, and interdisciplinary collaboration for widespread application. Finally, ongoing efforts to address these challenges are key to ensure that aptasensors can be effectively implemented in diverse healthcare systems.

Application of PS2M Aptamer as Receptor Layer for Electrochemical Detection of Lead Ions

Since lead can cause severe effects on living organisms' health and life, the regular monitoring of Pb levels in water and soil is of particular significance. Recently, it was shown that lead ions can also be detected using affinity-based biosensors, namely, using aptamers as recognition elements. In most cases, thrombin binding aptamer (TBA) was utilized; however, there are more examples of DNA aptamers which could also serve that purpose. Herein, we present studies on the electrochemical detection of lead ions using PS2M aptamer, which contains several guanine nucleotides, as the receptor element. Firstly, the method of aptamer-based layer fabrication was optimized along with the choice of a redox active indicator, which was a source of current signal. The experiments revealed the possibility of lead ion detection from 50 to 600 nM, which covers the range below and above the maximum accepted limit stated by US EPA (72 nM). Moreover, the sensing layer exhibited high selectivity towards lead ions and was successfully applied both for the analysis of tap water spiked with Pb2+ ions and as a miniaturized sensor. Finally, stability and regeneration studies on the aptamer-based receptor layer were executed to confirm the utility of the elaborated tool.

Pyridyl/Pyrimidyl-Containing Ligands Modulating Two Cd(II)-MOFs with Distinct Architectures and Al3+ Sensing Abilities

It is a challenging task to develop metal-organic frameworks (MOFs) with fascinating architectures and outstanding performance. In this work, two novel Cd(II)-MOFs, [Cd2(L1)(BDC)2·1.5i-PrOH]n (1) and [Cd(L2)0.5(BDC)(H2O)]n (2), with distinct sensing performances are successfully synthesized by pyridyl/pyrimidyl-containing functional ligands 9,10-bis(di(pyridine-4-yl)methylene)-9,10-dihydroanthracene (L1) and 9,10-bis(di(pyrimidin-5-yl)methylene)-9,10-dihydroanthracene (L2). 1 exhibits a 3D (4,6,10)-connected multicylindrical framework with compartments, constructed by 4-connected L1 and BDC2- in modes A and B, 6-connected Cd1, and 10-connected [Cd2(COO)2]2+. 2 is fabricated by 4-connected BDC2-, 7-connected Cd, and L2 bridges to generate a 3D (4,7)-connected pillar-layered framework with uncoordinated pyrimidyl N active sites. More importantly, their topologies have not been reported thus far. 1 and 2 have excellent water, pH, and thermal stabilities. 1 can efficiently sense TNP and MDZ in H2O, but its Al3+ sensing ability is relatively average. In sharp contrast, 2 has ultrahigh Al3+ sensitivity. Its limit of detection (LOD) toward Al3+ (2.93 × 10-7 M) is nearly 2 orders of magnitude and 25 times lower than that of 1 (1.18 × 10-5 M) and the WHO's maximum Al3+ limit (7.41 × 10-6 M) in drinking water, respectively. Their sensing mechanisms and different sensing performances are explored in depth.

Biosafety and pharmacokinetic characteristics of polyethylene pyrrolidone modified nano selenium in rats

OBJECTIVE

This study aims to investigate the biocompatibility and pharmacokinetic characteristics of polyvinyl pyrrolidone-modified selenium nanoparticles (PVP-Se NPs). Understanding the biosafety of PVP-Se NPs is crucial due to their potential applications in mitigating oxidative stress-related diseases and improving drug delivery systems.

METHODS

Selenium nanoparticles were prepared using a sodium selenite solution, followed by PVP modification. Particle size analysis was conducted using dynamic light scattering (DLS), and particle morphology was observed using transmission electron microscopy (TEM). Different concentrations of PVP-Se NPs were intraperitoneally injected into SD rats, and the survival rate was observed. Liver and kidney tissues, urine, feces, and blood samples were collected at the highest safe dose, and the concentration of selenium ions was measured.

RESULTS

The average particle size of PVP-Se NPs was 278.4 ± 124.8 nm, exhibiting a semi-spherical shape. The maximum safe dose of PVP-Se NPs for intraperitoneal injection in rats was approximately 320 µg/kg. At this dose, the content of PVP-Se NPs significantly increased in the liver and kidney tissues from day 1 to day 3, in urine and feces during the first 8 h, and in blood during the first 2 h, followed by a gradual decrease.

CONCLUSION

When administered at a safe dose, PVP-Se NPs do not damage liver and kidney tissues and can be eliminated from the body through liver and kidney metabolism without accumulation.

Overcoming Debye screening effect in field-effect transistors for enhanced biomarker detection sensitivity

Field-effect transistor (FET)-based biosensors not only enable label-free detection by measuring the intrinsic charges of biomolecules, but also offer advantages such as high sensitivity, rapid response, and ease of integration. This enables them to play a significant role in disease diagnosis, point-of-care detection, and drug screening, among other applications. However, when FET sensors detect biomolecules in physiological solutions (such as whole blood, serum, etc.), the charged molecules will be surrounded by oppositely charged ions in the solution. This causes the effective charge carried by the biomolecules to be shielded, thereby significantly weakening their ability to induce charge rearrangement at the sensing interface. Such shielding hinders the change of carriers inside the sensing material, reduces the variation of current between the source and drain electrodes of the FET, and seriously limits the sensitivity and reliability of the device. In this article, we summarize the research progress in overcoming the Debye screening effect in FET-based biosensors over the past decade. Here, we first elucidate the working principles of FET sensors for detecting biomarkers and the mechanism of the Debye screening. Subsequently, we emphasize optimization strategies to overcome the Debye screening effect. Finally, we summarize and provide an outlook on the research on FET biosensors in overcoming the Debye screening effect, hoping to help the development of FET electronic devices with high sensitivity, specificity, and stability. This work is expected to provide new ideas for next-generation biosensing technology.

Tag-free fluorometric aptasensor for detection of chromium(VI) in foods via SYBR Green I signal amplification and aptamer structure transition

BACKGROUND

In response to growing concerns regarding heavy metal contamination in food, particularly chromium (Cr)(VI) contamination, this study presented a simple, sensitive and practical method for Cr(VI) detection.

RESULTS

A magnetic separation-based capture-exponential enrichment ligand system evolution (SELEX) method was used to identify and characterize DNA aptamers with a high affinity for Cr(VI). An aptamer, Cr-15, with a dissociation constant (Kd) of 4.42 ± 0.44 μmol L-1 was obtained after only eight rounds of selection. Further innovative methods combining molecular docking, dynamic simulation and thermodynamic analysis revealed that CrO4 2- could bind to the 19th and 20th guanine bases of Cr-15 via hydrogen bonds. Crucially, a label-free fluorometric aptasensor based on SYBR Green I was successfully constructed to detect CrO4 2-, achieving a linear detection range of 60-300 nmol L-1 with a lower limit of detection of 44.31 nmol L-1. Additionally, this aptasensor was able to quantitatively detect CrO4 2- in grapes and broccoli within 40 min, with spike recovery rates ranging from 89.22% to 108.05%. The designed fluorometric aptasensor exhibited high selectivity and could detect CrO4 2- in real samples without sample processing or target pre-enrichment.

CONCLUSION

The aptasensor demonstrated its potential as a reliable tool for monitoring Cr(VI) contamination in fruit and vegetable products. © 2024 Society of Chemical Industry.

Process, advances, and perspectives of graphene oxide-SELEX for the development of aptamer molecular probes: A comprehensive review

BACKGROUND

Aptamers are screened via the systematic evolution of ligands by exponential enrichment (SELEX) and are widely used in molecular diagnostics and targeted therapies. The development of efficient and convenient SELEX technology has facilitated rapid access to high-performance aptamers, thereby advancing the aptamer industry. Graphene oxide (GO) serves as an immobilization matrix for libraries in GO-SELEX, making it suitable for screening aptamers against diverse targets.

RESULTS

This review summarizes the detailed steps involved in GO-SELEX, including monitoring methods, various sublibrary acquisition methods, and practical applications from its inception to the present day. In addition, the potential of GO-SELEX in the development of broad-spectrum aptamers is explored, and its current limitations for future development are emphasized. This review effectively promotes the application of the GO-SELEX technique by providing valuable insights and assisting researchers interested in conducting related studies.

SIGNIFICANCE AND NOVELTY

To date, no review on the topic of GO-SELEX has been published, making it challenging for researchers to initiate studies in this area. We believe that this review will broaden the SELEX options available to researchers, ensuring that they can meet the growing demand for molecular probes in the scientific domain.

Viral aptamer screening and aptamer-based biosensors for virus detection: A review

Virus-induced infectious diseases have a detrimental effect on public health and exert significant influence on the global economy. Therefore, the rapid and accurate detection of viruses is crucial for effectively preventing and diagnosing infections. Aptamer-based detection technologies have attracted researchers' attention as promising solutions. Aptamers, small single-stranded DNA or RNA screened via systematic evolution of ligands by exponential enrichment (SELEX), possess a high affinity towards their target molecules. Numerous aptamers targeting viral marker proteins or virions have been developed and widely employed in aptamer-based biosensors (aptasensor) for virus detection. This review introduces SELEX schemes for screening aptamers and discusses distinctive SELEX strategies designed explicitly for viral targets. Furthermore, recent advances in aptamer-based biosensing methods for detecting common viruses using different virus-specific aptamers are summarized. Finally, limitations and prospects associated with developing of aptamer-based biosensors are discussed.

Based on mutated aptamer-smartphone colorimetric detection of metronidazole in milk

Excessive residue of metronidazole (MNZ) in food is harmful to the human body. There is an urgent demand to develop a portable tool for MNZ detection on-site. In this study, fifteen aptamers were prepared through targeted base mutation. Apt1-3 with the highest enrichment was chosen for further study. Its affinity was characterized by molecular docking simulation, AuNPs colorimetric assay, graphene oxide (GO) fluorescence assay, and exonuclease assay. Kd was determined by GO fluorescence assay (Kd: 92.60 ± 25.59 nM). Its specificity was also characterized by an exonuclease assay. A novel aptasensor was constructed by using the newly identified aptamer combined with the smartphone dark box. The principle of color change is caused by the aggregation state of AuNPs. Smartphones act as reading instruments. The detection can be completed in just a few seconds without the aid of instruments, achieving a detection limit of 0.15 nmol/mL and a range of 6.7-44.4 nmol/mL (R 2 = 0.9810). Therefore, the constructed smartphone colorimetric sensor based on mutant aptamers has important applications in food detection.

Aptamer Screening: Current Methods and Future Trend towards Non-SELEX Approach

Aptamers are nucleic acid sequences that specifically bind with target molecules and are vital to applications such as biosensing, drug development, disease diagnostics, etc. The traditional selection procedure of aptamers is based on the Systematic Evolution of Ligands by an Exponential Enrichment (SELEX) process, which relies on repeating cycles of screening and amplification. With the rapid development of aptamer applications, RNA and XNA aptamers draw more attention than before. But their selection is troublesome due to the necessary reverse transcription and transcription process (RNA) or low efficiency and accuracy of enzymes for amplification (XNA). In light of this, we review the recent advances in aptamer selection methods and give an outlook on future development in a non-SELEX approach, which simplifies the procedure and reduces the experimental costs. We first provide an overview of the traditional SELEX methods mostly designed for screening DNA aptamers to introduce the common tools and methods. Then a section on the current screening methods for RNA and XNA is prepared to demonstrate the efforts put into screening these aptamers and the current difficulties. We further predict that the future trend of aptamer selection lies in non-SELEX methods that do not require nucleic acid amplification. We divide non-SELEX methods into an immobilized format and non-immobilized format and discuss how high-resolution partitioning methods could facilitate the further improvement of selection efficiency and accuracy.

Identification of the Binding Site between Aptamer sgc8c and PTK7

Aptamers are single-stranded RNA or DNA molecules that can specifically bind to targets and have found broad applications in cancer early-stage detection, accurate drug delivery, and precise treatment. Although various aptamer screening methods have been developed over the past several decades, the accurate binding site between the target and the aptamer cannot be characterized during a typical aptamer screening process. In this research, we chose a widely used aptamer screened by our group, sgc8c, and its target protein tyrosine kinase 7 (PTK7) as the model aptamer and target and tried to determine the binding site between aptamer sgc8c and PTK7. Through sequential protein truncation, we confirmed that the exact binding site of sgc8c was within the region of Ig 3 to Ig 4 in the extracellular domain of PTK7. Using in vitro expressed Ig (3-4), we successfully acquired the crystal of an sgc8c-Ig (3-4) binding complex. The possible sgc8c-binding amino acid residues on PTK7 and PTK7-binding nucleotide residues on sgc8c were further identified and simulated by mass spectrometry and molecular dynamics simulation and finally verified by aptamer/protein truncation and mutation.

Flexible electronics for heavy metal ion detection in water: a comprehensive review

Flexible electronics offer a versatile, rapid, cost-effective and portable solution to monitor water contamination, which poses serious threat to the environment and human health. This review paper presents a comprehensive exploration of the versatile platforms of flexible electronics in the context of heavy metal ion detection in water systems. The review overviews of the fundamental principles of heavy metal ion detection, surveys the state-of-the-art materials and fabrication techniques for flexible sensors, analyses key performance metrics and limitations, and discusses future opportunities and challenges. By highlighting recent advances in nanomaterials, polymers, wireless integration, and sustainability, this review aims to serve as an essential resource for researchers, engineers, and policy makers seeking to address the critical challenge of heavy metal contamination in water resources. The versatile promise of flexible electronics is thoroughly elucidated to inspire continued innovation in this emerging technology arena.

Aptamer and Electrochemical Aptasensor towards Selenate Ions (SeO42-)

Selenium is an essential inorganic compound in human and animal nutrition, involved in the proper functioning of the body. As a micronutrient, it actively contributes to the regulation of various metabolic activities, i.e., thyroid hormone, and protection against oxidative stress. However, Se exhibits a narrow concentration window between having a positive effect and exerting a toxic effect. In higher doses, it negatively affects living organisms and causes DNA damage through the formation of free radicals. Increased reactivity of Se anions can also disrupt the integrity and function of DNA-repairing proteins. As the permissible concentration of Se in drinking water is 10 µg/L, it is vital to develop sensitive and robust methods of Se detection in aqueous samples. In this study, for the first time, we proposed a selective aptamer for selenate ion detection, chosen following the SELEX process, and its application in the construction of an electrochemical aptasensor towards SeO42- ions. Measurement conditions such as the used redox marker and pH value of the measurement solution were chosen. The proposed aptasensor is characterized by good selectivity and an LOD of 1 nM. Conditions for biosensor regeneration and storage were also investigated in this research.

Electrochemical detection of manganese ions using aptamer-based layers

Heavy metals are one of the major pollutants found in drinking water and their abnormal level may pose a threat to human's health and life. Manganese also belongs to heavy metals group, and it is generally used in production of batteries, fertilizers, and ceramics. Even though, Mn is necessary for proper development of central nervous system, its elevated concentration might lead to certain diseases such as epilepsies, cell death in focal cerebral ischemia as well as neurodegenerative diseases such as Huntington and Alzheimer. Hence, it is crucial to elaborate novel methods for manganese ions detection that could be applied for in situ analysis of water samples. Herein, we present the studies on the electrochemical detection of manganese ions using aptamer-modified electrodes. This is the first attempt of application of aptamer strands as receptor layers for electrochemical analysis of manganese ions and for that purpose gold disk electrodes served as transducers, which were further modified with disulfide - based aptamers and 6-mercapto-1-hexanol blocking agent. The electrochemical measurements concerned the choice of the conditions for formation of aptamer receptor layer as well as the type of redox indicator that served as the source of current signal. The studies referred to the definition of aptasensor working parameters including the verification of the possibility of manganese ion detection in cell culture media. It was shown that it was possible to detect Mn2+ ions within 25 nM-1 μM concentration and the proposed aptasensor exhibited high selectivity towards target analyte for which at least 2 - times higher response was recorded than for interfering ions. Moreover, the possibility of Mn2+ detection in real samples was depicted followed by stability and regeneration studies.

Mercury (II) sensing using a simple turn-on fluorescent graphene oxide based aptasensor in serum and water samples

A simple, highly sensitive, and selective fluorometric aptasensing platform based on aptamer and graphene oxide (GO) is proposed for the determination of mercury (II) ion (Hg2+). In the designed assay, two aptamer probes, a carboxy-fluorescein (FAM) labeled aptamer (aptamer A) and its complementary (aptamer B) with partial complement containing several mismatches and GO as the quencher were used. In the absence of Hg2+, both A and B aptamers were adsorbed on the surface of GO by π-π-stacking, leading to fluorescence quenching of FAM due to fluorescence resonance energy transfer (FRET). Upon exposure to Hg2+, the A and B aptamer strands bind Hg2+ and form T-Hg2+-T complexes, leading to the formation of a stable double-stranded aptamer. The double-stranded aptamer is detached from the GO surface, resulting in the recovery of FAM fluorescence. The fluorescence intensity (FI) of the developed sensor was correlated with the Hg2+ concentration under optimized experimental conditions in two wide linear ranges, even in the presence of 10 divalent cations as interferences. The linear ranges were obtained from 200.0 to 900.0 fM and 5.0 to 33.0 pM, a limit of detection (LOD) of 106.0 fM, and a limit of quantification (LOQ) of 321.3 fM. The concentration of Hg2+ was determined in five real samples containing three water and two serum samples, using spiking and standard addition methods and the results were compared with the spiked amounts and atomic absorption (AAS) as standard method respectively, with acceptable recoveries. Furthermore, in the standard addition method, to overcome the effects of matrix influence of real samples in quantitative predictions, the excitation-emission matrix (EEM) data for samples was simultaneously analyzed by multivariate curve resolution with alternating least squares (MCR-ALS) as a second-order standard addition method (SOSAM).

An electrochemical aptasensor based on silver-thiolated graphene for highly sensitive detection of Pb2

The presence of lead ions (Pb2+) in the environment not only leads to environmental contamination but also poses a significant risk to public health through their migration into food and drinking water. Therefore, the development of rapid and effective techniques for detection of trace amounts of Pb2+ is crucial for safeguarding both the environment and biosafety. In this study, an aptamer-based electrochemical sensor was developed for specific detection of Pb2+ by modifying a polylysine (PLL) coated silver-thiolated graphene (Ag-SH-G) nanocomposite (PLL/Ag-SH-G) on the surface of a glassy carbon electrode, which was further modified with gold nanoparticles (AuNPs) for attachment of aptamers (Apt) that specifically recognized Pb2+. The Ag-SH-G particles were synthesized using a one-step in situ method, resulting in significantly enhanced electrochemical properties upon incorporating Ag nanoparticles into the PLL/Ag-SH-G composite. Coating of the covalently or no-covalently bonded Ag-SH-G particles with PLL provides an excellent supporting matrix, facilitating the assembly of AuNPs and a thiol-modified aptamer for Pb2+. Under optimized conditions, Apt/AuNPs/PLL/Ag-SH-G/GCE exhibited excellent sensing performance for Pb2+ with a wide linear response range (10-1000 nM), a low detection limit (0.047 nM) and extraordinary selectivity. The sensor was employed and satisfactory results were obtained in river water, soil and vegetable samples for the detection of Pb2+.

Two AIE-Ligand-Based 2-D Luminescent Metal-Organic Frameworks as Fe3+ Sensors

The design and synthesis of high-performance sensors are very important but remain great challenges. In this work, a new aggregation-induced-emission (AIE) molecule 4,4'-(((9H-fluoren-9-ylidene)methylene)bis(4,1-phenylene))dipyridine (L) was successfully synthesized and first developed as a functional ligand to construct two isomorphic metal-organic frameworks (MOFs) [M(L)(OBBA)]n [M2+ = Cd2+ (1), Co2+ (2); H2OBBA = 4,4'-oxybisbenzoic acid]. They adopt [M2(COO)4] flywheel clusters, OBBA2- bridges, and terminal L ligands as building units to form isomorphic 2-D networks with Lewis base active cites (uncoordinated pyridyl N). Both 1 and 2 exhibit excellent water, pH, and thermal stabilities and extremely efficient Fe3+ sensing abilities in the water environment. The quenching constants and detection limits reach the best levels reported so far. The sensing mechanism of 1 and 2 toward Fe3+ is studied in depth, and the difference in their sensing performance is also explained.

Sensitive electrochemical sensor for Cd2+ with engineered short high-affinity aptamer undergoing large conformation change

Cadmium ion (Cd2+) is a highly toxic heavy metal ion that threatens the environment and human health. To achieve rapid and sensitive detection of Cd2+, here we developed a reagent-less aptamer electrochemical sensor by immobilizing an engineered high-affinity DNA aptamer with a redox tag of methylene blue (MB) on the gold electrode. After testing a series of engineered aptamer sequences, we employed an optimal and new 15-mer aptamer with a short 3-bp stem for sensor fabrication, which underwent large conformation change upon Cd2+ binding. This aptamer retained high affinity with a Kd about 360 nM, verified by isothermal titration calorimetry (ITC) analysis. In the presence of Cd2+, this aptamer folded into a stem-loop structure, drawing the MB into a close proximity to the electrode surface and generating enhanced current in square wave voltammetry (SWV). Under the optimized conditions, this aptamer sensor enabled us to sensitively detect Cd2+ in a wide concentration range from 0.5 nM to 4 μM, and the detection limit was 90 pM. The developed electrochemical aptasensor has the advantages in easy preparation, rapid response, high stability, high selectivity and easy regeneration and reuse, showing the potential for Cd2+ detection in broad applications.

Xanthan gum-capped Chromia Nanoparticles (XG-CrNPs): A promising nanoprobe for the detection of heavy metal ions

The present study reports on the selective and sensitive detection of metals using xanthan gum-capped chromia nanoparticles (XG-CrNPs). The nanoparticles were synthesized by the chemical reduction method using sodium borohydride and xanthan gum as the reducing and capping agents, respectively. The synthesis of XG-CrNPs was confirmed by the appearance of the two absorption peaks at 272 nm and 371 nm in the UV-visible region. The nanoparticles have been extensively characterized by FTIR, TEM-EDX, XRD, and TGA analyses. The well-dispersed XG-CrNPs exhibited a quasi-spherical structure with an average particle size of 3 nm. A significantly low amount (2 μg/L) of XG-CrNPs was used for selective and sensitive detection of heavy metal ions. It showed excellent metal detecting properties by quenching its band gap signal which was extraordinarily conspicuous for Co(II), Hg(II), and Cd(II) in comparison to other metal ions like Ag(I), Ba(II), Mg(II), Mn(II), Ni(II), and Zn(II). The limit of detection of Co(II), Cd(II), and Hg(II) with this nanoprobe was found to be 2.167 μM, 1.065 μM, and 0.601 μM respectively. The nanoparticles manifested higher shelf-life and can be reused up to three consecutive cycles where most of its activity was conserved even after being used. Thus, it may find use in metal sensor devices for the detection of hazardous metals.

Detection of Cadmium(II) in Aquatic Products Using a Rolling-Circle Amplification-Coupled Ratio Fluorescent Probe Based on an Aptamer-Peptide Conjugate

The existing aptamers for cadmium (Cd2+), the common toxic heavy metal contaminant in food, cannot meet the requirements for detecting Cd2+ in rapid detection methods. In previous work, we found that coupling aptamer-peptide conjugates (APCs) with peptides and aptamers can provide a less disruptive method with a significantly improved affinity. Moreover, we found that the spatial conformation of aptamers and peptides is crucial for obtaining proper affinity in APC. Therefore, we describe a simple design strategy to obtain a series of APCs with different affinities by designing peptide orientations (N-terminal, C-terminal). The best affinity was found for APC(C1-N) with a binding constant (Ka) of 2.23 × 106 M-1, indicating that the APC(C1-N) affinity was significantly increased by 829.17% over aptamer. Finally, a rolling-circle amplification (RCA)-coupled ratio fluorescence-based biosensor for Cd2+ detection was established with a detection limit of 0.0036 nM, which has great potential for practical aquatic product detection.

Fast detection of bacterial gut pathogens on miniaturized devices: an overview

INTRODUCTION

Gut microbes pose challenges like colon inflammation, deadly diarrhea, antimicrobial resistance dissemination, and chronic disease onset. Development of early, rapid and specific diagnosis tools is essential for improving infection control. Point-of-care testing (POCT) systems offer rapid, sensitive, low-cost and sample-to-answer methods for microbe detection from various clinical and environmental samples, bringing the advantages of portability, automation, and simple operation.

AREAS COVERED

Rapid detection of gut microbes can be done using a wide array of techniques including biosensors, immunological assays, electrochemical impedance spectroscopy, mass spectrometry and molecular biology. Inclusion of Internet of Things, machine learning, and smartphone-based point-of-care applications is an important aspect of POCT. In this review, the authors discuss various fast diagnostic platforms for gut pathogens and their main challenges.

EXPERT OPINION

Developing effective assays for microbe detection can be complex. Assay design must consider factors like target selection, real-time and multiplex detection, sample type, reagent stability and storage, primer/probe design, and optimizing reaction conditions for accuracy and sensitivity. Mitigating these challenges requires interdisciplinary collaboration among scientists, clinicians, engineers, and industry partners. Future efforts are essential to enhance sensitivity, specificity, and versatility of POCT systems for gut microbe detection and quantification, advancing infectious disease diagnostics and management.

Luminescent lanthanide complexes based on 4,5-di(3,5-dicarboxylphenoxy)phthalic acid as enhanced fluorescence probes for highly selective detection of lead(II) ions in water

Six novel lanthanide complexes ([Nd2(L)(H2O)6]n·4.58n(H2O) (1), [Ln(H3L)(H2O)]n·0.5n(H2O), Ln = Sm (2), Eu (3), Gd (4), Tb (5), Eu0.18Gd0.62Tb0.20 (6)) have been hydrothermally synthesized based on the ligand 4,5-di(3,5-dicarboxylphenoxy)phthalic acid (H6L). Single crystal X-ray diffraction reveals that complexes 1-6 are 2D structures, where 2-6 are isomorphic. Complexes 3 and 5 exhibit the characteristic fluorescence of Eu(III) and Tb(III) ions respectively, while complex 4 shows blue-green light emission based on the ligand. In particular, the ternary Eu/Gd/Tb complex 6 shows white light emission with a CIE (Commission International del'Eclairage) chromaticity coordinate of (0.330, 0.339) and hence close to pure white light emission. Moreover, complexes 3 and 5 display specific fluorescence-enhanced detection performance for Pb2+ ions: The interaction between Pb2+ ions and the ligand enhances the charge transfer efficiency between the ligand and the Eu(III) and Tb(III) ions and thus leads to fluorescence enhancement of complexes 3 and 5. More importantly, complex 3 exhibits the lowest detection limit of 4.72 nM for Pb2+ ions among the existing complex fluorescent probes. In addition, both complexes 3 and 5 show good performance for recycling and for the detection of Pb2+ in real water samples.

Heavy Metal-Induced Assembly of DNA Network Biosensor from Double-Loop Hairpin Probes for Ultrasensitive Detection of UO22+ in Water and Soil Samples

The uranyl ion (UO22+) is the most stable form of uranium, which exhibits high toxicity and bioavailability posing a severe risk to human health. The construction of ultrasensitive, reliable, and robust sensing techniques for UO22+ detection in water and soil samples remains a challenge. Herein, a DNA network biosensor was fabricated for UO22+ detection using DNAzyme as the heavy metal recognition element and double-loop hairpin probes as DNA assembly materials. UO22+-activated specific cleavage of the DNAzyme will liberate the triggered DNA fragment, which can be utilized to launch a double-loop hairpin probe assembly among Hab, Hbc, and Hca. Through multiple cyclic cross-hybridization reactions, hexagonal DNA duplex nanostructures (n[Hab•Hbc•Hca]) were formed. This DNA network sensing system generates a high fluorescence response for UO22+ monitoring. The biosensor is ultrasensitive, with a detection limit of 2 pM. This sensing system also displays an excellent selectivity and robustness, enabling the DNA network biosensor to work even in complex water and soil samples with excellent accuracy and reliability. With the advantages of enzyme-free operation, outstanding specificity, and high sensitivity, our proposed DNA network biosensor provides a reliable, simple, and robust method for trace levels of UO22+ detection in environmental samples.

Toward the Ultimate Limit of Analyte Detection, in Graphene-Based Field-Effect Transistors

The ultimate sensitivity of field-effect-transistor (FET)-based devices for ionic species detection is of great interest, given that such devices are capable of monitoring single-electron-level modulations. It is shown here, from both theoretical and experimental perspectives, that for such ultimate limits to be approached the thermodynamic as well as kinetic characteristics of the (FET surface)-(linker)-(ion-receptor) ensemble must be considered. The sensitivity was probed in terms of optimal packing of the ensemble, through a minimal charge state/capacitance point of view and atomic force microscopy. Through the fine-tuning of the linker and receptor interaction with the sensing surface, a record limit of detection as well as specificity in the femtomolar range, orders of magnitude better than previously obtained and in excellent accord with prediction, was observed.

FAM Tag Size Separation-Based Capture-Systematic Evolution of Ligands by Exponential Enrichment for Sterigmatocystin-Binding Aptamers with High Specificity

Sterigmatocystin (ST) is a known toxin whose aptamer has rarely been reported because ST is a water-insoluble small-molecule target with few active sites, leading to difficulty in obtaining its aptamer using traditional target fixation screening methods. To obtain aptamer for ST, we incorporated FAM tag size separation into the capture-systematic evolution of ligands by exponential enrichment and combined it with molecular activation for aptamer screening. The screening process was monitored using a quantitative polymerase chain reaction fluorescence amplification curve and recovery of negative-, counter-, and positive-selected ssDNA. The affinity and specificity of the aptamer were verified by constructing an aptamer-affinity column, and the binding sites were predicted using molecular docking simulations. The results showed that the Kd value of the H Seq02 aptamer was 25.3 nM. The aptamer-affinity column based on 2.3 nmol of H Seq02 exhibited a capacity of about 80 ng, demonstrating better specificity than commercially available antibody affinity columns. Molecular simulation docking predicted the binding sites for H Seq02 and ST, further explaining the improved specificity. In addition, circular dichroism and isothermal titration calorimetry were used to verify the interaction between the aptamer and target ST. This study lays the foundation for the development of a new ST detection method.

Highly-efficient selection of aptamers for detecting various HPV subtypes in clinical samples

Nucleic acid aptamers are of great potentials in diagnostic and therapeutic applications because of their unique molecular recognition capabilities. However, satisfactory aptamers with high affinity and specificity are still in short supply. Herein, we have developed new selection methods allowing the free interactions between the targets and potential aptamers in solution. In our selection system, the protein targets (biotinylated randomly or site-specifically) were first incubated with the random DNA library, followed by the pull-down with the streptavidin magnetic beads or biolayer-interferometry (BLI) sensors. By comparing the two biotinylation strategies (random or site-specific) and two states of the targets (free or immobilized), we have found that the combination of the site-specific biotinylation and free-target strategies was most successful. Based on these highly-efficient selection strategies, HPV L1 aptamers were obtained. By designing the sandwich aptasensor assisted with RCA and CRISPR/Cas12a, we have diagnosed various HPV subtypes in clinical samples, such as easily-collected urine samples. In summary, our new strategy can allow efficient selection of aptamers with high affinity and specificity for clinical applications.

Current advancements and prospects of enzymatic and non-enzymatic electrochemical glucose sensors

This review discusses the most current developments and future perspectives in enzymatic and non-enzymatic glucose sensors, which have notably evolved over the preceding quadrennial period. Furthermore, a thorough exploration encompassed the sensor's intricate fabrication processes, the diverse range of materials employed, the underlying principles of detection, and an in-depth assessment of the sensors' efficacy in detecting glucose levels within essential bodily fluids such as human blood serums, urine, saliva, and interstitial fluids. It is worth noting that the accurate quantification of glucose concentrations within human blood has been effectively achieved by utilizing classical enzymatic sensors harmoniously integrated with optical and electrochemical transduction mechanisms. Monitoring glucose levels in various mediums has attracted exceptional attention from industrial to academic researchers for diabetes management, food quality control, clinical medicine, and bioprocess inspection. There has been an enormous demand for the creation of novel glucose sensors over the past ten years. Research has primarily concentrated on succeeding biocompatible and enhanced sensing abilities related to the present technologies, offering innovative avenues for more effective glucose sensors. Recent developments in wearable optical and electrochemical sensors with low cost, high stability, point-of-care testing, and online tracking of glucose concentration levels in biological fluids can aid in managing and controlling diabetes globally. New nanomaterials and biomolecules that can be used in electrochemical sensor systems to identify glucose concentration levels are developed thanks to advances in nanoscience and nanotechnology. Both enzymatic and non-enzymatic glucose electrochemical sensors have garnered much interest recently and have made significant strides in detecting glucose levels. In this review, we summarise several categories of non-enzymatic glucose sensor materials, including composites, non-precious transition metals and their metal oxides, hydroxides, precious metals and their alloys, carbon-based materials, conducting polymers, metal-organic framework (MOF)-based electrocatalysts, and wearable device-based glucose sensors deeply.

Label free electrochemical sensors for Pb(II) detection based on hemicellulose extracted from Opuntia Ficus Indica cactus

We aim to develop an electrochemical sensor for a divalent metal ion (lead II), a highly toxic water contaminant. We explore a sensor formed with a hemicellulose polysaccharide extracted from the Opuntia Ficus Indica cactus associated with agarose as a sensitive layer deposited on a gold electrode. This sensor combines the functional groups of hemicellulose that could form a complex with metal ions and agarose with gelling properties to form a stable membrane. The sensor demonstrated a loading ability of Pb2+, with higher affinity compared to other metal ions such as Hg2+, Ni2+, and Cu2+, thanks to the chemical structure of hemicellulose. The detection was measured by square wave voltammetry based on a well-defined redox peak of the metal ions. The sensor shows high sensitivity towards Pb2+ with a detection limit of 1.3 fM. The application in river and sea water using the standard addition method for lead detection was studied.

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.

Screen and Optimization of an Aptamer for Alexandrium tamarense-A Common Toxin-Producing Harmful Alga

Among all the paralytic shellfish toxins (PSTs)-producing algae, Alexandrium tamarense is one of the most widespread harmful species posing a serious threat to marine resources and human health. Therefore, it is extremely important to establish a rapid and accurate monitoring method for A. tamarense that can provide early warnings of harmful algal blooms (HABs) caused by this alga and limit the contamination due to PSTs. In this study, an ssDNA library was first obtained by whole cell systematic evolution of ligands by exponential enrichment after 18 consecutive rounds of iterative screening. After sequencing in combination with subsequent multiple alignment of sequences and secondary structure simulation, the library could be classified into 2 families, namely, Family1 and Family2, according to sequence similarity. Flow cytometry was used to test the affinity and cross-reactivity of Ata19, Ata6, Ata25 and Ata29 belonging to Family2. Ata19 was selected to be modified by truncation, through which a new resultant aptamer named as Ata19-1-1 was obtained. Ata19-1-1 with a KD of 75.16 ± 11.10 nM displayed a much higher affinity than Ata19. The specificity test showed that Ata19-1-1 has the same discrimination ability as Ata19 and can at least distinguish the target microalga from other microalgae. The observation under a fluorescence microscopy showed that the A. tamarense cells labeled with Ata19-1-1 are exhibiting bright green fluorescence and could be easily identified, factually confirming the binding of the aptamer with target cells. In summary, the aptamer Ata19-1-1 produced in this study may serve as an ideal molecular recognition element for A. tamarense, which has the potential to be developed into a novel detection method for this harmful alga in the future.

Aptasensors: employing molecular probes for precise medical diagnostics and drug monitoring

Accurate detection and monitoring of therapeutic drug levels are vital for effective patient care and treatment management. Aptamers, composed of single-stranded DNA or RNA molecules, are integral components of biosensors designed for both qualitative and quantitative detection of biological samples. Aptasensors play crucial roles in target identification, validation, detection of drug-target interactions and screening potential of drug candidates. This review focuses on the pivotal role of aptasensors in early disease detection, particularly in identifying biomarkers associated with various diseases such as cancer, infectious diseases and cardiovascular disorders. Aptasensors have demonstrated exceptional potential in enhancing disease diagnostics and monitoring therapeutic drug levels. Aptamer-based biosensors represent a transformative technology in the field of healthcare, enabling precise diagnostics, drug monitoring and disease detection.

Nanomaterials-based aptasensors: An efficient detection tool for heavy-metal and metalloid ions in environmental and biological samples

In light of potential risks of heavy metal exposure, diverse aptasensors have been developed through the combination of aptamers with nanomaterials for the timely and efficient detection of metals in environmental and biological matrices. Aptamer-based sensors can benefit from multiple merits such as heightened sensitivity, facile production, uncomplicated operation, exceptional specificity, enhanced stability, low immunogenicity, and cost-effectiveness. This review highlights the detection capabilities of nanomaterial-based aptasensors for heavy-metal and metalloid ions based on their performance in terms of the basic quality assurance parameters (e.g., limit of detection, linear dynamic range, and response time). Out of covered studies, dendrimer/CdTe@CdS QDs-based ECL aptasensor was found as the most sensitive option with an LOD of 2.0 aM (atto-molar: 10-18 M) detection for Hg2+. The existing challenges in the nanomaterial-based aptasensors and their scientific solutions are also discussed.

Nucleic Acid Aptamer-Based Biosensors: A Review

Aptamers, short strands of either DNA, RNA, or peptides, known for their exceptional specificity and high binding affinity to target molecules, are providing significant advancements in the field of health. When seamlessly integrated into biosensor platforms, aptamers give rise to aptasensors, unlocking a new dimension in point-of-care diagnostics with rapid response times and remarkable versatility. As such, this review aims to present an overview of the distinct advantages conferred by aptamers over traditional antibodies as the molecular recognition element in biosensors. Additionally, it delves into the realm of specific aptamers made for the detection of biomarkers associated with infectious diseases, cancer, cardiovascular diseases, and metabolomic and neurological disorders. The review further elucidates the varying binding assays and transducer techniques that support the development of aptasensors. Ultimately, this review discusses the current state of point-of-care diagnostics facilitated by aptasensors and underscores the immense potential of these technologies in advancing the landscape of healthcare delivery.

Mechanisms of ssDNA aptamer binding to Cd2+ in aqueous solution: A molecular dynamics study

ssDNA aptamers have been increasingly used to detect heavy metal ions as recognition elements due to their high affinity and specificity. However, the specific recognition and binding mechanisms between aptamers and most heavy metals were still unclear, which limits the development of aptamer-based detection methods. In this work, the interaction mechanisms of CD-2-1 aptamers with Cd2+ in aqueous solutions were investigated using molecular dynamic simulations. The most stable complex was found where Cd2+ binding at aptamer's stem-loop junction and preferred at the phosphate backbone or bases. Noteworthily, two binding modes of Cd2+ combining aptamer in aqueous solution were discovered: direct and indirect. In the former mode, Cd2+ directly coordinated O atoms of bases. For the latter, Cd2+ connected to bases with coordinated water molecules as bridges. Electrostatic interaction was found to be the main driving force, and differences of residues role between two binding modes were elucidated. Buffer molecules in aqueous solutions can stabilize aptamer-Cd2+ complex by hydrogen bonds. This study revealed the specific interaction mechanisms of aptamer with Cd2+ at an atomic level, which provided theoretical references for aptamer-based Cd2+ detection methods establishment as well as an efficient technical route of screening potential aptamers for heavy metal ions.

Supramolecular Nucleic Acid-Based Organosilica Nanoparticles Responsive to Physical and Biological Inputs

Organosilica nanoparticles that contain responsive organic building blocks as constitutive components of the silica network offer promising opportunities for the development of innovative drug formulations, biomolecule delivery, and diagnostic tools. However, the synthetic challenges required to introduce dynamic and multifunctional building blocks have hindered the realization of biomimicking nanoparticles. In this study, capitalizing on our previous research on responsive nucleic acid-based organosilica nanoparticles, we combine the supramolecular programmability of nucleic acid (NA) interactions with sol-gel chemistry. This approach allows us to create dynamic supramolecular bridging units of nucleic acids in a silica-based scaffold. Two peptide nucleic acid-based monoalkoxysilane derivatives, which self-assemble into a supramolecular bis-alkoxysilane through direct base pairing, were chosen as the noncovalent units inserted into the silica network. In addition, a bridging functional NA aptamer leads to the specific recognition of ATP molecules. In a one-step bottom-up approach, the resulting supramolecular building blocks can be used to prepare responsive organosilica nanoparticles. The supramolecular Watson-Crick-Franklin interactions of the organosilica nanoparticles result in a programmable response to external physical (i.e., temperature) and biological (i.e., DNA and ATP) inputs and thus pave the way for the rational design of multifunctional silica materials with application from drug delivery to theranostics.

Development of a Novel H-Shaped Electrochemical Aptasensor for Detection of Hg2+ Based on Graphene Aerogels-Au Nanoparticles Composite

Hg2+, a highly toxic heavy metal, poses significant environmental and health risks, necessitating rapid detection methods. In this study, we employed an electrochemical aptasensor for rapid and sensitive detection of Hg2+ based on DNA strands (H2 and H3) immobilized graphene aerogels-Au nanoparticles (GAs-AuNPs) hybrid recognition interface and exonuclease III (Exo III)-mediated cyclic amplification. Firstly, Gas-AuNPs were modified on the surface of the ITO electrode to form a sensing interface to increase DNA loading and accelerate electron transfer. Then, DNA helper was generated with the addition of Hg2+ via Exo III-mediated cycling. Finally, the hairpin structures of H2 and H3 were opened with the DNA helper, and then the methylene blue (MB) functionalized DNA (A1 and A2) combined with the H2 and H3 to form an H-shaped structure. The current response of MB as an electrochemical probe was proportional to the concentration of Hg2+. Under optimal conditions, the aptasensor showed excellent performance for Hg2+, achieving a linear range from 1 fM to 10 nM and a detection limit of 0.16 fM. Furthermore, the aptasensor was used to detect Hg2+ in spiked milk samples, achieving a high recovery rate and demonstrating promising application prospects.

A smart TESTER for reliable discrimination of cancer-derived small extracellular vesicles

Cancer-derived small extracellular vesicles (csEVs) are crucial liquid biopsy indicators that reflect the presence and progression of many malignancies. However, reliable discrimination of csEVs remains a great challenge owing to the interference from normal sEVs (nsEVs) and low abundance in the early stages of cancer. In this work, we developed a Two-Elements Selectively Triggered csEVs Recognization (TESTER) strategy for selective identification of csEVs from the complex clinical body fluid samples. This method was based on the MNAzyme-controlled synchronous recognition to EpCAM and CD63 proteins on the membrane of csEVs. Efficient recognition to csEVs via EpCAM aptamer and CD63 aptamer prompted the release of Partzyme A and Partzyme B probes to induce a MNAzyme structure formation, resulting in the cyclic cleavage of substrate chain to produce cascade fluorescence signal amplification. The detection threshold of the developed TESTER approach for csEVs in complicated biological samples was 72 particles μL-1, accomplishing the highly sensitive and selective quantification of csEVs. At the same time, we successfully constructed a new platform for bimolecular simultaneous recognition, which provides a good idea for the construction of bimolecular-activated detection switch in the future.

Paper-Based Aptasensors: Working Principles, Detection Modes, and Applications

Aptamers are short oligonucleotides designed to possess high binding affinity towards specific target compounds (ions, molecules, or cells). Due to their function and unique advantages, aptamers are considered viable alternatives to antibodies as biorecognition elements in bioassays and biosensors. On the other hand, paper-based devices (PADs) have emerged as a promising and powerful technology for the fabrication of low-cost analytical tools, mainly intended for on-site and point-of-care applications. The present work aims to provide a comprehensive overview of paper-based aptasensors. The review describes the fabrication methods and working principles of paper-based devices, the properties of aptamers as bioreceptors, the different modes of detection used in conjunction with aptasensing PADs, and representative applications for the detection of ions, small molecules, proteins, and cells. The future challenges and prospects of these devices are also discussed.