Preparation of DNA aptamer and development of lateral flow aptasensor combining recombinase polymerase amplification for detection of erythromycin

Portable smartphone-assisted amperometric immunosensor based on CoCe-layered double hydroxide for rapidly immunosensing erythromycin

Herein, we have manufactured a newly designed bifunctional impedimetric and amperometric immunosensor for rapidly detecting erythromycin (ERY) in complicated environments and food stuffs. For this, bimetallic cobalt/cerium-layered double hydroxide nanosheets (CoCe-LDH NSs), which was derived from Co-based zeolite imidazole framework via the structure conversion, was simultaneously utilized as the bioplatform for anchoring the ERY-targeted antibody and for modifying the gold and screen printed electrode. Basic characterizations revealed that CoCe-LDH NSs was composed of mixed metal valences, enrich redox, and abundant oxygen vacancies, facilitating the adhesion on the electrode, the antibody adsorption, and the electron transfers. The manufactured impedimetric and amperometric immunosensor based on CoCe-LDH has showed the comparable sensing performance, having a wide linear detection range from 1.0 fg mL-1 to 1.0 ng mL-1 with the ultralow detection limit toward ERY. Also, the portable, visualized, and efficient analysis of ERY was then attained at the smartphone-assisted CoCe-LDH-based SPE.

Lateral flow assay for simultaneous detection of multiple mycotoxins using nanozyme to amplify signals

Co-contamination of multiple mycotoxins produces synergistic toxic effects, leading to more serious hazards. Therefore, the simple, rapid and accurate simultaneous detection of multiple mycotoxins is crucial. Herein, a three-channel aptamer-based lateral flow assay (Apt-LFA) was established for the detection of aflatoxin M1 (AFM1), aflatoxin B1 (AFB1) and ochratoxin A (OTA). The multi-channel Apt-LFA utilized gold‑iridium nanozyme to catalyze the chromogenic substrate, which effectively achieved signal amplification. Moreover, the positions and lengths of the complementary sequences were screened by changes in fluorescence intensity. After grayscale analysis, the semi-quantitative results showed that the detection limits of AFM1, AFB1 and OTA were 0.39 ng/mL, 0.36 ng/mL and 0.82 ng/mL. The recoveries of the multiplexed competitive sensors in complex matrices of real samples were 93.33%-97.01%, 95.72%-102.67%, and 106.88%-109.33%, respectively. In conclusion, the assembly principle of the three-channel Apt-LFA is simple, which can provide a new idea for the simultaneous detection of small molecule targets.

Mobile phone-assisted imprinted nanozyme for bicolor colorimetric visual detection of erythromycin in river water and milk samples

The residues of erythromycin (ERY) may have negative impacts on the ecological environment, health, and food safety. How to detect ERY effectively and visually is a challenging issue. Herein, we synthesized a molecularly imprinted polymer based nanozymes for selective detection of erythromycin (ERY-MIPNs) at neutral pH, and developed a mobile phone-assisted bicolor colorimetric detection system. This system produced a wide range of color changes from blue to pinkish purple as the ERY concentration increased, making it easy to capture the visualization result. Also, the system showed good sensitivity to ERY ranging from 15 to 135 μM, with a detection limit of 1.78 μM. In addition, the system worked well in the detection of ERY in river water and milk, with the recoveries of 95.57% ∼ 103.20%. These data suggests that this strategy is of considerable potential for practical applications and it provides a new idea for visual detection with portable measurement.

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.

A comprehensive review of aptamer screening and application for lateral flow strip: Current status and future perspectives

The detection of biomarkers is of great significance for medical diagnosis, food safety, environmental monitoring, and agriculture. However, bio-detection technology at present often necessitates complex instruments, expensive reagents, specialized expertise, and prolonged procedures, making it challenging to fulfill the demand for rapid, sensitive, user-friendly, and economical testing. In contrast, lateral flow strip (LFS) technology offers simple, fast, and visually accessible detection modality, allowing real-time analysis of clinical specimens, thus finding widespread utility across various domains. Within the realm of LFS, the application of aptamers as molecular recognition probes presents distinct advantages over antibodies, including cost-effectiveness, smaller size, ease of synthesis, and chemical stability. In recent years, aptamer-based LFS has found extensive application in qualitative, semi-quantitative, and quantitative detection across food safety, environmental surveillance, clinical diagnostics, and other domains. This review provided a concise overview of different aptamer screening methodologies, selection strategies, underlying principles, and procedural, elucidating their respective advantages, limitations, and applications. Additionally, we summarized recent strategies and mechanisms for aptamer-based LFS, such as the sandwich and competitive methods. Furthermore, we classified LFSs constructed based on aptamers, considering the rapid advancements in this area, and discussed their applications in biological and chemical detection. Finally, we delved into the current challenges and future directions in the development of aptamer and aptamer-based LFS. Although this review was not thoroughly, it would serve as a valuable reference for understanding the research progress of aptamer-based LFS and aid in the development of new types of aptasensors.

Noncompetitive Determination of Small Analytes by Sandwich-Type Lateral Flow Assay Based on an Aptamer Kissing Complex

Here, we present the proof-of-concept of a lateral flow assay (LFA) that is capable of detecting small-molecule targets in a noncompetitive manner by deploying a sandwich-type format based on the aptamer kissing complex (AKC) strategy. A fluorescently labeled hairpin aptamer served as the signaling agent, while a specific RNA hairpin grafted onto the strip served as the capture element. The hairpin aptamer switched from an unfolded to a folded form in the presence of the target, resulting in kissing interactions between the loops of the reporter and the capture agents. This design triggered a target-dependent fluorescent signal at the test line. The AKC-based LFA was developed for the detection of adenosine, achieving a detection limit in the micromolar range. The assay revealed the presence of the same analyte in urine. The method also proved effective with another small molecule (theophylline). We believe that the AKC-based LFA approach could overcome many of the shortcomings associated with conventional signal-off methods and competitive processes.

A review on magnetic beads-based SELEX technologies: Applications from small to large target molecules

This review summarizes the stepwise strategy and key points for magnetic beads (MBs)-based aptamer selection which is suitable for isolating aptamers against small and large molecules via systematic evolution of ligands by exponential enrichment (SELEX). Particularities, if any, are discussed according to the target size. Examples targeting small molecules (<1000 Da) such as xenobiotics, toxins, pesticides, herbicides, illegal additives, hormones, and large targets such as proteins (biomarkers, pathogens) are discussed and presented in tabular formats. Of special interest are the latest advances in more efficient alternatives, which are based on novel instrumentation, materials or microelectronics, such as fluorescence MBs-SELEX or microfluidic chip system-assisted MBs-SELEX. Limitations and perspectives of MBs-SELEX are also reviewed. Taken together, this review aims to provide practical insights into MBs-SELEX technologies and their ability to screen multiple potential aptamers against targets from small to large molecules.

Recent progress of SELEX methods for screening nucleic acid aptamers

Nucleic acid aptamers are oligonucleotide sequences screened by an in vitro methodology called Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Known as "chemical antibodies", aptamers can achieve specific recognition towards the targets through conformational changes with high affinity, and possess multiple attractive features including, but not limited to, easy and inexpensive to prepare by chemical synthesis, relatively stable and low batch-to-batch variability, easy modification and signal amplification, and low immunogenicity. Now, aptamers are attracting researchers' attentions from more than 25 disciplines, and have showed great potential for application and economic benefits in disease diagnosis, environmental detection, food security, drug delivery and discovery. Although some aptamers exist naturally as the ligand-binding elements of riboswitches, SELEX is a recognized method for aptamers screening. After thirty-two years of development, a series of SELEX methods have been investigated and developed, as well as have shown unique advantages to improve sequence performances or to explore screening mechanisms. This review would mainly focus on the novel or improved SELEX methods that are available in the past five years. Firstly, we present a clear overview of the aptamer's history, features, and SELEX development. Then, we highlight the specific examples to emphasize the recent progress of SELEX methods in terms of carrier materials, technical improvements, real sample-improved screening, post-SELEX and other methods, as well as their respects of screening strategies, implementation features, screening parameters. Finally, we discuss the remaining challenges that have the potential to hinder the success of SELEX and aptamers in practical applications, and provide the suggestions and future directions for developing more convenient, efficient, and stable SELEX methods in the future.

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.

Employing the Anchor DSPE-PEG as a Redox Probe for Ratiometric Electrochemical Detection of Surface Proteins on Extracellular Vesicles with Aptamers

Quantitative analysis of surface proteins on extracellular vesicles (EVs) has been considered to be a crucial approach for reflecting the status of diseases. Due to the diverse composition of surface proteins on EVs and the interference from nonvesicular proteins, accurately detecting the expression of surface proteins on EVs remains a challenging task. While membrane affinity molecules have been widely employed as EVs capture probes to address this issue, their inherent biochemical properties have not been effectively harnessed. In this paper, we found that the electrochemical redox activity of the DSPE-PEG molecule was diminished upon its insertion into the membrane of EVs. This observation establishes the DSPE-PEG molecule modified on the Au electrode surface as a capture and a redox probe for the electrochemical detection of EVs. By utilizing methylene blue-labeled aptamers, the targeted surface proteins of EVs can be detected by recording the ratio of the oxidation peak current of methylene blue and DSPE-PEG. Without complicated signal amplification, the detection limit for EVs is calculated to be 8.11 × 102 particles/mL. Using this platform, we directly analyzed the expression of CD63 and HER2 proteins on the surface of EVs in human clinical plasma samples, demonstrating its significant potential in distinguishing breast cancer patients from healthy individuals.

Pharmaceutical residues in the ecosystem: Antibiotic resistance, health impacts, and removal techniques

Hospital wastewater has emerged as a major category of environmental pollutants over the past two decades, but its prevalence in freshwater is less well documented than other types of contaminants. Due to compound complexity and improper operations, conventional treatment is unable to remove pharmaceuticals from hospital wastewater. Advanced treatment technologies may eliminate pharmaceuticals, but there are still concerns about cost and energy use. There should be a legal and regulatory framework in place to control the flow of hospital wastewater. Here, we review the latest scientific knowledge regarding effective pharmaceutical cleanup strategies and treatment procedures to achieve that goal. Successful treatment techniques are also highlighted, such as pre-treatment or on-site facilities that control hospital wastewater where it is used in hospitals. Due to the prioritization, the regulatory agencies will be able to assess and monitor the concentration of pharmaceutical residues in groundwater, surface water, and drinking water. Based on the data obtained, the conventional WWTPs remove 10-60% of pharmaceutical residues. However, most PhACs are eliminated during the secondary or advanced therapy stages, and an overall elimination rate higher than 90% can be achieved. This review also highlights and compares the suitability of currently used treatment technologies and identifies the merits and demerits of each technology to upgrade the system to tackle future challenges. For this reason, pharmaceutical compound rankings in regulatory agencies should be the subject of prospective studies.

Recent Uses of Paper Microfluidics in Isothermal Nucleic Acid Amplification Tests

Isothermal nucleic acid amplification tests have recently gained popularity over polymerase chain reaction (PCR), as they only require a constant temperature and significantly simplify nucleic acid amplification. Recently, numerous attempts have been made to incorporate paper microfluidics into these isothermal amplification tests. Paper microfluidics (including lateral flow strips) have been used to extract nucleic acids, amplify the target gene, and detect amplified products, all toward automating the process. We investigated the literature from 2020 to the present, i.e., since the onset of the COVID-19 pandemic, during which a significant surge in isothermal amplification tests has been observed. Paper microfluidic detection has been used extensively for recombinase polymerase amplification (RPA) and its related methods, along with loop-mediated isothermal amplification (LAMP) and rolling circle amplification (RCA). Detection was conducted primarily with colorimetric and fluorometric methods, although a few publications demonstrated flow distance- and surface-enhanced Raman spectroscopic (SERS)-based detection. A good number of publications could be found that demonstrated both amplification and detection on paper microfluidic platforms. A small number of publications could be found that showed extraction or all three procedures (i.e., fully integrated systems) on paper microfluidic platforms, necessitating the need for future work.

Updates on developing and applying biosensors for the detection of microorganisms, antimicrobial resistance genes and antibiotics: a scoping review

Background

The inappropriate use of antibiotics in clinical and non-clinical settings contributes to the increasing prevalence of multidrug-resistant microorganisms. Contemporary endeavours are focused on exploring novel technological methodologies, striving to create cost-effective and valuable alternatives for detecting microorganisms, antimicrobial resistance genes (ARGs), and/or antibiotics across diverse matrices. Within this context, there exists an increasingly pressing demand to consolidate insights into potential biosensors and their implications for public health in the battle against antimicrobial resistance (AMR).

Methods

A scoping review was carried out to map the research conducted on biosensors for the detection of microorganisms, ARGs and/or antibiotics in clinical and environmental samples. The Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) checklist was used. Articles published from 1999 to November 2022 and indexed in the following databases were included: MEDLINE, EMBASE, Web of Science, BIOSIS Citation index, Derwent Innovations index, and KCI-Korean Journal.

Results

The 48 studies included in the scoping review described the development and/or validation of biosensors for the detection of microorganisms, ARGs and/or antibiotics. At its current stage, the detection of microorganisms and/or ARGs has focused primarily on the development and validation of biosensors in clinical and bacterial samples. By contrast, the detection of antibiotics has focused primarily on the development and validation of biosensors in environmental samples. Asides from target and samples, the intrinsic characteristics of biosensors described in the scoping review were heterogenous. Nonetheless, the number of studies assessing the efficacy and validation of the aforementioned biosensor remained limited, and there was also a lack of comparative analyses against conventional molecular techniques.

Conclusion

Promoting high-quality research is essential to facilitate the integration of biosensors as innovative technologies within the realm of public health challenges, such as antimicrobial resistance AMR. Adopting a One-Health approach, it becomes imperative to delve deeper into these promising and feasible technologies, exploring their potential across diverse sample sets and matrices.

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

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

3D Printed Materials for Combating Antimicrobial Resistance

Three-dimensional (3D) printing is a rapidly growing technology with a significant capacity for translational applications in both biology and medicine. 3D-printed living and non-living materials are being widely tested as a potential replacement for conventional solutions for testing and combating antimicrobial resistance (AMR). The precise control of cells and their microenvironment, while simulating the complexity and dynamics of an in vivo environment, provides an excellent opportunity to advance the modeling and treatment of challenging infections and other health conditions. 3D-printing models the complicated niches of microbes and host-pathogen interactions, and most importantly, how microbes develop resistance to antibiotics. In addition, 3D-printed materials can be applied to testing and delivering antibiotics. Here, we provide an overview of 3D printed materials and biosystems and their biomedical applications, focusing on ever increasing AMR. Recent applications of 3D printing to alleviate the impact of AMR, including developed bioprinted systems, targeted bacterial infections, and tested antibiotics are presented.

Selection of allosteric dnazymes that can sense phenylalanine by expression-SELEX

Aptamers are ligand-binding RNA or DNA molecules and have been widely examined as biosensors, diagnostic tools, and therapeutic agents. The application of aptamers as biosensors commonly requires an expression platform to produce a signal to report the aptamer-ligand binding event. Traditionally, aptamer selection and expression platform integration are two independent steps and the aptamer selection requires the immobilization of either the aptamer or the ligand. These drawbacks can be easily overcome through the selection of allosteric DNAzymes (aptazymes). Herein, we used the technique of Expression-SELEX developed in our laboratory to select for aptazymes that can be specifically activated by low concentrations of l-phenylalanine. We chose a previous DNA-cleaving DNAzyme known as II-R1 as the expression platform for its low cleavage rate and used stringent selection conditions to drive the selection of high-performance aptazyme candidates. Three aptazymes were chosen for detailed characterization and these DNAzymes were found to exhibit a dissociation constant for l-phenylalanine as low as 4.8 μM, a catalytic rate constant improvement as high as 20 000-fold in the presence of l-phenylalanine, and the ability to discriminate against closely related l-phenylalanine analogs including d-phenylalanine. This work has established the Expression-SELEX as an effective SELEX method to enrich high-quality ligand-responsive aptazymes.

Ready-to-use interactive dual-readout differential lateral flow biosensor for two genotypes of human papillomavirus

Ready-to-use in vitro diagnosis of multiple genotypes is vital for the prevention and treatment of cervical cancer. Herein, a paper-film-based interactive dual readout differential lateral flow biosensor is proposed to simultaneously assay two high-risk types of human papillomavirus (HPV) within the body-fluid. The CuCo₂S₄/ZnIn₂S₄ heterostructure is fabricated on the paper-film compound chip with high thermostability, and surface sulfur vacancy is introduced by mild annealing treatment to endow unexceptionable photoexcitation activity, such structure can be served as an initial energy harvester and converter. With the assistance of differential channels, the dual-target-propelled self-assembly of annular DNA and the cleavage activity of CRISPR-Cas12a are stepwise activated by sequential solution transfer. Accordingly, the input and release of polydopamine-coated gold nanoparticles with photothermal/photoelectric characteristic were implemented. The fabricated biosensor not only realized intelligent thermal-response without large instruments, but also actuated dynamic interfacial charge separation and transfer kinetics to further transmit photoelectric-signal, resulting in desirable interactive dual-signal with low limit-of-detection (0.21 pM for HPV-18 and 42.92 pM for HPV-16). Thanks to the sophisticated design of differential lateral flow paper-film compound chip and interactive dual-signal amplification strategy, sensitive detection of two HPV genotypes is realized, which provides a promising candidate for home medical intelligent diagnosis.

Semi-automated and efficient parallel SELEX of aptamers for multiple targets

In this study, we constructed and optimized a semi-automatic instrument to perform aptamer SELEX targeting multiple proteins simultaneously. Our work provides a simple SELEX platform characterized by real-time feedback, which is time efficient and can reduce human intervention. A number of aptamers were rapidly screened by this method. Moreover, the binding affinities of these aptamers were verified by various methods, including SPR and flow cytometry, which supports the applicability and reliability of our newly established aptamer SELEX system.

A Rapid Antimicrobial Resistance Diagnostic Platform for Staphylococcus aureus Using Recombinase Polymerase Amplification

Antimicrobial resistance (AMR) has posed a global threat to public health. The Staphylococcus aureus strains have especially developed AMR to practically all antimicrobial medications. There is an unmet need for rapid and accurate detection of the S. aureus AMR. In this study, we developed two versions of recombinase polymerase amplification (RPA), the fluorescent signal monitoring and lateral flow dipstick, for detecting the clinically relevant AMR genes retained by S. aureus isolates and simultaneously identifying such isolates at the species level. The sensitivity and specificity were validated with clinical samples. Our results showed that this RPA tool was able to detect antibiotic resistance for all the 54 collected S. aureus isolates with high sensitivity, specificity, and accuracy (all higher than 92%). Moreover, results of the RPA tool are 100% consistent with that of PCR. In sum, we successfully developed a rapid and accurate AMR diagnostic platform for S. aureus. The RPA might be used as an effective diagnostic test in clinical microbiology laboratories to improve the design and application of antibiotic therapy. IMPORTANCE Staphylococcus aureus is a species of Staphylococcus and belongs to Gram-positive. Meanwhile, S. aureus remains one of the most common nosocomial and community-acquired infections, causing blood flow, skin, soft tissue, and lower respiratory tract infections. The identification of the particular nuc gene and the other eight genes of drug-resistant S. aureus can reliably and quickly diagnose the illness, allowing doctors to prescribe treatment regimens sooner. The detection target in this work is a particular gene of S. aureus, and a POCT is built to simultaneously recognize S. aureus and analyze genes representing four common antibiotic families. We developed and assessed a rapid and on-site diagnostic platform for the specific and sensitive detection of S. aureus. This method allows the determination of S. aureus infection and 10 different AMR genes representing four different families of antibiotics within 40 min. It was easily adaptable in low-resource circumstances and professional-lacking circumstances. It should be supported in overcoming the continuous difficulty of drug-resistant S. aureus infections, which is a shortage of diagnostic tools that can swiftly detect infectious bacteria and numerous antibiotic resistance indicators.

Biosensors based on functional nucleic acids and isothermal amplification techniques

In the past few years, with the in-depth research of functional nucleic acids and isothermal amplification techniques, their applications in the field of biosensing have attracted great interest. Since functional nucleic acids have excellent flexibility and convenience in their structural design, they have significant advantages as recognition elements in biosensing. At the same time, isothermal amplification techniques have higher amplification efficiency, so the combination of functional nucleic acids and isothermal amplification techniques can greatly promote the widespread application of biosensors. For the purpose of further improving the performance of biosensors, this review introduces several widely used functional nucleic acids and isothermal amplification techniques, as well as their classification, basic principles, application characteristics, and summarizes their important applications in the field of biosensing. We hope to provide some references for the design and construction of new tactics to enhance the detection sensitivity and detection range of biosensing.

Capture-SELEX: Selection Strategy, Aptamer Identification, and Biosensing Application

Small-molecule contaminants, such as antibiotics, pesticides, and plasticizers, have emerged as one of the substances most detrimental to human health and the environment. Therefore, it is crucial to develop low-cost, user-friendly, and portable biosensors capable of rapidly detecting these contaminants. Antibodies have traditionally been used as biorecognition elements. However, aptamers have recently been applied as biorecognition elements in aptamer-based biosensors, also known as aptasensors. The systematic evolution of ligands by exponential enrichment (SELEX) is an in vitro technique used to generate aptamers that bind their targets with high affinity and specificity. Over the past decade, a modified SELEX method known as Capture-SELEX has been widely used to generate DNA or RNA aptamers that bind small molecules. In this review, we summarize the recent strategies used for Capture-SELEX, describe the methods commonly used for detecting and characterizing small-molecule-aptamer interactions, and discuss the development of aptamer-based biosensors for various applications. We also discuss the challenges of the Capture-SELEX platform and biosensor development and the possibilities for their future application.

Systematic bio-fabrication of aptamers and their applications in engineering biology

Aptamers are single-stranded DNA or RNA molecules that have high affinity and selectivity to bind to specific targets. Compared to antibodies, aptamers are easy to in vitro synthesize with low cost, and exhibit excellent thermal stability and programmability. With these features, aptamers have been widely used in biology and medicine-related fields. In the meantime, a variety of systematic evolution of ligands by exponential enrichment (SELEX) technologies have been developed to screen aptamers for various targets. According to the characteristics of targets, customizing appropriate SELEX technology and post-SELEX optimization helps to obtain ideal aptamers with high affinity and specificity. In this review, we first summarize the latest research on the systematic bio-fabrication of aptamers, including various SELEX technologies, post-SELEX optimization, and aptamer modification technology. These procedures not only help to gain the aptamer sequences but also provide insights into the relationship between structure and function of the aptamers. The latter provides a new perspective for the systems bio-fabrication of aptamers. Furthermore, on this basis, we review the applications of aptamers, particularly in the fields of engineering biology, including industrial biotechnology, medical and health engineering, and environmental and food safety monitoring. And the encountered challenges and prospects are discussed, providing an outlook for the future development of aptamers.

Non-thiolated nucleic acid functionalized gold nanoparticle-based aptamer lateral flow assay for rapid detection of kanamycin

A novel Apt-LFA has been established for kanamycin based on non-thiolated nucleic acid-modified colloidal gold nanoprobe (AuNPs@polyA-DNA). The improvement in nucleic acid hybridization speed and efficiency was verified by modifying AuNPs with polyA-DNA strands instead of thiolated oligonucleotides (SH-DNA) strands. Moreover, the AuNPs@polyA-DNA was explored to apply in an Apt-LFA. The experimental factors including the concentration of the aptamer, the concentration of SA-DNA_T conjugate, the incubation time, and temperature were carefully investigated. In addition, the kanamycin aptamer was modified by extending several bases at its end to modulate the hybridization complementary strand, which was found to significantly improve the performance of Apt-LFA. Under optimal experimental conditions, the Apt-LFA can detect kanamycin in honey with a LOD of 250 ng mL^-1 by the naked eyes. A linear range of 50-1250 ng mL^-1 was obtained with a LOD of 15 ng mL^-1 in honey by a portable reader. The Apt-LFA was successfully applied to the detection of kanamycin in honey with recoveries of 95.1-105.2%.

Dual Gold Nanoparticle/Chemiluminescent Immunoassay for Sensitive Detection of Multiple Analytes

Multiple antibiotics and mycotoxins usually simultaneously exist in foods, which poses a serious threat to human health. How to detect them in one test with high sensitivity and fidelity is challenging. In this study, we develop a dual readout lateral flow immunodetection platform that can quantitatively detect five kinds of antibiotics and five kinds of mycotoxins within one sample. The platform is composed of a chip and a portable readout instrument where gold nanoparticle (AuNP)-based and chemiluminescence immunoassays could be performed to reach a maximum throughput of 220 analytes in one setting. For a rapid screen, qualitative analysis by detecting the color change of the deposited AuNPs on the chip could be realized. For quantitative results, chemiluminescence imaging and analysis can be completed within 15 min. Apart from the high throughput and high efficiency, this platform has a high detection sensitivity. For instance, the limit of detection (LOD) for thiamphenicol (a representative antibiotic) and fumonisins B1 (a representative mycotoxin) is 8 times and 40 times lower than those of the previously reported methods, respectively. Thus, this dual readout immunodetection platform is promising as a universal device for rapid and quantitative detection of multiple analytes with high throughput, high sensitivity, and high fidelity.

Integration of an Expression Platform in the SELEX Cycle to Select DNA Aptamer Binding to a Disease Biomarker

Aptamers can be developed for biosensors, diagnostic tools, and therapeutic reagents. These applications usually require a fusion of aptamers and expression platforms. However, the fusion process is usually time-consuming and laborious. In this study, we integrated the deoxyribozyme (I-R3) as an expression platform in the SELEX cycle (called Expression-SELEX) to select aptazymes that can sense diverse molecules. We used the Maple syrup urine disease (MSUD) biomarker L-allo-isoleucine to test the selection model. After five rounds of screening, the cleavage products were sufficiently enriched to be visualized on polyacrylamide gel electrophoresis (PAGE) gel. Through high-throughput sequencing analysis, several candidates were identified. One such candidate, IR3-I-DNA, binds L-allo-isoleucine with a dissociation constant (K _D) of 0.57 mM. When the ligand was present, the cleavage fraction of IR3-I-DNA increased from 0.3 to 0.5, and its K _obs value improved from 1.38 min^-1 to 1.97 min^-1. Our selection approach can also be applied to produce aptazymes that can bind to variable ligands and be used more directly as biosensors.

Assays to Estimate the Binding Affinity of Aptamers

Aptamers have become coming-of-age molecular recognition elements in both diagnostic and therapeutic applications. Generated by SELEX, the 'quality control' of aptamers, which involves the validation of their binding affinity against their respective targets is pivotal to ascertain their potency prior to use in any downstream assays or applications. Several aptamers have been isolated thus far, however, the usage of inappropriate validation assays renders some of these aptamers dubitable in terms of their binding capabilities. Driven by this need, we provide an up-to-date critical review of the various strategies used to determine the aptamer-target binding affinity with the aim of providing researchers a better comprehension of the different analytical approaches in respect to the molecular properties of aptamers and their intended targets. The techniques reported have been classified as label-based techniques such as fluorescence intensity, fluorescence anisotropy, filter-binding assays, gel shift assays, ELISA; and label-free techniques such as UV-Vis spectroscopy, circular dichroism, isothermal titration calorimetry, native electrospray ionization-mass spectrometry, quartz crystal microbalance, surface plasmon resonance, NECEEM, backscattering interferometry, capillary electrophoresis, HPLC, and nanoparticle aggregation assays. Hybrid strategies combining the characteristics of both categories such as microscale thermophoresis have been also additionally emphasized. The fundamental principles, complexity, benefits, and challenges under each technique are elaborated in detail.

High sensitivity and rapid detection of hepatitis B virus DNA using lateral flow biosensors based on Au@Pt nanorods in the absence of hydrogen peroxide

Au@Pt nanorods with enhanced oxidase-like activity were designed and used as signal probes to construct LFBs for the high sensitivity detection of hepatitis B virus DNA (HBV-DNA).

Current Advances in Paper-Based Biosensor Technologies for Rapid COVID-19 Diagnosis

The global coronavirus disease 2019 (COVID-19) pandemic has had significant economic and social impacts on billions of people worldwide since severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in Wuhan, China, in November 2019. Although polymerase chain reaction (PCR)-based technology serves as a robust test to detect SARS-CoV-2 in patients with COVID-19, there is a high demand for cost-effective, rapid, comfortable, and accurate point-of-care diagnostic tests in medical facilities. This review introduces the SARS-CoV-2 viral structure and diagnostic biomarkers derived from viral components. A comprehensive introduction of a paper-based diagnostic platform, including detection mechanisms for various target biomarkers and a COVID-19 commercial kit is presented. Intrinsic limitations related to the poor performance of currently developed paper-based devices and unresolved issues are discussed. Furthermore, we provide insight into novel paper-based diagnostic platforms integrated with advanced technologies such as nanotechnology, aptamers, surface-enhanced Raman spectroscopy (SERS), and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas. Finally, we discuss the prospects for the development of highly sensitive, accurate, cost-effective, and easy-to-use point-of-care COVID-19 diagnostic methods.

Aptamer-based lateral flow assay on-site biosensors

The lateral flow assay (LFA) is a widely used paper-based on-site biosensor that can detect target analytes and obtain test results in several minutes. Generally, antibodies are utilized as the biorecognition molecules in the LFA. However, antibodies selected using an in vivo process not only may risk killing the animal hosts and causing errors between different batches but also their range is restricted by the refrigerated conditions used to store them. To avoid these limitations, aptamers screened by an in vitro process have been studied as biorecognition molecules in LFAs. Based on the sandwich or competitive format, the aptamer-based LFA can accomplish on-site detection of target analytes. Since aptamers have a distinctive ability to undergo conformational changes, the adsorption-desorption format has also been exploited to detect target analytes in aptamer-based LFAs. This paper reviews developments in aptamer-based LFAs in the last three years for the detection of target analytes. Three formats of aptamer-based LFAs, i.e., sandwich, competitive, and adsorption-desorption, are described in detail. Based on these formats, signal amplification strategies and multiplexed detection are discussed in order to provide an overview of aptamer-based LFAs for on-site detection of target analytes. In addition, the potential commercialization and future perspectives of aptamer-based LFAs for rapid detection of SARS-CoV-2 are given to support the COVID-19 pandemic.