Selection and characterization of aptamers against Salmonella typhimurium using whole-bacterium Systemic Evolution of Ligands by Exponential Enrichment (SELEX)

Novel antibody- and aptamer-based approaches for sensitive detection of mycotoxin fusaric acid in cereal

This study presents the first successful generation of polyclonal antibodies (pAbs) and oligonucleotide aptamers specifically targeting fusaric acid (FA). Utilizing these pAbs and aptamers, three highly sensitive and specific assays were developed for the detection of FA in cereals with limits of detection (LOD) ranging from 5 to 50 ng/g: an antibody-based enzyme-linked immunosorbent assay (ELISA), an aptamer-based enzyme-linked aptamer-sorbent assay (ELASA), and a hybrid enzyme-linked aptamer-antibody sandwich assay (ELAAA). The recovery rates of FA in spiked cereal samples ranged from 87 % to 112 % across all assays. Analysis of 15 cereal feed samples revealed FA contamination levels of 459 to 1743 ng/g (ELISA), 427 to 1960 ng/g (ELASA), and 381 to 1987 ng/g (ELAAA). These results were further validated by HPLC analysis, confirming high consistency within developed assays. Overall, the ELISA, ELASA, and ELAAA are promising tools for the rapid detection of FA, significantly contributing to food safety monitoring.

Target-inhibited MCOF-Apt-AuNPs self-assembly for multicolor colorimetric detection of Salmonella Typhimurium

Pathogens detection is a crucial measure in the prevention of foodborne diseases. This study developed a novel multicolor colorimetric assay to visually detect Salmonella Typhimurium (S. Typhimurium), by utilizing the etching process of gold nanorods (AuNRs) with TMB2+. The strategy involved the construction of nanozyme by assembling magnetic covalent organic framework (MCOF) with aptamer-conjugated AuNPs (Apt-AuNPs), exhibiting remarkable peroxidase-like activity to catalyze the oxidation of TMB/H2O2 and inducing the etching of AuNRs. The presence of S. Typhimurium could inhibit this process, resulting in the generation of vivid colors. The multicolor colorimetric assay could specifically determine S. Typhimurium from 102 to 108 CFU mL-1 in 60 min with visual detection limit of 102 CFU mL-1, and instrumental detection limit of 2.3 CFU mL-1. Moreover, detecting S. Typhimurium in chicken, milk, pork and lettuce samples has shown promise in practical applications.

Engineered exosomes as a prospective therapy for diabetic foot ulcers

Diabetic foot ulcer (DFU), characterized by high recurrence rate, amputations and mortality, poses a significant challenge in diabetes management. The complex pathology involves dysregulated glucose homeostasis leading to systemic and local microenvironmental complications, including peripheral neuropathy, micro- and macro-angiopathy, recurrent infection, persistent inflammation and dysregulated re-epithelialization. Novel approaches to accelerate DFU healing are actively pursued, with a focus on utilizing exosomes. Exosomes are natural nanovesicles mediating cellular communication and containing diverse functional molecular cargos, including DNA, mRNA, microRNA (miRNA), lncRNA, proteins, lipids and metabolites. While some exosomes show promise in modulating cellular function and promoting ulcer healing, their efficacy is limited by low yield, impurities, low loading content and inadequate targeting. Engineering exosomes to enhance their curative activity represents a potentially more efficient approach for DFUs. This could facilitate focused repair and regeneration of nerves, blood vessels and soft tissue after ulcer development. This review provides an overview of DFU pathogenesis, strategies for exosome engineering and the targeted therapeutic application of engineered exosomes in addressing critical pathological changes associated with DFUs.

Precision in cancer diagnostics: ultra-sensitive detection of MCF-7 breast cancer cells by gold nanostructure-enhanced electrochemical biosensing

Timely identification of cancers is pivotal in optimizing treatment efficacy and reducing their widespread impact. This study introduces a novel biosensor for the sensitive electrochemical detection of cancer cells overexpressing mucin 1 (MUC1), a well-established model for breast cancer. The sensor substrate comprises gold columnar nanostructures obtained through glancing angle deposition (GLAD) of copper nanostructures, subsequently replaced by gold via a facile galvanic replacement process. Functionalizing these gold nanostructures with aptamers targeting the MUC1 glycoproteins, a prominent cancer biomarker, enables specific recognition of MCF-7 breast cancer cells. The proposed electrochemical sensing platform offers several advantages, including high selectivity, a wide linear range of detection, a low detection limit of 30 cells per mL, and long-term stability, rendering this sensor highly desirable for definitive breast cancer diagnosis.

Research progress on the detection of foodborne pathogens based on aptamer recognition

Foodborne diseases caused by bacterial contamination are a serious threat to food safety and human health. The classical plate culture method has the problems of long detection cycle, low sensitivity and specificity, and complicated operation, which cannot meet the growing demand for rapid quantitative detection of pathogenic bacteria. The frequent outbreak of foodborne diseases has put forward higher requirements for rapid and simple detection technology of foodborne pathogens. Aptamer is a kind of oligonucleotide fragment that can recognize targets with the advantages of high affinity and good specificity. The target can be range from proteins, small molecules, cells bacteria, and even viruses. Herein, the latest advances in sensitive and rapid detection of foodborne pathogens based on aptamer recognition was reviewed. Special attention has been paid to the obtained sequences of aptamers to various foodborne pathogens, the optimization of sequences, and the mechanism of aptamer recognition. Then, the research progress of biosensors for the detection of pathogenic bacteria based on aptamer recognition were summarized. Some challenges and prospects for the detection of foodborne pathogens based on aptamer recognition were prospected. In summary, with the further deepening of aptamer research and improvement of detection technology, aptamer-based recognition can meet the needs of rapid, sensitive, and accurate detection in practical applications.

Colorimetry/fluorescence dual-mode detection of Salmonella typhimurium based on self-assembly of MCOF with Au NPs nanozyme coupled AIEgen

Sensitive, accurate, simple and quick monitoring of Salmonella typhimurium (S. typhimurium) in food is significant for preventing food poisoning, but still remains a challenge. Herein, a colorimetry/fluorescence dual-mode sensing strategy was fabricated to detect S. typhimurium by integrating the self-assembly of magnetic covalent organic framework (MCOF) with gold nanoparticles (Au NPs) as the peroxidase-mimicking nanozyme and aggregation-induced emission luminogen (AIEgen). S. typhimurium could competitive bind to aptamer conjugated Au NPs (Au NPs@apt), inhibit the self-assembly of MCOF with Au NPs, and shield the catalytic activity of AuNPs. After adding H2O2 and TPE-4A, the dark green solution changed to light with increasing S. typhimurium concentration, on the contrary, the fluorescent signals were generated. As a result, in colorimetry/fluorescence modes, S. typhimurium could be detected in the linear ranges of 103-108 CFU mL-1 and 101-107 CFU mL-1, with LODs of 1000 and 10 CFU mL-1, respectively. Importantly, different colors consistent with various S. typhimurium concentrations can be accurately classified by smartphone app and linear discriminant analysis (LDA). The smartphone-assisted data interpretation can generate complementary colorimetry and fluorescence signals without any sophisticated equipment and achieve on-site detection. Moreover, the proposed strategy could be explored for S. typhimurium monitoring in milk with satisfactory recoveries (97.6-100.4 %) in colorimetry and fluorescence mode and good classification and prediction performance in smartphone/LDA system, suggesting the feasibility and potential applications of the sensing platform.

Novel enzyme-linked aptamer-antibody sandwich assay and hybrid lateral flow strip for SARS-CoV-2 detection

We have successfully generated oligonucleotide aptamers (Apts) and monoclonal antibodies (mAbs) targeting the recombinant nucleocapsid (N) protein of SARS-CoV-2. Apts were obtained through seven rounds of systematic evolution of ligands by exponential enrichment (SELEX), while mAbs were derived from the 6F6E11 hybridoma cell line. Leveraging these Apts and mAbs, we have successfully devised two innovative and remarkably sensitive detection techniques for the rapid identification of SARS-CoV-2 N protein in nasopharyngeal samples: the enzyme-linked aptamer-antibody sandwich assay (ELAAA) and the hybrid lateral flow strip (hybrid-LFS). ELAAA exhibited an impressive detection limit of 0.1 ng/mL, while hybrid-LFS offered a detection range of 0.1 - 0.5 ng/mL. In the evaluation using ten nasopharyngeal samples spiked with known N protein concentrations, ELAAA demonstrated an average recovery rate of 92%. Additionally, during the assessment of five nasopharyngeal samples from infected individuals and ten samples from healthy volunteers, hybrid-LFS displayed excellent sensitivity and specificity. Our study introduces a novel and efficient on-site approach for SARS-CoV-2 detection in nasopharyngeal samples. The reliable hybrid Apt-mAb strategy not only advances virus diagnostic methods but also holds promise in combating the spread of related diseases.

Advanced diagnostic methods for identification of bacterial foodborne pathogens: contemporary and upcoming challenges

It is a public health imperative to have safe food and water across the population. Foodborne infections are one of the primary causes of sickness and mortality in both developed and developing countries. An estimated 100 million foodborne diseases and 120 000 foodborne illness-related fatalities occur each year in India. Several factors affect foodborne illness, such as improper farming methods, poor sanitary and hygienic conditions at all levels of the food supply chain, the lack of preventative measures in the food processing industry, the misuse of food additives, as well as improper storage and handling. In addition, chemical and microbiological combinations also play a key role in disease development. But recent disease outbreaks indicated that microbial pathogens played a major role in the development of foodborne diseases. Therefore, prompt, rapid, and accurate detection of high-risk food pathogens is extremely vital to warrant the safety of the food items. Conventional approaches for identifying foodborne pathogens are labor-intensive and cumbersome. As a result, a range of technologies for the rapid detection of foodborne bacterial pathogens have been developed. Presently, many methods are available for the instantaneous detection, identification, and monitoring of foodborne pathogens, such as nucleic acid-based methods, biosensor-based methods, and immunological-based methods. The goal of this review is to provide a complete evaluation of several existing and emerging strategies for detecting food-borne pathogens. Furthermore, this review outlines innovative methodologies and their uses in food testing, along with their existing limits and future possibilities in the detection of live pathogens in food.

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.

Applications and Challenges of Bacteriostatic Aptamers in the Treatment of Common Pathogenic Bacteria Infections

The continuous evolution and spread of common pathogenic bacteria is a major challenge in diagnosis and treatment with current biotechnology and modern molecular medicine. To confront this challenge, scientists urgently need to find alternatives for traditional antimicrobial agents. Various bacteriostatic aptamers obtained through SELEX screening are one of the most promising strategies. These bacteriostatic aptamers can reduce bacterial infection by blocking bacterial toxin infiltration, inhibiting biofilm formation, preventing bacterial invasion of immune cells, interfering with essential biochemical processes, and other mechanisms. In addition, aptamers may also help enhance the function of other antibacterial materials/drugs when used in combination. This paper has reviewed the bacteriostatic aptamers in the treatment of common pathogenic bacteria infections. For this aspect, first, bacteriostatic aptamers and their screening strategies are summarized. Then, the effect of molecular tailoring and modification on the performance of the bacteriostatic aptamer is analyzed, and the antibacterial mechanism and antibacterial strategy based on aptamers are introduced. Finally, the key technical challenges and their development prospects in clinical treatment are also carefully discussed.

Smartphone-assisted colorimetric detection of Salmonella typhimurium based on the catalytic reduction of 4-nitrophenol by β-cyclodextrin-capped gold nanoparticles

Salmonella typhimurium (S. typhimurium) is one of the most common pathogens in the environment, such as in drinking water and soil. Herein, an on-site detection method was developed by combining silver-coated magnetic nanoparticles (Fe₃O₄@Ag NPs) with the β-cyclodextrin-capped gold nanoparticles (β-CD-Au NPs) to achieve sensitive detection of S. typhimurium. After they formed a sandwich structure in the presence of S. typhimurium, the 4-nitrophenol was reduced to 4-aminophenol based on the nitro-reductase activity of β-CD-Au NPs. The naked eyes were able to observe the color change from yellow to colorless. Under optimal conditions, the detection range of S. typhimurium was 10-10⁷ CFU mL^-1, and the limit of detection (LOD) was 10 CFU mL^-1. The total detection time was 90 min, showing satisfactory performance in real samples. We combined a smartphone app with the colorimetric method, making it possible to semi-quantitatively detect S. typhimurium by analyzing the grey value. In conclusion, this assay detects S. typhimurium in environmental samples, offering an accurate and sensitive detection method without sophisticated equipment.

Molecular Targets for Foodborne Pathogenic Bacteria Detection

The detection of foodborne pathogenic bacteria currently relies on their ability to grow on chemically defined liquid and solid media, which is the essence of the classical microbiological approach. Such procedures are time-consuming and the quality of the result is affected by the selectivity of the media employed. Several alternative strategies based on the detection of molecular markers have been proposed. These markers may be cell constituents, may reside on the cell envelope or may be specific metabolites. Each marker provides specific advantages and, at the same time, suffers from specific limitations. The food matrix and chemical composition, as well as the accompanying microbiota, may also severely compromise detection. The aim of the present review article is to present and critically discuss all available information regarding the molecular targets that have been employed as markers for the detection of foodborne pathogens. Their strengths and limitations, as well as the proposed alleviation strategies, are presented, with particular emphasis on their applicability in real food systems and the challenges that are yet to be effectively addressed.

Advances in Aptamer-Based Biosensors and Cell-Internalizing SELEX Technology for Diagnostic and Therapeutic Application

Aptamers are a group of synthetic single-stranded nucleic acids. They are generated from a random library of single-stranded DNA or RNA by a technology named systematic evolution of ligands by exponential enrichment (SELEX). SELEX is a repetitive process to select and identify suitable aptamers that show high affinity and specificity towards target cells. Great strides have been achieved in the design, construction, and use of aptamers up to this point. However, only a small number of aptamer-based applications have achieved widespread commercial and clinical acceptance. Additionally, finding more effective ways to acquire aptamers with high affinity remains a challenge. Therefore, it is crucial to thoroughly examine the existing dearth and advancement in aptamer-related technologies. This review focuses on aptamers that are generated by SELEX to detect pathogenic microorganisms and mammalian cells, as well as in cell-internalizing SELEX for diagnostic and therapeutic purposes. The development of novel aptamer-based biosensors using optical and electrical methods for microbial detection is reported. The applications and limitations of aptamers are also discussed.

Aptamers: A prospective tool for infectious diseases diagnosis

It is well known that people's health is seriously threatened by various pathogens (such as Mycobacterium tuberculosis, Treponema pallidum, Novel coronavirus, HIV, Mucor, etc.), which leads to heavy socioeconomic burdens. Therefore, early and accurate pathogen diagnosis is essential for timely and effective therapies. Up to now, diagnosing human contagious diseases at molecule and nano levels is remarkably difficult owing to insufficient valid probes when it comes to determining the biological markers of pathogens. Aptamers are a set of high‐specificity and high‐sensitivity plastic oligonucleotides screened in vitro via the selective expansion of ligands by exponential enrichment (SELEX). With the advent of aptamer‐based technologies, their merits have aroused mounting academic interest. In recent years, as new detection and treatment tools, nucleic acid aptamers have been extensively utilized in the field of biomedicine, such as pathogen detection, new drug development, clinical diagnosis, nanotechnology, etc. However, the traditional SELEX method is cumbersome and has a long screening cycle, and it takes several months to screen out aptamers with high specificity. With the persistent development of SELEX‐based aptamer screening technologies, the application scenarios of aptamers have become more and more extensive. The present research briefly reviews the research progress of nucleic acid aptamers in the field of biomedicine, especially in the diagnosis of contagious diseases.

Future perspectives on aptamer for application in food authentication

Food fraudulence and food contamination are major concerns, particularly among consumers with specific dietary, cultural, lifestyle, and religious requirements. Current food authentication methods have several drawbacks and limitations, necessitating the development of a simpler, more sensitive, and rapid detection approach for food screening analysis, such as an aptamer-based biosensor system. Although the use of aptamer is growing in various fields, aptamer applications for food authentication are still lacking. In this review, we discuss the limitations of existing food authentication technologies and describe the applications of aptamer in food analyses. We also project several potential targets or marker molecules to be targeted in the SELEX process. Finally, this review highlights the drawbacks of current aptamer technologies and outlines the potential route of aptamer selection and applications for successful food authentication. This review provides an overview of the use of aptamer in food research and its potential application as a molecular reporter for rapid detection in food authentication process. Developing databases to store all biochemical profiles of food and applying machine learning algorithms against the biochemical profiles are urged to accelerate the identification of more reliable biomarker molecules as aptamer targets for food authentication.

Label-free fluorescent aptasensor for chloramphenicol based on hybridization chain reaction amplification and G-quadruplex/N-methyl mesoporphyrin IX complexation

The use of the broad-spectrum antibiotic chloramphenicol (CAP) in food is strictly regulated or banned in many countries. Herein, for the sensitive, rapid, and specific detection of CAP in milk, a label-free fluorescence strategy was established based on guanine (G)-quadruplex/N-methyl mesoporphyrin IX (NMM) complex formation and hybridization chain reaction (HCR) amplification. In this system, CAP can specifically bind to an aptamer (Apt) to release an Apt-C sequence from double-stranded DNA (Apt·Apt-C). Apt-C, can further hybridize with a functional hairpin DNA probe to release a primer sequence. The released primer sequence causes HCR and the formation of a nicked double-helix polymer, which contains G-quadruplex DNA. The recognition of G-quadruplex DNA by the NMM fluorochrome results in fluorescence enhancement. Consequently, CAP can be quantitatively detected by measuring the fluorescence intensity at 612 nm. The reliability of the aptasensor method was confirmed by comparison with an enzyme-linked immunosorbent assay. The proposed aptasensor was found to have a limit of detection of 0.8 pg mL-1 for CAP. Moreover, when the aptasensor was applied to the detection of CAP in milk samples, the average recoveries were 99.8-108.3% with relative standard deviations of 4.5-5.2%. Thus, this CAP detection method, which is rapid with high sensitivity and selectivity, has considerable potential for a wide range of food analysis applications.

SELEX against whole-cell bacteria resulted in lipopolysaccharide binding aptamers

Nucleic acid aptamers are target-specific oligonucleotides selected from combinatorial libraries through an iterative in vitro screening process known as Systemic Evolution of Ligands by Exponential Enrichment (SELEX). In this report, the selection of bacteria differentiating ssDNA aptamer candidates from a combinatorial library through the whole-cell SELEX method was performed. The enriched SELEX pool was sequenced using Illumina Next-Generation Sequencing (NGS) technology and analyzed for the most abundant sequences using CLC Genomics Workbench. The sequencing data resulted in several oligonucleotide families from which three individual sequences were chosen per SELEX based on the copy numbers. The binding performance of the selected aptamers was assessed by flow cytometry and fluorescence spectroscopy, and the binding constants were estimated using binding saturation curves. Varying results were obtained from two independent SELEX procedures where the SELEX against the model gram-negative bacterium Escherichia coli provided more selective sequences while the SELEX library used against gram-positive bacterium Listeria monocytogenes did not evolve as expected. The sequences that emerged from E. coli SELEX were shown to bind Lipopolysaccharide residues (LPS) and inhibit LPS-induced macrophage polarization. Thus, it can be said that, performed whole-cell SELEX could be resulted as the selection of aptamers which can bind LPS and inhibit LPS induced inflammation response and thus can be candidates for the inhibition of bacterial infections. In future studies, the selected aptamer sequences could be structurally and chemically modified and exploited as potential diagnostic tools and therapeutic agents as LPS antagonists.

Single-stranded DNA aptamer-based rolling circle amplification as anti-chicken Salmonella bacteriostatic

Background and Aim:

Salmonella is a major foodborne pathogen in the poultry industry, wherein the control measures may include sanitation and antibacterial and vaccines. However, there have been severe global restrictions on using anti-Salmonella antibacterial agents in livestock. This situation, along with rapidly increasing drug-resistant bacterial species, has led to the exploration of unconventional methods to control Salmonella infection in poultry. In recent years, selection techniques of promising DNA aptamers have begun to permeate several medical branches, resulting in the development of numerous anti-Salmonella DNA aptamers, most of which are used as sensing molecules for diagnostic purposes. These DNA aptamers have been demonstrated to interfere with bacterial growth, multiplication, and viability. Aptamers formed in rolling circle amplification products (RCA-p) could improve the potential action of aptamer interference with bacteria. This study aimed to test the use of single-stranded DNA aptamers in the form of RCA-p as a bacteriostatic to Salmonellain vitro.

Materials and Methods:

Salmonella Typhimurium and Salmonella Enteritidis isolates were subjected to the action of anti-ST and anti-SE DNA aptamers in the form of RCA-p. Each isolate was grown on MacConkey and Luria-Bertani agar media separately in different concentrations in the presence or absence of the cognate RCA-p.

Results:

The anti-Salmonella species DNA aptamer-based RCA-p were capable of reducing bacterial growth to significant levels in vitro.

Conclusion:

We describe a potential solution for the rapidly developing drug resistance of several bacterial species. Our findings suggested that the use of non-toxic, non-immunogenic, and low-cost DNA aptamers targeting Salmonella in the form of RCA-p could inhibit the bacterial growth rate. Unlike polymerase chain reaction, RCA yields tandem repeats of single-stranded DNA at isothermal conditions, which would increase the probability of receptor-ligand clustering and increase affinity. Furthermore, as our RCA template was bivalent with two DNA aptamer sequences, we could target multiple sites or antigens on a bacterial cell.

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

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

Selection, truncation and fluorescence polarization based aptasensor for Weissella viridescens detection

Weissella viridescens is a spoilage bacterium commonly found in low-temperature meat products. In this work, after fifteen rounds including three counter selection rounds of whole-cell systemic evolution of ligands by exponential enrichment (SELEX) in vitro, a novel aptamer L3 that can specifically recognize W. viridescens was obtained with a dissociation constant (K_d) value of 68.25 ± 5.32 nM. The sequence of aptamer L3 was optimized by truncation and a new aptamer sequence TL43 was obtained with a lower K_d value of 32.11 ± 3.01 nM. Finally, a simple and rapid fluorescence polarization (FP) platform was constructed to detect W. viridescens, in which FAM-labeled complementary sequence (FAM-cDNA) was employed to generate FP signal and streptavidin was used to amplify FP signal. In the presence of target bacteria, FP value decreased owning to the dissociation of FAM-cDNA from streptavidin/biotin-TL43/FAM-cDNA complex. Under optimal conditions, the concentration of W. viridescens and FP value displayed a good linear relationship with the detection range from 10² to 10⁶ cfu/mL. Moreover, the designed detection system had a good recovery rate of 90.6%-107.7% in smoked ham samples compared with classical plate counting method, indicating the great potential of the selected and truncated aptamer in practical biosensing applications.

DNA aptamers specific for Legionella pneumophila: systematic evolution of ligands by exponential enrichment in whole bacterial cells

Legionella pneumophila is the major causative agent of Legionnaires' disease and Pontiac fever, which pose major public health problems. Rapid detection of L. pneumophila is important for global control of these diseases. Aptamers, short oligonucleotides that bind to targets with high affinity and specificity, have great potential for use in pathogenic bacterium detection, diagnostics, and therapy. Here, we used a whole-cell SELEX (systematic evolution of ligands by exponential enrichment) method to isolate and characterize single-stranded DNA (ssDNA) aptamers against L. pneumophila. A total of 60 ssDNA sequences were identified after 17 rounds of selection. Other bacterial species (Escherichia coli, Bacillus subtilis, Pseudomonas syringae, Staphylococcus aureus, Legionella quateirensis, and Legionella adelaidensis) were used for counterselection to enhance the specificity of ssDNA aptamers against L. pneumophila. Four ssDNA aptamers showed strong affinity and high selectivity for L. pneumophila, with K_d values in the nanomolar range. Bioinformatic analysis of the most specific aptamers revealed predicted conserved secondary structures that might bind to L. pneumophila cell walls. In addition, the binding of these four fluorescently labeled aptamers to the surface of L. pneumophila was observed directly by fluorescence microscopy. These aptamers identified in this study could be used in the future to develop medical diagnostic tools and public environmental detection assays for L. pneumophila.

Aptasensors versus immunosensors-Which will prevail?

Since the invention of the first biosensors 70 years ago, they have turned into valuable and versatile tools for various applications, ranging from disease diagnosis to environmental monitoring. Traditionally, antibodies have been employed as the capture probes in most biosensors, owing to their innate ability to bind their target with high affinity and specificity, and are still considered as the gold standard. Yet, the resulting immunosensors often suffer from considerable limitations, which are mainly ascribed to the antibody size, conjugation chemistry, stability, and costs. Over the past decade, aptamers have emerged as promising alternative capture probes presenting some advantages over existing constraints of immunosensors, as well as new biosensing concepts. Herein, we review the employment of antibodies and aptamers as capture probes in biosensing platforms, addressing the main aspects of biosensor design and mechanism. We also aim to compare both capture probe classes from theoretical and experimental perspectives. Yet, we highlight that such comparisons are not straightforward, and these two families of capture probes should not be necessarily perceived as competing but rather as complementary. We, thus, elaborate on their combined use in hybrid biosensing schemes benefiting from the advantages of each biorecognition element.

Selection and Characterization of ssDNA Aptamers Targeting Largemouth Bass Virus Infected Cells With Antiviral Activities

Largemouth bass virus (LMBV) is one of the most devastating viral pathogens in farmed Largemouth bass. Aptamers are novel molecule probes and have been widely applied in the field of efficient therapeutic and diagnostic agents development. LMBV-infected fathead minnow cells (LMBV-FHM) served as target cells in this study, and three DNA aptamers (LBVA1, LBVA2, and LBVA3) were generated against target cells by SELEX technology. The selected aptamers could specifically bind to LMBV-FHM cells, with rather high calculated dissociation constants (Kd) of 890.09, 517.22, and 249.31 nM for aptamers LBVA1, LBVA2, and LBVA3, respectively. Three aptamers displayed efficient antiviral activities in vitro. It indicates that the selected aptamers have great potentials in developing efficient anti-viruses treatments. The targets of aptamers LBVA1, LBVA2, and LBVA3 could be membrane proteins on host cells. The targets of aptamers (LBVA1, LBVA2, and LBVA3) come out on the cells surface at 8, 10, 8 h post-infection. As novel molecular probes for accurate recognition, aptamer LBVA3 could detect LMBV infection in vitro and in vivo, it indicates that the selected aptamers could be applied in the development of rapid detective technologies, which are characterized by high sensitivity, accuracy, and easy operation.

New analytical methods using carbon-based nanomaterials for detection of Salmonella species as a major food poisoning organism in water and soil resources

Salmonella is one of the most prevalent causing agents of food- and water-borne illnesses, posing an ongoing public health threat. These food-poisoning bacteria contaminate the resources at different stages such as production, aggregation, processing, distribution, as well as marketing. According to the high incidence of salmonellosis, effective strategies for early-stage detection are required at the highest priority. Since traditional culture-dependent methods and polymerase chain reaction are labor-intensive and time-taking, identification of early and accurate detection of Salmonella in food and water samples can prevent significant health economic burden and lessen the costs. The immense potentiality of biosensors in diagnosis, such as simplicity in operation, the ability of multiplex analysis, high sensitivity, and specificity, have driven research in the evolution of nanotechnology, innovating newer biosensors. Carbon nanomaterials enhance the detection sensitivity of biosensors while obtaining low levels of detection limits due to their possibility to immobilize huge amounts of bioreceptor units at insignificant volume. Moreover, conjugation and functionalization of carbon nanomaterials with metallic nanoparticles or organic molecules enables surface functional groups. According to these remarkable properties, carbon nanomaterials are widely exploited in the development of novel biosensors. To be specific, carbon nanomaterials such as carbon nanotubes, graphene and fullerenes function as transducers in the analyte recognition process or surface immobilizers for biomolecules. Herein the potential application of carbon nanomaterials in the development of novel Salmonella biosensors platforms is reviewed comprehensively. In addition, the current problems and critical analyses of the future perspectives of Salmonella biosensors are discussed.

Systematic Evolution of Ligands by Exponential Enrichment Technologies and Aptamer-Based Applications: Recent Progress and Challenges in Precision Medicine of Infectious Diseases

Infectious diseases are considered as a pressing challenge to global public health. Accurate and rapid diagnostics tools for early recognition of the pathogen, as well as individualized precision therapy are essential for controlling the spread of infectious diseases. Aptamers, which were screened by systematic evolution of ligands by exponential enrichment (SELEX), can bind to targets with high affinity and specificity so that have exciting potential in both diagnosis and treatment of infectious diseases. In this review, we provide a comprehensive overview of the latest development of SELEX technology and focus on the applications of aptamer-based technologies in infectious diseases, such as targeted drug-delivery, treatments and biosensors for diagnosing. The challenges and the future development in this field of clinical application will also be discussed.

Oligonucleotide aptamers for pathogen detection and infectious disease control

During an epidemic or pandemic, the primary task is to rapidly develop precise diagnostic approaches and effective therapeutics. Oligonucleotide aptamer-based pathogen detection assays and control therapeutics are promising, as aptamers that specifically recognize and block pathogens can be quickly developed and produced through simple chemical synthesis. This work reviews common aptamer-based diagnostic techniques for communicable diseases and summarizes currently available aptamers that target various pathogens, including the SARS-CoV-2 virus. Moreover, this review discusses how oligonucleotide aptamers might be leveraged to control pathogen propagation and improve host immune system responses. This review offers a comprehensive data source to the further develop aptamer-based diagnostics and therapeutics specific for infectious diseases.

Dual-mode aptasensor for simultaneous detection of multiple food-borne pathogenic bacteria based on colorimetry and microfluidic chip using stir bar sorptive extraction

A dual-mode aptasensor using colorimetry and microfluidic chip (MC) together with stir bar sorptive extraction (SBSE) has been developed for firstly qualifying samples contaminated with Vibrio parahaemolyticus (V.P) and Salmonella typhimurium (S.T), then precisely determine both of them in positive samples. For this purpose, the aptamer-streptavidin encoded probes (Apt-SAEs) corresponding to different bacteria were prepared in advance. Then, a stir bar modified with 4-mercaptophenylboronic acid (MPBA) was made to extract bacteria together with Apt-SAE probes. The binding event of aptamer and target triggered the formation of two sandwich structures containing Apt-SAE, V.P or S.T. The concentration of bacteria could be enriched by 1000 times within 15 min to avoid long-time enrichment process. Finally, the stir bar was immersed in the 3,3',5,5'-Tetramethylbenzidine (TMB)-H₂O₂ solution for color development. The color could be observed by naked eyes to judge whether the analytes were present. The colorless samples were judged to be negative. For the positive samples, the adsorbed encoded probes corresponding to different bacteria would be eluted from the stir bar and rapidly analyzed by the MC. Under the optimized conditions, 100 CFU/mL of V.P or S.T or both of them could be observed by colorimetry and 35 CFU/mL of them could be detected (S/N = 3) by the MC. The assay has significant application value for on-site screening and multiple detection of food-borne pathogenic bacteria.

Aptamers and Aptamer-Coupled Biosensors to Detect Water-Borne Pathogens

Aptamers can serve as efficient bioreceptors for the development of biosensing detection platforms. Aptamers are short DNA or RNA oligonucleotides that fold into specific structures, which enable them to selectively bind to target analytes. The method used to identify aptamers is Systematic Evolution of Ligands through Exponential Enrichment (SELEX). Target properties can have an impact on aptamer efficiencies. Therefore, characteristics of water-borne microbial targets must be carefully considered during SELEX for optimal aptamer development. Several aptamers have been described for key water-borne pathogens. Here, we provide an exhaustive overview of these aptamers and discuss important microbial aspects to consider when developing such aptamers.

Novel Detection of Nasty Bugs, Prevention Is Better than Cure

Hospital-acquired infections (HAIs) are a growing concern around the world. They contribute to increasing mortality and morbidity rates and are an economic threat. All hospital patients have the potential to contract an HAI, but those with weakened or inferior immune systems are at highest risk. Most hospital patients will contract at least one HAI, but many will contract multiple ones. Bacteria are the most common cause of HAIs and contribute to 80-90% of all HAIs, with Staphylococcus aureus, Clostridium difficile, Escherichia coli, Acinetobacter baumannii, Pseudomonas aeruginosa and Klebsiella pneumoniae accounting for the majority. Each of these bacteria are highly resistant to antibiotics and can produce a protective film, known as a biofilm, to further prevent their eradication. It has been shown that by detecting and eradicating bacteria in the environment, infection rates can be reduced. The current methods for detecting bacteria are time consuming, non-specific, and prone to false negatives or false positives. Aptamer-based biosensors have demonstrated specific, time-efficient and simple detection, highlighting the likelihood that they could be used in a similar way to detect HAI-causing bacteria.

Application of Multiplexed Aptasensors in Food Contaminants Detection

The existence of contaminants in food poses a serious threat to human health. In recent years, aptamer sensors (aptasensors) have been developed rapidly for the detection of food contaminants because of their high specificity, design flexibility, and high efficiency. However, the development of high-throughput, highly sensitive, on-site, and cost-effective methods for simultaneous detection of food contaminants is still restricted due to multiple signal overlap or mutual interference and cross-reaction between different analytes with similar molecular structures. To overcome these problems, this Review summarizes some effective strategies from the articles published in recent years about multiplexed aptasensors for the simultaneous detection of food contaminants. This work focuses on the application of multiplexed aptasensors to simultaneously detect antibiotics, pathogens, and mycotoxins in food. These aptasensors mainly contain fluorescent aptasensors, electrochemical aptasensors, surface-enhanced Raman scattering-based aptasensors, microfluidic chip aptasensors, and paper-based multiplexed aptasensors. In addition, this Review also covers the application of nucleic acid cycle amplification and nanomaterial amplification strategies to improve the detection sensitivity. Finally, the limitations and challenges in the design of multiplexed aptasensor are also taken into account.

Application and development of aptamer in cancer: from clinical diagnosis to cancer therapy

Traditional anticancer therapies can cause serious side effects in clinical treatment due to their nonspecific of tumor cells. Aptamers, also termed as 'chemical antibodies', are short DNA or RNA oligonucleotides selected from the synthetic large random single-strand oligonucleotide library by systematic evolution of ligands by exponential enrichment (SELEX) to bind to lots of different targets, such as proteins or nucleic acid structures. Aptamers have good affinities and high specificity with target molecules, thus may be able to act as drugs themselves to directly inhibit the proliferation of tumor cells, or own great potentialities in the targeted drug delivery systems which can be used in tumor diagnosis and target specific tumor cells, thereby minimizing the toxicity to normal cells. Here we review the unique properties of aptamer represents a great opportunity when applied to the rapidly developing fields of biotechnology and discuss the recent developments in the use of aptamers as powerful tools for analytic, diagnostic and therapeutic applications for cancer.

Recent advances on functional nucleic acid-based biosensors for detection of food contaminants

It has seen increasing development of reliable, robust, and flexible biosensors for rapid food-safety analysis in the past few decades. Recently, functional nucleic acid-based biosensors have attracted attention because of their programmability, bottom-up characteristics, and structural switches. However, few systematic reviews devoted to categorizing the potential of DNA nanostructures and devices were found for detecting food contaminants. Hence, the applications of functional nucleic acid-based biosensors were reviewed for analyzing food contaminants, including foodborne pathogen bacteria, biotoxins, heavy metals, and et al. In addition to categorizing the various biosensors, multiple signal readout strategies, such as optical, electrochemical, and mass-based signals were also examined. Finally, the future changes and potential opportunities, as well as practical applications of functional nucleic acid-based biosensors were discussed.

Enhancement of the peroxidase-like activity of aptamers modified gold nanoclusters by bacteria for colorimetric detection of Salmonella typhimurium

A colorimetric aptasensor was developed for selective and sensitive detection of Salmonella typhimurium (S. typhimurium) based on the enhancement of bacteria for the peroxidase-like activity of dual aptamers modified bovine serum albumin stabilized-gold nanoclusters (aptamers@BSA-AuNCs). Micro-sized bacteria was found to be able to capture aptamers@BSA-AuNCs and 3,3',5,5'-tetramethylbenzidine (TMB), thus promoting the proximity of aptamers@BSA-AuNCs to TMB and greatly increasing the local concentrations of the enzyme-mimetic nanoparticles and their substrate. As a result, addition of bacteria promoted the formation of blue products in the catalytic system, which was utilized to achieve bacteria detection by colorimetry. The parameters influencing the colorimetric aptasensor were optimized by an orthogonal test. Under the selected conditions, the aptasensor exhibited a wide linear response to S. typhimurium in the concentration range of 10¹-10⁶ cfu mL^-1 with a detection limit as low as 1 cfu mL^-1. The feasibility of the aptasensor was verified by successful detection of S. typhimurium in egg samples with recoveries in the range of 92.4%-110%.

A sensitive fluorometric sensor for Ag+ based on the hybridization chain reaction coupled with a glucose oxidase dual-signal amplification strategy

In this work, an efficient and sensitive fluorometric sensor was developed to detect silver ions (Ag⁺). It is based on the cytosine–Ag⁺–cytosine (C–Ag⁺–C) structure via a dual-signal amplification strategy using glucose oxidase (GOx) and the hybridization chain reaction (HCR). A silver-coated glass slide (SCGS) acts as an ideal material for separation. Cytosine rich (C-rich) capture DNA (C-DNA) assembled themselves on the SCGS via Ag–S bonds and hybridized with signal DNA (S-DNA) to trigger the HCR. With specific base-pairing, the S-DNA and HCR products bind on the SCGS. Then, the GOx–biotin–streptavidin (SA) complexes bind to the HCR products through SA–biotin interactions. Owing to the formation of a particular C–Ag⁺–C structure between two neighboring C-rich C-DNA on the SCGS, the C-DNA/S-DNA/HP1-GOx/HP2-GOx complex gradually moved away from the SCGS as the concentration of Ag⁺ increased and the combined GOx fell into the buffer. H₂O₂ could be generated during the oxidation of glucose, catalyzed by GOx in the buffer. Afterward, H₂O₂ could oxidize the substrate (3-(p-hydroxyphenyl)-propanoic acid) when Horseradish peroxidase was present, giving rise to blue fluorescence. The proposed strategy reached a limit of detection (LOD) of 1.8 pmol L⁻¹ with a linear detection range of 5 to 1000 pmol L⁻¹ for Ag⁺. Moreover, this assay has been commendably used for the detection of Ag⁺ in actual samples with fairly good results.

An assay for Ag⁺ based on a C–Ag⁺–C structure by utilizing a HCR/GOx dual-signal amplification strategy and SCGS as an ideal separation material.

An overview and future prospects on aptamers for food safety

Introduction

Many bacteria are responsible for infections in humans and plants, being found in vegetables, water, and medical devices. Most bacterial detection methods are time-consuming and take days to give the result. Aptamers are a promising alternative for a quick and reliable measurement technique to detect bacteria present in food products. Selected aptamers are DNA or RNA oligonucleotides that can bind with bacteria or other molecules with affinity and specificity for the target cells by the SELEX or cell-SELEX technique. This method is based on some rounds to remove the non-ligand oligonucleotides, leaving the aptamers specific to bind to the selected bacteria. Compared with conventional methodologies, the detection approach using aptamers is a rapid, low-cost form of analysis.

Objective

This review summarizes obtention methods and applications of aptamers in the food industry and biotechnology. Besides, different techniques with aptamers are presented, which enable more effective target detection.

Conclusion

Applications of aptamers as biosensors, or the association of aptamers with nanomaterials, may be employed in analyses by colorimetric, fluorescence, or electrical devices. Additionally, more efficient ways of sample preparation are presented, which can support food safety to provide human health, with a low-cost method for contaminant detection.

Key points • Aptamers are promising for detecting contaminants outbreaks. • Studies are needed to identify aptamers for different targets.

Selection of potential aptamers for specific growth stage detection of Yersinia enterocolitica

Yersinia enterocolitica remains a threat to public health, and a sensitive detection method is a prerequisite due to its complicated diagnosis associated with slow growth. Recently, aptamer-based detection systems have played a vital role in the development of simple, rapid, sensitive, and specific detection methods. Herein, highly specific ssDNA aptamers were screened against Y. enterocolitica at the different growth stages by whole cell-SELEX. Cells at different growth stages were harvested and incubated with an ssDNA library to get an enriched pool of specific aptamer candidates. After the 10th round of SELEX, the enriched pool was sequenced and grouped into seven families based on homology and similarity of the secondary structure. Flow cytometry analysis revealed that the aptamers M1, M5, and M7 with K d values of 37.93 ± 7.88 nM, 74.96 ± 21.34 nM, and 73.02 ± 18.76 nM had the highest affinity and specificity to the target, respectively. The selected aptamers showed binding to the different growth stages of Y. enterocolitica with a significant increase in the gated fluorescence. Our aptamer selection strategy is convenient, and the developed aptamer can be useful for an accurate and reliable detection system.

Delivery of antibacterial silver nanoclusters to Pseudomonas aeruginosa using species-specific DNA aptamers

Introduction. The use of silver as an antimicrobial therapeutic is limited by its toxicity to host cells compared with that required to kill bacterial pathogens.Aim. To use aptamer targeting of DNA scaffolded silver nanoclusters as an antimicrobial agent for treating Pseudomonas aeruginosa infections.Methodology. Antimicrobial activity was assessed in planktonic cultures and in vivo using an invertebrate model of infection.Results. The aptamer conjugates that we call aptabiotics have potent antimicrobial activity. Targeted silver nanoclusters were more effective at killing P. aeruginosa than the equivalent quantity of untargeted silver nanoclusters. The aptabiotics have an IC₅₀ of 1.3-2.6 µM against planktonically grown bacteria. Propidium iodide staining showed that they rapidly depolarize bacterial cells to kill approximately 50 % of the population within 10 min following treatment. In vivo testing in the Galleria mellonella model of infection prolonged survival from an otherwise lethal infection.Conclusion. Using P. aeruginosa as a model, we show that targeting of DNA-scaffolded silver nanoclusters with an aptamer has effective fast-acting antimicrobial activity in vitro and in an in vivo animal model.

Aptamer-Based Biosensors for Environmental Monitoring

Due to their relative synthetic and chemical simplicity compared to antibodies, aptamers afford enhanced stability and functionality for the detection of environmental contaminants and for use in environmental monitoring. Furthermore, nucleic acid aptamers can be selected for toxic targets which may prove difficult for antibody development. Of particular relevance, aptamers have been selected and used to develop biosensors for environmental contaminants such as heavy metals, small-molecule agricultural toxins, and water-borne bacterial pathogens. This review will focus on recent aptamer-based developments for the detection of diverse environmental contaminants. Within this domain, aptamers have been combined with other technologies to develop biosensors with various signal outputs. The goal of much of this work is to develop cost-effective, user-friendly detection methods that can complement or replace traditional environmental monitoring strategies. This review will highlight recent examples in this area. Additionally, with innovative developments such as wearable devices, sentinel materials, and lab-on-a-chip designs, there exists significant potential for the development of multifunctional aptamer-based biosensors for environmental monitoring. Examples of these technologies will also be highlighted. Finally, a critical perspective on the field, and thoughts on future research directions will be offered.

Computer-Aided aptamer design for sulfadimethoxine antibiotic: step by step mutation based on MD simulation approach

This study introduces a computational method to design a new aptamer with higher binding affinity to a special target in comparison with the experimentally available aptamers. The method is called step by step mutation based on MD simulation, which includes some steps. First, MD simulation is performed for the SELEX-introduced (native) aptamer in the presence of the target. Afterwards, conformational factor (P_i) is calculated for the simulated system, which obtains the affinity of the aptamer residues to the target. A nucleotide exchange is done for the residue with the least P_i parameter to the nucleotide with the highest P_i value that results in a mutant aptamer. MD simulation is performed for the target-mutant complex, and P_i values are calculated again. The nucleotide exchange is performed similarly, and the designing process is proceeded repeatedly that results in a mutant with the improved specificity to the target. The aptamer affinity to the target is also determined in each step through calculating the binding Gibbs energy (ΔG_Bind) as a reliable parameter. The introduced strategy is utilized efficiently to design a mutant aptamer with improved specificity toward sulfadimethoxine (SDM) antibiotic as a case study. The great difference in the ΔG_Bind values about 579.856 kJ mol^-1 highlights that the M5 mutant possesses the improved specificity toward SDM in comparison with the native aptamer. Besides, the selectivity of the M5 aptamer toward SDM is examined among some conventional interfering compounds by using MD simulation that confirms the applicability of the designed aptamer for further experimental studies.

A SERS aptasensor for simultaneous multiple pathogens detection using gold decorated PDMS substrate

An aptamer-based sensitive method was developed here for detection of multiple foodborne pathogens in food matrix by surface-enhanced Raman scattering (SERS) technology. Polydimethylsiloxane (PDMS) film was first prepared and then coated with gold nanoparticles (AuNP) to act as an active substrate for the enhancement of Raman scattering. The as-prepared Au-PDMS film was functionalized with specific pathogen aptamers (Apt) to capture the targets. In addition, aptamers functionalized AuNP integrated with Raman reporters (4-Mercaptobenzoic acid (4-MBA)/Nile blue A (NBA)) were fabricated as pathogen-specific SERS probes. In this scheme, pathogens were first captured by Apt-Au-PDMS film and then bind with SERS probes to allow the formation of a sandwich assay to complete the sensor module for the detection of multiple pathogens. With Vibrio parahaemolyticus and Salmonella typhimurium as model targets, this protocol can selectively detect 18 cfu/mL and 27 cfu/mL, respectively. Furthermore, this platform can be successfully applied to detect pathogens in seafood samples with recoveries ranging from 82.9% to 95.1%.

Aptamers coupled to nanoparticles in the diagnosis and treatment of microbial infections

There are nanoparticles with remarkable antibacterial characteristics and aptamers able to recognize specific pathogenic bacteria with high affinity and specificity. The combination of both systems has been used to design rapid bacterial detection methods with excellent detection limits. Likewise, the synergism between aptamers and nanoparticles have allowed to optimize the antimicrobial activity of antibiotics and other nanostructures providing them with activity bacterium-specific, turning into attractive and promising tools to fight against bacteria resistant to multiple antimicrobials.

Rapid isolation of bacteria-specific aptamers with a non-SELEX-based method

Usually, isolation of bacteria-specific aptamers by SELEX is a time-consuming process due to the required repeated rounds of binding, separation, and amplification of the probes to target bacteria. Here, we show that it is possible to isolate bacteria-specific DNA aptamers omitting the repeated rounds of binding incubation, separation, and amplification that are indispensable for SELEX. The serial removal of unbound DNAs to the bacterial cells from an initial mixture of bacteria and DNA libraries through serial centrifugation, one-time separation, and further one-time amplification of DNA bound to the target bacterial cells applied in this non-SELEX-based method allows successful aptamer isolation.