Identification and characterization of two high affinity aptamers specific for Salmonella Enteritidis

Metal Nanocomposites as Biosensors for Biological Fluids Analysis

Metal nanocomposites are rapidly emerging as a powerful platform for biosensing applications, particularly in the analysis of biological fluids. This review paper examines the recent advancements in the development and application of metal nanocomposites as biosensors for detecting various analytes in complex biological matrices such as blood, serum, urine, and saliva. We discuss the unique physicochemical properties of metal nanocomposites, including their high surface area, enhanced conductivity, and tunable optical and electrochemical characteristics, which contribute to their superior sensing capabilities. The review will cover various fabrication techniques, focusing on their impact on the sensitivity, selectivity, and stability of the resulting biosensors. Furthermore, we will analyze the diverse applications of these biosensors in the detection of disease biomarkers, environmental toxins, and therapeutic drugs within biological fluids. Finally, we will address the current challenges and future perspectives of this field, highlighting the potential for improved diagnostic tools and personalized medicine through the continued development of advanced metal nanocomposite-based biosensors.

Whole-cell aptamer-based techniques for rapid bacterial detection: Alternatives to traditional methods

Controlling the spread of bacterial infectious diseases is a major public health issue, particularly in view of the pandemic of bacterial resistance to antibiotics. In this context, the detection and identification of pathogenic bacteria is a prerequisite for the implementation of control measures. Current reference methods are mainly based on culture methods, which generate a delay in obtaining a result and requires equipment. Consequently, focusing on the detection of the whole bacterium represents a very attractive alternative, since no culture is required. Several techniques have already been deployed to identify whole-cell bacteria. In recent decades, growing interest in nucleic acid aptamers has emerged as a viable alternative to antibodies as recognition elements, offering preferable stability, cost-efficiency, good specificity and affinity. This review explores current alternative methods for the detection of whole-cell bacteria, with particular emphasis on aptamer-based assays. These assays have shown promising results in various transduction mechanisms, including optical, electrochemical, and mechanical approaches, enhancing their versatility in different diagnostic platforms. The integration of aptamers in these detection methods offers rapid, sensitive, versatile and portable solutions for pathogen identification, positioning them as valuable tools in the fight against bacterial infections.

Aptamer and DNAzyme Based Colorimetric Biosensors for Pathogen Detection

The detection of pathogens is critical for preventing and controlling health hazards across clinical, environmental, and food safety sectors. Functional nucleic acids (FNAs), such as aptamers and DNAzymes, have emerged as versatile molecular tools for pathogen detection due to their high specificity and affinity. This review focuses on the in vitro selection of FNAs for pathogens, with emphasis on the selection of aptamers for specific biomarkers and intact pathogens, including bacteria and viruses. Additionally, the selection of DNAzymes for bacterial detection is discussed. The integration of these FNAs into colorimetric biosensors has enabled the development of simple, cost-effective diagnostic platforms. Both non-catalytic and catalytic colorimetric biosensors are explored, including those based on gold nanoparticles, polydiacetylenes, protein enzymes, G-quadruplexes, and nanozymes. These biosensors offer visible detection through color changes, making them ideal for point-of-care diagnostics. The review concludes by highlighting current challenges and future perspectives for advancing FNA-based colorimetric biosensing technologies for pathogen detection.

Hybrid chain reaction-based and Au/Bi4NbO8Cl/In2S3 layer-by-layer assembled dual-mode photoelectrochemical-electrochemical aptasensor for the detection of Salmonella enteritidis

Salmonella enteritidis (SE) is a food-borne pathogens that can cause acute gastroenteritis. With the increasing social attention to food safety, the detection method of SE has attracted wide attention. In response to the demand for efficient detection methods of SE, this study constructed a novel dual-mode photoelectrochemical-electrochemical (PEC-EC) aptamer-based biosensor. The sensor was constructed using Bi4NbO8Cl/In2S3 heterojunction as the electrode substrate material, the hybridization chain reaction (HCR) and dye sensitization were used as the signal amplification strategies. Bi4NbO8Cl/In2S3 heterojunction could provide an excellent initial photocurrent response for the sensing platform, and the HCR was opened by the end of complementary DNA (cDNA) and generated an ultra-long DNA double-stranded (dsDNA) "super structure" on the surface of the electrode, which could be embedded with a large number of methylene blue (MB) as the bifunctional probes. Thus, dual-mode output was achieved via the PEC and EC activity of MB. Under the optimized conditions, the PEC and EC signal responses of the system were linear to the logarithm of SE concentration in a range from 1.5 × 102 CFU/mL to 1.5 × 107 CFU/mL. The detection limits were found to be 12.9 CFU/mL and 12.3 CFU/mL using the PEC and EC methods, respectively. The constructed dual-mode biosensor exhibited good performance for real sample analysis, and demonstrated great application potential in the field of SE rapid detection. Moreover, this dual-mode detection strategy provided more accurate and reliable results than the single-mode output.

The non-negligible non-specific adsorption of oligonucleotides in target-immobilized Mag-SELEX

Target-immobilized magnetic beads-based Systematic Evolution of Ligands by Exponential Enrichment (target-immobilized Mag-SELEX) has emerged as a powerful tool for aptamer selection owing to its convenience, efficiency, and versatility. However, in this study we systematically investigated non-specific adsorption in target-immobilized Mag-SELEX and found that the non-specific adsorption of the oligonucleotides to target-labeled magnetic beads was comparable to that of the screening libraries, indicating a substantial portion of captured sequences likely stem from non-specific adsorption. Longer nucleic acid sequences (80 nt and above, such as polyA80 and yeast tRNA) were found to attenuate this non-specific adsorption, with more complex higher-order structures demonstrating greater efficacy, while dNTP and short sequences such as primer sequences (20 nt), polyT(59), or polyA(59), did not possess this capability. Various evidence suggested that hydrophobic interactions and other weak interactions may be the primary underlying cause of non-specific adsorption. Additionally, surface modification of magnetic beads with polar molecule polyethylene glycol (PEG) also yielded a significant reduction in non-specific adsorption. In conclusion, our research underscores the critical importance of closely monitoring non-specific adsorption in target-immobilized Mag-SELEX.

The Biomedical Applications of Biomolecule Integrated Biosensors for Cell Monitoring

Cell monitoring is essential for understanding the physiological conditions and cell abnormalities induced by various stimuli, such as stress factors, microbial invasion, and diseases. Currently, various techniques for detecting cell abnormalities and metabolites originating from specific cells are employed to obtain information on cells in terms of human health. Although the states of cells have traditionally been accessed using instrument-based analysis, this has been replaced by various sensor systems equipped with new materials and technologies. Various sensor systems have been developed for monitoring cells by recognizing biological markers such as proteins on cell surfaces, components on plasma membranes, secreted metabolites, and DNA sequences. Sensor systems are classified into subclasses, such as chemical sensors and biosensors, based on the components used to recognize the targets. In this review, we aim to outline the fundamental principles of sensor systems used for monitoring cells, encompassing both biosensors and chemical sensors. Specifically, we focus on biosensing systems in terms of the types of sensing and signal-transducing elements and introduce recent advancements and applications of biosensors. Finally, we address the present challenges in biosensor systems and the prospects that should be considered to enhance biosensor performance. Although this review covers the application of biosensors for monitoring cells, we believe that it can provide valuable insights for researchers and general readers interested in the advancements of biosensing and its further applications in biomedical fields.

Emerging Biomimetic Sensor Technologies for the Detection of Pathogenic Bacteria: A Commercial Viability Study

Ensuring a rapid and accurate identification of harmful bacteria is crucial in various fields including environmental monitoring, food safety, and clinical diagnostics. Conventional detection methods often suffer from limitations such as long analysis time, complexity, and the need for qualified personnel. Therefore, a lot of research effort is devoted to developing technologies with the potential to revolutionize the detection of pathogenic bacteria by offering rapid, sensitive, and user-friendly platforms for point-of-care analysis. In this light, biosensors have gained significant commercial attention in recent years due to their simplicity, portability, and rapid analysis capabilities. The purpose of this review is to identify a trend by analyzing which biosensor technologies have become commercially successful in the field of bacteria detection. Moreover, we highlight the characteristics that a biosensor must possess to finally arrive in the market and therefore in the hands of the end-user, and we present critical examples of the market applications of various technologies. The aim is to investigate the reason why certain technologies have achieved commercial success and extrapolate these trends to the future economic viability of a new subfield in the world of biosensing: the development of biomimetic sensor platforms. Therefore, an overview of recent advances in the field of biomimetic bacteria detection will be presented, after which the challenges that need to be addressed in the coming years to improve market penetration will be critically evaluated. We will zoom into the current shortcomings of biomimetic sensors based on imprinting technology and aptamers and try to come up with a recommendation for further development based on the trends observed from previous commercial success stories in biosensing.

Electrochemical Aptasensor for the Detection of the Key Virulence Factor YadA of Yersinia enterocolitica

New point-of-care (POC) diagnosis of bacterial infections are imperative to overcome the deficiencies of conventional methods, such as culture and molecular methods. In this study, we identified new aptamers that bind to the virulence factor Yersinia adhesin A (YadA) of Yersinia enterocolitica using cell-systematic evolution of ligands by exponential enrichment (cell-SELEX). Escherichia coli expressing YadA on the cell surface was used as a target cell. After eight cycles of selection, the final aptamer pool was sequenced by high throughput sequencing using the Illumina Novaseq platform. The sequencing data, analyzed using the Geneious software, was aligned, filtered and demultiplexed to obtain the key nucleotides possibly involved in the target binding. The most promising aptamer candidate, Apt1, bound specifically to YadA with a dissociation constant (Kd) of 11 nM. Apt1 was used to develop a simple electrochemical biosensor with a two-step, label-free design towards the detection of YadA. The sensor surface modifications and its ability to bind successfully and stably to YadA were confirmed by cyclic voltammetry, impedance spectroscopy and square wave voltammetry. The biosensor enabled the detection of YadA in a linear range between 7.0 × 104 and 7.0 × 107 CFU mL−1 and showed a square correlation coefficient >0.99. The standard deviation and the limit of detection was ~2.5% and 7.0 × 104 CFU mL−1, respectively. Overall, the results suggest that this novel biosensor incorporating Apt1 can potentially be used as a sensitive POC detection system to aid the diagnosis of Y. enterocolitica infections. Furthermore, this simple yet innovative approach could be replicated to select aptamers for other (bacterial) targets and to develop the corresponding biosensors for their detection.

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.

The systemic characterization of aptamer cocktail for bacterial detection studied by graphene oxide-based fluorescence resonance energy transfer aptasensor

Aptamers have gained significant attention as the molecular recognition element to replace antibodies in sensor development and target delivery. Nevertheless, it is noteworthy that unlike the wide application of polyvalent antibodies, existing researches on the combined use of heterologous aptamers with similar recognition affinity and specificity for target detection were sporadic. Herein, first, the wide existence of polyaptamer for bacteria was revealed through the summary of existing literature. Furthermore, based on the establishment of a sensitive aptamer cocktail/graphene oxide fluorescence resonance energy transfer polyaptasensor with a detection limit as low as 10 CFU/ml, the systemic characterization of aptamer cocktails in bacterial detection was carried out by taking E. coli, Vi. parahemolyticus, S. typhimurium, and C. sakazakii as the assay targets. It was turned out that the polyaptasensors for C. sakazakii and S. typhimurium owned prevalence in the broader concentration range of target bacteria. While the polyaptasensors for E. coli and V. parahemolyticus outperformed monoaptasensor mainly in the lower concentration of target bacteria. The linear relationships between fluorescence recovery and the concentration of bacteria were also discussed. The different characteristics of the bacterial cellular membrane, including the binding affinity and the robustness to variation, are analyzed to be the main reason for the diverse detection performance of aptasensors. The study here enhances a sensor detection strategy with super sensitivity. More importantly, this systemic study on the aptamer cocktail in reference to antibodies will advance the in-depth understanding and rational design of aptamer based biological recognition, detection, and targeting.

An Enhanced Lateral Flow Assay Based on Aptamer-Magnetic Separation and Multifold AuNPs for Ultrasensitive Detection of Salmonella Typhimurium in Milk

In this paper, a novel and ultrasensitive lateral flow assay (LFA) based on aptamer-magnetic separation, and multifold Au nanoparticles (AuNPs) was developed for visual detecting Salmonella enterica ser. Typhimurium (S. Typhimurium). The method realized magnetic enrichment and signal transduction via magnetic separation and achieved signal amplification through hybridizing AuNPs-capture probes and AuNPs-amplification probes to form multifold AuNPs. Two different thiolated single-strand DNA (ssDNA) on the AuNPs-capture probe played different roles. One was combined with the AuNPs-amplification probe on the conjugate pad to achieve enhanced signals. The other was connected to transduction ssDNA1 released by aptamer-magnetic capture of S. Typhimurium, and captured by the T-line, forming a positive signal. This method had an excellent linear relationship ranging from 8.6 × 102 CFU/mL to 8.6 × 107 CFU/mL with the limit of detection (LOD) as low as 8.6 × 100 CFU/mL in pure culture. In actual samples, the visual LOD was 4.1 × 102 CFU/mL, which did not carry out nucleic acid amplification and pre-enrichment, increasing three orders of magnitudes than unenhanced assays with single-dose AuNPs and no magnetic separation. Furthermore, the system showed high specificity, having no reaction with other nontarget strains. This visual signal amplificated system would be a potential platform for ultrasensitive monitoring S. Typhimurium in milk samples.

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.