Selection of aptamers against pathogenic bacteria and their diagnostics application

Recent Advances in Recognition Receptors for Electrochemical Biosensing of Mycotoxins-A Review

Mycotoxins are naturally occurring toxic secondary metabolites produced by fungi in cereals and foodstuffs during the stages of cultivation and storage. Electrochemical biosensing has emerged as a rapid, efficient, and economical approach for the detection and quantification of mycotoxins in different sample media. An electrochemical biosensor consists of two main units, a recognition receptor and a signal transducer. Natural or artificial antibodies, aptamers, molecularly imprinted polymers (MIP), peptides, and DNAzymes have been extensively employed as selective recognition receptors for the electrochemical biosensing of mycotoxins. This article affords a detailed discussion of the recent advances and future prospects of various types of recognition receptors exploited in the electrochemical biosensing of mycotoxins.

Physical and Functional Characterization of PLGA Nanoparticles Containing the Antimicrobial Peptide SAAP-148

Synthetic antimicrobial and antibiofilm peptide (SAAP-148) commits significant antimicrobial activities against antimicrobial resistant (AMR) planktonic bacteria and biofilms. However, SAAP-148 is limited by its low selectivity index, i.e., ratio between cytotoxicity and antimicrobial activity, as well as its bioavailability at infection sites. We hypothesized that formulation of SAAP-148 in PLGA nanoparticles (SAAP-148 NPs) improves the selectivity index due to the sustained local release of the peptide. The aim of this study was to investigate the physical and functional characteristics of SAAP-148 NPs and to compare the selectivity index of the formulated peptide with that of the peptide in solution. SAAP-148 NPs displayed favorable physiochemical properties [size = 94.1 ± 23 nm, polydispersity index (PDI) = 0.08 ± 0.1, surface charge = 1.65 ± 0.1 mV, and encapsulation efficiency (EE) = 86.7 ± 0.3%] and sustained release of peptide for up to 21 days in PBS at 37 °C. The antibacterial and cytotoxicity studies showed that the selectivity index for SAAP-148 NPs was drastically increased, by 10-fold, regarding AMR Staphylococcus aureus and 20-fold regarding AMR Acinetobacter baumannii after 4 h. Interestingly, the antibiofilm activity of SAAP-148 NPs against AMR S. aureus and A. baumannii gradually increased overtime, suggesting a dose-effect relationship based on the peptide's in vitro release profile. Using 3D human skin equivalents (HSEs), dual drug SAAP-148 NPs and the novel antibiotic halicin NPs provided a stronger antibacterial response against planktonic and cell-associated bacteria than SAAP-148 NPs but not halicin NPs after 24 h. Confocal laser scanning microscopy revealed the presence of SAAP-148 NPs on the top layers of the skin models in close proximity to AMR S. aureus at 24 h. Overall, SAAP-148 NPs present a promising yet challenging approach for further development as treatment against bacterial infections.

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.

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.

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.

Regulation Mechanism of ssDNA Aptamer in Nanozymes and Application of Nanozyme-Based Aptasensors in Food Safety

Food safety issues are a worldwide concern. Pathogens, toxins, pesticides, veterinary drugs, heavy metals, and illegal additives are frequently reported to contaminate food and pose a serious threat to human health. Conventional detection methods have difficulties fulfilling the requirements for food development in a modern society. Therefore, novel rapid detection methods are urgently needed for on-site and rapid screening of massive food samples. Due to the extraordinary properties of nanozymes and aptamers, biosensors composed of both of them provide considerable advantages in analytical performances, including sensitivity, specificity, repeatability, and accuracy. They are considered a promising complementary detection method on top of conventional ones for the rapid and accurate detection of food contaminants. In recent years, we have witnessed a flourishing of analytical strategies based on aptamers and nanozymes for the detection of food contaminants, especially novel detection models based on the regulation by single-stranded DNA (ssDNA) of nanozyme activity. However, the applications of nanozyme-based aptasensors in food safety are seldom reviewed. Thus, this paper aims to provide a comprehensive review on nanozyme-based aptasensors in food safety, which are arranged according to the different interaction modes of ssDNA and nanozymes: aptasensors based on nanozyme activity either inhibited or enhanced by ssDNA, nanozymes as signal tags, and other methods. Before introducing the nanozyme-based aptasensors, the regulation by ssDNA of nanozyme activity via diverse factors is discussed systematically for precisely tailoring nanozyme activity in biosensors. Furthermore, current challenges are emphasized, and future perspectives are discussed.

Oligonucleotide aptamers: Recent advances in their screening, molecular conformation and therapeutic applications

Aptamers are single stranded oligonucleotides with specific recognition and binding ability to target molecules, which can be obtained by Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Aptamers have the advantages of low molecular weight, low immunogenicity, easy modification and high stability. They play promising role in promoting food safety, monitoring the environment and basic research, especially in clinical diagnosis and therapeutic drugs. To date, great achievements regarding the selection, modifications and application of aptamers have been made. However, since it is still a challenge to obtain aptamers with high affinity in a more effective way, few aptamer-based products have already successfully entered into clinical use. This review aims to provide a thorough overview of the latest advances in this rapidly developing field, focusing on aptamer screening methods for different targets, the structure of the interaction between aptamers and target substances, and the challenges and potential of current therapeutic aptamers.

Selective Capture and Identification of Methicillin-Resistant Staphylococcus aureus by Combining Aptamer-Modified Magnetic Nanoparticles and Mass Spectrometry

A nucleic acid aptamer that specifically recognizes methicillin-resistant Staphylococcus aureus (MRSA) has been immobilized on magnetic nanoparticles to capture the target bacteria prior to mass spectrometry analysis. After the MRSA species were captured, they were further eluted from the nanoparticles and identified using matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). The combination of aptamer-based capture/enrichment and MS analysis of microorganisms took advantage of the selectivity of both techniques and should enhance the accuracy of MRSA identification. The capture and elution efficiencies for MRSA were optimized by examining factors such as incubation time, temperature, and elution solvents. The aptamer-modified magnetic nanoparticles showed a capture rate of more than 90% under the optimized condition, whereas the capture rates were less than 11% for non-target bacteria. The as-prepared nanoparticles exhibited only a 5% decrease in the capture rate and a 9% decrease in the elution rate after 10 successive cycles of utilization. Most importantly, the aptamer-modified nanoparticles revealed an excellent selectivity towards MRSA in bacterial mixtures. The capture of MRSA at a concentration of 10² CFU/mL remained at a good percentage of 82% even when the other two species were at 10⁴ times higher concentration (10⁶ CFU/mL). Further, the eluted MRSA bacteria were successfully identified using MALDI mass spectrometry.

Rapid Detection of Escherichia coli Antibiotic Susceptibility Using Live/Dead Spectrometry for Lytic Agents

Antibiotic resistance is a serious threat to public health. The empiric use of the wrong antibiotic occurs due to urgency in treatment combined with slow, culture-based diagnostic techniques. Inappropriate antibiotic choice can promote the development of antibiotic resistance. We investigated live/dead spectrometry using a fluorimeter (Optrode) as a rapid alternative to culture-based techniques through application of the LIVE/DEAD® BacLightTM Bacterial Viability Kit. Killing was detected by the Optrode in near real-time when Escherichia coli was treated with lytic antibiotics-ampicillin and polymyxin B-and stained with SYTO 9 and/or propidium iodide. Antibiotic concentration, bacterial growth phase, and treatment time used affected the efficacy of this detection method. Quantification methods of the lethal action and inhibitory action of the non-lytic antibiotics, ciprofloxacin and chloramphenicol, respectively, remain to be elucidated.

In Vivo Production of RNA Aptamers and Nanoparticles: Problems and Prospects

RNA aptamers are becoming increasingly attractive due to their superior properties. This review discusses the early stages of aptamer research, the main developments in this area, and the latest technologies being developed. The review also highlights the advantages of RNA aptamers in comparison to antibodies, considering the great potential of RNA aptamers and their applications in the near future. In addition, it is shown how RNA aptamers can form endless 3-D structures, giving rise to various structural and functional possibilities. Special attention is paid to the Mango, Spinach and Broccoli fluorescent RNA aptamers, and the advantages of split RNA aptamers are discussed. The review focuses on the importance of creating a platform for the synthesis of RNA nanoparticles in vivo and examines yeast, namely Saccharomyces cerevisiae, as a potential model organism for the production of RNA nanoparticles on a large scale.

Recent advances on aptamer-based biosensors for detection of pathogenic bacteria

As a significant constituent in biosphere, bacteria have a great influence on human activity. The detection of pathogen bacteria is closely related to the human health. However, the traditional methods for detection of pathogenic bacteria are time-consuming and difficult for quantification, although they are practical and reliable. Therefore, novel strategies for rapid, sensitive, and cost-effective detection are in great demand. Aptamer is a kind of oligonucleotide that selected by repeated screening in vitro or systematic evolution of ligands by exponential enrichment (SELEX) technology. Over the past years, owing to high affinity and specificity of aptamers, a variety of aptamer-based biosensors have been designed and applied for pathogen detection. In this review, we have discussed the recent advances on the applications of aptamer-based biosensors in detection of pathogenic bacteria. In addition, we also point out some problems in current methods and look forward to the further development of aptamer-based biosensors for pathogen detection.

Electrochemical Immuno- and Aptamer-Based Assays for Bacteria: Pros and Cons over Traditional Detection Schemes

Microbiological safety of the human environment and health needs advanced monitoring tools both for the specific detection of bacteria in complex biological matrices, often in the presence of excessive amounts of other bacterial species, and for bacteria quantification at a single cell level. Here, we discuss the existing electrochemical approaches for bacterial analysis that are based on the biospecific recognition of whole bacterial cells. Perspectives of such assays applications as emergency-use biosensors for quick analysis of trace levels of bacteria by minimally trained personnel are argued.

Generation of ssDNA aptamers as diagnostic tool for Newcastle avian virus

Aptamers are short single-stranded DNA (ssDNA), RNA or synthetic XNA molecules, which are used as a class of affinity binders recognizing target molecules with a very high affinity and specificity. The aim of this study was to generate and characterize ssDNA aptamers for the detection of Newcastle disease virus (NDV). These aptamers were selected using systematic evolution of ligands by exponential enrichment (SELEX) in combination with quantitative high-throughput DNA sequencing. After three rounds of selections, a highly enriched ssDNA pool was sequenced, and the results were analyzed using FASTAptamer Toolkit. Sequencing reads were sorted by copy numbers and clustered into groups, according to their sequence homology. Top aptameric sequences were used to develop a sandwich enzymatic linked aptamer assay (ELAA) for rapid and sensitive detection of NDV in farm samples. The selected aptamers have an affinity within the nanomolar range, and a high specificity with no cross-reactivity towards other avian viruses. Following optimization of the sandwich ELAA method, the results demonstrated that both selected aptamers Apt_NDV01 and Apt_NDV03 with dissociation constant values of 31 nM and 78.1 nM, respectively, showed the highest specificity and affinity for NDV detection. The ELAA results were verified by quantitative real-time PCR, demonstrating strong concordance, and showing outstanding accuracy for detection of NDV in field sample. In summary, combination of SELEX with high-throughput DNA sequencing allowed rapid screening and selection of aptamers. The selected aptamers allowed recognition of NDV with high affinities. This is the first report that uses a validated sandwich ELAA for rapid and specific detection of NDV in poultry samples.

Selective Binding and Elution of Aptamers for Pesticides Based on Sol-Gel-Coated Nanoporous Anodized Aluminum Oxide Membrane

Sol-gel-based mesopores allow the entry of target small molecules retained in their cavity and aptamers to bind to target molecules. Herein, sol-gel-based materials are applied to screen-selective aptamers for small molecules, such as pesticides. To enhance the efficiency of aptamer screening using a sol-gel, it is necessary to increase the binding surface. In this study, we applied the sol-gel to an anodized aluminum oxide (AAO) membrane, and the morphological features were observed via electron microscopy after spin coating. The binding and elution processes were conducted and confirmed by fluorescence microscopy and polymerase chain reaction. The sol-gel coating on the AAO membrane formed a hollow nanocolumn structure. A diazinon-binding aptamer was bound to the diazinon-containing sol-gel-coated AAO membrane, and the bound aptamer was effectively retrieved from the sol-gel matrix by thermal elution. As a proof of concept, a sol-gel-coated AAO disc was mounted on the edge of a pipette tip, and the feasibility of the prepared platform for the systematic evolution of ligands by exponential enrichment (SELEX) of the aptamer binding was also confirmed. The proposed approach will be applied to an automated SELEX cycle using an automated dispenser, such as a pipetting robot, in the near future.

Chemical Modification of Aptamers for Increased Binding Affinity in Diagnostic Applications: Current Status and Future Prospects

Aptamers are short single stranded DNA or RNA oligonucleotides that can recognize analytes with extraordinary target selectivity and affinity. Despite their promising properties and diagnostic potential, the number of commercial applications remains scarce. In order to endow them with novel recognition motifs and enhanced properties, chemical modification of aptamers has been pursued. This review focuses on chemical modifications, aimed at increasing the binding affinity for the aptamer's target either in a non-covalent or covalent fashion, hereby improving their application potential in a diagnostic context. An overview of current methodologies will be given, thereby distinguishing between pre- and post-SELEX (Systematic Evolution of Ligands by Exponential Enrichment) modifications.

Inhibitory effects of aptamer targeted teicoplanin encapsulated PLGA nanoparticles for Staphylococcus aureus strains

Emergence of resistance to traditional antibiotic treatments necessitates alternative delivery systems. Teicoplanin is a glycopeptide antibiotic used in the treatments of serious infections caused by Gram-positive bacteria, including Methicillin Resistant Staphylococcus aureus (MRSA). One strategy to keep up with antibiotic resistance development is to limit dose and amount during treatments. Targeted delivery systems of antibiotics have been suggested as a mechanism to slow-down the evolution of resistance and to increase efficiency of the antimicrobials on already resistant pathogens. In this study, we report teicoplanin delivery nanoparticles of Poly Lactic-co-Glycolic Acid (PLGA), which are functionalized with S. aureus specific aptamers. A 32-fold decrease in minimum inhibitory concentration (MIC) values of teicoplanin for S. aureus was demonstrated for susceptible strains and about 64-fold decline in MIC value was achieved for moderately resistant clinical isolates of MRSA upon teicoplanin treatment with aptamer-PLGA nanoparticles. Although teicoplanin delivery in PLGA nanoparticles without targeting demonstrated eightfold decrease in MIC of susceptible strains of S. aureus and S. epidermidis and twofold in MIC of resistant strains, the aptamer targeting specifically decreased MIC for S. aureus, but not for S. epidermidis. Therefore, aptamer-targeted PLGA delivery of antibiotic can be an attractive alternative to combat with some of the multi-drug resistant bacterial pathogens.

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.

Aptamer-based biosensor for detecting carcinoembryonic antigen

Carcinoembryonic antigen (CEA), as one of the common tumor markers, is a human glycoprotein involved in cell adhesion and is expressed during human fetal development. Since the birth of human, CEA expression is largely inhibited, with only low levels in the plasma of healthy adults. Generally, CEA will overexpressed in many cancers, including gastric, breast, ovarian, lung, and pancreatic cancers, especially colorectal cancer. As one of the important tumor markers, the detection of CEA has great significance in differential diagnosis, condition monitoring and therapeutic evaluation of diseases. Conventional CEA testing typically uses immunoassay methods. However, immunoassay methods require complex and expensive instruments and professional personnel to operate. Moreover, radioactive element may cause certain damage to the human body, which limits their wide application. In the past few years, biosensors, especially aptamer-based biosensors, have attracted extensive attention due to their high sensitivity, good selectivity, high accuracy, fast response and low cost. This review briefly classifies and describes the advance in optical and electrochemical aptamer biosensors for CEA detection, also explains and compares their advantages and disadvantages.

Rapid and label-free detection of Brucella melitensis in milk and milk products using an aptasensor

In this work, a novel quartz crystal microbalance (QCM) aptasensor is designed for the diagnosis of Brucella melitensis bacteria, which affects the Mediterranean fever (brucellosis) from the zoonotic diseases that are very common in the Middle East Countries. The method is based on the selection of B. melitensis bacterium from solutions using B. melitensis specific binding aptamer (Apt) attached magnetic nanoparticles. The surface of the magnetic nanoparticles (i.e.,Fe₃O₄) was modified by 3-aminopropyltriethoxysilane (APTES) and then grafted with a hydrophilic macromonomer poly(ethyleneglycol)-methacrylate (PEG-MA) as a first block polymer and glycidylmethacrylate (GMA) as a second block functional polymer via atom transfer radical polymerization (ATRP) method [Fe₃O₄ @SiO₂ @p(PEG-MA-GMA)], then, the specific binding aptamer was immobilized. The aptamer immobilized magnetic nanoparticles were used for the pre-concentration of the target bacterium, and the same aptamer sequence was also immobilized on the QCM chip and used for the quantitative detection of B. melitensis using QCM aptasensor. The detection limits of the QCM aptasensor were in the range 1.0²-1.0⁷ CFU mL^-1, with recoveries up to 79%. The synthesized [Fe₃O₄ @SiO₂ @p(PEGMA-GMA)] nanoparticles showed a good permanence and high isolation recoveries for the pull down of the target bacterium from food samples, after recycling eight times. The method was successfully applied to target bacterium determinations in milk and milk product samples.

Aptamers: an emerging class of bioaffinity ligands in bioactive peptide applications

The food and health applications of bioactive peptides have grown remarkably in the past few decades. Current elucidations have shown that bioactive peptides have unique structural arrangement of amino acids, conferring distinct functionalities, and molecular affinity characteristics. However, whereas interest in the biological potency of bioactive peptides has grown, cost-effective techniques for monitoring the structural changes in these peptides and how these changes affect the biological properties have not grown at the same rate. Due to the high binding affinity of aptamers for other biomolecules, they have a huge potential for use in tracking the structural, conformational, and compositional changes in bioactive peptides. This review provides an overview of bioactive peptides and their essential structure-activity relationship. The review further highlights on the types and methods of synthesis of aptamers before the discussion of the prospects, merits, and challenges in the use of aptamers for bioaffinity interactions with bioactive peptides.