Colorimetric Aptasensor Based on Truncated Aptamer and Trivalent DNAzyme for Vibrio parahemolyticus Determination

Generating robust aptamers for food analysis by sequence-based configuration optimization

Advanced analytical techniques are emerging in the food industry. Aptamer-based biosensors achieve rapid and highly selective analysis, thus drawing particular attention. Aptamers are oligonucleotide probes screened via in vitro Systematic Evolution of Ligands by EXponential Enrichment (SELEX), which can bind with their specific targets by folding into three-dimensional configurations and accept various modifications to be incorporated into biosensors, showing great potential in food analysis. Unfortunately, aptamers obtained by SELEX may not possess satisfactory affinity. Post-SELEX strategies were proposed to optimize aptamers' configuration and enhance the binding affinity, with specificity confirmed. Sequence-based optimization strategies exhibit great advantages in simple operation, good generalization, low cost, etc. This review summarizes the latest study (2015-2023) on generating robust aptamers for food targets by sequence-based configuration optimization, as well as the generated aptamers and aptasensors, with an expectation to provide inspirations for developing aptamer and aptasensors with high performance for food analysis and to safeguard food quality and safety.

Recent progress on DNAzyme-based biosensors for pathogen detection

Pathogens endanger food safety, agricultural productivity, and human health. Those pathogens are spread through direct/indirect contact, airborne transmission and food/waterborne transmission, and some cause severe health consequences. As the population grows and global connections intensify, the transmission of infectious diseases expands. Traditional detection methods for pathogens still have some shortcomings, such as time-consuming procedures and high operational costs. To fulfil the demands for simple and effective detection, numerous biosensors have been developed. DNAzyme, a unique DNA structure with catalytic activity, is gradually being applied in the field of pathogen detection owing to its ease of preparation and use. In this review, we concentrated on the two main types of DNAzyme, hemin/G-quadruplex DNAzyme (HGD) and RNA-cleaving DNAzyme (RCD), explaining their research progress in pathogen detection. Furthermore, we introduced two additional novel DNAzymes, CLICK 17 DNAzyme and Supernova DNAzyme, which showed promising potential in pathogen detection. Finally, we summarize the strengths and weaknesses of these four DNAzymes and offer feasible recommendations for the development of biosensors.

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.

Selection and application of highly specific Salmonella typhimurium aptamers against matrix interference

In practical applications, the structure and performance of aptamers can be influenced by the presence of sample matrices, which interferes with the specific binding between the aptamer and its target. In this work, to obtain aptamer chains resistant to matrix interference, four typical food matrices were introduced as negative selection targets and selection environments in the process of selecting aptamers for Salmonella typhimurium using the systematic evolution of ligands by exponential enrichment (SELEX) technology. As a result, some highly specific candidate aptamers for Salmonella typhimurium (BB-34, BB-37, ROU-8, ROU-9, ROU-14, ROU-24, DAN-3, NAI-12, and NAI-21) were successfully obtained. Based on the characterization results of secondary structure, affinity, and specificity of these candidate aptamers, ROU-24 selected in the pork matrix and BB-34 selected in the binding buffer were chosen to develop label-free fluorescence aptasensors for the sensitive and rapid detection of the Salmonella typhimurium and verify the performance against matrix interference. The ROU-24-based aptasensor demonstrated a larger linear range and better specificity compared to the BB-34-based aptasensor. Meanwhile, the recovery rate of the ROU-24-based aptasensor in real sample detection (ranging from 94.2% to 110.7%) was significantly higher than that of the BB-34-based aptasensor. These results illustrated that the negative selection of food matrices induced in SELEX could enhance specific binding between the aptamer and its target and the performance against matrix interference. Overall, the label-free fluorescence aptasensors were developed and successfully validated in different foodstuffs, demonstrating a theoretical and practical basis for the study of aptamers against matrix interference.

High-affinity truncated aptamers for detection of Cronobacter spp with magnetic separation-assisted DNAzyme-driven 3D DNA walker

After optimizing the original aptamer sequence by truncation strategy, a magnetic separation-assisted DNAzyme-driven 3D DNA walker fluorescent aptasensor was developed for detecting the food-borne pathogen Cronobacter species. Iron oxide magnetic nanoparticles (MNPs) modified with a hybrid of truncated aptamer probe and DNAzyme strand (AP-E1) denoted as MNPs@AP-E1, were employed as capture probes. Simultaneously, a DNAzyme-driven 3D-DNA walker was utilized as the signal amplification element. The substrate strand (Sub) was conjugated with the gold nanoparticles (AuNPs), resulting in the formation of AuNPs@Sub, which served as a 3D walking track. In the presence of the target bacteria and Mg2+, E1-DNAzyme was activated and moved along AuNPs@Sub, continuously releasing the signal probe. Under optimized conditions, a strong linear correlation was observed for Cronobacter sakazakii (C. sakazakii) in the concentration range 101 to 106 CFU mL-1, with a low detection limit of 2 CFU mL-1. The fluorescence signal responses for different Cronobacter species exhibited insignificant differences, with a relative standard deviation of 3.6%. Moreover, the aptasensor was successfully applied to determine  C. sakazakii in real samples with recoveries of 92.86%-108.33%. Therefore, the novel method could be a good candidate for ultra-sensitive and selective detection of Cronobacter species without complex manipulation.

Detection of acrylamide in food based on MIL-glucose oxidase cascade colorimetric aptasensor

BACKGROUND

Maillard reaction involves the polymerization, condensation, and other reactions between compounds containing free amino groups and reducing sugars or carbonyl compounds during heat processing. This process endows unique flavors and colors to food, while it can also produce numerous hazards. Acrylamide (AAm) is one of Maillard's hazards with neurotoxicity and carcinogenicity, these effects can trigger mutations and alternations in gene expression in human cells and accelerate organ aging. An accurate and reliable acrylamide detection method with high sensitivity and specificity for future regulatory activities is urgently needed.

RESULTS

Herein, we constructed a colorimetric aptasensor with the hybridization of MIL-glucose oxidase (MGzyme)-cDNA and magnetic nanoparticle-aptamer (MNP-Apt) to specifically detect AAm. The incorporation of MB-Apt and AAm released MGzyme-cDNA in the supernatant, took the supernatant out, with the addition of glucose and TMB, MGzyme would oxidize glucose, the resulting •OH facilitated the oxidation of colorless TMB to blue ox-TMB. The absorbance value at 652 nm, which indicates the characteristic absorption peak of ox-TMB, exhibited a proportion to the concentration of AAm. MGzyme avoided the addition of harmful intermediate H2O2 and created an acid microenvironment for the catalytic reaction. MNP-Apt possessed the advantages of high specificity and simplified separation. Under optimal conditions, this method displayed a linear range of 0.01-100 μM with the limit of detection of 1.53 nM. With the spiked analysis data cross-verified by ELISA kit, this aptasensor was proven to specifically detect AAm at low concentrations.

SIGNIFICANCE

This colorimetric aptasensor was the integration of aptamer and the enzyme-cascade system, which could broaden the applicable range of enzyme-cascade system, break the limits of specific detection of substrates, eliminate the need for harmful intermediates, improve the reaction efficiency, implement the specific detection, whilst enabling the accurate detection of AAm. Given these remarkable performances, this method has shown significant potential in the field of food safety inspection.

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.

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.

Improving aptamer performance: key factors and strategies

Aptamers are functional single-stranded oligonucleotide fragments isolated from randomized libraries by Systematic Evolution of Ligands by Exponential Enrichment (SELEX), exhibiting excellent affinity and specificity toward targets. Compared with traditional antibody reagents, aptamers display many desirable properties, such as low variation and high flexibility, and they are suitable for artificial and large-scale synthesis. These advantages make aptamers have a broad application potential ranging from biosensors, bioimaging to therapeutics and other areas of application. However, the overall performance of aptamer pre-selected by SELEX screening is far from being satisfactory. To improve aptamer performance and applicability, various post-SELEX optimization methods have been developed in the last decade. In this review, we first discuss the key factors that influence the performance or properties of aptamers, and then we summarize the key strategies of post-SELEX optimization which have been successfully used to improve aptamer performance, such as truncation, extension, mutagenesis and modification, splitting, and multivalent integration. This review shall provide a comprehensive summary and discussion of post-SELEX optimization methods developed in recent years. Moreover, by discussing the mechanism of each approach, we highlight the importance of choosing the proper method to perform post-SELEX optimization.

A dual-mode ratiometric aptasensor for accurate detection of pathogenic bacteria based on recycling of DNAzyme activation

Pathogenic bacteria have a significant impact on food safety. Herein, an innovative dual-mode ratiometric aptasensor was constructed for ultrasensitive and accurate detection of Staphylococcus aureus (S. aureus) based on recycling of DNAzyme activation on gold nanoparticles-functionalized MXene nanomaterials (MXene@Au NPs). Electrochemiluminescent (ECL) emitter-labeled probe DNA (probe 2-Ru) containing the blocked DNAzyme was partly hybridized with aptamer and then captured by electrochemical (EC) indicator-labeled probe DNA (probe 1-MB) on electrode surface. When S. aureus presented, the conformation vibration of probe 2-Ru activated the blocked DNAzymes, leading to recycling cleavage of probe 1-MB and ECL tag close to electrode surface. Based on the reverse change tendencies of ECL and EC signals, aptasensor achieved S. aureus quantification from 5 to 10⁸ CFU/mL. Moreover, the self-calibration characteristic of the aptasensor with dual-mode ratiometric readout ensured the reliable measurement of S. aureus in real samples. This work showed useful insight into sensing foodborne pathogenic bacteria.

Induced ultrasensitive electrochemical biosensor for target MDA-MB-231 cell cytoplasmic protein detection based on RNA-cleavage DNAzyme catalytic reaction

Herein, we implemented RNA-cleaving DNAzymes specific for the endogenous protein of breast cancer cells (MDA-MB -231) and programmed for electrochemical detection. Thionine-modified gold nanoparticles and modified magnetic nanoparticles are attached to the two ends of the DNAzyme molecule. The prepared probe is pulled to the surface of the electrode with the help of a magnetic field, and the signal caused by the electrochemical activity of thionine is observed on the surface of the electrode. The presence of a covalent gold nanoparticle-thionine hybrid as a highly electroactive/enhanced electrochemical label ensures a strong detection signal. After addition of the enzyme activator cofactor (MDA-MB -231 cytoplasmic cell protein), it reacts with the catalytic core of the enzyme sequence in the DNAzyme molecule and triggers the cleavage reaction in the substrate sequence of the DNAzyme molecule. During this process, the gold nanoparticle-thionine labels are detached from the probe and released into the solution. Inductive removal of gold nanoparticles leads to a decrease in the current related to the reduction of thionine on the electrode surface. The results show that this biosensor can detect this protein marker in the linear range of (1.0E-06 to 1.0E+01) pg/ml, with a detection limit (1.0129E-07 pg/ml), using differential pulse voltammetry as a measuring technique. As well as, electrochemical impedance spectroscopy (EIS).

Study of binding mechanism of aptamer to kanamycin and the development of fluorescent aptasensor in milk detection

Aptasensors being versatile sensing platforms presented higher sensitivity toward target detection. However, lacking theoretical basis of recognition between most targets and their corresponding aptamers has impeded their applications. Herein, we conducted a study to explore the binding mechanism of aptamer to kanamycin (Kana) and developed rapid fluorescent aptasensing methods. Based on the fluorescence polarization results, base mutations were performed at different sites of the aptamer. The key binding nucleotides of Kana was identified as T7, T8, C13 and A15 by using isothermal titration calorimetry (ITC). The Kmut3 (2.18 μM) with lower dissociation constants (Kd), one-third of the native aptamer (6.91 μM), was also obtained. In addition, the lower K⁺ concentration and temperature were found to be conducive to Kana binding. Circular dichroism (CD) results revealed that the binding of Kana can trigger the change of base stacking force and helix force. On the aforementioned basis, a fluorescent sensor was designed with the native aptamer and Kmut3 as recognition elements. The comparison results proved that the Kmut3 presented a 3 times lower limit of detection of 59 nM compared to the native aptamer (148 nM). Notably, this developed aptasensor can be finished in 45 min and was convenient to operate.

Cluster-bomb type magnetic biosensor for ultrasensitive detection of Vibrio parahaemolyticus based on low field nuclear magnetic resonance

Herein, a novel cluster-bomb type signal sensing and amplification strategy in low field nuclear magnetic resonance was proposed, and a magnetic biosensor for ultrasensitive homogeneous immunoassay of Vibrio parahaemolyticus (VP) was developed. The capture unit MGO@Ab was magnetic graphene oxide (MGO) immobilized by VP antibody (Ab) to capture VP. And, the signal unit PS@Gd-CQDs@Ab was polystyrene (PS) pellets covered by Ab to recognize VP and Gd-CQDs i.e. carbon quantum dots (CQDs) containing lots of magnetic signal labels Gd³⁺. In presence of VP, the immunocomplex signal unit-VP-capture unit could be formed and separated by magnetic force conveniently from the sample matrix. With the successive introduction of disulfide threitol and hydrochloric acid, signal units were cleaved and disintegrated, resulting in a homogeneous dispersion of Gd³⁺. Thus, cluster-bomb type dual signal amplification was achieved through increasing the amount and the dispersity of signal labels simultaneously. Under optimal experimental conditions, VP could be detected in the concentration range of 5-1.0 × 10⁶ CFU/mL, with a limit of quantitation (LOQ) 4 CFU/mL. In addition, satisfactory selectivity, stability and reliability could be obtained. Therefore, this cluster-bomb type signal sensing and amplification strategy is powerful in designing magnetic biosensor and detecting pathogenic bacteria.

Programmable Nanostructures Based on Framework-DNA for Applications in Biosensing

DNA has been actively utilized as bricks to construct exquisite nanostructures due to their unparalleled programmability. Particularly, nanostructures based on framework DNA (F-DNA) with controllable size, tailorable functionality, and precise addressability hold excellent promise for molecular biology studies and versatile tools for biosensor applications. In this review, we provide an overview of the current development of F-DNA-enabled biosensors. Firstly, we summarize the design and working principle of F-DNA-based nanodevices. Then, recent advances in their use in different kinds of target sensing with effectiveness have been exhibited. Finally, we envision potential perspectives on the future opportunities and challenges of biosensing platforms.

Isolation of Bacteria Aptamers with Non-SELEX for the Development of a Highly Sensitive Colorimetric Assay Based on Dual Signal Amplification

In this work, an aptamer against Escherichia coli is isolated via non-SELEX, which executes efficient selection by employing repetitive cycles of centrifugation-based partitioning, and the binding site of the aptamer on E. coli cell surfaces is inferred to be a membrane protein. Moreover, truncated sequence 2-17-2 with a higher affinity (K_d = 101.76 nM) is employed for highly sensitive colorimetric detection of bacteria based on the dual signal amplification strategy. When targets exist, the release of DNA 1 from the polymer activates a hybridization chain reaction (HCR) between DNA 1 and DNA 2, thereby inducing the aggregation of probe 1. Subsequently, DNA 3 dissociated from probe 1 as a linker DNA further assembles probe 2/3. In this system, two types of DNA@gold nanoparticles (AuNPs) coexist and successively aggregate AuNPs based on divergent triggering mechanisms. Under optimal conditions, the dual signal amplification strategy presents excellent sensitivity (10 CFU mL^-1) and specificity, as well as the realization of real sample analysis.

Fluorescent aptasensor for detection of live foodborne pathogens based on multicolor perovskite-quantum-dot-encoded DNA probes and dual-stirring-bar-assisted signal amplification

In this study, a fluorescent (FL) aptasensor was developed for on-site detection of live Salmonella typhimurium (S.T.) and Vibrio parahaemolyticus (V.P.). Complementary DNA (cDNA) of aptamer (Apt)-functionalized multicolor polyhedral oligomeric silsesquioxane-perovskite quantum dots (cDNA-POSS-PQDs) were used as encoded probes and combined with dual-stirring-bar-assisted signal amplification for pathogen quantification. In this system, bar 1 was labeled with the S.T. and V.P. Apts, and then bar 2 was functionalized with cDNA-POSS-PQDs. When S.T. and V.P. were introduced, pathogen-Apt complexes would form and be released into the supernatant from bar 1. Under agitation, the two complexes reached bar 2 and subsequently reacted with cDNA-POSS-PQDs, which were immobilized on MXene. Then, the encoded probes would be detached from bar 2 to generate FL signals in the supernatant. Notably, the pathogens can resume their free state and initiate next cycle. They swim between the two bars, and the FL signals can be gradually enhanced to maximum after several cycles. The FL signals from released encoded probes can be used to detect the analytes. In particular, live pathogens can be distinguished from dead ones by using an assay. The detection limits and linear range for S.T. and V.P. were 30 and 10 CFU/mL and 10²-10⁶ CFU/mL, respectively. Therefore, this assay has broad application potential for simultaneous on-site detection of various live pathogenic bacteria in water.

Discovery and Optimization of an Aptamer and Its Sensing Ability to Amantadine Based on SERS via Binary Metal Nanoparticles

With the growing concern of illegal abuse of amantadine (AMD) and its potential harmful impact on humans, detection of AMD has become an urgent food safety and environmental topic. Biosensing is a promising method for this, but the effective recognition of AMD still remains a challenge. Herein, we isolated an aptamer (Am-20) for AMD through a 14-round iterative selection based on capture-SELEX. The preliminary interaction mechanism between AMD and Am-20 was clarified with the help of docking simulations. Facilitated by a base mutation and truncation strategy, an optimized aptamer Am-20-1 with a short length of 62-mer was obtained, which exhibited competitive affinity with a K_d value of 33.90 ± 5.16 nM. A structure-switching SERS-based aptasensor based on Am-20-1 was then established for AMD quantification via a binary metal nanoparticle-embedded Raman reporter substrate (AuNRs@ATP@AgNPs). The fabricated strategy showed a wide linear range (0.005∼25 ng/mL) and a low limit of detection (0.001 ng/mL) for AMD determination. We envision that the novel aptamer identified in this study will provide a complementary tool for specific recognition and detection of AMD and could assist in the supervision of illegal abuse of AMD.

Toward intelligent food packaging of biosensor and film substrate for monitoring foodborne microorganisms: A review of recent advancements

Microorganisms in food do harms to human. They can cause serious adverse reactions and sometimes even death. So it is an urgent matter to find an effective method to control them. The research of intelligent- biosensor packaging is in the ascendant in recent years, which is mainly promoted by reflecting on food safety and reducing resource waste. Intelligent biosensor-packaging is an instant and efficient intelligent packaging technology, which can directly and scientifically manifest the quality of food without complex operation. In this review, the purposes of providing relevant information on intelligent biosensor-packaging are reviewed, such as types of biosensors for monitoring foodborne microorganism, the suitable material for intelligent biosensor-packaging and design and fabrication of intelligent biosensor-packaging. The potential of intelligent biosensor-packaging in the detection of foodborne microorganisms is emphasized. The challenges and directions of the intelligent biosensor-packaging in the detection of foodborne pathogens are discussed. With the development of science and technology in the future, the intelligent biosensor-packaging should be commercialized in a real sense. And it is expected that commercial products can be manufactured in the future, which will provide a far-reaching approach in food safety and food prevention. HighlightsSeveral biosensors are suitable for the detection of food microorganisms.Plastic polymer is an excellent choice for the construction of intelligent biosensor packaging.Design and fabrication can lay the foundation for intelligent-biosensor packaging.Intelligent biosensor-packaging can realize fast and real-time detection of microorganisms in food.

Advances in magnetic nanoparticles for the separation of foodborne pathogens: Recognition, separation strategy, and application

Foodborne pathogens contamination is one of the main sources of food safety problems. Although the existing detection methods have been developed for a long time, the complexity of food samples is still the main factor affecting the detection time and sensitivity, and the rapid separation and enrichment of pathogens is still an objective to be studied. Magnetic separation strategy based on magnetic nanoparticles (MNPs) is considered to be an effective tool for rapid separation and enrichment of foodborne pathogens in food. Therefore, this study comprehensively reviews the development of MNPs in the separation of foodborne pathogens over the past decade. First, various biorecognition reagents for identification of foodborne pathogens and their modifications on the surface of MNPs are introduced. Then, the factors affecting the separation of foodborne pathogens, including the size of MNPs, modification methods, separation strategies and separation forms are discussed. Finally, the application of MNPs in integrated detection methods is reviewed. Moreover, current challenges and prospects of MNPs for the analysis of foodborne pathogens are discussed. Further research should focus on the design of multifunctional MNPs, the processing of large-scale samples, the simultaneous analysis of multiple targets, and the development of all-in-one small analytical device with separation and 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.

Split aptamer acquisition mechanisms and current application in antibiotics detection: a short review

Antibiotic contamination is becoming a prominent global issue. Therefore, sensitive, specific and simple technology is desirable the demand for antibiotics detection. Biosensors based on split aptamer has gradually attracted extensive attention for antibiotic detection due to its higher sensitivity, lower cost, false positive/negative avoidance and flexibility in sensor design. Although many of the reported split aptamers are antibiotics aptamers, the acquisition and mechanism of splitting is still unknow. In this review, six reported split aptamers in antibiotics are outlined, including Enrofloxacin, Kanamycin, Tetracycline, Tobramycin, Neomycin, Streptomycin, which have contributed to promote interest, awareness and thoughts into this emerging research field. The study introduced the pros and cons of split aptamers, summarized the assembly principle of split aptamer and discussed the intermolecular binding of antibiotic-aptamer complexes. In addition, the recent application of split aptamers in antibiotic detection are introduced. Split aptamers have a promising future in the design and development of biosensors for antibiotic detection in food and other field. The development of the antibiotic split aptamer meets many challenges including mechanism discovery, stability improvement and new biosensor development. It is believed that split aptamer could be a powerful molecular probe and plays an important role in aptamer biosensor.

Recent advances in aptamer applications for analytical biochemistry

Aptamers are typically defined as relatively short (20-60 nucleotides) single-stranded DNA or RNA molecules that bind with high affinity and specificity to various types of targets. Aptamers are frequently referred to as "synthetic antibodies" but are easier to obtain, less expensive to produce, and in several ways more versatile than antibodies. The beginnings of aptamers date back to 1990, and since then there has been a continual increase in aptamer publications. The intent of the present account was to focus on recent original research publications, i.e., those appearing in 2019 through April 2020, when this account was written. A Google Scholar search of this recent literature was performed for relevance-ranking of articles. New methods for selection of aptamers were not included. Nine categories of applications were organized and representative examples of each are given. Finally, an outlook is offered focusing on "faster, better, cheaper" application performance factors as key drivers for future innovations in aptamer applications.

Fast and sensitive graphene oxide-DNAzyme-based biosensor for Vibrio alginolyticus detection

DNAzymes have been widely and effectively used for the detection of pathogenic bacteria, which pose a serious public health threat. However, the rapid and cost-effective detection of such bacteria remains a major challenge. In this study, we successfully selected Vibrio alginolyticus-specific DNAzymes. The activity of the candidates was assessed via fluorescence intensity and gel electrophoresis. The DNAzyme DT1 had a detection limit of 31 CFU/ml for V. alginolyticus and exhibited high specificity. Graphene oxide (GO) was used to develop a DNAzyme-based fluorescent sensor for the detection of V. alginolyticus, which significantly improved detection performance and shortened the reaction time as little as 10 s. The proposed method was then validated using crab, shrimp, fish, clam, and oyster samples. This study thus provides a new method for the rapid and sensitive detection of V. alginolyticus.

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.

Bio-Receptors Functionalized Nanoparticles: A Resourceful Sensing and Colorimetric Detection Tool for Pathogenic Bacteria and Microbial Biomolecules

Pathogenic bacteria and several biomolecules produced by cells and living organisms are common biological components posing a harmful threat to global health. Several studies have devised methods for the detection of varying pathogenic bacteria and biomolecules in different settings such as food, water, soil, among others. Some of the detection studies highlighting target pathogenic bacteria and biomolecules, mechanisms of detection, colorimetric outputs, and detection limits have been summarized in this review. In the last 2 decades, studies have harnessed various nanotechnology-based methods for the detection of pathogenic bacteria and biomolecules with much attention on functionalization techniques. This review considers the detection mechanisms, colorimetric prowess of bio-receptors and compares the reported detection efficiency for some bio-receptor functionalized nanoparticles. Some studies reported visual, rapid, and high-intensity colorimetric detection of pathogenic bacteria and biomolecules at a very low concentration of the analyte. Other studies reported slight colorimetric detection only with a large concentration of an analyte. The effectiveness of bio-receptor functionalized nanoparticles as detection component varies depending on their selectivity, specificity, and the binding interaction exhibited by nanoparticles, bio-receptor, and analytes to form a bio-sensing complex. It is however important to note that the colorimetric properties of some bio-receptor functionalized nanoparticles have shown strong and brilliant potential for real-time and visual-aided diagnostic results, not only to assess food and water quality but also for environmental monitoring of pathogenic bacteria and a wide array of biomolecules.

Ferrocene-Doped Polystyrene Nanoenzyme and DNAzyme Cocatalytic SERS Quantitative Assay of Ultratrace Pb2+

A new, stable and high-catalytic activity ferrocene-doped polystyrene nanosphere (PN_Fer) sol was prepared by the hydrogel procedure and characterized by electron microscopy and molecular spectroscopy. Results show that the nanosol exhibits excellent catalysis of the new indicator nanoreaction between AgNO₃ and sodium formate to generate nanosilver with strong surface-enhanced Raman scattering (SERS), resonance Rayleigh scattering (RRS) and surface plasmon resonance absorption (Abs) trimode molecular spectral signals. This new nanocatalytic amplification trimode indicator reaction was coupled with the G-quadruplex DNAzyme catalytic amplification of Pb²⁺ aptamer to fabricate a new SERS quantitative/RRS/Abs assay platform for the determination of ultratrace amounts of Pb²⁺. The Pb²⁺ content in water samples was analyzed with satisfactory results.

G-quadruplex based biosensors for the detection of food contaminants

G-quadruplex (G4) is a very interesting DNA structure, commonly associated with cancer and its treatment. With flexible binding ability, G4 has been extended as a significant component in biosensors. On account of its simple operation, high sensitivity and low cost, G4-based biosensors have attracted considerable interest for the detection of food contaminants. In this review, research published in recent 5 years is collated from a principle perspective, that is target recognition and signal transduction. Contaminants with G4 binding capacity are illustrated, emerging G4-based biosensors including colorimetric, electrochemical and fluorescent sensors are also elaborated. The current review indicates that G4 has provided an efficient and effective solution for the rapid detection of food contaminants. A distinctive feature of G4 as recognition unit is the simple composition, but the selectivity is still unsatisfactory. As signal reporter, G4/hemin DNAzyme has not only achieved amplified signals, but also enabled visualized detection, which offers great potential for on-site measurement. With improved selectivity and visualized signal, the combination of aptamer and G4 seems to be an ideal strategy. This promising combination should be developed for the real-time monitor of multiple contaminants in food matrix.

Sensitive colorimetric aptasensor based on stimuli-responsive metal-organic framework nano-container and trivalent DNAzyme for zearalenone determination in food samples

Zearalenone (ZEN) poses a serious threat to human and animal health. The development of sensitive determination methods for ZEN is of great significance for ensuring the quality and safety of food. Herein, based on a stimuli-responsive aptamer-functionalized metal-organic framework (MOF) nano-container and trivalent DNA peroxidase mimicking enzyme (DNAzyme), an efficient aptasensor was constructed initially for the colorimetric determination of ZEN. The proposed aptasensor only required simple operations but exhibited outstanding specificity, reproducibility, storage stability and reusability simultaneously. Under the optimal conditions, there was a good linear relationship between the changed absorbance and logarithm concentration of ZEN within 0.01-100 ng mL^-1, and the limit of detection (LOD) could reach 0.36 pg mL^-1. Moreover, the proposed aptasensor was reliable in quantifying ZEN in spiked food samples. The current bioassay provides a promising scheme for constructing stable, specific and rapid colorimetric platforms with potential applications in the fields of food safety.

A Novel Truncated DNAzyme Modified Paper Analytical Device for Point-of-Care Test of Copper Ions in Natural Waters

On-site determination of trace copper ions in natural waters is of great significance to environmental monitoring, and how to develop accurate and specific point-of-care test methods is one critical issue. In the study, a paper-based analytical device (PAD) being modified with a new truncated DNAzyme (CLICK-T, which was derived from a reported DNAzyme-CLICK-17) was developed for Cu ions detection. The detection mechanism was based on Cu(II)-catalyzed azide-alkyne cycloaddition (Cu(II)AAC) reaction. It can directly conduct on-site analysis of Cu(II) ions based on fluorescent signals detected using a mobile phone. In the assay, the CLICK-T was firstly modified on the PADs. Then, water samples containing Cu ions mixed with 3-azido-7-hydroxycoumarin and 3-butyn-1-ol were instantly dripped on PADs and incubated for 20 min. Finally, the PADs were excited at 365 nm and emitted fluorescence which could be analyzed on site using smart phones. The Cu(II) concentration could be quantified through RGB analysis with the aid of iPhone APP software. The limit of detection is 0.1 µM by the naked eye due to the fact that CLICK-T exhibited a good catalytic effect on Cu(II)AAC. The Cu(II) concentration could also be directly detected without using reductant, such as ascorbic acid, which is prone to be oxidized in air. This simplifies the PDA detection process improves its efficiency. The PAD is convenient for the on-site analysis of Cu ions in natural waters.

A novel aptamer RRS assay platform for ultratrace melamine based on COF-loaded Pd nanocluster catalytic amplification

Two COFs of BzBD and BzBD loaded Pd nanoclusters (BzBD_Pd) were prepared using 1,3,5-benzenetricarboxaldehyde (Bz), benzidine (BD) and CO reducing agent, and were characterized by transmission electron microscopy (TEM), X-ray powder diffraction (XRD), infrared spectroscopy (IR) and other techniques. BzBD_Pd can strongly catalyze the new and stable Au@NiP nanoreaction that exhibit a strong resonance Rayleigh scattering (RRS) peak at 538 nm and a surface plasmon resonance (SPR) absorption peak at 395 nm, and the sensitive and facile RRS technique was used to study the indicator reaction. Combining the nanocatalytic amplification reaction with specific aptamer (Apt) of some target molecules such as melamine (ML), urea (UR) and bisphenol A (BPA), a simple, sensitive and selective Apt RRS assay platform was established. The linear range of the RRS detection platform for melamine is 0.0025-0.04 nmol/L, and the detection limit (DL) is 1.96 × 10^-4 nmol/L. In addition, ML in real sample was analyzed, the stability of BzBD, BzBD_Pd, PdNPs and the catalytic mechanism of COF_Pd were also considered.

Graphene Based Nanohybrid Aptasensors in Environmental Monitoring: Concepts, Design and Future Outlook

In view of ever-increasing environmental pollution, there is an immediate requirement to promote cheap, multiplexed, sensitive and fast biosensing systems to monitor these pollutants or contaminants. Aptamers have shown numerous advantages in being used as molecular recognition elements in various biosensing devices. Graphene and graphene-based materials/nanohybrids combined with several detection methods exhibit great potential owing to their exceptional optical, electronic and physicochemical properties which can be employed extensively to monitor environmental contaminants. For environmental monitoring applications, aptamers have been successfully combined with graphene-based nanohybrids to produce a wide range of innovative methodologies. Aptamers are immobilized at the surface of graphene based nanohybrids via covalent and non-covalent strategies. This review highlights the design, working principle, recent developmental advances and applications of graphene based nanohybrid aptasensors (GNH-Apts) (since January 2014 to September 2021) with a special emphasis on two major signal-transduction methods, i.e., optical and electrochemical for the monitoring of pesticides, heavy metals, bacteria, antibiotics, and organic compounds from different environmental samples (e.g., water, soil and related). Lastly, the challenges confronted by scientists and the possible future outlook have also been addressed. It is expected that high-performance graphene-based nanohybrid aptasensors would find broad applications in the field of environmental monitoring.

Aptasensors for the detection of infectious pathogens: design strategies and point-of-care testing

The epidemic of infectious diseases caused by contagious pathogens is a life-threatening hazard to the entire human population worldwide. A timely and accurate diagnosis is the critical link in the fight against infectious diseases. Aptamer-based biosensors, the so-called aptasensors, employ nucleic acid aptamers as bio-receptors for the recognition of target pathogens of interest. This review focuses on the design strategies as well as state-of-the-art technologies of aptasensor-based diagnostics for infectious pathogens (mainly bacteria and viruses), covering the utilization of three major signal transducers, the employment of aptamers as recognition moieties, the construction of versatile biosensing platforms (mostly micro and nanomaterial-based), innovated reporting mechanisms, and signal enhancement approaches. Advanced point-of-care testing (POCT) for infectious disease diagnostics are also discussed highlighting some representative ready-to-use devices to address the urgent needs of currently prevalent coronavirus disease 2019 (COVID-19). Pressing issues in aptamer-based technology and some future perspectives of aptasensors are provided for the implementation of aptasensor-based diagnostics into practical application.

Aptamer-Based Antibacterial and Antiviral Therapy against Infectious Diseases

Nucleic acid aptamers are single-stranded DNA or RNA molecules selected in vitro that can bind to a broad range of targets with high affinity and specificity. As promising alternatives to conventional anti-infective agents, aptamers have gradually revealed their potential in the combat against infectious diseases. This article provides an overview on the state-of-art of aptamer-based antibacterial and antiviral therapeutic strategies. Diverse aptamers targeting pathogen-related components or whole pathogenic cells are summarized according to the species of microorganisms. These aptamers exhibited remarkable in vitro and/or in vivo inhibitory effect for pathogenic invasion, enzymatic activities, or viral replication, even for some highly drug-resistant strains and biofilms. Aptamer-mediated drug delivery and controlled drug release strategies are also included herein. Critical technical barriers of therapeutic aptamers are briefly discussed, followed by some future perspectives for their implementation into clinical utility.

A Short- and Long-Range Fluorescence Resonance Energy Transfer-Cofunctionalized Fluorescence Quenching Collapsar Probe Regulates Amplified and Accelerated Detection of Salmonella

Accurate and rapid quantification of foodborne pathogens is of great significance for food safety and human health. In this work, we have successfully constructed a fluorescence quenching collapsar probe (FQCP) on the basis of a conventional aptamer-encoded molecular beacon (AEMB) and applied it for the detection of Salmonella. In structure, the FQCP is assembled by AEMBs in fours via specific streptavidin and biotin binding. Such a simple format makes the FQCP cofunctionalized with short- and long-range fluorescence resonance energy transfer (FRET) effects, thereby leading to a significantly suppressed inherent background fluorescence that is much lower than that of the conventional AEMB. Moreover, the FQCP exhibits superior biostability because of the blocking of its 3' terminal. The reaction kinetics of the FQCP for Salmonella recognition is obviously improved since the probe designed with four binding sites increases the probability to react with Salmonella. As a result, the FQCP-based sensing platform can rapidly output the target detection signal within 30 min associated with a greatly improved signal-to-noise ratio up to 32.4. The system was also demonstrated with a well antimatrix effect for ultrasensitive detection of Salmonella from tap water, milk, red bull, green tea, orange juice, and Coca-Cola. Our study provides insights into the facile tailoring of functional nucleic acids for amplified and mix-to-answer detection of foodborne pathogens, which could become a powerful analytical tool for straightforward sensing of pathogens in the fields of food safety analysis, clinical diagnostics, and environmental monitoring.

Lateral flow colorimetric biosensor for detection of Vibrio parahaemolyticus based on hybridization chain reaction and aptamer

Vibrio parahaemolyticus (V. parahaemolyticus) is the causative agent for acute hepatopancreatic necrosis disease (AHPND) of shrimp, and it is also a common seafood-borne pathogen for humans. Rapid and accurate identification of V. parahaemolyticus is helpful to diagnose the AHPND and ensure food safety. Common detection methods suffer the deficiency of time-consuming and complexed operation. Based on the increased development of aptamer and our previous study, a new detection assay of V. parahaemolyticus was introduced, in which the aptamer combined with magnetic nanoparticles (MNPs) was the recognizer, hybridization chain reaction (HCR) was the signal amplifier, and lateral flow nucleotide biosensor (LFNB) was the signal exporter. The assay possessed high specificity of distinguishing the target with other bacteria, and the calculated limit of detection was 2.6 × 10³ cells. Furthermore, the whole process just needs 67 min, free of thermocycle instruments and signal readout instruments, which means it is suitable for low-resource laboratories or districts.

DEOXYRIBOZYMES IN DETECTION OF PATHOGENIC BACTERIA

Aim. The purpose of the review was to analyze the use of DNAzyme biosensors for the detection of pathogens. In the recent years, deoxyribozymes (DNAzymes) have a significant impact as biosensors in diverse fields, from detection of metal ions in the environment to theranostic applications and detection of microorganisms. Although routinely used sophisticated instrumental methods are available to detect pathogenic bacterial contamination, they involve time-consuming, complicated sample pre-treatment and expensive instruments. As an alternative, pathogen-specific DNAzymes have demonstrated a series of advantages: a non-destructive rapid analysis technique with in situ and real-time detection of bacteria with high sensitivity and selectivity. A wide range of pathogen-specific DNAzymes has been developed using colorimetric and fluorescence-based detections for pathogenic bacterial contamination in various samples. The current review summarizes the in vitro selection of pathogen-specific DNAzymes, various strategies utilized in the sensor designs, and their potential use in theranostic applications.

DNAzyme-Based Biosensors: Immobilization Strategies, Applications, and Future Prospective

Since their discovery almost three decades ago, DNAzymes have been used extensively in biosensing. Depending on the type of DNAzyme being used, these functional oligonucleotides can act as molecular recognition elements within biosensors, offering high specificity to their target analyte, or as reporters capable of transducing a detectable signal. Several parameters need to be considered when designing a DNAzyme-based biosensor. In particular, given that many of these biosensors immobilize DNAzymes onto a sensing surface, selecting an appropriate immobilization strategy is vital. Suboptimal immobilization can result in both DNAzyme detachment and poor accessibility toward the target, leading to low sensing accuracy and sensitivity. Various approaches have been employed for DNAzyme immobilization within biosensors, ranging from amine and thiol-based covalent attachment to non-covalent strategies involving biotin-streptavidin interactions, DNA hybridization, electrostatic interactions, and physical entrapment. While the properties of each strategy inform its applicability within a proposed sensor, the selection of an appropriate strategy is largely dependent on the desired application. This is especially true given the diverse use of DNAzyme-based biosensors for the detection of pathogens, metal ions, and clinical biomarkers. In an effort to make the development of such sensors easier to navigate, this paper provides a comprehensive review of existing immobilization strategies, with a focus on their respective advantages, drawbacks, and optimal conditions for use. Next, common applications of existing DNAzyme-based biosensors are discussed. Last, emerging and future trends in the development of DNAzyme-based biosensors are discussed, and gaps in existing research worthy of exploration are identified.

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.

Recent Advances in Aptamer-Based Biosensors for Global Health Applications

Since aptamers were first reported in the early 2000s, research on their use for the detection of health-relevant analytical targets has exploded. This review article provides a brief overview of the most recent developments in the field of aptamer-based biosensors for global health applications. The review provides a description of general aptasensing principles and follows up with examples of recent reports of diagnostics-related applications. These applications include detection of proteins and small molecules, circulating cancer cells, whole-cell pathogens, extracellular vesicles, and tissue diagnostics. The review also discusses the main challenges that this growing technology faces in the quest of bringing these new devices from the laboratory to the market.

Designing of Nanomaterials-Based Enzymatic Biosensors: Synthesis, Properties, and Applications

Among the many biological entities employed in the development of biosensors, enzymes have attracted the most attention. Nanotechnology has been fostering excellent prospects in the development of enzymatic biosensors, since enzyme immobilization onto conductive nanostructures can improve characteristics that are crucial in biosensor transduction, such as surface-to-volume ratio, signal response, selectivity, sensitivity, conductivity, and biocatalytic activity, among others. These and other advantages of nanomaterial-based enzymatic biosensors are discussed in this work via the compilation of several reports on their applications in different industrial segments. To provide detailed insights into the state of the art of this technology, all the relevant concepts around the topic are discussed, including the properties of enzymes, the mechanisms involved in their immobilization, and the application of different enzyme-derived biosensors and nanomaterials. Finally, there is a discussion around the pressing challenges in this technology, which will be useful for guiding the development of future research in the area.

Enlarging the Toolbox Against Antimicrobial Resistance: Aptamers and CRISPR-Cas

In the post-genomic era, molecular treatments and diagnostics have been envisioned as powerful techniques to tackle the antimicrobial resistance (AMR) crisis. Among the molecular approaches, aptamers and CRISPR-Cas have gained support due to their practicality, sensibility, and flexibility to interact with a variety of extra- and intracellular targets. Those characteristics enabled the development of quick and onsite diagnostic tools as well as alternative treatments for pan-resistant bacterial infections. Even with such potential, more studies are necessary to pave the way for their successful use against AMR. In this review, we highlight those two robust techniques and encourage researchers to refine them toward AMR. Also, we describe how aptamers and CRISPR-Cas can work together with the current diagnostic and treatment toolbox.

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.

A turn-on-type fluorescence resonance energy transfer aptasensor for vibrio detection using aptamer-modified polyhedral oligomeric silsesquioxane-perovskite quantum dots/Ti3C2 MXenes composite probes

A pair of composite probes based on aptamer modified polyhedral oligomeric silsesquioxane-perovskite quantum dots (POSS-PQDs-Apt) as signal probe and titanium carbide (Ti₃C₂) MXenes as quencher were prepared for the first time. They were employed to fabricate one turn-on-type aptasensor relying on fluorescence resonance energy transfer (FRET) for Vibrio parahaemolyticus (VP) determination. The POSS-PQDs-Apt can be adsorbed on the MXenes nanosheets, and its fluorescence was quenched due to the FRET. After the composite probes were incubated with VP for 50 min, the POSS-PQDs-Apt binding with VP can be released from the surface of MXenes, and the signal recovered due to its higher affinity to the VP than MXenes. The fluorescence intensity from 519 nm emission of the system was measured at 480 nm excitation. Under In optimized conditions, the assay can determine VP in the concentration range 10² - 10⁶ cfu/mL, and the detection limit (LOD) was 30 cfu/mL using fluorescence detection. The LOD is still 100 cfu/mL by naked eye detection which is proper for on-line monitoring VP in aquaculture water. This method was also used to detect VP in actual samples of seawater, the recovery of spiked samples was between 93% and 106%, and relative standard deviation (RSD) was between 2.7% and 6.7%. The result is consistent with the plate count. Therefore, this assay could provide a candidate platform for screening VP in aquaculture industry.

The universal dual-mode aptasensor for simultaneous determination of different bacteria based on naked eyes and microfluidic-chip together with magnetic DNA encoded probes

It was critically important to develop some sensitive, convenient and on-site methods for simultaneous assay of different pathogenic bacteria in foods. In this work, a dual-mode aptasensor was established for fulfilling above aims combing colorimetry with microfluidic chip. This as-prepared dual-mode aptasensor not only realized rapid screening by naked eye on-site, but also the simultaneous quantification of multiple bacteria. Namely, the presence of pathogenic bacteria was firstly judged by naked eyes with Salmonella typhimurium (S.T) and Vibrio parahaemolyticus (V.P) as models. And then, S.T and V.P in positive samples were simultaneously quantified by microfluidic chip. In order to obtain the multiple signals, a series of magnetic DNA encoded-probes (MDEs) was fabricated containing rolling cycle amplified long DNA chain (RCA-DNA) rich in G-quadruplex sequences. They can combine with hemin as DNAzyme to catalyze 3,3'-5,5'-Tetramethyl benzidine (TMB)-H₂O₂ system for color development and be cleaved by EcoRV endonuclease to produce DNA fragments with different lengths. The microfluidic chip was employed to separate and quantify the fragments for quantifying S.T and V.P simultaneously. For this protocol, 100 CFU·mL^-1 of V.P or S.T could be observed by the naked eye and as low as 32 S.T and 30 CFU·mL^-1 V.P could be detected by the chip within 3 min. The dual-mode aptasensor could quickly screen positive samples, and simultaneously perform quantitative detection of the bacteria in positive samples. Our protocol demonstrated its potential in on-site qualification & simultaneous quantification of foodborne bacteria in foods.