Highly sensitive detection of lipopolysaccharides using an aptasensor based on hybridization chain reaction

Aptasensors: employing molecular probes for precise medical diagnostics and drug monitoring

Accurate detection and monitoring of therapeutic drug levels are vital for effective patient care and treatment management. Aptamers, composed of single-stranded DNA or RNA molecules, are integral components of biosensors designed for both qualitative and quantitative detection of biological samples. Aptasensors play crucial roles in target identification, validation, detection of drug-target interactions and screening potential of drug candidates. This review focuses on the pivotal role of aptasensors in early disease detection, particularly in identifying biomarkers associated with various diseases such as cancer, infectious diseases and cardiovascular disorders. Aptasensors have demonstrated exceptional potential in enhancing disease diagnostics and monitoring therapeutic drug levels. Aptamer-based biosensors represent a transformative technology in the field of healthcare, enabling precise diagnostics, drug monitoring and disease detection.

An optical aptasensor for real-time quantification of endotoxin: From ensemble to single-molecule resolution

Endotoxin is a deadly pyrogen, rendering it crucial to monitor with high accuracy and efficiency. However, current endotoxin detection relies on multistep processes that are labor-intensive, time-consuming, and unsustainable. Here, we report an aptamer-based biosensor for the real-time optical detection of endotoxin. The endotoxin sensor exploits the distance-dependent scattering of gold nanoparticles (AuNPs) coupled to a gold nanofilm. This is enabled by the conformational changes of an endotoxin-specific aptamer upon target binding. The sensor can be used in an ensemble mode and single-particle mode under dark-field illumination. In the ensemble mode, the sensor is coupled with a microspectrometer and exhibits high specificity, reliability (i.e., linear concentration to signal profile in logarithmic scale), and reusability for repeated endotoxin measurements. Individual endotoxins can be detected by monitoring the color of single AuNPs via a color camera, achieving single-molecule resolution. This platform can potentially advance endotoxin detection to safeguard medical, food, and pharmaceutical products.

Gut-derived low-grade endotoxaemia, atherothrombosis and cardiovascular disease

Systemic inflammation has been suggested to have a pivotal role in atherothrombosis, but the factors that trigger systemic inflammation have not been fully elucidated. Lipopolysaccharide (LPS) is a component of the membrane of Gram-negative bacteria present in the gut that can translocate into the systemic circulation, causing non-septic, low-grade endotoxaemia. Gut dysbiosis is a major determinant of low-grade endotoxaemia via dysfunction of the intestinal barrier scaffold, which is a prerequisite for LPS translocation into the systemic circulation. Experimental studies have demonstrated that LPS is present in atherosclerotic arteries but not in normal arteries. In atherosclerotic plaques, LPS promotes a pro-inflammatory status that can lead to plaque instability and thrombus formation. Low-grade endotoxaemia affects several cell types, including leukocytes, platelets and endothelial cells, leading to inflammation and clot formation. Low-grade endotoxaemia has been described in patients at risk of or with overt cardiovascular disease, in whom low-grade endotoxaemia was associated with atherosclerotic burden and its clinical sequelae. In this Review, we describe the mechanisms favouring the development of low-grade endotoxaemia, focusing on gut dysbiosis and changes in gut permeability; the plausible biological mechanisms linking low-grade endotoxaemia and atherothrombosis; the clinical studies suggesting that low-grade endotoxaemia is a risk factor for cardiovascular events; and the potential therapeutic tools to improve gut permeability and eventually eliminate low-grade endotoxaemia.

Environmental protection based on the nanobiosensing of bacterial lipopolysaccharides (LPSs): material and method overview

Lipopolysaccharide (LPS) or endotoxin control is critical for environmental and healthcare issues. LPSs are responsible for several infections, including septic and shock sepsis, and are found in water samples. Accurate and specific diagnosis of endotoxin is one of the most challenging issues in medical bacteriology. Enzyme-linked immunosorbent assay (ELISA), plating and culture-based methods, and Limulus amebocyte lysate (LAL) assay are the conventional techniques in quantifying LPS in research and medical laboratories. However, these methods have been restricted due to their disadvantages, such as low sensitivity and time-consuming and complicated procedures. Therefore, the development of new and advanced methods is demanding, particularly in the biological and medical fields. Biosensor technology is an innovative method that developed extensively in the past decade. Biosensors are classified based on the type of transducer and bioreceptor. So in this review, various types of biosensors, such as optical (fluorescence, SERS, FRET, and SPR), electrochemical, photoelectrochemical, and electrochemiluminescence, on the biosensing of LPs were investigated. Also, the critical role of advanced nanomaterials on the performance of the above-mentioned biosensors is discussed. In addition, the application of different labels on the efficient usage of biosensors for LPS is surveyed comprehensively. Also, various bio-elements (aptamer, DNA, miRNA, peptide, enzyme, antibody, etc.) on the structure of the LPS biosensor are investigated. Finally, bio-analytical parameters that affect the performance of LPS biosensors are surveyed.

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.

A rapid aptamer-based fluorescence assay for the detection of lipopolysaccharides using SYBR Green I

Lipopolysaccharides (endotoxins), found on Gram-negative bacteria, can trigger a severe immune response in humans leading to septic shock and in extreme cases, even death. Therefore, the detection and neutralization of lipopolysaccharides (LPS) is of utmost importance in the pharmaceutical and medical industries. The United States Food and Drug Administration (US FDA) recommended detection method for LPS, the Limulus amebocyte lysate (LAL) assay, is expensive, time consuming, complex, and is prone to interference from proteases. As an alternative, this paper proposes a rapid, label-free fluorescence-based assay using LPS-specific aptamers and the SYBR Green DNA stain. The proposed method has a detection limit of 0.1 ng/ml, which is sufficient to detect the permissible levels of LPS in many pharmaceutical drugs and medical products. The fluorescence signal was found to be a linear function of the concentration of LPS in the range from 0.1 ng/ml to 10⁵ ng/ml.

Hydrazone ligation assisted DNAzyme walking nanomachine coupled with CRISPR-Cas12a for lipopolysaccharide analysis

In this work, hydrazone ligation assisted DNAzyme walking nanomachine is explored to couple with CRISPR-Cas12a trans-cleavage. Hydrazone ligation with high efficiency can mediate signal input which can be induced by target binding, thereby regulating the performance of DNAzyme walking nanomachine. The product strand from DNAzyme walking nanomachine can further activate the trans-cleavage of Cas12a. So, cascade signal amplification can be achieved to enhance the sensitivity for target detection. Subsequently, hydrazone ligation assisted DNAzyme walking nanomachine coupled with CRISPR-Cas12a has been further developed as a biosensor to analyze lipopolysaccharides. The developed biosensor exhibits a linear range from 0.05 ng/mL to 10⁶ ng/mL and a lowest limit of detection of 7.31 fg/mL. This research provides a new mode for the signal output of DNAzyme walking nanomachine, so as to sensitively analyze different biomolecules.

Recent Advances and a Roadmap to Aptamer-Based Sensors for Bloodstream Infections

The present review is intended to describe bloodstream infections (BSIs), the major pathogens responsible for BSIs, conventional tests and their limitations, commercially available methods used, and the aptamer and nanomaterials-based approaches developed so far for the detection of BSIs. The advantages associated with aptamers and the aptamer-based sensors, the comparison between the aptamers and the antibodies, and the various types of aptasensors developed so far for the detection of bloodstream infections have been described in detail in the present review. Also, the future outlook and roadmap toward aptamer-based sensors and the challenges associated with the aptamer development have also been concluded in this review.

dsDNA-templated fluorescent copper nanoparticles for the detection of lipopolysaccharides

The introduction of lipopolysaccharides (LPS) or endotoxins that originate from Gram-negative bacteria into the human blood stream induces a severe immune response that can lead to septic shock, and even death. Hence, the accurate detection of LPS is of great importance in the medical and pharmaceutical sectors. This paper proposes a novel label-free fluorescence assay for the detection of LPS utilizing aptamers and the interference synthesis of dsDNA-templated copper nanoparticles. The assay can be performed at room temperature and does not require expensive reagents. The proposed assay has a limit of detection of 0.95 ng ml-1 of LPS, and the fluorescence emission from the copper nanoparticles was found to vary linearly with the concentration of LPS over a wide range (1 to 105 ng ml-1) with R2 = 0.9877.

Prospective Application of Aptamer-based Assays and Therapeutics in Bloodstream Infections

Sepsis is still a severe health problem worldwide with high morbidity and mortality. Blood bacterial culture remains the gold standard for the detection of pathogenic bacteria in bloodstream infections, but it is time-consuming, and both the sophisticated equipment and well-trained personnel are required. Immunoassays and genetic diagnosis are expensive and limited to specificity and sensitivity. Aptamers are single-stranded deoxyribonucleic acid (ssDNA) and ribonucleic acid (RNA) oligonucleotide or peptide sequence generated in vitro based on the binding affinity of aptamer-target by a process known as Systematic Evolution of Ligands by Exponential Enrichment (SELEX). By taking several advantages over monoclonal antibodies and other conventional small-molecule therapeutics, such as high specificity and affinity, negligible batch-to-batch variation, flexible modification and production, thermal stability, low immunogenicity and lack of toxicity, aptamers are presently becoming promising novel diagnostic and therapeutic agents. This review describes the prospective application of aptamerbased laboratory diagnostic assays and therapeutics for pathogenic bacteria and toxins in bloodstream infections.

Recent Progress in the Identification of Aptamers Against Bacterial Origins and Their Diagnostic Applications

Aptamers have gained an increasing role as the molecular recognition element (MRE) in diagnostic assay development, since their first conception thirty years ago. The process to screen for nucleic acid-based binding elements (aptamers) was first described in 1990 by the Gold Laboratory. In the last three decades, many aptamers have been identified for a wide array of targets. In particular, the number of reports on investigating single-stranded DNA (ssDNA) aptamer applications in biosensing and diagnostic platforms have increased significantly in recent years. This review article summarizes the recent (2015 to 2020) progress of ssDNA aptamer research on bacteria, proteins, and lipids of bacterial origins that have implications for human infections. The basic process of aptamer selection, the principles of aptamer-based biosensors, and future perspectives will also be discussed.

Chitosan Stabilized Silver Nanoparticles for the Electrochemical Detection of Lipopolysaccharide: A Facile Biosensing Approach for Gram-Negative Bacteria

Negatively charged lipopolysaccharide (LPS), a major endotoxin and component of the outer membrane of several Gram-negative bacteria, provides a useful biomarker for the indirect detection of these pathogens. For instance, Escherichia coli (E. coli) is a pathogenic bacterium that causes infections in almost all age groups, and has been implicated in food and water contamination. Current diagnostic and detection methods tend to be labor-intensive or expensive, necessitating the need for an easy, sensitive, rapid, and low-cost method. We report on the synthesis and use of positively charged chitosan stabilized silver nanoparticles (Chi-AgNPs) as a sensitive electrochemical nanobiosensor for the detection of LPS. Chi-AgNPs were synthesized through a facile, single step protocol, and characterized for size, charge, and morphology. Glassy carbon electrodes modified with Chi-AgNPs resulted in an enhancement of signal in the presence of both LPS and E. coli. Detection was accomplished over a large concentration range (several orders of magnitude) of 0.001–100 ng/mL and 10–10⁷ CFU/mL. The biosensors can reliably detect LPS and E. coli at very low concentrations. Chi-AgNPs have potential as low cost, sensitive nanobiosensors for Gram-negative bacteria due to strong electrostatic interaction with LPS present in their outer membranes.

Sensors, Biosensors, and Analytical Technologies for Aquaculture Water Quality

In aquaculture industry, fish, shellfish, and aquatic plants are cultivated in fresh, salt, or brackish waters. The increasing demand of aquatic products has stimulated the rapid growth of aquaculture industries. How to effectively monitor and control water quality is one of the key concerns for aquaculture industry to ensure high productivity and high quality. There are four major categories of water quality concerns that affect aquaculture cultivations, namely, (1) physical parameters, e.g., pH, temperature, dissolved oxygen, and salinity, (2) organic contaminants, (3) biochemical hazards, e.g., cyanotoxins, and (4) biological contaminants, i.e., pathogens. While the physical parameters are affected by climate changes, the latter three are considered as environmental factors. In this review, we provide a comprehensive summary of sensors, biosensors, and analytical technologies available for monitoring aquaculture water quality. They include low-cost commercial sensors and sensor network setups for physical parameters. They also include chromatography, mass spectrometry, biochemistry, and molecular methods (e.g., immunoassays and polymerase chain reaction assays), culture-based method, and biophysical technologies (e.g., biosensors and nanosensors) for environmental contamination factors. According to the different levels of sophistication of various analytical techniques and the information they can provide (either fine fingerprint, highly accurate quantification, semiquantification, qualitative detection, or fast screening), we will comment on how they may be used as complementary tools, as well as their potential and gaps toward current demand of real-time, online, and/or onsite detection.

Hydrazone chemistry assisted DNAzyme for the analysis of double targets

In this work, a hydrazone chemistry assisted DNAzyme has been designed and constructed. The introduction of hydrazone chemistry increases the versatility of DNAzymes. With superior catalytic capability, the hydrazone chemistry assisted DNAzyme has been successfully applied for the analysis of double targets. Taking 5-hydroxymethylfurfural (HMF) and lipopolysaccharide (LPS) as samples, the hydrazone chemistry assisted DNAzyme can be used for the detection of different combinations of targets. Moreover, because hydrazone chemistry is popular in nature, this work may also provide a new insight for the development of DNAzymes and their multifunctionality.

Application of Aptamer-Based Biosensor for Rapid Detection of Pathogenic Escherichia coli

Pathogenic Escherichia coli (E. coli) widely exist in Nature and have always been a serious threat to the human health. Conventional colony forming units counting-based methods are quite time consuming and not fit for rapid detection for E. coli. Therefore, novel strategies for improving detection efficiency and sensitivity are in great demand. Aptamers have been widely used in various sensors due to their extremely high affinity and specificity. Successful applications of aptamers have been found in the rapid detection of pathogenic E. coli. Herein, we present the latest advances in screening of aptamers for E. coli, and review the preparation and application of aptamer-based biosensors in rapid detection of E. coli. Furthermore, the problems and new trends in these aptamer-based biosensors for rapid detection of pathogenic microorganism are also discussed.

Chemical and Biological Sensing Using Hybridization Chain Reaction

Since the advent of its theoretical discovery more than 30 years ago, DNA nanotechnology has been used in a plethora of diverse applications in both the fundamental and applied sciences. The recent prominence of DNA-based technologies in the scientific community is largely due to the programmable features stored in its nucleobase composition and sequence, which allow it to assemble into highly advanced structures. DNA nanoassemblies are also highly controllable due to the precision of natural and artificial base-pairing, which can be manipulated by pH, temperature, metal ions, and solvent types. This programmability and molecular-level control have allowed scientists to create and utilize DNA nanostructures in one, two, and three dimensions (1D, 2D, and 3D). Initially, these 2D and 3D DNA lattices and shapes attracted a broad scientific audience because they are fundamentally captivating and structurally elegant; however, transforming these conceptual architectural blueprints into functional materials is essential for further advancements in the DNA nanotechnology field. Herein, the chemical and biological sensing applications of a 1D DNA self-assembly process known as hybridization chain reaction (HCR) are reviewed. HCR is a one-dimensional (1D) double stranded (ds) DNA assembly process initiated only in the presence of a specific short ssDNA (initiator) and two kinetically trapped DNA hairpin structures. HCR is considered an enzyme-free isothermal amplification process, which shows substantial promise and offers a wide range of applications for in situ chemical and biological sensing. Due to its modular nature, HCR can be programmed to activate only in the presence of highly specific biological and/or chemical stimuli. HCR can also be combined with different types of molecular reporters and detection approaches for various analytical readouts. While the long dsDNA HCR product may not be as structurally attractive as the 2D and 3D DNA networks, HCR is highly instrumental for applied biological, chemical, and environmental sciences, and has therefore been studied to foster a variety of objectives. In this review, we have focused on nucleic acid, protein, metabolite, and heavy metal ion detection using this 1D DNA nanotechnology via fluorescence, electrochemical, and nanoparticle-based methodologies.

Nucleic acid aptamer-based methods for diagnosis of infections

Infectious diseases are a serious global problem, which not only take an enormous human toll but also incur tremendous economic losses. In combating infectious diseases, rapid and accurate diagnostic tests are required for pathogen identification at the point of care (POC). In this review, investigations of diagnostic strategies for infectious diseases that are based on aptamers, especially nucleic acid aptamers, oligonucleotides that have high affinities and specificities toward their targets, are described. Owing to their unique features including low cost of production, easy chemical modification, high chemical stability, reproducibility, and low levels of immunogenicity and toxicity, aptamers have been widely utilized as bio-recognition elements (bio-receptors) for the development of infection diagnostic systems. We discuss nucleic acid aptamer-based methods that have been developed for diagnosis of infections using a format that organizes discussion according to the target pathogenic analytes including toxins or proteins, whole cells and nucleic acids. Also included is, a summary of recent advances made in the sensitive detection of pathogenic bacteria utilizing the isothermal nucleic acid amplification method. Lastly, a nucleic acid aptamer-based POC system is described and future directions of studies in this area are discussed.

Optical nano-biosensing interface via nucleic acid amplification strategy: construction and application

Modern optical detection technology plays a critical role in current clinical detection due to its high sensitivity and accuracy. However, higher requirements such as extremely high detection sensitivity have been put forward due to the clinical needs for the early finding and diagnosing of malignant tumors which are significant for tumor therapy. The technology of isothermal amplification with nucleic acids opens up avenues for meeting this requirement. Recent reports have shown that a nucleic acid amplification-assisted modern optical sensing interface has achieved satisfactory sensitivity and accuracy, high speed and specificity. Compared with isothermal amplification technology designed to work completely in a solution system, solid biosensing interfaces demonstrated better performances in stability and sensitivity due to their ease of separation from the reaction mixture and the better signal transduction on these optical nano-biosensing interfaces. Also the flexibility and designability during the construction of these nano-biosensing interfaces provided a promising research topic for the ultrasensitive detection of cancer diseases. In this review, we describe the construction of the burgeoning number of optical nano-biosensing interfaces assisted by a nucleic acid amplification strategy, and provide insightful views on: (1) approaches to the smart fabrication of an optical nano-biosensing interface, (2) biosensing mechanisms via the nucleic acid amplification method, (3) the newest strategies and future perspectives.

Ultrasensitive colorimetric detection of circulating tumor DNA using hybridization chain reaction and the pivot of triplex DNA

This work presents an amplified colorimetric biosensor for circulating tumor DNA (ctDNA), which associates the hybridization chain reaction (HCR) amplification with G-Quadruplex DNAzymes activity through triplex DNA formation. In the presence of ctDNA, HCR occurs. The resulting HCR products are specially recognized by one sequence to include one GGG repeat and the other containing three GGG repeats, through the synergetic effect of triplex DNA and asymmetrically split G-Quadruplex forming. Such design takes advantage of the amplification property of HCR and the high peroxidase-like catalytic activity of asymmetrically split G-Quadruplex DNAzymes by means of triplex DNA formation, which produces color signals in the presence of ctDNA. Nevertheless, in the absence of ctDNA, no HCR happens. Thus, no triplex DNA and G-Quadruplex structure is formed, producing a negligible background. The colorimetric sensing platform is successfully applied in complex biological environments such as human blood plasma for ctDNA detection, with a detection limit corresponding to 0.1 pM. This study unambiguously uses triplex DNA forming as the pivot to integrate nucleic acid amplification and DNAzymes for producing a highly sensitive signal with low background.