A novel assay strategy based on isothermal amplification and cascade signal amplified electrochemical DNA sensor for sensitive detection of Helicobacter pylori

Nanobody-based immunosensor for the detection of H. pylori in saliva

Helicobacter pylori (H. pylori) infection is highly prevalent worldwide, affecting more than 43% of world population. The infection can be transmitted through different routes, like oral-oral, fecal-oral, and gastric-oral. Electrochemical sensors play a crucial role in the early detection of various substances, including biomolecules. In this study, the development of nanobody (Nb)-based immunosensor for the detection of H. pylori antigens in saliva samples was investigated. The D2_Nb was isolated and characterized using Western blot and ELISA and employed in the fabrication of the immunosensor. The sensor was prepared using gold screen-printed electrodes, with the immobilization of Nb achieved through chemical linkage using cysteamine-glutaraldehyde. The surface of the electrode was characterized using EIS, FTIR and SEM. Initially, the Nb-based immunosensor's performance was evaluated through cyclic voltammetry (CV), differential pulse voltammetry (DPV), and square wave voltammetry (SWV). The sensor exhibited excellent linearity with an R2 value of 0.96. However, further assessment with the DPV technique revealed both a low limit of detection (5.9 ng/mL, <1 cfu/mL) and high selectivity when exposed to a mixture of similar antigens. Moreover, the immunosensor demonstrated robust recovery rates (96.2%-103.4%) when spiked into artificial saliva and maintained its functionality when stored at room temperature for 24 days.

DNA nanoassembly based turn-on amplification probe for sensitive colorimetric CRISPR/Cas12a-mediated detection of pathogen DNA

Clustered regularly interspaced short palindromic repeat (CRISPR) system has been explored as an efficient tool for nucleic acid diagnostics. However, it normally needs instrumentation or produces turn-off signals. Herein, a bulged Y-shape DNA (Y-DNA) nanoassembly was designed and synthesized as a novel turn-on probe. A CRISPR/Cas12a and Y-DNA probe mediated colorimetric assay (named as CYMCOA) strategy was developed for visual detection of pathogen DNA. Upon activating Cas12a with pathogen DNA, the Y-DNA bulge is catalytically trans-cleaved, releasing the G-quadruplex sequence embedded in the Y-DNA nanoassembly as a peroxidase-like DNAzyme. Visible signals with chromogen substrates are thus produced. The CYMCOA strategy was combined with recombinase polymerase amplification (RPA), an isothermal amplification technique, in detecting Helicobacter pylori (Hp) bacteria and SARS-CoV-2 N plasmids as two model pathogens. The bioassay has very excellent detection sensitivity and specificity, owing to the triple cascade amplification reactions and the very low mismatch tolerance. The lower limit of detection values were 0.16 cfu⋅mL-1, 1.5 copies⋅μL-1, and 0.17 copies⋅μL-1 for Hp bacteria, Hp plasmids, and SARS-CoV-2 N plasmids respectively. The detection is fast and accurate. The colorimetric bioassay strategy provides to be a simple, accurate, fast and instrumentation-free platform for nucleic acids detections in various settings, including crude and emergent situations.

Advances in signal amplification strategies applied in pathogenic bacteria apta-sensing analysis-A review

Pathogenic bacteria are primarily kinds of food hazards that provoke serious harm to human health via contaminated or spoiled food. Given that pathogenic bacteria continue to reproduce and expand once they contaminate food, pathogenic bacteria of high concentration triggers more serious losses and detriments. Hence, it is essential to detect low-dose pollution at an early stage with high sensitivity. Aptamers, also known as "chemical antibodies", are oligonucleotide sequences that have attracted much attention owing to their merits of non-toxicity, small size, variable structure as well as easy modification of functional group. Aptamer-based bioanalysis has occupied a critical position in the field of rapid detection of pathogenic bacteria. This is attributed to the unique advantage of using aptamers as recognition elements in signal amplification strategies. The signal amplification strategy is an effective means to improve the detection sensitivity. Some diverse signal amplification strategies emphasize the synthesis and assembly of nanomaterials with signal amplification capabilities, while others introduce various nucleic acid amplification techniques into the detection system. This review focuses on a variety of signal amplification strategies employed in aptamer-based detection approaches to pathogenic bacteria. Meanwhile, we provided a detailed introduction to the design principles and characteristics of signal amplification strategies, as well as the improvement of sensor sensitivity. Ultimately, the existing issues and development trends of applying signal amplification strategies in apta-sensing analysis of pathogenic bacteria are critically proposed and prospected. Overall, this review discusses from a new perspective and is expected to contribute to the further development of this field.

Strategy of functional nucleic acids-mediated isothermal amplification for detection of foodborne microbial contaminants: A review

Foodborne microbial contamination (FMC) is the leading cause of food poisoning and foodborne illness. The foodborne microbial detection methods based on isothermal amplification have high sensitivity and short detection time, and functional nucleic acids (FNAs) could extend the detectable object of isothermal amplification to mycotoxins. Therefore, the strategy of FNAs-mediated isothermal amplification has been emergingly applied in biosensors for foodborne microbial contaminants detection, making biosensors more sensitive with lower cost and less dependent on nanomaterials for signal output. Here, the mechanism of six isothermal amplification technologies and their application in detecting FMC is firstly introduced. Then the strategy of FNAs-mediated isothermal amplification is systematically discussed from perspectives of FNAs' versatility including recognition elements (Aptamer, DNAzyme), programming tools (DNA tweezer, DNA walker and CRISPR-Cas) and signal units (G-quadruplex, FNAs-based nanomaterials). Finally, challenges and prospects are presented in terms of addressing the issue of nonspecific amplification reaction, developing better FNAs-based sensing elements and eliminating food matrix effects.

Aptamer-based technology for gastric cancer theranostics

Gastric cancer is one of the most common causes of cancer death worldwide. This cancer exhibits high molecular and phenotype heterogeneity. The overall survival rate for gastric cancer is very low because it is always diagnosed in the advanced stages. Therefore, early detection and treatment are of great significance. Currently, biomedical studies have tapped the potential clinical applicability of aptamer-based technology for gastric cancer diagnosis and targeted therapy. Herein, we summarize the enrichment and evolution of relevant aptamers, followed by documentation of the recent developments in aptamer-based techniques for early diagnosis and precision therapy for gastric cancers.

Harnessing enhanced CRISPR/Cas12a trans-cleavage activity with extended reporters and reductants for early diagnosis of Helicobacter pylori, the causative agent of peptic ulcers and stomach cancer

Developing rapid and non-invasive diagnostics for Helicobacter pylori (HP) is imperative to prevent associated diseases such as stomach gastritis, ulcers, and cancers. Owing to HP strain heterogeneity, not all HP-infected individuals incur side effects. Cytotoxin-associated gene A (CagA), and vacuolating cytotoxin A (VacA) genes predominantly drive HP pathogenicity. Therefore, diagnosing CagA and VacA genotypes could alert active infection and decide suitable therapeutics. We report an enhanced LbCas12a trans-cleavage activity with extended reporters and reductants (CEXTRAR) for early detection of HP. We demonstrate that extended ssDNA reporter acts as an excellent signal amplifier, making it a potential alternative substrate for LbCas12a collateral activity. Through a systematic investigation of various buffer components, we demonstrate that reductants improve LbCas12a trans-cleavage activity. Overall, our novel reporter and optimal buffer increased the trans-cleavage activity to an order of 16-fold, achieving picomolar sensitivity (171 pM) without target pre-amplification. Integrated with loop-mediated isothermal amplification (LAMP), CEXTRAR successfully attained attomolar sensitivity for HP detection using real-time fluorescence (43 and 96 aM), in-tube fluorescence readouts (430 and 960 aM), and lateral flow (4.3 and 9.6 aM) for CagA and VacA, respectively. We also demonstrate a rapid 2-min Triton X-100 lysis for clinical sample analysis, which could provide clinicians with actionable information for rapid diagnosis. CEXTRAR could potentially spot the ¹³C urea breath test false-negatives. For the first time, our study unveils an experimental outlook to manipulate reporters and reconsider precise cysteine substitution via protein engineering for Cas variants with enhanced catalytic activities for use in diagnostics and genetic engineering.

Advanced Sensing Strategies Based on Different Types of Biomarkers toward Early Diagnosis of H. pylori

Helicobacter pylori (H. pylori) is a bacterium that can colonize human gastric epithelial cells and cause H. pylori infection, closely related to many gastric diseases. Compared with conventional H. pylori detection methods, emerging diagnostic approaches (such as biosensors) have become potentially more effective alternatives due to their high sensitivity, good selectivity and noninvasiveness. This review begins with a brief overview of H. pylori infection, the processes that lead to diseases, and current diagnostic methods. Subsequently, advanced biosensors in different target-based for diagnosing H. pylori infection are focused, including the detection of H. pylori-related nucleic acid, H. pylori-related protein (such as the cytotoxin, urease), and intact H. pylori. In addition, prospects for the development of H. pylori detection methods are also discussed in the end.

Evolution of Diagnostic Methods for Helicobacter pylori Infections: From Traditional Tests to High Technology, Advanced Sensitivity and Discrimination Tools

Rapid diagnosis and treatment application in the early stages of H. pylori infection plays an important part in inhibiting the transmission of this infection as this bacterium is involved in various gastric pathologies such as gastritis, gastro-duodenal ulcer, and even gastric neoplasia. This review is devoted to a quick overview of conventional and advanced detection techniques successfully applied to the detection of H. pylori in the context of a compelling need to upgrade the standards of the diagnostic methods which are currently being used. Selecting the best diagnostic method implies evaluating different features, the use of one or another test depending on accessibility, laboratories equipment, and the clinical conditions of patients. This paper aims to expose the diagnosis methods for H. pylori that are currently available, highlighting their assets and limitations. The perspectives and the advantages of nanotechnology along with the concept of nano(bio)sensors and the development of lab-on-chip devices as advanced tools for H. pylori detection, differentiation, and discrimination is also presented, by emphasizing multiple advantages: simple, fast, cost-effective, portable, miniaturized, small volume of samples required, highly sensitive, and selective. It is generally accepted that the development of intelligent sensors will completely revolutionize the acquisition procedure and medical decision in the framework of smart healthcare monitoring systems.

Recent advances in the biosensors application for the detection of bacteria and viruses in wastewater

The presence of disease-causing pathogens in wastewater can provide an excellent diagnostic tool for infectious diseases. Biosensors are far superior to conventional methods used for regular infection screening and surveillance testing. They are rapid, sensitive, inexpensive portable and carry no risk of exposure in their detection schemes. In this context, this review summarizes the most recently developed biosensors for the detection of bacteria and viruses in wastewater. The review also provides information on the new detection methods aimed at screening for SARS-CoV-2, which has now caused more than 4 million deaths. In addition, the review highlights the potential behind on-line and real-time detection of pathogens in wastewater pipelines. Most of the biosensors reported were not targeted to wastewater samples due to the complexity of the matrix. However, this review highlights on the performance factors of recently developed biosensors and discusses the importance of nanotechnology in amplifying the output signals, which in turn increases the accuracy and reliability of biosensors. Current research on the applicability of biosensors in wastewater promises a dramatic change to the conventional approach in the field of medical screening.

Protein recognition-initiated exponential amplification reaction (PRIEAR) and its application in clinical diagnosis

The isothermal exponential amplification technology have rarely been fabricated as the universal sensing platform for the detection of various proteins. To broaden its application, we here developed a strategy named protein recognition-initiated exponential amplification reaction (PRIEAR) using protein recognition to induce the DNA assembly which converts protein recognition events into ssDNA amplicons and combining two-stage amplification to achieve exponential amplification technology. Taking advantage of this principle, diverse biomarkers can be quantified at sub-picomolar concentrations in the homogenous manner, making the PRIEAR suitable for clinical practice. Therefore, this strategy can expand the powerful isothermal exponential amplification technology to protein targets and thus provide a new toolbox into the clinical and biomedical applications.

A DNAzyme-catalyzed label-free aptasensor based on multifunctional dendrimer-like DNA assembly for sensitive detection of carcinoembryonic antigen

Carcinoembryonic antigen (CEA) is an important malign tumor marker. In this study, a simple, label-free and antibody-free aptasensor was fabricated based on a multifunctional dendrimer-like DNA nanoassembly. The DNA nanoassembly was embedded with multiple G-quadruplex DNAzyme motifs and a hanging CEA aptamer motif. It was prepared from short DNA sequences by autonomous-assembly. The aptasensor was prepared simply by self-assembly of a capture DNA (cpDNA) on a gold electrode, followed by hybridization with a CEA aptamer (AptGAC-P). CEA as a model target was detected through competitive binding of CEA with AptGAC-P, exposing cpDNA to bind with the DNA nanoassembly. The detection process only contains 2 incubation steps. The high load of G-quadruplex DNAzyme motifs and their catalytic activity resulted in an amplified and label-free differential pulse voltammetry (DPV) electrochemical signal. The peak current correlated linearly with the CEA concentration, with a linear range of 2-45 ng mL^-1, and an LOD value of 0.24 ng mL^-1. The aptasensor showed high specificity and reproducibility, and retained 96.5% of detection signal intensities after 31 days of storage. The recovery rates for spiked CEA in human serum were within 100 ± 5%, and the coincidence rates for clinical human serum samples with ELISA kits were 80.7-111%. Conceivably, possessing simplicity, sensitivity, reproducibility, storage stability, and accuracy, the aptasensor should be a very prominent and applicable tool for clinical CEA detection and cancer diagnosis, and is promisingly applicable as a platform for detecting other targets of interests.