DNA-Walker-Induced Allosteric Switch for Tandem Signal Amplification with Palladium Nanoparticles/Metal-Organic Framework Tags in Electrochemical Biosensing

Emergence of infectious diseases and role of advanced nanomaterials in point-of-care diagnostics: a review

Infectious outbreaks are the foremost global public health concern, challenging the current healthcare system, which claims millions of lives annually. The most crucial way to control an infectious outbreak is by early detection through point-of-care (POC) diagnostics. POC diagnostics are highly advantageous owing to the prompt diagnosis, which is economical, simple and highly efficient with remote access capabilities. In particular, utilization of nanomaterials to architect POC devices has enabled highly integrated and portable (compact) devices with enhanced efficiency. As such, this review will detail the factors influencing the emergence of infectious diseases and methods for fast and accurate detection, thus elucidating the underlying factors of these infections. Furthermore, it comprehensively highlights the importance of different nanomaterials in POCs to detect nucleic acid, whole pathogens, proteins and antibody detection systems. Finally, we summarize findings reported on nanomaterials based on advanced POCs such as lab-on-chip, lab-on-disc-devices, point-of-action and hospital-on-chip. To this end, we discuss the challenges, potential solutions, prospects of integrating internet-of-things, artificial intelligence, 5G communications and data clouding to achieve intelligent POCs.

Emerging insights into the application of metal-organic framework (MOF)-based materials for electrochemical heavy metal ion detection

Heavy metal ions are one of the main sources of water pollution, which has become a major global problem. Given the growing need for heavy metal ion detection, electrochemical sensor stands out for its high sensitivity and efficiency. Metal-organic frameworks (MOFs) have garnered much interest as electrode modifiers for electrochemical detection of heavy metal ions owing to their significant specific surface area, tailored pore size, and catalytic activity. This review summarizes the progress of MOF-based materials, including pristine MOFs and MOF composites, in the electrochemical detection of various heavy metal ions. The synthetic methods of pristine MOFs, the detection mechanisms of heavy metal ions and the modification strategies of MOFs are introduced. Besides, the diverse applications of MOF-based materials in detecting both single and multiple heavy metal ions are presented. Furthermore, we present the current challenges and prospects for MOF-based materials in electrochemical heavy metal ion detection.

Metalation of metal-organic frameworks: fundamentals and applications

Metalation of metal-organic frameworks (MOFs) has been developed as a prominent strategy for materials functionalization for pore chemistry modulation and property optimization. By introducing exotic metal ions/complexes/nanoparticles onto/into the parent framework, many metallized MOFs have exhibited significantly improved performance in a wide range of applications. In this review, we focus on the research progress in the metalation of metal-organic frameworks during the last five years, spanning the design principles, synthetic strategies, and potential applications. Based on the crystal engineering principles, a minor change in the MOF composition through metalation would lead to leveraged variation of properties. This review starts from the general strategies established for the incorporation of metal species within MOFs, followed by the design principles to graft the desired functionality while maintaining the porosity of frameworks. Facile metalation has contributed a great number of bespoke materials with excellent performance, and we summarize their applications in gas adsorption and separation, heterogeneous catalysis, detection and sensing, and energy storage and conversion. The underlying mechanisms are also investigated by state-of-the-art techniques and analyzed for gaining insight into the structure-property relationships, which would in turn facilitate the further development of design principles. Finally, the current challenges and opportunities in MOF metalation have been discussed, and the promising future directions for customizing the next-generation advanced materials have been outlined as well.

Signal amplification strategy of DNA self-assembled biosensor and typical applications in pathogenic microorganism detection

Biosensors have emerged as ideal analytical devices for various bio-applications owing to their low cost, convenience, and portability, which offer great potential for improving global healthcare. DNA self-assembly techniques have been enriched with the development of innovative amplification strategies, such as dispersion-to-localization of catalytic hairpin assembly, and dumbbell hybridization chain reaction, which hold great significance for building biosensors capable of realizing sensitive, rapid and multiplexed detection of pathogenic microorganisms. Here, focusing primarily on the signal amplification strategies based on DNA self-assembly, we concisely summarized the strengths and weaknesses of diverse isothermal nucleic acid amplification techniques. Subsequently, both single-layer and cascade amplification strategies based on traditional catalytic hairpin assembly and hybridization chain reaction were critically explored. Furthermore, a comprehensive overview of the recent advances in DNA self-assembled biosensors for the detection of pathogenic microorganisms is presented to summarize methods for biorecognition and signal amplification. Finally, a brief discussion is provided about the current challenges and future directions of DNA self-assembled biosensors.

Efficient DNA walker guided by ordered cruciform-shaped DNA track for ultrasensitive and rapid electrochemical detection of lead ion

The rational design of DNA tracks is an effective pathway to guide the autonomous movement and high-efficiency recognition in DNA walkers, showing outstanding advantages for the cascade signal amplification of electrochemical biosensors. However, the uncontrolled distance between two adjacent tracks on the electrode could increase the risk of derailment and interruption of the reaction. Hence, a novel four-way balanced cruciform-shaped DNA track (C-DNT) was designed as a structured pathway to improve the effectiveness and stability of the reaction in DNA walkers. In this work, two kinds of cruciform-shaped DNA were interconnected as a robust structure that could avoid the invalid movement of the designed DNA walker on the electrode. When hairpin H2 was introduced onto the electrode, the strand displacement reaction (SDR) effectively triggered movements of the DNA walker along the cruciform-shaped track while leaving ferrocene (Fc) on the electrode, leading to a significant enhancement of the electrochemical signal. This design enabled the walker to move in an excellent organized and controllable manner, thus enhancing the reaction speed and walking efficiency. Compared to other walkers moving on random tracks, the reaction time of the C-DNT-based DNA walker could be reduced to 20 min. Lead ion (Pb2+) was used as a model target to evaluate the analytical performance of this biosensor, which exhibited a low detection limit of 0.033 pM along with a wide detection ranging from 0.1 pM to 500 nM. This strategy presented a novel concept for designing a high-performance DNA walker-based sensing platform for the detection of contaminants.

DNA Polymerase-Steered Self-Propelled and Self-Enhanced DNA Walker for Rapid and Distinctly Amplified Electrochemical Sensing

The development of a simple, rapid, easy-to-operate, and ultrasensitive DNA walker-based sensing system is challenging but would be very intriguing for the enormous applications in biological analysis and disease monitoring. Herein, a new self-propelled and self-enhanced DNA walking strategy was developed on the basis of a simple DNA polymerase-steered conversion from a typical alternate DNA assembly process. The sensing platform was fabricated easily by immobilizing only one hairpin probe (H1) and the sensing process was based on a simple one-step mixing with another hairpin-like DNA probe (H2) and DNA polymerase. The DNA polymerization could achieve target recycling and successive DNA walking steps. Interestingly, along with each DNA walking step, the new DNA walker sequence could be autonomously accumulated for a self-enhanced DNA walking effect. This provided a multilevel signal amplification ability for the ultrasensitive detection of the target with a low detection limit of 0.18 fM. Moreover, it could greatly reduce the reaction time with the sensing process finished within 1 h. The detection selectivity and the applicative potential in a complicated biological matrix were also demonstrated. Furthermore, the flexible control of sensing modes (self-enhanced DNA walking or the alternate DNA assembly) by using DNA polymerase or not offered a powerful means for sensing performance modulation. It thus opens a new avenue toward the development of a DNA walker-based sensing platform with both rapid and ultrasensitive features and might hold a huge potential for point-of-care diagnostic applications.

Signal-Amplified Nanobiosensors for Virus Detection Using Advanced Nanomaterials

Rapid diagnosis and treatment of infectious illnesses are crucial for clinical outcomes and public health. Biosensing developments enhance diagnostics at the point of care. This is superior to traditional procedures, which need centralized lab facilities, specialized personnel, and large equipment. The emerging coronavirus epidemic threatens global health and economic security. Increasing viral surveillance and regulatory actions against disease transmission necessitate rapid, sensitive testing tools for viruses. Due to their sensitivity and specificity, biosensors offer a possible reliable and quantifiable viral detection method. Current advances in genetic engineering, such as genetic alteration and material engineering, have provided several opportunities to enhance biosensors' sensitivity, selectivity, and recognition efficiency. This chapter explains biosensing techniques, biosensor varieties, and signal amplification technologies. Challenges and potential developments for viral microorganisms based on biosensors and signal amplification were also investigated.

Advances in Bioelectrode Design for Developing Electrochemical Biosensors

The critical performance factors such as selectivity, sensitivity, operational and storage stability, and response time of electrochemical biosensors are governed mainly by the function of their key component, the bioelectrode. Suitable design and fabrication strategies of the bioelectrode interface are essential for realizing the requisite performance of the biosensors for their practical utility. A multifaceted attempt to achieve this goal is visible from the vast literature exploring effective strategies for preparing, immobilizing, and stabilizing biorecognition elements on the electrode surface and efficient transduction of biochemical signals into electrical ones (i.e., current, voltage, and impedance) through the bioelectrode interface with the aid of advanced materials and techniques. The commercial success of biosensors in modern society is also increasingly influenced by their size (and hence portability), multiplexing capability, and coupling in the interface of the wireless communication technology, which facilitates quick data transfer and linked decision-making processes in real-time in different areas such as healthcare, agriculture, food, and environmental applications. Therefore, fabrication of the bioelectrode involves careful selection and control of several parameters, including biorecognition elements, electrode materials, shape and size of the electrode, detection principles, and various fabrication strategies, including microscale and printing technologies. This review discusses recent trends in bioelectrode designs and fabrications for developing electrochemical biosensors. The discussions have been delineated into the types of biorecognition elements and their immobilization strategies, signal transduction approaches, commonly used advanced materials for electrode fabrication and techniques for fabricating the bioelectrodes, and device integration with modern electronic communication technology for developing electrochemical biosensors of commercial interest.

Room-Temperature Synthesized Iron/Cobalt Metal-Organic Framework Nanosheets with Highly Efficient Catalytic Activity toward Luminol Chemiluminescence Reaction

Two-dimensional (2D) iron/cobalt metal-organic framework nanosheets (Fe/Co-MOF NSs) were synthesized via the cooperative self-assembly reaction of Fe3+/Co2+ and terephthalic acid at room temperature. The as-prepared 2D Fe/Co-MOF NSs display superior performance in catalysis of the chemiluminescence (CL) reaction between luminol and H2O2. The CL spectrum, UV-vis absorption spectroscopy, radical scavenger experiments, and electron spin resonance (ESR) spectroscopy are utilized to research the possible CL mechanism of the luminol-H2O2-Fe/Co-MOF NSs system. All results indicate that Fe/Co-MOF NSs present outstanding peroxidase-like activity and could catalyze H2O2 to produce 1O2, O2·-, and ·OH, which could react rapidly with the luminol anion radical and result in strong CL. With the highly efficient CL of the luminol-H2O2-Fe/Co-MOF NSs system, a sensitive sensor for the detection of dopamine (DA) is developed based on the inhibitory effect of DA on the CL intensity. Good linearity over the range of 50-800 nM is achieved with a limit of detection of 20.88 nM (S/N = 3). This research demonstrates that 2D Fe/Co-MOF NSs is a highly effective catalyst for luminol CL reaction and has great application potential in the CL field.

Allosteric switch for electrochemical aptasensor toward heavy metals pollution of Lentinus edodes sensitized with porphyrinic metal-organic frameworks

BACKGROUND

Lentinan medicament from Lentinus edodes has been considered as natural medicinal products with minimal side effects for cancer therapy, but Lentinus edodes are easily polluted by nonbiodegradable heavy metals, especially silver ion (Ag+). Therefore, it is highly desirable to monitor Ag + pollution in Lentinus edodes considering their adverse impact on lentinan medicament. Electrochemical sensor isn't affected from the interference of matrix turbidity and color, and offers a powerful means for determination of variant analytes. As for electrochemical sensing toward Ag+, there is a great need to design efficient signal probes for specific recognition and signal generation.

RESULTS

We present an appropriate electrochemical aptasensor for Ag + assay based on biomimetic catalysis of porphyrin-encapsulated MOF (PorMOF) and allosteric switch of C-rich DNA. Thanks to the excellent biocompatibility, PorMOFs as nanozyme are used to design signal probes by loading duplex-like DNA scaffold. Owing to the specific recognition of Ag+ toward cytosine (C) base-rich DNA, PorMOF at the distal end was close to the underlying electrode via C-Ag+-C formation, leading to an enhanced current of catalytic hydroxylamine oxidation for signal generation. Using the positive correlation between current response and Ag+ level, the electrochemical system provides a promising means for on-line monitoring of Ag+ in Lentinus edodes with recoveries from 92.8% to 106.4% and relative standard deviation from 3.98% to 8.24%, verifying the applicability of the electrochemical aptasensor toward Ag+ in Lentinus edodes.

SIGNIFICANCE AND NOVELTY

With merits of portability, simple operation, and rapid response, the electrochemical pattern offers a useful solution for on-line monitoring of Ag+ in Lentinus edodes. By altering the DNA sequence, the proposed aptasensor provides a powerful way for monitoring other heavy metals, capable of protecting medicament production from heavy metal pollution.

DNA tetrahedral scaffold-corbelled 3D DNAzyme walker for electrochemiluminescent aflatoxin B1 detection

The reaction efficiency of surface-based DNA walker can directly affect the properties of a biosensor. Herein, three-dimensional (3D) DNAzyme walker were first fixed on the top of DNA tetrahedral scaffold to improve the immobilization efficiency. Ferrocene (Fc) that labeled at substrate strand ends effectively quenched the electrochemiluminescence (ECL) signal of Ru(bpy)₂(cpaphen)²⁺, yielding the sensor in a "signal-off" state. Upon the addition of aflatoxin B₁ (AFB₁), 3D DNAzyme walker was activated and fueled by Na⁺, accordingly releasing Fc and recovering the ECL signal of Ru(bpy)₂(cpaphen)²⁺. Due to the high movement efficiency of such 3D DNAzyme walker, ultrasensitive detection of AFB₁ was achieved in the range of 1.0 fg mL^-1-10 ng mL^-1, with a detection limit of 0.58 fg mL^-1. Moreover, satisfactory results were obtained while detecting AFB₁ in corn and peanut samples, suggesting it has a potential application in food safety analysis.

A novel electrochemical biosensor based on signal amplification of Au HFGNs/PnBA-MXene nanocomposite for the detection of miRNA-122 as a biomarker of breast cancer

Cancer is one of the leading causes of death worldwide and a crisis for global health. Breast cancer is the second most common cancer globally. In the perusal, a novel electrochemical biosensor amplified with hierarchical flower-like gold, poly (n-butyl acrylate), and MXene (AuHFGNs/PnBA-MXene) nanocomposite and activated by highly special antisense ssDNA (single-stranded DNA) provide a promising alternative for miRNA-122 detection as a biomarker of breast cancer. The biosensor presented a detection limit of 0.0035 aM (S/N = 3) with a linear range from 0.01 aM to 10 nM. The platform was tried on 20 breast cancer miRNAs extracted from actual serum specimens (10 positives and 10 negatives). Founded on the quantitatively obtained outcomes and statistic analysis (t-test, box-graph, receiver performance characteristic curve, and cut-off amount), the biosensor showed a meaningful discrepancy between the native and positive groups with 100% specificity and 100% sensitivity. While, RT-qPCR showed less specificity and sensitivity (70% specificity, 100% sensitivity) than the proposed biosensor. To assess the quantitative capacity and biosensor detection limit for clinical tests, the biosensor diagnosis performance for continually diluted miRNA extracted from patients was compared to that gained by RT-qPCR results, indicating that the biosensor detection limit was lower than RT-qPCR. ssDNA/AuHFGN/PnBA-MXene/GCE displayed little cross-reaction with other sequences and also showed desirable stability, reproducibility, and specificity and stayed stable until 32 days. As a result, the designed biosensor can perform as a hopeful method for diagnosis applications.

A visual detection strategy for SARS-CoV-2 based on dual targets-triggering DNA walker

SARS-CoV-2, a highly transmissible and mutagenic virus, made huge threats to global public health. The detection strategies, which are free from testing site requirements, and the reagents and instruments are portable, are vital for early screening and play a significant role in curbing the spread. This work proposed a silver-coated glass slide (SCGS)/DNA walker based on a dual targets-triggering mechanism, enzyme-catalyzed amplification, and smartphone data analysis, which build a portable visual detection strategy for the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) gene. By this method, the detection was reflected by the ultraviolet absorbance changes and visible color changes to the naked eye which was analyzed by Red-Green-Blue (RGB) data analysis via smartphone within 30 min, simplifying the detection process and shortening the detection time. Meanwhile, the dual targets-triggering mechanism and dual signal amplification strategy ensured detection specificity and sensitivity. Further, the practicability was verified by the detection of the real sample which provided this method an application potential in SARS-CoV-2 rapid detection.

Wedged DNA Walker Coupled with a Bimetallic Metal-Organic Framework Electrocatalyst for Rapid and Sensitive Monitoring of DNA Methylation

The dissociation of the walking strand from the track gives rise to decreased efficiency and long reaction time of DNA walkers. In this work, we constructed a DNA walker combining the introduction of a wedge segment with a bimetallic metal-organic framework (MOF) electrocatalyst to solve this problem. The target methylated DNA acted as a single-legged walker, and the immobilization probe assembled on the track contained a wedge segment that was complementary to the target methylated DNA persistently, inhibiting its dissociation from the track. The fuel strand modified with a bimetallic MOF would drive the target strand to conduct branch migration and move processively along the track. The stepwise movement of the target strand resulted in the loading of numerous bimetallic MOF catalysts to reduce H₂O₂ at the electrode interface, thereby a significantly increased current response would be obtained for the detection of methylated DNA. This DNA walker achieved a detection limit of 200 aM within 20 min and effectively distinguished DNA with different methylation statuses, which would pave a way for rapid and sensitive monitoring of DNA methylation.

Telomerase-initiated three-dimensional DNAzyme motor for monitoring of telomerase activity in living cells

Telomerase (TE) is recognized as a potential biomarker for early diagnosis, monitoring and treatment of cancer. At present, most of the methods for TE detection are only applicable to in vitro assays, and unsuitable for in vivo applications. Though a few intracellular probes have been reported to have good specificity for TE, they do not involve signal amplification, which hinders their applicability in scenarios requiring high sensitivity. It is rather challenging to develop highly sensitive biosensors for intracellular TE detection due to the difficulty in design TE probes with both high specificity and compatibility with signal amplification in living cells. Herein, a highly sensitive and selective three-dimensional DNAzyme motor for monitoring of TE activity in living cells was developed by innovatively integrating TE-mediated chain replacement reaction with a three-dimensional DNA walker. Specifically, the DNAzyme motor was constructed by assembling both DNAzyme substrates and swing arms made up of a hairpin-structured DNAzyme and a telomeric primer onto gold nanoparticles. TE in cells can activate the DNAzyme motor to carry out continuous chain replacement and substrate cutting reactions, and hence realize signal amplification in living cells. The DNAzyme motor was successfully utilized to monitor the dynamic changes of TE activity in four types of cells. Due to the advantages of simple synthesis, good biocompatibility and high sensitivity and specificity for TE, the proposed DNAzyme motor is expected to have great application potential in the early diagnosis of cancer.

Defined metal atom aggregates precisely incorporated into metal-organic frameworks

Nanosized metal aggregates (MAs), including metal nanoparticles (NPs) and nanoclusters (NCs), are often the active species in numerous applications. In order to maintain the active form of MAs in "use", they need to be anchored and stabilised, preventing agglomeration. In this context, metal-organic frameworks (MOFs), which exhibit a unique combination of properties, are of particular interest as a tunable and porous matrix to host MAs. A high degree of control in the synthesis towards atom-efficient and application-oriented MA@MOF composites is required to derive specific structure-property relationships and in turn to enable design of functions on the molecular level. Due to the versatility of MA@MOF (derived) materials, their applications are not limited to the obvious field of catalysis, but increasingly include 'out of the box' applications, for example medical diagnostics and theranostics, as well as specialised (bio-)sensoring techniques. This review focuses on recent advances in the controlled synthesis of MA@MOF materials en route to atom-precise MAs. The main synthetic strategies, namely 'ship-in-bottle', 'bottle-around-ship', and approaches to achieve novel hierarchical MA@MOF structures are highlighted and discussed while identifying their potential as well as their limitations. Hereby, an overview of standard characterisation methods that enable a systematic analysis procedure and state-of-art techniques that localise MA within MOF cavities are provided. While the perspectives of MA@MOF materials in general have been reviewed various times in the recent past, few atom-precise MAs inside MOFs have been reported so far, opening opportunities for future investigation.

Split aptamer remodeling-initiated target-self-service 3D-DNA walker for ultrasensitive detection of 17β-estradiol

DNA walker machines, as one of the dynamic DNA nanodevices, have attracted extensive interest in the field of analysis due to their inherent superiority. Herein, we reported a split aptamer remodeling-initiated target-self-service 3D-DNA walker for ultrasensitive, specific, and high-signal-background ratio determination of 17β-estradiol (E2) in food samples. Two split probes (STWS-a and STWS-b) were rationally designed that can undergo structural reassembled to serve as walking strands (STWS) under the induction of the target. Meanwhile, an intact E6-DNAzyme region was formed and activated at the tail of STWS. The activated E6-DNAzyme then continuously drives the 3D-DNA walker for signal amplification and specific detection of E2. Under optimal conditions, the proposed DNA walker-based biosensor exhibited excellent linearity in the range of 1 pM to 50 nM with a low limit of detection (LOD) of 0.28 pM, and good precision (2.7%) for 11 replicate determinations of 1 nM of E2. Furthermore, the developed DNA walker-based biosensor achieved excellent sensitive analysis of E2 in the complex food matrix with recoveries of 95.6-106.5%. This newly proposed split aptamer-based strategy has the advantages of ultrasensitive, high signal-to-background ratio, and high stability. Noteworthy, the successful operation of the DNA walker initiated by the split aptamer expands the principles of DNA walker design and provides a universal signal amplification platform for trace analysis.

Metal-Organic Framework UiO-66-Mediated Dual-Signal Ratiometric Electrochemical Sensor for microRNA Detection with DNA Walker Amplification

Electrochemical nanotags with strong signal input are necessary for a ratiometric electrochemical sensor to overcome the drawbacks of inaccurate detection results. In this paper, the metal-organic framework (MOF) UiO-66 was utilized as an electrochemical signal tag. A stable and strong current response at +0.9 V can be detected in neutral conditions. MicroRNA (miRNA) was employed as the model analyte. Herein, an enzyme-free DNA-walker-based ultrasensitive ratiometric electrochemical biosensor in combination with Zr MOF (UiO-66) signal tags to detect miRNA was demonstrated. In the presence of miRNA, the autonomous walker movement can be initiated by miRNA, leading to the release of biotin-modified fragments. Thus, streptavidin-labeled UiO-66 nanomaterials were not bound to the electrode, generating a low signal response of UiO-66 at +0.9 V. However, the current signal of electrolyte solution as reference at +0.2 V was increased due to the enhancement of electrode conductivity. This ratiometic sensor demonstrated high sensitivity, selectivity, and reproducibility. It can eliminate the disturbance of environmental factors and basic electrode characteristics, providing more accurate signals. A limit of detection (LOD) of 0.17 fM was achieved. Moreover, the method was also used to detect miRNA-21 spiked in real serum samples.

Ultrasensitive dual-signal electrochemical ratiometric aptasensor based on Co-MOFs with intrinsic self-calibration property for Mucin 1

The concentration of tumor biomarker Mucin 1 (MUC 1) is highly related with many diseases, which can be employed for the early diagnosis of cancer. In this paper, an electrochemical ratiometric aptasensor with intrinsic self-calibration property for the detection of MUC 1 is presented. In this paper, Co-MOFs themselves were employed as signal substances. This strategy was fabricated by using gold nanoparticles@black phosphorus (BP) as the substrate on the electrode, followed by modification of DNA nanotetrahedrons (DTN) via Au-S bond. The terminal of DTN contains MUC 1 aptamer. In the presence of MUC 1, the signal of DNA-labeled Co-MOFs can be detected. The current signal of Co-MOFs increased and that of thionine (as reference) was unchanged upon the addition of MUC 1. Thus, an intrinsic self-calibration aptasensor was achieved. In order to simplify the modification procedure, the electrolyte solution thionine was employed as an inner reference probe. Moreover, coupling of the hybridization chain reaction (HCR) with these MOFs signal tags presents an enzyme-free method for signal amplification, endowing the proposed ratiometric biosensor detection with high reproducibility and high sensitivity. The current ratio (I_IR/I_SP) remained stable over 30 individual measurements performed on ten different working electrodes. Even ten repeated scans performed on a single electrode exhibited a constant current ratio. The electrochemical ratiometric aptasensor is highly sensitivity for MUC 1 with the detection limit of 1.34 fM. Our proposed ratiometric sensor has great potential for the detection of cancer-related biomarkers.

Multiregion Linear DNA Walker-Mediated Ultrasensitive Electrochemical Biosensor for miRNA Detection

In this work, an intelligent multiregion linear DNA walker (MLDW) with a high walking rate and a high amplification efficiency was explored for ultrasensitive detection of miRNA. Significantly, amounts of functional domain could be concentrated in a long linear DNA obtained by the target miRNA-mediated rolling-circle amplification to simultaneously increase the local concentration and collision probability, resulting in an obviously improved reaction rate. Impressively, the MLDW can accomplish the reaction within 30 min, which is at least 4 times beyond that of traditional single-leg and multiple-leg DNA walkers. As a proof of concept, the high-efficiency MLDW was used to develop an electrochemical biosensing platform for ultrasensitive detection of target miRNA-21 with a low detection limit down to 36 aM. Therefore, the MLDW we designed puts forward an innovative insight to construct a functional DNA nanodevice and promote the investigation of the inherent performance of nucleic acid signal amplification for ultimate application in the detection of biomolecules and clinical disease diagnosis.

A cascade amplification strategy for ultrasensitive Salmonella typhimurium detection based on DNA walker coupling with CRISPR-Cas12a

Salmonella typhimurium (S. typhimurium) infection is one of leading causes of severe foodborne illness, which poses grievous threats to public health. Thus, the detection with ultra-sensitivity is highly demanded for timely prevention and diagnosis of S. typhimurium. In this study, we developed a novel detection machinery based on DNA walker and CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas12a technologies. Mechanistically, the S. typhimurium specific sequence triggers Nt.AlwI nicking endonuclease and produces particular signaling nucleotide, which further activates Cas12a for strong fluorescence signal output. This cascade amplification strategy exhibits excellent specificity and successfully decreases the limit of detection (LOD) of DNA walker by 2,000 folds to 5 CFU/mL. Collectively, this combinatorial approach offers great promises to effectively reduce foodborne diseases by ultrasensitive detection of S. typhimurium. As a proof of concept, this innovative design also shows prominent potential in detections of other biomolecules, cells and pathogens.

Engineering DNA walkers for bioanalysis: A review

Considerable advances have been made in the design, modularization, functionalization, and regulation of DNA nanostructures over the past 40 years. These advances have accelerated the development of DNA nanomachines such as DNA walkers, dynamic nanomachines with walking feet, tracks, and driven forces, which have highly sensitive detection and signal amplification abilities that can be applied to various bioanalytical contexts and therapeutic strategies. Here, we describe a rational design of the nano-bio interface, the kinetics of DNA walkers and the strategies for improving their efficiency and sensitivity. We also outline the various bioanalytic and imaging applications to which DNA walkers have been applied, such as electrochemical and optical measurements, when integrated with other simulation and activation tools. Finally, we compare the performances of novel DNA walker-based strategies for bioanalysis and propose a method to improve DNA walker design.

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.

A glucose/O2 biofuel cell integrated with an exonuclease-powered DNA walker for self-powered sensing of microRNA

With the aid of an exonuclease-powered DNA walker, the amount of glucose oxidase immobilized on the bioanode can be facilely tailored by varying the concentration of microRNA-141, so a glucose/O₂ biofuel cell is employed as a self-powered sensor for sensitive and selective detection of microRNA-141.

Integration of a capacitor to a 3-D DNA walker and a biofuel cell-based self-powered system for ultrasensitive bioassays of microRNAs

A self-powered microRNA biosensor with triple signal amplification systems was assembled through the integration of three-dimensional DNA walkers, enzymatic biofuel cells and a capacitor. The DNA walker is designed from an enzyme-free target triggered catalytic hairpin assembly of modified gold nanoparticles. When triggered by the target microRNA, the DNA walker will move along the catalytic hairpin track, resulting in a payload release of glucose oxidase. The enzymatic biofuel cell contains the glucose oxidase bioanode and a bilirubin oxidase biocathode that bring a dramatic open circuit voltage to realize the self-powered bioassays of microRNA. A capacitor is further coupled with the enzymatic biofuel cell to further amplify the electrochemical signal, and the sensitivity increases 28.82 times through optimizing the matching capacitor. Based on this design, the present biosensor shows high performance, especially for detection limit and sensitivity. Furthermore, the present biosensor was successfully applied for serum samples, directly demonstrating its good application in clinical biomedicine and disease diagnosis.

Dual-mode sensor based on the synergy of magnetic separation and functionalized probes for the ultrasensitive detection of Clostridium perfringens

Clostridium perfringens is an important foodborne pathogen, which has caused serious public health problems worldwide. So, there is an urgent need for rapid and ultrasensitive detection of C. perfringens. In this paper, a dual-mode sensing platform using the synergy between fluorescent and electrochemical signals for Clostridium perfringens detection was proposed. An electrochemical aptasensor was constructed by a dual-amplification technology based on a DNA walker and hybridization chain reaction (HCR). When the C. perfringens genomic DNA was present, it specifically bonded with FAM-labeled aptamer which triggered the DNA walker on hairpin DNA (hDNA) tracks to start the synthesis of double-stranded DNA. HCR occurred subsequently and produced long-chain DNA to absorb more methylene blue (MB). In this cycle, the fluorescent signals of released FAM-labeled aptamer could also be detected. The synergistic effects of MB and FAM significantly improved the sensitivity and accuracy of the dual-mode sensor. As a result, the biosensor displayed an excellent analytical performance for C. perfringens at a concentration of 1 to 10⁸ CFU g⁻¹. A minimum concentration of 1 CFU g⁻¹ and good accuracy were detected in real samples. The proposed ultrasensitive detection method for detecting C. perfringens in food showed great potential in controlling foodborne diseases.

Clostridium perfringens is an important foodborne pathogen, which has caused serious public health problems worldwide.

MOF-assisted antifouling material: application in rapid determination of TB gene in whole-serum specimens

Biofouling is a nuisance in the practical applications of biosensors, which seriously affects the reliability and accuracy of detection. The utilization of antifouling interface materials is a promising option for mitigating biofouling. Only highly accumulated antifouling polymeric surfaces tend to offer "zero" nonspecific protein adsorption. Herein, superior antifouling coatings based on chondroitin sulfate (CS) were prepared by the NH₂-MIL-53 (Al) assisted strategy. This is a novel design to improve the antifouling property of material by taking advantage of the high specific surface area of the three-dimensional MOF to increase the accumulation degree of antifouling functional groups per unit area. And the related chemical technology is simple and easy to operate. As expected, this novel CS-loaded MOF demonstrated an excellent antifouling performance in various biological samples, even in 100% goat serum. Only 8.48% changes of differential pulse voltammetry (DPV) were found. Furthermore, this antifouling interface material is successfully applied for the specific detection of the tuberculosis (TB) gene in undiluted biofluids. This developed TB biosensor showed a high analytical performance with a wide linear range (1.00 × 10^-16 M to 1.00 × 10^-11 M) and a low detection limit, indicating that it may open new avenues for direct biosensing of disease markers for clinical samples.

Electrochemical Sensor for the Detection of 1-Hydroxypyrene Based on Composites of PAMAM-Regulated Chromium-Centered Metal-Organic Framework Nanoparticles and Graphene Oxide

A nanocomposite was formed by combining graphene oxide (GO) with chromium-centered metal-organic framework (Cr-MOF) nanoparticles regulated by the dendrimer polyamidoamine (PAMAM). PAMAM can successfully regulate the synthesis of Cr-MOF; in doing so, the size of Cr-MOF is reduced, its original morphology is maintained, and it has good crystallinity. A simple ultrasonication method was used to make the Cr-MOF/GO hybrid nanocomposite. Various characterization methods confirmed the successful synthesis of PAMAM/Cr-MOF/GO nanocomposites. The PAMAM/Cr-MOF/ERGO modified electrode could be used with cyclic voltammetry (CV) and differential pulse voltammetry (DPV) to study the electrochemical behaviors of 1-hydroxypyrene (1-OHPyr). The results indicated that the constructed PAMAM/Cr-MOF/ERGO electrochemical sensor had a significantly enhanced electrocatalytic effect on the electrochemical reduction of 1-OHPyr compared with the sensors with no PAMAM and the ERGO sensor, which could be ascribed to the synergetic effect from the high porosity of Cr-MOF and the high conductivity of ERGO, as well as the further electron transport action of the nanocomposite. Under the optimal conditions, the reduction peak current and concentration of 1-OHPyr showed a good linear relationship in the range of 0.1-1.0 and 1.0-6.0 μM, and the detection limit of 1-OHPyr was calculated to be 0.075 μM. Moreover, the PAMAM/Cr-MOF/ERGO electrochemical sensor constructed in this paper can be expected to provide some instructions for the construction of electrochemical sensing platforms and wider potential applications.

Direct electrochemistry of silver nanoparticles-decorated metal-organic frameworks for telomerase activity sensing via allosteric activation of an aptamer hairpin

A direct electrochemistry of silver nanoparticles (AgNPs)-anchored metal-organic frameworks (MOFs) is developed for detection of telomerase activity based on allosteric activation of an aptamer hairpin. AgNPs in situ decorated on PCN-224 (AgNPs/PCN-224) constituted the direct electrochemical labels that were further biofunctionalized by recognition moiety of streptavidin (SA). To achieve the target biosensing, an allosteric hairpin-structured DNA was elaborately designed for signal transduction. The presence of telomerase elongated its primer in the hairpin to displace partial stem strand, thus resulted in the formation of SA aptamer-open structure. Through the specific interaction with aptamer, SA-biofunctionalized AgNPs/PCN-224 probe was attached onto the electrode surface, generating electrochemical signal at + 0.072 V of AgNPs centralized by MOF structure. The direct electrochemical biosensor showed target activity-dependent response from 1.0 × 10^-7 to 1.0 × 10^-1 IU L^-1 with a detection limit of 5.4 × 10^-8 IU L^-1. Moreover, the sensor was applied in evaluation of telomerase activity in living cancer cells. The established electrochemical detection approach in this work avoids the critical deoxygenation conditions and additional electrocatalytic reagents, which opens a novel biosensing perspective for direct electrochemistry of MOF-based nanocomposites.

Highly sensitive fluorescent quantification of acid phosphatase activity and its inhibitor pesticide Dufulin by a functional metal-organic framework nanosensor for environment assessment and food safety

Developing a rapid and accurate strategy of sensing Dufulin is a vital challenge for risk assessment and food crops along with its spreading usage. Herein a dye-encapsulated azoterephthalate metal-organic framework (MOF)-based fluorescent sensing system was designed for Dufulin analysis by acid phosphatase (ACP) enzyme-controlled collapse of MOF framework and subsequent release of the encapsulated dye. The fluorescence intensity of the DMOF/AAP/ACP system was negatively related to the dosage of Dufulin (0-5 μg mL^-1) with detection limit of 2.96 ng mL^-1. The sensing system able to rapidly and sensitively sense the activity of ACP and Dufulin, and was also applicable for assessment of the real samples including paddy water and soil, polished rice and cucumber. Accordingly, this study illustrated the feasibility and the potential of MOF-derived nanosensors for improving pesticide analysis and opening up the design of the enzyme-based probes for pesticide sensing in environmental assessment and food safety.

DNA walker-mediated biosensor for target-triggered triple-mode detection of Vibrio parahaemolyticus

Herein, we have constructed a target-triggered and DNA walker-mediated biosensor with triple signal (BTS) outputs mode for sensitive and reliable detection of pathogenic bacteria. Vibrio parahaemolyticus (VP) being the detection target model, the aptamer conformational changes induced by VP have been designed to activate the DNA walk on the modifiable and conductive surface of Fe3O4 nanoparticles to generate triple signal outputs, including electrochemiluminescence (ECL), fast scan cyclic voltammetry (FSCV) and fluorescent pixel counting (FLPC). Limits of quantification (LOQ) of VP were as low as 1 CFU⋅mL-1 by ECL with a linear range of 1-106 CFU⋅mL-1, 1 CFU⋅mL-1 by FSCV with a linear range of 1-106 CFU⋅mL-1, and 10 CFU⋅mL-1 by FLPC with a linear range of 10-107 CFU⋅mL-1 respectively, all squared correlation coefficients R2 being > 0.99. In addition, optical and electrochemical results, signal-on and signal-off results, electrode phase and solution phase results could be mutually verified by integrating of multiple detection techniques in one biosensor, greatly improving the accuracy and reliability. Therefore, the designed BTS has provided a powerful strategy for pathogenic bacteria detection considering its high detection sensitivity and accuracy, exhibiting great potential in food safety, water quality and biological contamination.

Label-Free and Sensitive Electrochemical Biosensor for Amplification Detection of Target Nucleic Acids Based on Transduction Hairpins and Three-Leg DNAzyme Walkers

Nucleic acids are regarded as reliable biomarkers for the early diagnosis of various diseases. By ingeniously combining a transduction hairpin (THP) with the toehold-mediated strand displacement reaction (TSDR) to form three-leg DNAzyme walkers, for the first time, we constructed a label-free and sensitive electrochemical sensing system for the amplification detection of target nucleic acids. With microRNA-155 (miR-155) as a model target, the feasibility of the biosensing strategy and the conformational states of DNA in the recognition process were studied in detail on the basis of electrochemical and dual polarization interferometry techniques. With the assistance of THP, miR-155 indirectly triggered the TSDR between three hairpins (H1, H2, and H3), then massive Mg2+-dependent three-leg DNAzyme walkers were formed in aqueous solutions. After the binding/cleaving/moving process of three-leg DNAzyme walkers on the electrode surface modified with substrate hairpins (SHPs), a number of single-stranded DNAs (ssDNAs) were generated. Hence, the interaction of methylene blue (MB) with the duplex section of SHPs was impeded, which brought about a decreased electrochemical signal. Benefiting from the cyclic amplification of the TSDR and the higher cleavage activity of three-leg DNAzyme walkers, the proposed sensing strategy showed remarkable improvement in sensitivity with a low detection limit of 0.27 fM for miR-155. Owing to the precise design of the THP, this method exhibited excellent specificity to distinguish miR-155 from the single-base and triplex-base mismatched sequences. This sensing strategy importing the flexible THP can be utilized to detect various nucleic acid biomarkers by only redesigning the THP without changing the main circuit or reporter constructs, showing the great versatility and potential for the early diagnostics and biological analysis.

Rational Engineering of the DNA Walker Amplification Strategy by Using a Au@Ti3C2@PEI-Ru(dcbpy)32+ Nanocomposite Biosensor for Detection of the SARS-CoV-2 RdRp Gene

The detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is crucial for preventing and controlling infectious diseases and disease treatment. In this work, a Au@Ti3C2@PEI-Ru(dcbpy)32+ nanocomposite-based electrochemiluminescence (ECL) biosensor was rationally designed, which realized sensitive detection of the RNA-dependent RNA polymerase (RdRp) gene of SARS-CoV-2. In addition, a DNA walker was also used to excise the hairpin DNAs under the action of Nb.BbvCI endonuclease. Furthermore, model DNA-Ag nanoclusters (model DNA-AgNCs) were used to quench the initial ECL signal. As a result, the ECL biosensor was used to sensitively detect the SARS-CoV-2 RdRp gene with a detection range of 1 fM to 100 pM and a limit of detection of 0.21 fM. It was indicated that the ECL biosensor had a great application potential for clinical medical detection. Furthermore, the DNA walker amplification also played a reliable candidate strategy for other detection methods.

Immobilization-free electrochemical DNA sensor based on signal cascade amplification strategy

The development of convenient and efficient strategies without using complex nanomaterials or enzymes for signal amplification is very important for bioanalytical applications. Herein, a novel electrochemical DNA sensor was developed by harnessing the signal amplification efficiency of catalytic hairpin assembly (CHA) and a brand-new signal marker tetraferrocene. The prepared sensor had both ends of the probe H2 labeled with tetraferrocene; both ends have a large number of unhybridized T bases, which cause tetraferrocene to move closer to the electrode surface, generating a high-efficiency amplification signal. In the presence of target DNA, it induced strand exchange reactions promoting the formation of double-stranded DNA and recycling of target DNA. Under optimal conditions, the sensor showed a good linear correlation between the peak currents and logarithm of target DNA concentrations (ranging from 0.1 fM to 0.3125 pM) with a detection limit of 0.06 fM, which is obtained by a triple signal-to-noise ratio. Additionally, the prepared sensor possesses excellent selectivity, reproducibility, and stability, demonstrating efficient and stable DNA detection methodology.

Recent advances in DNA walker machines and their applications coupled with signal amplification strategies: A critical review

DNA walkers, a type of dynamic nanomachines, have become the subject of burgeoning research in the field of biology. These walkers are powered by driving forces based on strand displacement reactions, protein enzyme/DNAzyme reactions and conformational transitions. With the unique properties of high directionality, flexibility and efficiency, DNA walkers move progressively and autonomously along multiple dimensional tracks, offering abundant and promising applications in biosensing, material assembly and synthesis, and early cancer diagnosis. Notably, DNA walkers identified as signal amplifiers can be combined with various amplification approaches to enhance signal transduction and amplify biosensor sensing signals. Herein, we systematically and comprehensively review the walking principles of various DNA walkers and the recent progress on multiple dimensional tracks by presenting representative examples and an insightful discussion. We also summarized and categorized the diverse signal amplification strategies with which DNA walkers have coupled. Finally, we outline the challenges and future trends of DNA walker machines in emerging analytical fields.

Epoxy-functionalized macroporous carbon with embedded platinum nanoparticles for electrochemical detection of telomerase activity via telomerase-triggered catalytic hairpin assembly

Telomerase is regarded as a crucial biomarker for the early diagnosis of malignant tumors and a valuable therapeutic target. In this work, a telomerase-triggered amplification strategy was designed on the basis of a catalyzed hairpin assembly (CHA) for bridging a signal probe of platinum nanoparticles (Pt NPs) anchored on three-dimensional (3D) epoxy-functionalized macroporous carbon (Pt/MPC-COOH) in an ultrasensitive electrochemical biosensor. Pt/MPC-COOH nanomaterials with interconnected macroporous structure not only immobilized hairpin DNA probe 2 (H2) via an amide reaction (Pt/MPC-COOH-H2), but they also generated an obvious electrochemical signal in response to acetaminophen (AP) oxidation. After the introduction of telomerase, telomerase primer (TP) was extended to a telomerase extension product (TEP) with several hexamer repeats (TTAGGG)n to initiate the CHA cycle, leading to signal amplification. Subsequently, with the TEP-triggered CHA cycle amplification strategy, a large amount of Pt/MPC-COOH-H2 was introduced on the electrode surface for the construction of the electrochemical platform, which realized the sensitive detection of telomerase activity from 10² to10⁷ cells mL^-1 with a limit of detection (LOD) of 9.02 cells mL^-1. This strategy provides a sensitive method for the detection of biomolecules that could be useful for bioanalysis and early clinical diagnoses of diseases.

Interaction between the functionalized probes: The depressed efficiency of dual-amplification strategy on ratiometric electrochemical aptasensor for aflatoxin B1

Signal amplification is one of the most effective ways to develop the high-performance electrochemical sensors. However, it can be more complicated for ratiometric detections. Herein, a ratiometric electrochemical aptasensor for aflatoxin B1 (AFB1) was proposed by taking advantage of a dual-amplification strategy by coupling of DNA walker (DW) with hybridization chain reaction (HCR). The special binding of AFB1 with ferrocene (Fc)-labelled aptamer triggers DW on hairpin DNA (hDNA) tracks to produce abundant double-stranded DNA (dsDNA). HCR-based strand amplification occurs on these dsDNA to absorb more methylene blue (MB). Then current ratio of MB (I_MB) and Fc (I_Fc) is designed as a yardstick to detect AFB1. Our experiments reveal that the interaction between Fc and MB (i.e., steric hindrance, electron mediator) varies. In addition to steric hindrance, the presence of MB also acts as electron mediator, thereby facilitating the electron transfer between Fc and electrode. Such combined effect consequently depresses the efficiency of dual-amplification strategy to improve the detection. The developed ratiometric electrochemical aptasensor allows the accurate detection of AFB1 in the 0.003-3 pg mL^-1 range. Our work has shed light on the amplification strategy for ratiometric sensing, and provided a new route in integrating different amplification strategies.

A signal-on photoelectrochemical aptasensor for chloramphenicol assay based on 3D self-supporting AgI/Ag/BiOI Z-scheme heterojunction arrays

Severe challenges are still remained for development of highly sensitive, selective and stable photoelectrochemical (PEC) sensing technology, albeit with its broad application for chloramphenicol (CAP) detection. Herein, a novel "signal-on" PEC aptasensor was fabricated based on a 3D self-supporting Z-scheme AgI/Ag/BiOI heterojunction arrays subtly integrated with in-situ formed biocatalytic precipitation (BCP) for highly sensitive and selective determination of CAP. Impressively, the HRP modified CAP aptamer (HRP-CAP aptamer) was released from the electrode by its strong affinity to the introduced CAP, and gradually terminated the BCP reaction, in turn recovering the photocurrent. By virtues of the 3D self-supporting AgI/Ag/BiOI Z-scheme heterojunction arrays and BCP signal amplification strategy, the resultant PEC sensor exhibited a wide linear range of 2-250 nM with a limit of detection (LOD) as low as 0.226 nM (S/N = 3). This work opens a new avenue for design of PEC aptasensing strategy and exhibits the marvelous potential in bioanalysis of environmental samples.

Three-dimensional bipedal DNA walker enabled logic gates responding to telomerase and miRNA

In this work, we have developed a simple and reliable platform for simultaneous analysis of telomerase and miRNA. A three-dimensional bipedal DNA walking strategy is designed utilizing gold nanoparticles and MnO2 nanosheets. Given the merits of fast, sensitive and selective analysis, the developed method has great potential application in early clinical diagnosis.