DNA Hairpins and Dumbbell-Wheel Transitions Amplified Walking Nanomachine for Ultrasensitive Nucleic Acid Detection

Ultrahigh-Speed 3D DNA Walker with Dual Self-Protected DNAzymes for Ultrasensitive Fluorescence Detection and Intracellular Imaging of microRNA

Herein, a dual self-protected DNAzyme-based 3D DNA walker (dSPD walker), composed of activated dual self-protected walking particles (ac-dSPWPs) and track particles (TPs), was constructed for ultrasensitive and ultrahigh-speed fluorescence detection and imaging of microRNAs (miRNAs) in living cells. Impressively, compared with the defect that "one" target miRNA only initiates "one" walking arm of the conventional single self-protected DNAzyme walker, the dSPD walker benefits from the secondary amplification and spatial confinement effect and could guide "one" target miRNA to generate "n" secondary targets, thereby initiating "n" nearby walking strands immediately, realizing the initial rate over one-magnitude-order faster than that of the conventional one. Moreover, in the process of relative motion between ac-dSPWPs and TPs, the ac-dSPWPs could cleave multiple substrate strands simultaneously to speed up movement and reduce the derailment rate, as well as combine with successive TPs to facilitate a large amount of continuous signal accumulation, achieving an ultrafast detection of miRNA-221 within 10 min in vitro and high sensitivity with a low detection limit of 0.84 pM. In addition, the DNA nanospheres obtained by the rolling circle amplification reaction can capture the Cy5 fluorescence dispersed in liquids, which achieves the high-contrast imaging of miRNA-221, resulting in further ultrasensitive imaging of miRNA-221 in cancer cells. The proposed strategy has made a bold innovation in the rapid and sensitive detection as well as intracellular imaging of low-abundance biomarkers, offering promising application in early diagnosis and relevant research of cancer and tumors.

A Fluorescence Light-Up 3D DNA Walker Driven and Accelerated by Endogenous Adenosine-5'-triphosphate for Sensitive and Rapid Label-Free MicroRNA Detection and Imaging in Living Cells

Herein, a fluorescence light-up 3D DNA walker (FLDW) was powered and accelerated by endogenous adenosine-5'-triphosphate (ATP) molecules to construct a biosensor for sensitive and rapid label-free detection and imaging of microRNA-221 (miRNA-221) in malignant tumor cells. Impressively, ATP as the driving force and accelerator for FLDW could significantly accelerate the operation rate of FLDW, reduce the likelihood of errors in signaling, and improve the sensitivity of detection and imaging. When FLDW was initiated by output DNA H1-op transformed by target miRNA-221, G-rich sequences in the S strand, anchored to AuNP, were exposed to form G-quadruplexes (G4s), and thioflavin T (ThT) embedded in the G4s emitted intense fluorescence to realize sensitive and rapid detection of target miRNA-221. Meanwhile, the specific binding of ThT to G4 with a weak background fluorescence response was utilized to enhance the signal-to-noise ratio of the label-free assay straightforwardly and cost-effectively. The proposed FLDW system could realize sensitive detection of the target miRNA-221 in the range of 1 pM to 10 nM with a detection limit of 0.19 pM by employing catalytic hairpin assembly (CHA) to improve the conversion of the target. Furthermore, by harnessing the abundant ATP present in the tumor microenvironment, FLDW achieved rapid and accurate imaging of miRNA-221 in cancer cells. This strategy provides an innovative and high-speed label-free approach for the detection and imaging of biomarkers in cancer cells and is expected to be a powerful tool for bioanalysis, diagnosis, and prognosis of human diseases.

Multiplexed electrochemical nucleic acid sensor based on visible light-mediated metal-free thiol-yne click reaction for simultaneous detection of different nucleic acid targets

Simultaneous detection of multiple tumor biomarkers with a simple and low-cost assay is crucial for early cancer detection and diagnosis. Herein, we presented a low-cost and simple assay for multiplexed detection of tumor biomarkers using a spatially separated electrodes strategy. The sensor is fabricated based on a metal-free thiol-yne click reaction, which is mediated by visible light, on commercially available indium tin oxide (ITO) electrodes. Four biomarkers, including p53 DNA, Brca2 DNA, K-ras DNA, and MicroRNA-204 RNA, were used as model analytes, and the corresponding oligonucleotide probes were modified on the desired electrode units sequentially with 530 nm irradiation light in the presence of photosensitizer Eosin Y. By this visible light-mediated coupling reaction, oligonucleotide probe densities of up to 9.2 ± 0.7 × 1010 molecules/cm2 were readily obtained on the ITO electrode surface. The proposed multiplexed E-NA sensor could detect four different nucleic acid targets concurrently without crosstalk among adjacent electrodes and was also successfully applied for detecting targets in a 20% fetal calf serum sample. The detection limits for p53 DNA, Brca2 DNA, K-ras DNA, and MicroRNA-204 RNA were 0.72 nM, 0.97 nM, 2.15 nM, and 1.73 nM, respectively. The developed approach not only has a great potential for developing cost-effective biosensors on affordable substrates for nucleic acid target detection, but also be easily extended to detect other targets by modifying the specific oligonucleotide probes anchored on the electrode.

The combination of DNA nanostructures and materials for highly sensitive electrochemical detection

Due to the wide range of electrochemical devices available, DNA nanostructures and material-based technologies have been greatly broadened. They have been actively used to create a variety of beautiful nanostructures owing to their unmatched programmability. Currently, a variety of electrochemical devices have been used for rapid sensing of biomolecules and other diagnostic applications. Here, we provide a brief overview of recent advances in DNA-based biomolecular assays. Biosensing platform such as electrochemical biosensor, nanopore biosensor, and field-effect transistor biosensors (FET), which are equipped with aptamer, DNA walker, DNAzyme, DNA origami, and nanomaterials, has been developed for amplification detection. Under the optimal conditions, the proposed biosensor has good amplification detection performance. Further, we discussed the challenges of detection strategies in clinical applications and offered the prospect of this field.

Ultrasensitive and Rapid Circulating Tumor DNA Liquid Biopsy Using Surface-Confined Gene Amplification on Dispersible Magnetic Nano-Electrodes

Circulating tumor DNA (ctDNA) detection has been acknowledged as a promising liquid biopsy approach for cancer diagnosis, with various ctDNA assays used for early detection and treatment monitoring. Dispersible magnetic nanoparticle-based electrochemical detection methods have been proposed as promising candidates for ctDNA detection based on the detection performance and features of the platform material. This study proposes a nanoparticle surface-localized genetic amplification approach by integrating Fe3O4-Au core-shell nanoparticles into polymerase chain reactions (PCR). These highly dispersible and magnetically responsive superparamagnetic nanoparticles act as nano-electrodes that amplify and accumulate target ctDNA in situ on the nanoparticle surface upon PCR amplification. These nanoparticles are subsequently captured and subjected to repetitive electrochemical measurements to induce reconfiguration-mediated signal amplification for ultrasensitive (∼3 aM) and rapid (∼7 min) metastatic breast cancer ctDNA detection in vitro. The detection platform can also detect metastatic biomarkers from in vivo samples, highlighting the potential for clinical applications and further expansion to rapid and ultrasensitive multiplex detection of various cancers.

Logic Signal Amplification System for Sensitive Electrochemiluminescence Detection and Subtype Identification of Cancer Cells

Achieving sensitive detection and accurate identification of cancer cells is vital for diagnosing and treating the disease. Here, we developed a logic signal amplification system using DNA tetrahedron-mediated three-dimensional (3D) DNA nanonetworks for sensitive electrochemiluminescence (ECL) detection and subtype identification of cancer cells. Specially designed hairpins were integrated into DNA tetrahedral nanostructures (DTNs) to perform a catalytic hairpin assembly (CHA) reaction in the presence of target microRNA, forming hyperbranched 3D nanonetworks. Benefiting from the "spatial confinement effect," the DNA tetrahedron-mediated catalytic hairpin assembly (DTCHA) reaction displayed significantly faster kinetics and greater cycle conversion efficiency than traditional CHA. The resulting 3D nanonetworks could load a large amount of Ru(phen)32+, significantly enhancing its ECL signal, and exhibit detection limits for both miR-21 and miR-141 at the femtomolar level. The biosensor based on modular logic gates facilitated the distinction and quantification of cancer cells and normal cells based on miR-21 levels, combined with miR-141 levels, to further identify different subtypes of breast cancer cells. Overall, this study provides potential applications in miRNA-related clinical diagnostics.

Electrochemical Monitoring of Sphingosine-1-phosphate-Induced ATP Release Using a Microsensor Based on an Entropy-Driven Bipedal DNA Walker

Neuropathic pain is a chronic and severe syndrome for which effective therapy is insufficient and the release of ATP from microglia induced by sphingosine-1-phosphate (S1P) plays a vital role in neuropathic pain. Therefore, there is an urgent demand to develop highly sensitive and selective ATP biosensors for quantitative monitoring of low-concentration ATP in the complex nervous system, which helps in understanding the mechanism involved in neuropathic pain. Herein, we developed an electrochemical microsensor based on an entropy-driven bipedal DNA walker. First, the microsensor specifically recognized ATP via ATP aptamers, initiating the entropy-driven bipedal DNA walker. Subsequently, the bipedal DNA walker autonomously traversed the microelectrode interface, introducing methylene blue to the electrode surface and achieving cascade signal amplification. This microsensor showed excellent selectivity, stability, and a low limit of detection at 1.13 nM. The S1P-induced ATP release from BV2 cells was successfully monitored, and it was observed that dicumarol could inhibit this release, suggesting dicumarol as a potential treatment for neuropathic pain. The microsensor's small size exhibited significant potential for monitoring ATP level changes in neuropathic pain in vivo, which provides a new strategy for in situ and quantitative monitoring of nonelectroactive biomolecules associated with neurological diseases.

Controllable and reusable seesaw circuit based on nicking endonucleases

Seesaw circuits are essential for molecular computing and biosensing. However, a notable limitation of seesaw circuits lies in the irreversible depletion of components, precluding the attainment of system recovery and rendering nucleic acid circuits non-reusable. We developed a brand-new method for creating controllable and reusable seesaw circuits. By using the nicking endonucleases Nt.BbvCI and Nt.Alwi, we removed "functional components" while keeping the "skeletal components" for recurrent usage. T-inputs were introduced, increasing the signal-to-noise ratio of AND logic from 2.68 to 11.33 and demonstrating compatibility. We identified the logic switching feature and verified that it does not impair circuit performance. We also built intricate logic circuits, such as OR-AND gate, to demonstrate the versatility of our methodology. This controllable reusability extends the applications of nanotechnology and bioengineering, enhancing the practicality and efficiency of these circuits across various domains.

Ratiometric electrochemical biosensor based on lateral movement of multi-pedal DNA tetrahedron machine on biomimetic interface

In this work, a lateral moving multi-pedal DNA tetrahedron machine (MTM) is designed and coupled with dual-signal output system to construct a biomimetic electrochemical ratiometric strategy for ultrasensitive target DNA analysis. The tetrahedral structure provided rigid support for the pedal, ensuring efficient replacement of the rail chain modified with ferrocene. By conjugating cholesterol molecules to one vertex of MTM, it is decorated on a lipid bilayer. This molecular architecture confers lateral movement of MTM on an electrode surface while prevents its detachment from the system. The methylene blue tagged hairpin probe provides constant power to support MTM swim on lipid bilayer. Compared with the conventional motion mode, the lateral moving mechanism has the fastest reaction rate and the highest signal-to-noise ratio. Additionally, the dual-signal reporting system further improves the accuracy of target detection on the basis of ensuring motion efficiency. The work improved movement efficiency and shortened time fragment. A linear relationship between the ratio value of two reporters and target DNA concentration was observed from 0.5 fM to 50 pM with a detection limit of 28 aM. The lateral motion mode of DNA machine coalescing with ratiometric system made this sensing platform ultrasensitive and accurate, which holds new avenue of early diagnosis.

NIR-driven photoelectrochemical-fluorescent dual-mode biosensor based on bipedal DNA walker for ultrasensitive detection of microRNA

Optical biosensors have become powerful tools for bioanalysis, but most of them are limited by optic damage, autofluorescence, as well as poor penetration ability of ultraviolet (UV) and visible (Vis) light. Herein, a near-infrared light (NIR)-driven photoelectrochemical (PEC)-fluorescence (FL) dual-mode biosensor has been proposed for ultrasensitive detection of microRNA (miRNA) based on bipedal DNA walker with cascade amplification. Fueled by toehold-mediated strand displacement (TMSD), the bipedal DNA walker triggered by target miRNA-21 is formed through catalytic hairpin assembly (CHA), which can efficiently move along DNA tracks on CdS nanoparticles (CdS NPs)-modified fluorine doped tin oxide (FTO) electrode, resulting in the introduction of upconversion nanoparticles (UCNPs) on electrode surface. Under 980 nm laser irradiation, the UCNPs serve as the energy donor to emit UV/Vis light and excite CdS NPs to generate photocurrent for PEC detection, while the upconversion luminescence (UCL) at 803 nm is monitored for FL detection. This PEC-FL dual-mode biosensor has achieved the ultrasensitive and accurate analysis of miRNA-21 in human serum and different gynecological cancer cells. Overall, the proposed dual-mode biosensor can not only couple the inherent features of each single-mode biosensor but also provide mutual authentication of testing results, which opens up a new avenue for early diagnosis of miRNA-related diseases in clinic.

Exonuclease-catalyzed recycling and annular four-footed DNA walking amplification-assisted "on-off-super on" signal transitions for photoelectrochemical biosensing of kanamycin

Photoelectrochemical (PEC) biosensors have exhibited a promising potential for assays of a large variety of analytes; however, how to realize their low background-based "super on" signal output is still a great challenge. Herein, we report a novel multiple nucleic acid amplification-assisted "on-off-super on" signal transition mechanism for the PEC biosensing of kanamycin antibiotics. The biosensing platform was constructed on a perylene-3,4,9,10-tetracarboxylic dianhydride-based photoelectrode, and its strong photocurrent could be well inhibited by an anchored ferrocene (Fc)-labeled hairpin DNA to produce a low background signal. Two target biorecognition-triggered exonuclease III-catalytic reactions were adopted to produce an annular four-footed DNA walker (AFW) and a methylene blue (MB)-labeled DNA strand. By using their synergistic effect to release Fc quenchers and simultaneously capture MB sensitizers, a "super on" signal output was realized. As a result, a very wide linear range from 10 fg mL-1 to 10 ng mL-1 and an ultra-low detection limit of 7.8 fg mL-1 were obtained. Meanwhile, the aptamer recognition-based homogeneous reaction and AFW-based multiple nucleic acid amplification effectively simplified the assay manipulation and well ensured the repeatability of the method. The satisfactory sample experiment results indicated its good reliability and accuracy for the antibiotic residue analysis application.

Photocleavable DNA Nanotube-Based Dual-Amplified Resonance Rayleigh Scattering System for MicroRNA Detection Incorporating Molecular Computing-Cascaded Keypad Lock Functionality

Cascade molecular events in complex systems are of vital importance for enhancing molecular diagnosis and information processing. However, the conversion of a cascaded biosensing system into a multilayer encrypted molecular keypad lock remains a significant challenge in the development of molecular logic devices. In this study, we present a photocleavable DNA nanotube-based dual-amplified resonance Rayleigh scattering (RRS) system for detecting microRNA-126 (miR-126). The cascading dual-amplification biosensing system provides a multilayer-encrypted prototype with the functionality of a molecular computing cascade keypad lock. RRS signals were greatly amplified by using photocleavable DNA nanotubes and enzyme-assisted strand displacement amplification (SDA). In the presence of miR-126, enzyme-assisted SDA produced numerous identical nucleotide fragments as the target, which were then specifically attached to magnetic beads through the DNA nanotube by using a Y-shaped DNA scaffold. Upon ultraviolet irradiation, the DNA nanotube was released into the solution, resulting in an increase in the intensity of the RRS signal. This strategy demonstrated a low limit of detection (0.16 fM) and a wide dynamic range (1 fM to 1 nM) for miR-126. Impressively, the enzyme-assisted SDA offers a molecular computing model for generating the target pool, which serves as the input element for unlocking the system. By cascading the molecular computing process, we successfully constructed a molecular keypad lock with a multilevel authentication technique. The proposed system holds great potential for applications in molecular diagnosis and information security, indicating significant value in integrating molecular circuits for intelligent sensing.

Photoresponsive CHA-Integrated Self-Propelling 3D DNA Walking Amplifier within the Concentration Localization Effect of DNA Molecular Framework Enables Highly Efficient Fluorescence Bioimaging

While three-dimensional (3D) DNA walking amplifiers hold considerable promise in the construction of advanced DNA-based fluorescent biosensors for bioimaging, they encounter certain difficulties such as inadequate sensitivity, premature activation, the need for exogenous propelling forces, and low reaction rates. In this contribution, a variety of profitable solutions have been explored. First, a catalytic hairpin assembly (CHA)-achieved nonenzymatic isothermal nucleic acid amplification is integrated to enhance sensitivity. Subsequently, one DNA component is simply functionalized with a photocleavage-bond to conduct a photoresponsive manner, whereby the target recognition occurs only when the biosensor is exposed to an external ultraviolet light source, overcoming premature activation during biodelivery. Furthermore, a special self-propelling walking mechanism is implemented by reducing biothiols to MnO2 nanosheets, thereby propelling forces that are self-supplied to a Mn2+-reliant DNAzyme. By carrying the biosensing system with a DNA molecular framework to induce a unique concentration localization effect, the nucleic acid contact reaction rate is notably elevated by 6 times. Following these, an ultrasensitive in vitro detection performance with a limit of detection down to 2.89 fM is verified for a cancer-correlated microRNA biomarker (miRNA-21). Of particular importance, our multiple concepts combined 3D DNA walking amplifier that enables highly efficient fluorescence bioimaging in live cells and even bodies, exhibiting a favorable application prospect in disease analysis.

Novel fluorescence nano-orbital biosensor for highly sensitive microRNA detection

BACKGROUND

MicroRNAs play an important role in regulating cell function and gene expression. Early prevention and clinical diagnosis of diseases have high requirements for high-sensitivity detection of microRNAs. Due to the limitations of tedious operation and large sample size, miRNA with small molecular weight and low expression abundance cannot be accurately detected in traditional miRNA detection. To improve the sensitivity and accuracy of detection, we established a novel biosensor based on nucleic acid circuit of signal amplification, which converted miRNA recognition into a fluorescence signal for amplification.

RESULTS

We designed a biosensor based on an exponential amplification reaction with cascaded HCR and DNAzyme nucleic acid circuit (named E-NOF biosensor) by amplicon sub-fragments to trigger the construction of fluorescence nano-orbitals (NOF), which could be used to detect miRNA ultrasensitively. By modifying two fluorophores (Cy3 and Cy5) on the chain of constructing nano-orbitals, when the amplicon triggered the construction of nano-orbitals, fluorescence resonance energy transfer (FRET) occurred between Cy3 and Cy5, and then two fluorescence signals with different trends could be observed. Therefore, through the ratio of the two signals, we could quantitatively and quickly detect the miRNA from 1 fM to 100 nM, and the E-NOF biosensor detection limit was as low as 0.129 fM. Furthermore, the HCR nucleic acid circuit cascaded with DNAzyme could enrich the fluorophores on the nano-orbitals and significantly enhance the fluorescence signal by accelerating the reaction rate.

SIGNIFICANCE

According to our understanding, the E-NOF biosensor is the first strategy to cascade EXPAR with HCR and DNAzyme nucleic acid circuit for miRNA-1246 detection. Accurate results can be obtained in only 120 min. Compared with the traditional HCR system, the sensitivity of the new E-NOF biosensor is increased by 1 × 109 times. Furthermore, the biosensor can also detect biomarkers in human serum samples. It has great potential in miRNA detection and identification.

Engineering Assembly of Plasmonic Virus-Like Gold SERS Nanoprobe Guided by Intelligent Dual-Machine Nanodevice for High-Performance Analysis of Tetracycline

Accurate detection of trace tetracyclines (TCs) in complex matrices is of great significance for food and environmental safety monitoring. However, traditional recognition and amplification tools exhibit poor specificity and sensitivity. Herein, a novel dual-machine linkage nanodevice (DMLD) is proposed for the first time to achieve high-performance analysis of TC, with a padlock aptamer component as the initiation command center, nucleic acid-encoded multispike virus-like Au nanoparticles (nMVANs) as the signal indicator, and cascade walkers circuit as the processor. The existence of spike vertices and interspike nanogaps in MVANs enables intense electromagnetic near-field focusing, allowing distinct surface-enhanced Raman scattering (SERS) activity. Moreover, through the sequential activation between multistage walker catalytic circuits, the DLMD system converts the limited TC recognition into massive engineering assemblies of SERS probes guided by DNA amplicons, resulting in synergistic enhancement of bulk plasmonic hotspot entities. The continuously guaranteed target recognition and progressively promoted signal enhancement ensure highly specific amplification analysis of TC, with a detection limit as low as 7.94 × 10-16  g mL-1 . Furthermore, the reliable recoveries in real samples confirm the practicability of the proposed sensing platform, highlighting the enormous potential of intelligent nanomachines for analyzing the trace hazards in the environment and food.

Electrochemical aptasensor based on DNA-templated copper nanoparticles and RecJf exonuclease-assisted target recycling for lipopolysaccharide detection

An electrochemical aptasensor for detecting lipopolysaccharides (LPS) was fabricated based on DNA-templated copper nanoparticles (DNA-CuNPs) and RecJf exonuclease-assisted target recycling. The DNA-CuNPs were synthesized on a double-stranded DNA template generated through the hybridization of the LPS aptamer and its complementary chain (cDNA). In the absence of LPS, the CuNPs were synthesized on DNA double-strands, and a strong readout corresponding to the CuNPs was achieved at 0.10 V (vs. SCE). In the presence of LPS, the fabricated aptamer could detach from the DNA double-strand to form a complex with LPS, disrupting the template for the synthesis of CuNPs on the electrode. Meanwhile, RecJf exonuclease could hydrolyze the cDNA together with this single-stranded aptamer, releasing the LPS for the next round of aptamer binding, thereby enabling target recycling amplification. As a result, the electrochemical signal decreased and could be used to indicate the LPS content. The fabricated electrochemical aptasensor exhibited an extensive dynamic working range of 0.01 pg mL-1 to 100 ng mL-1, and its detection limit was 6.8 fg mL-1. The aptasensor also exhibited high selectivity and excellent reproducibility. Moreover, the proposed aptasensor could be used in practical applications for the detection of LPS in human serum samples.

Development of a regenerable dual-trigger tripedal DNA walker electrochemical biosensor for sensitive detection of microRNA-155

Since microRNAs (miRNAs) are valuable biomarkers for disease diagnosis and prognosis, the pursuit of enhanced detection sensitivity through signal amplification strategies has emerged as a prominent focus in low-abundance miRNA detection research. DNA walkers, as dynamic DNA nanodevice, have gained significant attention for their applications as signal amplification strategies. To overcome the limitations of unipedal DNA walkers with a restricted signal amplification efficiency, there is a great need for multi-pedal DNA walkers that offer improved walking and signal amplification capabilities. Here, we employed a combination of catalytic hairpin assembly (CHA) and APE1 enzymatic cleavage reactions to construct a tripedal DNA walker, driving its movement to establish a cascade signal amplification system for the electrochemical detection of miRNA-155. The biosensor utilizes tumor cell-endogenous microRNA-155 and APE1 as dual-trigger for DNA walker formation and walking movement, leading to highly efficient and controllable signal amplification. The biosensor exhibited high sensitivity, with a low detection limit of 10 pM for microRNA-155, and successfully differentiated and selectively detected microRNA-155 from other interfering RNAs. Successful detection in 20 % serum samples indicates its potential clinical application. In addition, we harnessed strand displacement reactions to create a gentle yet efficient electrode regeneration strategy, to addresses the time-consuming challenges during electrode modification processes. We have successfully demonstrated the stability of current signals even after multiple cycles of electrode regeneration. This study showcased the high-efficiency amplification potential of multi-pedal DNA walkers and the effectiveness and versatility of strand displacement in biosensing applications. It opens a promising path for developing regenerable electrochemical biosensors. This regenerable strategy for electrochemical biosensors is both label-free and cost-effective, and holds promise for detecting various disease-related RNA targets beyond its current application.

DNA Nanomachine-Driven Heterogeneous Quadratic Amplification for Sensitive and Programmable miRNA Profiling

Inspired by the molecular crowding effect in biological systems, a novel heterogeneous quadratic amplification molecular circuit (HEQAC) was developed for sensitive bimodal miRNA profiling (HEQAC-BMP) by combining an MNAzyme-based DNA nanomachine with an entropy-driven catalytic hairpin assembly (E-CHA) autocatalytic circuit. Utilizing ferromagnetic nanomaterials as the substrate for DNA nanomachines, a biomimetic heterogeneous interface was established; thus, a localized molecular crowding system was created that can elevate the local reaction concentration and accelerate the molecular recognition process for a significant threshold signal. Simultaneously, the threshold signal undergoes further amplification by E-CHA and is transformed into a chemical signal, enabling a colorimetric-fluorescence bimodal signal readout. The HEQAC-BMP enables miRNA detection from 10 aM to 10 nM with detection limits of 3.7 aM (colorimetry) and 4.8 aM (fluorometry), respectively. Moreover, the design principle and strategy of HEQAC-BMP can be customized to address other critical viruses or diseases with life-threatening and socioeconomic impacts, enhancing healthcare outcomes for individuals.

Cascade signal amplification electrochemical biosensor based on AgNPs and ring opening polymerization for determination of Ochratoxin A

An ochratoxin A (OTA) electrochemical biosensor based on a cascade signal amplification strategy with Ag nanoparticles (AgNPs) and ring opening polymerization (ROP) was constructed. The large specific surface area of AgNPs was used to increase the loading of OTA aptamer on the electrode surface, enhancing the ability to capture OTA as a way to achieve the first signal amplification. The OTA antibody modified with polyethylenimine specifically recognizes the OTA, forming an aptamer-OTA-antibody sandwich structure. The amino group on polyethylenimine initiates the ROP reaction with α-amino acid-n-carboxylic anhydride-ferrocene (NCA-Fc) as the monomer. A large number of electrochemical signal units of ferrocene are introduced into the sensing system for a second signal amplification. By amplifying the signal twice, the sensitivity of the sensor is improved. Under the optimal conditions, the detection range of the sensor is 1 pg·mL-1 ~ 1 μg·mL-1, while the detection limit is as low as 117 fg·mL-1. Moreover, the sensor has the advantages of high sensitivity, good stability and selectivity. Standard addition recovery experiment proved that the sensing system can be successfully used for the detection of OTA in four actual samples with recoveries in the range 90.0 to 113% with RSDs of 0.6 to 5.2%, providing a new idea for the pollution assessment of mycotoxins.

Current research status of tumor cell biomarker detection

With the annual increases in the morbidity and mortality rates of tumors, the use of biomarkers for early diagnosis and real-time monitoring of tumor cells is of great importance. Biomarkers used for tumor cell detection in body fluids include circulating tumor cells, nucleic acids, protein markers, and extracellular vesicles. Among them, circulating tumor cells, circulating tumor DNA, and exosomes have high potential for the prediction, diagnosis, and prognosis of tumor diseases due to the large amount of valuable information on tumor characteristics and evolution; in addition, in situ monitoring of telomerase and miRNA in living cells has been the topic of extensive research to understand tumor development in real time. Various techniques, such as enzyme-linked immunosorbent assays, immunoblotting, and mass spectrometry, have been widely used for the detection of these markers. Among them, the detection of tumor cell markers in body fluids based on electrochemical biosensors and fluorescence signal analysis is highly preferred because of its high sensitivity, rapid detection and portable operation. Herein, we summarize recent research progress in the detection of tumor cell biomarkers in body fluids using electrochemical and fluorescence biosensors, outline the current research status of in situ fluorescence monitoring and the analysis of tumor markers in living cells, and discuss the technical challenges for their practical clinical application to provide a reference for the development of new tumor marker detection methods.

Dual-layer 3D DNA nanostructure: The next generation of ultrafast DNA nanomachine for microRNA sensing and intracellular imaging

The working efficiency of traditional 3D DNA nanomachines is extremely restricted due to the complex DNA components modified on nanoparticles in the same spatial height. Herein, an ultrafast dual-layer 3D DNA nanomachine (UDDNM) based on catalytic hairpin assembly (CHA) was developed by assembling two different lengths of hairpin DNA on the surface of gold nanoparticles, the long hairpin 1 (H1), to capture the trigger, and the short hairpin 2 (H2), as the signal probe, to recycle the trigger. Compared to the traditional single-layer 3D DNA nanomachine, the dual-layer 3D DNA nanostructure greatly enhances the effective collision between trigger and targeted DNA probe, H1, since the H1 located in outer layer would react with the trigger, inhibiting the invalid collision between the trigger and residual DNA component, H2, and remarkably decreasing the steric hindrance associated with the nucleic acids layer around the nanoparticles. Especially, when the distance of two layers was fixed at 3 nm, the corresponding UDDNM could accomplish the overall reaction only in 3 min with a dramatically high initial rate of up to 5.93 × 10-7 M s-1, which was at least 5-fold beyond that of the typical single-layer 3D DNA nanomachines. As a proof of concept, the described UDDNM was successfully applied in ultrasensitive fluorescence detection and sensitive intracellular imaging of miRNA-21. Consequently, our strategy, based on the creation of dual-layer 3D DNA nanostructure, may create a new approach to designing the next generation of DNA nanomachine and has enormous potential for applications in bio-analysis, logic gate operations, and clinical diagnoses.

Electrochemical nucleic acid sensors: Competent pathways for mobile molecular diagnostics

Electrochemical nucleic acid biosensor has demonstrated great promise in clinical diagnostic tests, mainly because of its flexibility, high efficiency, low cost, and easy integration for analytical applications. Numerous nucleic acid hybridization-based strategies have been developed for the design and construction of novel electrochemical biosensors for diagnosing genetic-related diseases. This review describes the advances, challenges, and prospects of electrochemical nucleic acid biosensors for mobile molecular diagnosis. Specifically, the basic principles, sensing elements, applications in diagnosis of cancer and infectious diseases, integration with microfluidic technology and commercialization are mainly included in this review, aiming to provide new insights and directions for the future development of electrochemical nucleic acid biosensors.

Self-accelerated DNA walker mediated electrochemical biosensor for rapid and ultrasensitive detection of microRNA

Herein, we developed a novel three-dimensional (3D) self-accelerated DNA walker (SADW) which progressively expedite walking rate by unlocking the more walking arm continuously in walker process to construct electrochemical biosensor for ultrasensitive detection of microRNA. Particularly, we skillfully introduced a target analogue sequence in the double-loop hairpin, which could be released in the walking process of SADW, then rapidly activating more silenced walking strands to achieve the continuous self-acceleration, resulting in the expedited reaction rate. Surprisingly, the average reaction rate of SADW was quite higher than that of traditional 3D self-circulating DNA walkers (DW) under pretty low target miRNA concentration, which is ascribed to the outstanding acceleration process of the SADW, readily conquering the major predicaments of DW in detecting target with traces concentration: slow reaction rate and low sensitivity. This way, the elaborated SADW is favorably applied in the ultrasensitive and rapid detection of miRNA-21 in tumor cancer cell lysates with a detection limit down to 5.81 aM which was far from lower than the detection limit of DW. This approach develops the novel generation of widespread strategy for the applications in clinic diagnose, biosensing assay, and DNA nanobiotechnology.

Efficient Three-Dimensional DNA Nanomachine Guided by a Robust Tetrahedral DNA Nanoarray Structure for the Rapid and Ultrasensitive Electrochemical Detection of Matrix Metalloproteinase 2

Herein, a giant-sized DNA nanoarray was subtly assembled by two kinds of independent tetrahedral DNA structures as the DNA track for a multi-armed three-dimensional (3D) DNA nanomachine to perform signal transduction and amplification efficiently, which was developed as an electrochemical biosensor for the rapid and ultrasensitive detection of matrix metalloproteinase 2 (MMP-2). Impressively, in contrast to conventional DNA walkers with inefficiency, which walked on random DNA tracks composed of a two-dimensional (2D) probe or a one-dimensional (1D) single-stranded (ss)DNA probe, the multi-armed 3D DNA nanomachine from exonuclease III (Exo III) enzyme-assisted target recycling amplification would be endowed with faster reaction speed and better walking efficiency because of the excellent rigidity and orderliness of the tetrahedral DNA nanoarray structure. Once the hairpin H3-label with the signal substance ferrocene (Fc) was added to the modified electrode surface, the multi-armed 3D DNA nanomachine would be driven to move along the well-designed nanoarray tracks by toehold-mediated DNA strand displacement, resulting in most of the ferrocene (Fc) binding to the electrode surface and a remarkable increase in electrochemical signals within 60 min. As a proof of concept, the prepared biosensor attained a low detection limit of 11.4 fg/mL for the sensitive detection of the target MMP-2 and was applied in Hela and MCF-7 cancer cell lysates. As a result, this strategy provided a high-performance sensing platform for protein detection in tumor diagnosis.

Modular Engineering of a DNA Tetrahedron-Based Nanomachine for Ultrasensitive Detection of Intracellular Bioactive Small Molecules

Bioactive small molecules serve as invaluable biomarkers for recognizing modulated organismal metabolism in correlation with numerous diseases. Therefore, sensitive and specific molecular biosensing and imaging in vitro and in vivo are particularly critical for the diagnosis and treatment of a large group of diseases. Herein, a modular DNA tetrahedron-based nanomachine was engineered for the ultrasensitive detection of intracellular small molecules. The nanomachine was composed of three self-assembled modules: an aptamer for target recognition, an entropy-driven unit for signal reporting, and a tetrahedral oligonucleotide for the transportation of the cargo (e.g., the nanomachine and fluorescent markers). Adenosine triphosphate (ATP) was used as the molecular model. Once the target ATP bonded with the aptamer module, an initiator was released from the aptamer module to activate the entropy-driven module, ultimately activating the ATP-responsive signal output and subsequent signal amplification. The performance of the nanomachine was validated by delivering it to living cells with the aid of the tetrahedral module to demonstrate the possibility of executing intracellular ATP imaging. This innovative nanomachine displays a linear response to ATP in the 1 pM to 10 nM concentration range and demonstrates high sensitivity with a low detection limit of 0.40 pM. Remarkably, our nanomachine successfully executes endogenous ATP imaging and is able to distinguish tumor cells from normal ones based on the ATP level. Overall, the proposed strategy opens up a promising avenue for bioactive small molecule-based detection/diagnostic assays.

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.

Self-Powered DNAzyme Walker Enables Dual-Mode Biosensor Construction for Electrochemiluminescence and Electrochemical Detection of MicroRNA

Herein, an electrochemiluminescence (ECL) and electrochemical (EC) dual-mode biosensor platform with a self-powered DNAzyme walking machine was established for accurate and sensitive detection of miRNA-21. By employing a magnesium ion (Mn²⁺)-dependent DNAzyme cleavage cycling reaction, the walking machine was built by assembling DNAzyme walking strands and ferrocene (Fc)-labeled substrate strands on the Au nanoparticles and graphitic carbon nitride nanosheet (g-C₃N₄ NS)-covered electrode. The DNAzyme walking strand was first prohibited by a blocker strand. After the addition of target miRNA-21 and Mn²⁺, the DNAzyme walker could be activated and produce autonomous movements along the electrode track fueled by Mn²⁺-dependent DNAzyme-catalyzed substrate cleavage without additional energy supply. Notably, each walking step resulted in the cleavage of a substrate strand and the release of a Fc-labeled DNA strand fragment, allowing us to acquire an extreme ECL signal recovery of g-C₃N₄ inhibited by Fc. Meanwhile, numerous Fc-labeled DNA fragments escaped from the surface of the electrode, directly producing an obvious decrease in the square wave voltammetry (SWV) signal from Fc on the same sensing platform. This work not only avoided difficultly assembling various signal indicators but also significantly improved the sensitivity through using self-powered DNAzyme-walker amplification. Moreover, the proposed design employed the same reaction to produce two signal output modes, which could eliminate the interference from diverse reactive pathways on the outcome to mutually improve the accuracy. Therefore, the dual-mode miRNA-21 biosensor exhibited wide detection ranges of 100 aM to 100 nM with low detection limits of 54.3 and 78.6 aM by ECL and SWV modes, respectively, which provided an efficient and universal biosensing approach with extensive applications in early disease diagnosis and bioanalysis.

A photoelectrochemical biosensor based on ZnIn2S4@AuNPs coupled with circular bipedal DNA walker for signal-on detection of circulating tumor DNA

The circulating tumor DNA (ctDNA) is a crucial cancer marker, its sensitive monitoring is useful for early diagnose and therapy of tumor-related diseases. Herein, a bipedal DNA walker with multiple recognition sites is designed through the transition of dumbbell-shaped DNA nanostructure to realize the dual amplification of the signal and achieve ultrasensitive photoelectrochemical (PEC) detection of ctDNA. Initially, the ZnIn₂S₄@AuNPs is obtained by combining the drop coating method with electrodeposition method. When the target is present, the dumbbell-shaped DNA structure transforms into an annular bipedal DNA walker that can walk unrestrictedly on the modified electrode. After the cleavage endonuclease (Nb.BbvCI) was added to the sensing system, the ferrocene (Fc) on the substrate is released from the electrode surface, and the transfer efficiency of photogenerated electron-hole pairs is extremely improved, enabling the "signal on" testing of ctDNA. The detection limit of the prepared PEC sensor is 0.31 fM, and the recovery of actual samples varied between 96.8 and 103.6% with an average relative standard deviation of about 8%. Meaningfully, the prepared PEC biosensor with an innovative bipedal DNA walker has potential application value for ultrasensitive detection of other nucleic acid-related biomarker.

Cooperative Amplification of Au@FeCo as Mimetic Catalytic Nanozymes and Bicycled Hairpin Assembly for Ultrasensitive Electrochemical Biosensing

Exploring the cooperative amplification of peroxidase-like metal nanocomposites and cycled hairpin assembly is intriguing for sensitive bioanalysis. Herein, we report the first design of a unique electrochemical biosensor based on mimicking Au@FeCo nanozymes and bicycled hairpin assembly (BHA) for synergistic signal amplification. By loading the enzyme-like FeCo alloy in Au nanoparticles (AuNPs), the as-synthesized Au@FeCo hybrids display great improvement of electronic conductivity and active surface area and excellent mimic catalase activity to H₂O₂ decomposition into ^•OH radicals. The immobilization of Au@FeCo in an electrode sensing interface is stabilized via the resulting electrodeposition in HAuCl₄ while efficiently accelerating the electron transfer of electroactive ferrocene (Fc). Upon the immobilization of a helping hairpin (HH) via Au-S bonds, a specific DNA trigger (T*) is introduced to activate BHA operation through competitive strand displacement reactions among recognizing hairpin (RH), signaling hairpin (SH), and HH. T* and RH are rationally released to catalyze two cycles, in which the transient depletion of dsDNA intermediates rapidly drives the progressive hairpin assemblies to output more products SH·HH. Thus, the efficient amplification of Au@FeCo mimic catalase activity combined with BHA leads to a significantly increased current signal of Fc dependent on miRNA-21 analogous to T*, thereby directing the creation of a highly sensitive electrochemical biosensor having applicable potential in actual samples.

Rational design of nonlinear hybridization immunosensor chain reactions for simultaneous ultrasensitive detection of two tumor marker proteins

Sensitive biomarker detection techniques are beneficial for both disease diagnosis and postoperative examinations. The nonlinear hybridization chain reaction (NHCR) is widely used as an output signal amplification technique for biosensor platforms. A novel hairpin-free NHCR was developed in this study as a flow cytometric immunoassay to detect alpha-fetoprotein (AFP) and prostate specific antigen (PSA). First, the target AFP is captured on magnetic beads (MBs) that are modified with capture antibodies. Then, the prepared biotin-streptavidin-biotin (B-S-B) system, which links biotinylated detection antibodies and biotinylated trigger DNA together through the high affinity between biotin-streptavidin interaction, is added to label the target AFP, forming a sandwich complex with three trigger DNA chains. Each trigger DNA chain grows a dendritic DNA nanostructure following a nonlinear hybridization chain reaction. As the substrate flue chains are labeled with fluorophores, the self-assembly process of dendritic DNA is accompanied by the continuous release of fluorophores. Dendrites with strong fluorescence then form on the surface of MBs. Finally, the target AFP is quantified by analyzing the fluorescent MBs using flow cytometry. The proposed immunoassay has a high selectivity along with isothermal, enzyme-free, and exponential amplification efficiency. It shows a limit of detection (LOD) of 1.74 pg mL^-1. The proposed biosensor was also successfully used to quantitatively detect AFP in serum samples. It may be utilized to detect multiple tumor markers simultaneously by changing the size of MBs and antibody-antigen pairs. Most tumor markers are only related to tumor diagnosis but without specificity, so the combined detection of multiple tumor markers can improve the accuracy of early tumor diagnoses.

A dual-modal electrochemical aptasensor based on intelligent DNA Walker with cascade signal amplification powered by Nb.BbvCI for Pb2

As a unique nanomachine, DNA Walker can move continuously along a specific orbit to amplify signal. Therefore, based on DNA Walker and endonuclease assisted signal amplification strategy, a novel dual-mode visual electrochemical aptasensor was constructed for the detection of Pb²⁺. Ceric dioxide@mesoporous carbon (CeO₂/CS)@AuNPs not only could improve the conductivity of sensing interface but also could fix the aptamer. DNA Walker moved on the surface of the electrode to realize the pairing with the Ag-γFe₂O₃/cDNA probe, forming a special base sequence that could be spliced by the Nb.BbvCI. Under the action of endonuclease Nb.BbvCI, the Ag-γFe₂O₃/cDNA probe was continuously sheared and the amount on the electrode was decreased to amplify the signal. Besides, the nanoenzyme of Ag-γFe₂O₃ could catalyze 3'3'5'5'-tetramethylbenzidine (TMB) to blue color realizing the visual detection of Pb²⁺. The sensor has been successfully applied to the visual and accurate rapid detection of Pb²⁺ in aquatic products. The fabricated method of the sensor open up a new way for visual and accurate the detection of environmental pollutants.

Self-Priming DNA Polymerization-Propelled Stochastic Walkers on Magnetic Microbeads for Amplified Detection of miRNA

Sensitive detection of miRNA targets in complex biological samples possesses great value in biopsy analysis and disease diagnosis but is still challenging because of low abundance and nonspecific interferences. In this work, self-primer DNA polymerization-propelled stochastic walkers (SWs) were proposed to detect miRNA-24 by combining magnetic microbeads (MMBs) and flow cytometry. The MMBs not only provide a three-dimensional interface for DNA walkers but also facilitate the enrichment and isolation of RNA targets from complex biological samples such as serum. The SWs can be initiated to walk through the entire surface of MMBs and transduce RNA walking into amplified fluorescence signals, with the detection limit of miRNA-24 at 0.95 pM. Moreover, this strategy integrating with flow cytometry was demonstrated to have good specificity with other homologous miRNAs. This platform offers promising applications in RNA biosensing and biomedical diagnostics.

A renewable platform based on the entropy-driven catalytic amplification and element labeling inductively coupled plasma mass spectrometry for microRNA analysis

The element labeling inductively coupled plasma mass spectrometry (ICP-MS) strategy has been increasingly applied to the bioanalysis for various bio-targets. Herein, a renewable analysis platform with element labeling ICP-MS was firstly proposed for microRNA (miRNA) analysis. The analysis platform was established on the magnetic bead (MB) with entropy-driven catalytic (EDC) amplification. When the EDC reaction was initiated by target miRNA, numerous strands labeled with Ho element were released from MBs, and ¹⁶⁵Ho in the supernatant detected by ICP-MS could reflect the amount of target miRNA. After detection, the platform was easily regenerated by adding strands to reassemble EDC complex on MBs. This MB platform could be used four times, and the limit of detection for miRNA-155 was 8.4 pmol L^-1. Moreover, the developed regeneration strategy based on EDC reaction can be easily expanded to other renewable analysis platforms, such as, the renewable platform involving EDC and rolling circle amplification technology. Overall, this work proposed a novel regenerated bioanalysis strategy to reduce the consumption of reagent and time for probe preparation, profiting the development of bioassay based on element labeling ICP-MS strategy.

Ultrasensitive Electrochemiluminescence Biosensor Based on 2D Co3O4 Nanosheets as a Coreaction Accelerator and Highly Ordered Rolling DNA Nanomachine as a Signal Amplifier for the Detection of MicroRNA

A novel ultrasensitive electrochemiluminescence (ECL) biosensor was constructed using two-dimensional (2D) Co₃O₄ nanosheets as a novel coreaction accelerator of the luminol/H₂O₂ ECL system for the detection of microRNA-21 (miRNA-21). Impressively, coreaction accelerator 2D Co₃O₄ nanosheets with effective mutual conversion of the Co²⁺/Co³⁺ redox pair and abundant active sites could promote the decomposition of coreactant H₂O₂ to generate more superoxide anion radicals (O₂^•-), which reacted with luminol for significantly enhancing ECL signals. Furthermore, the trace target miRNA-21 was transformed into a large number of G-wires through the strand displacement amplification (SDA) process to self-assemble the highly ordered rolling DNA nanomachine (HORDNM), which could tremendously improve the detection sensitivity of biosensors. Hence, on the basis of the novel luminol/H₂O₂/2D Co₃O₄ nanosheet ternary ECL system, the biosensor implemented ultrasensitive detection of miRNA-21 with a detection limit as low as 4.1 aM, which provided a novel strategy to design an effective ECL emitter for ultrasensitive detection of biomarkers for early disease diagnosis.

Electrostatic Interaction-Induced Aggregation-Induced Emission-Type AgAu Bimetallic Nanoclusters as a Highly Efficient Electrochemiluminescence Emitter for Ultrasensitive Detection of Glial Fibrillary Acidic Protein

Herein, the aggregation-induced emission (AIE)-type carboxymethyl chitosan (CMCS)@6-aza-2-thiothymine (ATT) templated AgAu bimetallic nanoclusters (CMCS@ATT-AgAu BMNCs) with superior electrochemiluminescence (ECL) emission were first synthesized to construct a biosensor for the ultrasensitive detection of glial fibrillary acidic protein (GFAP). Impressively, unlike the traditional AIE-type bimetallic nanoclusters (BMNCs) obtained by complicated multi-step synthesis, the AIE-type CMCS@ATT-AgAu BMNCs were prepared by the electrostatic interaction between the negatively charged ATT and positively charged CMCS, in which the molecule ATT was served as a capping and reducing agent of bimetal ions. In addition, a rapidly moving cholesterol labeled DNA walker was constructed to move freely on the lipid bilayer to increase its moving efficiency, and the well-regulated DNA was intelligently designed to further improve its walking efficiency for rapid and ultrasensitive detection of GFAP with a limit of detection (LOD) as low as 73 ag/mL. This strategy proposed an avenue to synthesize highly efficient BMNCs-based ECL emitters, which have great potential in ultrasensitive biosensing for early diagnosis of diseases.

A catalytic hairpin assembly-based Förster resonance energy transfer sensor for ratiometric detection of ochratoxin A in food samples

Ochratoxin A (OTA) poses severe risks to the environment and human health, making the development of an accurate and sensitive analytical method for OTA detection essential. In this study, a catalytic hairpin assembly (CHA)-based Förster resonance energy transfer (FRET) aptasensor was developed to detect OTA using carbon quantum dots (CDs) and 6-carboxy-fluorescein (FAM) as dual signal readout. In the presence of OTA, the aptamer specifically interacted with OTA to release the helper DNA (HP), which could open the hairpin structure of FAM-labeled hairpin DNA 1 (H₁-FAM) modified on the surface of gold nanoparticles (AuNPs). CHA between H₁-FAM and hairpin H₂ labeled with CDs (H₂-CDs) can release HP for the next cycle, resulting in the occurrence of FRET with CDs as the energy donor and FAM as the energy acceptor. According to the ratio of F_CDs/F_FAM, the proposed aptasensor showed a wide linear range from 5.0 pg/mL to 3.0 ng/mL and a low detection limit of 1.5 pg/mL for OTA detection. Moreover, satisfactory results were obtained for OTA detection in rice, suggesting the potential application of this sensor in food safety analysis.

Appraising the electrocatalytic performance of beta-cyclodextrin embellished supramolecular recognition system for pernicious food colorants

The current research presents the evaluation of supramolecular proficiency of the designed platform for electrocatalytic determination of pernicious food colorants, amaranth and fast green. The approach involving surface modification of glassy carbon electrode with beta cyclodextrin decorated strontium ferrite reduced graphene oxide nanocomposite (SFrGO-βCD) to ensure fast and reversible electro-oxidation of hydroxyl groups of the colorant molecules. The synergy between SF and rGO facilitated the sensor with enhanced surface area and conductivity through faradic redox reaction. Tremendous decrease in the obtained values of peak separation potential and impedance as manifested in CV and EIS analysis, enabled by electrostatic interactions between surface functionalities of rGO and βCD has resulted in the significant augmentation of sensitivity. The value of charge transfer coefficient, number of electrons involved, nature of electron transport process at electrode electrolyte interface during the analysis of electrochemical detection were explored through CV experiments. Food samples analysis (without spiking) utilizing screen printed electrode manifested the sensor as portable device for real time monitoring. Outstanding detection limit (0.022 nM for amaranth and 0.051 nM for fast green), excellent regenerability (Relative standard deviation less than 3%) and apparent recovery rate (above 90%) of the modified electrode presented a colossal potential for the development of sustainable and commercially competitive electrochemical sensor in food sector.

Controllable Three-Dimensional DNA Nanomachine-Mediated Electrochemical Biosensing Platform for Rapid and Ultrasensitive Detection of MicroRNA

In this work, a high-efficiency controllable three-dimensional (3D) DNA nanomachine (CDNM) was reasonably developed by regulating the diameter of the core and the length of the DNAzyme cantilever, which acquired greater amplification efficiency and speedier walking rate than traditional 3D DNA nanomachines with gold nanoparticles as the cores and DNAzymes as the walking arms. Significantly, once the target miRNA-21 existed, a large number of silent DNAzymes on the CDNM could be activated by enzyme-free-target-recycling amplification (EFTRA) to achieve fast cleavage and walking on the biosensor surface under the interaction of Mg²⁺. Impressively, when the diameter of the core was 40 nm and the length of the DNAzyme cantilever was 5 nm (15 bp), the CDNM could complete the reaction process in 60 min that was at least twice shorter than those of conventional DNA nanomachines. Moreover, the designed electrochemical biosensor successfully detected target miRNA-21 at an ultrasensitive level with a wide response range (100 aM to 1 nM) and a low detection limit (33.1 aM). Therefore, the developed CDNM provides a new idea for exploring functional DNA nanomachines in the field of biosensing for applications.

Nucleic acid and nanomaterial-assisted signal-amplified strategies in fluorescent analysis of circulating tumor cells and small extracellular vesicles

As two main types of liquid biopsy markers, both circulating tumor cells (CTCs) and small extracellular vesicles (sEVs) play important roles in the diagnosis and prognosis of cancers. CTCs are malignant cells that detach from the original tumor tissue and enter the circulation of body fluids. sEVs are nanoscale vesicles secreted by normal cells or pathological cells. However, CTCs and sEVs in body fluids are scarce, leading to great difficulties in the accurate analysis of related diseases. For the sensitive detection of CTCs and sEVs in body fluids, various types of nucleic acid and nanomaterial-assisted signal amplification strategies have been developed. In this review, we summarize the recent advances in fluorescent detection of CTCs and sEVs in liquid biopsy based on nucleic acid and nanomaterial-assisted signal amplification strategies. We also discuss their advantages, challenges, and future prospects.

Recent advancements in nucleic acid detection with microfluidic chip for molecular diagnostics

The coronavirus disease 2019 (COVID-19) has extensively promoted the application of nucleic acid testing technology in the field of clinical testing. The most widely used polymerase chain reaction (PCR)-based nucleic acid testing technology has problems such as complex operation, high requirements of personnel and laboratories, and contamination. The highly miniaturized microfluidic chip provides an essential tool for integrating the complex nucleic acid detection process. Various microfluidic chips have been developed for the rapid detection of nucleic acid, such as amplification-free microfluidics in combination with clustered regularly interspaced short palindromic repeats (CRISPR). In this review, we first summarized the routine process of nucleic acid testing, including sample processing and nucleic acid detection. Then the typical microfluidic chip technologies and new research advances are summarized. We also discuss the main problems of nucleic acid detection and the future developing trend of the microfluidic chip.

A novel DNA detection using spherical identification probe and strand displacement reaction-initiated silver nanocluster switch

Herein, we developed a novel fluorescent assay using spherical identification probes and toehold-mediated strand displacement reaction-initiated silver nanoclusters (AgNCs) "on-off" signal switch. In this strategy, the target was captured by the spherical probes to induce the activity of exonuclease III (Exo III), catalyzing the cyclic cleavage of substrates to produce a mass of trigger strands. After magnetic bead separation, the intermediates in the supernatant activated downstream toehold-mediated strand displacement reaction to change the structure of silver nanocluster templates, leading to fluorescence intensity reduction. Furthermore, it is demonstrated that the application of spherical identification probes could reduce the signal leakage and the limit of detection. In addition, AgNCs with perfect optical property were ingeniously combined to realize signal output, which reduced the cost and time of synthesis. Under the optimal conditions, the sensing method displayed a good linear range from 250 pM to 25 nM with a detectable minimum concentration of 250 pM. And the practical application potential in complex biological matrices was also evaluated. Considering these advantages, this constructed strategy opens a new path for nucleic acid detection with better performance. A simple, label- and hairpin-free fluorescent system based on spherical identification probe and toehold-mediated strand displacement reaction-initiated silver nanoclusters (AgNCs) "on-off" signal switch was successfully constructed to detect target DNA.

Pathogen Identification: Ultrasensitive Nucleic Acid Detection via a Dynamic DNA Nanosystem-Integrated Ratiometric Electrochemical Sensing Strategy

Sensitively determining trace nucleic acid is of great significance for pathogen identification. Herein, a dynamic DNA nanosystem-integrated ratiometric electrochemical biosensor was proposed to determine human immunodeficiency virus-associated DNA fragment (HIV-DNA) with high sensitivity and selectivity. The dynamic DNA nanosystem was composed of a target recycling unit and a multipedal DNA walker unit. Both of them could be driven by a toehold-mediated strand displacement reaction, enabling an enzyme-free and isothermal amplification strategy for nucleic acid determination. The target recycling unit could selectively recognize HIV-DNA and activate the multipedal DNA walker unit to roll on the electrode surface, which would lead to bidirectional signal variation for ratiometric readout with cascade signal amplification. Benefiting from the synergistic effect of the dynamic DNA nanosystem and the ratiometric output mode, the ultrasensitive detection of HIV-DNA was achieved in a wide linear range of 6 orders of magnitude with a limit of detection of 36.71 aM. The actual usability of the proposed sensor was also verified in complex biological samples with acceptable performance. This dynamic DNA nanosystem-integrated ratiometric sensing strategy might be promising in the development of reliable point-of-care diagnostic devices for highly sensitive and selective pathogen identification.

Electrochemical Aptasensing of SARS-CoV-2 Based on Triangular Prism DNA Nanostructures and Dumbbell Hybridization Chain Reaction

Development of convenient, accurate, and sensitive methods for rapid screening of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) infection is highly desired. In this study, we have developed a facile electrochemical aptasensor for the detection of the SARS-CoV-2 S1 protein amplified by dumbbell hybridization chain reaction (DHCR). A triangular prism DNA (TPDNA) nanostructure is first assembled and modified at the electrode interface. Due to the multiple thiol anchors, the immobilization is quite stable. The TPDNA nanostructure also provides an excellent scaffold for better molecular recognition efficiency on the top single-strand region (DHP0). The aptamer sequence toward the SARS-CoV-2 S1 protein is previously localized by partial hybridization with DHP0. In the presence of the target protein, the aptamer sequence is displaced and DHP0 is exposed. After further introduction of the fuel stands of DHCR, compressed DNA linear assembly occurs, and the product can be stacked on the TPDNA nanostructure for the enrichment of electrochemical species. This electrochemical method successfully detects the target protein in clinical samples, which provides a simple, robust, and accurate platform with great potential utility.

Strategies for Enhancing the Sensitivity of Electrochemiluminescence Biosensors

Electrochemiluminescence (ECL) has received considerable attention as a powerful analytical technique for the sensitive and accurate detection of biological analytes owing to its high sensitivity and selectivity and wide dynamic range. To satisfy the growing demand for ultrasensitive analysis techniques with high efficiency and accuracy in complex real sample matrices, considerable efforts have been dedicated to developing ECL strategies to improve the sensitivity of bioanalysis. As one of the most effective approaches, diverse signal amplification strategies have been integrated with ECL biosensors to achieve desirable analytical performance. This review summarizes the recent advances in ECL biosensing based on various signal amplification strategies, including DNA-assisted amplification strategies, efficient ECL luminophores, surface-enhanced electrochemiluminescence, and ratiometric strategies. Sensitivity-enhancing strategies and bio-related applications are discussed in detail. Moreover, the future trends and challenges of ECL biosensors are discussed.

Highly Efficient Quadruped DNA Walker Guided by Ordered DNA Tracks for Rapid and Ultrasensitive Electrochemical Detection of miRNA-21

Herein, a long period liner DNA tandem (Lr-DNT) was intelligently designed as DNA track for quadruped DNA walker (q-walker) to run in an orderly and efficient manner, which could be applied to construct an electrochemical biosensor for rapid and ultrasensitive detection of microRNA-21 (miRNA-21). Impressively, benefiting from the orderliness and equidistance of Lr-DNT, the q-walker could be endowed with a high controllability, directionality as well as a quite short reaction time down to 20 min compared with those of traditional DNA walkers walked on the stochastic tracks. Once the target miRNA-21 interacted with the locked q-walker, the q-walker could be activated to expeditiously cleave Lr-DNT for releasing amounts of signal probes ferrocene (Fc) with the assistance of the Nt.BbvCI enzyme. This way, the developed q-walker could not only readily overcome the problem of low reaction efficiency but also address the drawback of time consumption in a previous strategy. As a proof of concept, the prepared biosensor could accomplish sensitive detection of target miRNA-21 with a detection limit down to 31 aM. As a result, this tactic gave impetus to design high-performance sensing platform with ultimate application in clinical sample analysis and nucleic acid based cancer diagnostics.

Electrochemical Biosensors for Circulating Tumor DNA Detection

Early diagnosis and treatment have always been highly desired in the fight against cancer, and detection of circulating tumor DNA (ctDNA) has recently been touted as highly promising for early cancer-screening. Consequently, the detection of ctDNA in liquid biopsy is gaining much attention in the field of tumor diagnosis and treatment, which has also attracted research interest from industry. However, it is difficult to achieve low-cost, real-time, and portable measurement of ctDNA in traditional gene-detection technology. Electrochemical biosensors have become a highly promising solution to ctDNA detection due to their unique advantages such as high sensitivity, high specificity, low cost, and good portability. Therefore, this review aims to discuss the latest developments in biosensors for minimally invasive, rapid, and real-time ctDNA detection. Various ctDNA sensors are reviewed with respect to their choices of receptor probes, designs of electrodes, detection strategies, preparation of samples, and figures of merit, sorted by type of electrode surface recognition elements. The development of biosensors for the Internet of Things, point-of-care testing, big data, and big health is analyzed, with a focus on their portable, real-time, and non-destructive characteristics.

Nucleic acid isothermal amplification-based soft nanoarchitectonics as an emerging electrochemical biosensing platform

The emergence of nucleic acid isothermal amplification strategies based on soft nanoarchitectonics offers a new dimension to the traditional electrochemical technique, particularly because of its flexibility, high efficiency, and increased sensitivity for analytical applications. Various DNA/RNA isothermal amplification strategies have been developed for the design and fabrication of new electrochemical biosensors for efficient and important biomolecular detection. Herein, we provide an overview of recent efforts in this research field and the strategies for signal-amplified sensing systems, with their biological applications, current challenges and prospects in this promising new area.

Size-Discriminative DNA Nanocage Framework Enables Sensitive and High-Fidelity Imaging of Mature MicroRNA in Living Cells

Mature microRNAs (miRNAs) are closely associated with cell proliferation and differentiation, stress response, and carcinogenesis, and monitoring intracellular miRNAs can contribute to the studies of their regulatory roles and molecular mechanisms of disease progression. However, accurate and reliable detection of mature miRNAs in complex physiological environments encounters the challenge of undesired detection accuracy ascribed to the coexistence of their precursor microRNAs (pre-miRNAs) and degradation of sensing probes. Here, we demonstrate the synthesis of a new size-discriminative DNA nanocage framework (DNF) for the sensitive monitoring of mature miRNA-21 in living cells with high accuracy via cascaded toehold-mediated strand displacement reaction (TSDR) amplifications. The DNF is prepared by a simple self-assembly of six ssDNAs, and the signal probes are docked inside the DNF. Because of its rigid framework structure, the DNF shows enhanced enzyme stability. Upon entering cells, only the short target mature miRNA-21 sequences instead of the large-sized pre-miRNAs are allowed to be accommodated inside the cavity of the DNF owing to the size-discriminative capability of the DNF. The cascaded TSDR amplifications can thus be activated by the mature miRNA-21 together with endogenous ATP to result in magnified fluorescence for sensitive detection and selective discrimination of miRNA-21 from the interference pre-miRNAs. Our results indicate that the DNF probes can offer robust sensing means for detecting various intracellular mature miRNAs with high accuracy for disease diagnoses and biomedical studies.