Proximity hybridization induced molecular machine for signal-on electrochemical detection of α-synuclein oligomers

α-synuclein oligomer is a marker of Parkinson's disease. The traditional enzyme-linked immunosorbent assay for α-synuclein oligomer detection is not conducive to large-scale application due to its time-consuming, high cost and poor stability. Recently, DNA-based biosensors have been increasingly used in the detection of disease markers due to their high sensitivity, simplicity and low cost. In this study, based on the DNAzyme-driven DNA bipedal walking method, we developed a signal-on electrochemical sensor for the detection of α-syn oligomers. Bipedal DNA walkers have a larger walking area and faster walking kinetics, providing higher amplification efficiency compared to conventional DNA walkers. The DNA walker is driven via an Mg2+-dependent DNAzyme, and the binding-induced DNA walker will continuously clamp the MB, resulting in the proliferation of Fc confined near the GE surface. The linear range and limit of detection were 1 fg/mL to 10 pg/mL and 0.57 fg/mL, respectively. The proposed signal-on electrochemical sensing strategy is more selective. It will play a significant role in the sensitive and precise electrochemical analysis of other proteins.

Stimuli-responsive probes for amplification-based imaging of miRNAs in living cells

MicroRNAs (miRNAs) have emerged as important biomarkers in biomedicine and bioimaging due to their roles in various physiological and pathological processes. Real-time and in situ monitoring of dynamic fluctuation of miRNAs in living cells is crucial for understanding these processes. However, current miRNA imaging probes still have some limitations, including the lack of effective amplification methods for low abundance miRNAs bioanalysis and uncontrollable activation, leading to background signals and potential false-positive results. Therefore, researchers have been integrating activatable devices with miRNA amplification techniques to design stimuli-responsive nanoprobes for "on-demand" and precise imaging of miRNAs in living cells. In this review, we summarize recent advances of stimuli-responsive probes for the amplification-based imaging of miRNAs in living cells and discuss the future challenges and opportunities in this field, aiming to provide valuable insights for accurate disease diagnosis and monitoring.

Multiorbital DNA walker nanoprobe for portable photothermal detection based on H2S etching of cubic Prussian blue

In the developed assay, multiorbital 3D DNA walker (MO DNA walker) was applied as signal amplified protocol for enhancing the detection signal of the photothermal biosensor, which was designed for sensitive detection of miRNA based on the H2S triggered conversation of photothermal reagent. When the target molecule is present, the DNA walking strand was released and then hybridize with track strands. The landing of walking particles (WPT) on the tracking particles (TPT) promotes the relative movement of the WPT around TPT, thus releasing large amount of horseradish peroxidase (HRP) with the aid of DNAzyme. After reacting with Na2S2O3 and H2O2, multiple H2S can be generated in situ based on the catalytic ability of HRP. Meanwhile, cubic Prussian blue (CPB) was synthesized and exhibited superior photothermal response, which can be served as efficient photothermal reagent and H2S responsive acceptor. Significantly, the photothermal signal of CPB could be obviously reduced after challenged with H2S ascribed to synchronous reaction between the ferric ion (Fe3+) and H2S. The improved walking area and freedom enable significant signal amplification, enhancing the biosensor's performance. Under ideal circumstances, the proposed photothermal assay demonstrated excellent performance for determination of miRNA-21.

DNAzyme-driven bipedal DNA walker triggered to hybridize silver nanoparticle probes for electrochemical detection of amyloid-β oligomer

Amyloid-β oligomer has been considered as a promising molecular biomarker for the diagnosis of Alzheimer's disease due to their significant neural synapse toxicity. Therefore, it is essential to create an easy approach for the selective detection of Amyloid-β oligomer that has high sensitivity and cheap cost. In this work, we developed an innovative enzyme-free electrochemical aptasensor based on the DNAzyme-driven DNA bipedal walker tactics for sensing Amyloid-β oligomer. Bipedal DNA walkers demonstrate a wider walking region, better walking kinetics, and higher amplification effectiveness than typical DNA walkers. The Mg²⁺-dependent DNAzyme drove the DNA walker, and the binding-induced DNA walker can sequentially shear MBs and form MB fragment structure. Finally, the detection probes modified AgNPs hybridized with the MB fragment structure, resulting in the multiplication of AgNPs on the electrode surface. Electrochemical stripping of AgNPs was used to test the performance of the obtained electrochemical sensor. In particular, a low detection limit of 5.94 fM and a wide linear range of 0.01 pM-0.1 nM were attained. The detection of Amyloid-β oligomer in human serum was then carried out using this bipedal DNA walker biosensor, which shown good selectivity and outstanding reproducibility, indicating its usefulness in bioanalysis.

DNAzyme-driven bipedal DNA walker for label-free and signal-on electrochemical detection of amyloid-β oligomer

As a common technique for detecting AβO, the enzyme-linked immunosorbent assay (ELISA) method is time-consuming, high in cost, and poor in stability. Therefore, it is necessary to develop a highly sensitive, method-simple and low-cost method for the selective detection of AβO. Here, we created a novel signal-on and label-free electrochemical aptamer sensor for the detection of AβO based on a DNAzyme-driven DNA bipedal walking strategy. Compared with common DNA walkers, bipedal DNA walkers exhibit larger walking areas and faster walking kinetics, and provide higher amplification efficiency. The DNAwalker is powered by an Mg²⁺-dependent DNAzyme, and the binding-induced DNAwalker continuously clamps the MB, unlocking several active G-quadruplex-forming sequences. These G-quadruplexes can be further combined by hemin to generate a G-quadruplex/heme complex, resulting in an amperometric signal, resulting in a broad proportional band from 0.1 pM to 1 nM and an excellent detection range of 46 fM. A bipedal DNA walker aptamer sensor can detect human serum AβO with remarkable specificity, high reproducibility and practical application value.

Electrochemiluminescence nanoemitters for immunoassay of protein biomarkers

The family of electrochemiluminescent luminophores has witnessed quick development since the electrochemiluminescence (ECL) phenomenon of silicon nanoparticles was first reported in 2002. Moreover, these developed ECL nanoemitters have extensively been applied in sensitive detection of protein biomarker by combining with immunological recognition. This review firstly summarized the origin and development of various ECL nanoemitters including inorganic and organic nanomaterials, with an emphasis on metal-organic frameworks (MOFs)-based ECL nanoemitters. Several effective strategies to amplify the ECL response of nanoemitters and improve the sensitivity of immunosensing were discussed. The application of ECL nanoemitters in immunoassay of protein biomarkers for diagnosis of cancers and other diseases, especially lung cancer and heart diseases, was comprehensively presented. The recent development of ECL imaging with the nanoemitters as ECL tags for detection of multiplex protein biomarkers on single cell membrane also attracted attention. Finally, the future opportunities and challenges in the ECL biosensing field were highlighted.

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.

Construction of Fast-Walking Tetrahedral DNA Walker with Four Arms for Sensitive Detection and Intracellular Imaging of Apurinic/Apyrimidinic Endonuclease 1

Herein, a novel tetrahedral DNA walker with four arms was engineered to travel efficiently on the 3D-tracks via catalyzed hairpin assembly autonomously, realizing the sensitive detection and activity assessment as well as intracellular imaging of apurinic/apyrimidinic endonuclease 1 (APE1). In contrast to traditional DNA walkers, the tetrahedral DNA walker with the rigid 3D framework structure and nonplanar multi-sites walking arms endowed with high collision efficiency, showing a fast walking rate and high nuclease resistance. Impressively, the initial rate of the tetrahedral DNA walker with four arms was 4.54 times faster than that of the free bipedal DNA walker and produced a significant fluorescence recovery in about 40 min, achieving a sensitive detection of APE1 with a low detection limit of 5.54× 10^-6 U/μL as well as ultrasensitive intracellular APE1 fluorescence activation imaging. This strategy provides a novel DNA walker for accurate identification of low-abundance cancer biomarker and potential medical diagnosis.

Pyrenecarboxaldehyde encapsulated porous TiO2 nanoreactors for monitoring cellular GSH levels

Recently, ternary electrochemiluminescence (ECL) system has become a hot research topic due to its great potential for improving ECL efficiency by promoting the generation of intermediates. However, it is still a great challenge to increase the utilization rate of intermediates in a ternary ECL system. Herein, we propose a strategy to increase the utilization rate of intermediates by designing pyrenecarboxaldehyde (Pyc) encapsulated porous titania (pTiO₂) nanospheres (Pyc@pTiO₂) as ECL nanoreactors for an integrated ternary (luminophore/coreactant/co-reaction accelerator, Pyc/S₂O₈^2-/TiO₂) ECL system construction. Specifically, pTiO₂ acted as an ECL co-reaction accelerator, in which Pyc could obtain electrons from the conduction band of TiO₂ to produce more SO₄˙^-, increasing its emissions. Simultaneously, pTiO₂ could provide confined reaction spaces to effectively shorten the diffusion distance, extend the lifetime of free radicals, increase the utilization rate of intermediates and improve the efficiency of the ternary ECL system. As a proof of concept, the Pyc@pTiO₂ nanoreactors-based sensing platform was successfully constructed to sensitively monitor cellular GSH levels. Overall, this work for the first time proposed an avenue to increase the utilization rate of intermediates in a ternary ECL system, which opened a new route for ECL biosensing in cell analysis applications.

Nonenzymatic Target-Driven DNA Nanomachine for Monitoring Malathion Contamination in Living Cells and Bioaccumulation in Foods

Intensive applications of toxic malathion pesticides bring a vital threat to the environment and health. Hence, a credible and sensitive strategy is urgently needed for the respective detection of malathion. In this work, an aptamer-based nonenzymatic autonomous DNA walking machine was fabricated for monitoring trace malathion contamination in cells and foods. Along with the machine walking driven by malathion-triggered reaction entropy, multiple fluorescent signal outputs were thermodynamically generated for signal amplification. The proposed stable DNA nanomachine achieved satisfactory results with a detection limit of 81.9 pg L^-1 for testing malathion, which could be applied to actual samples including apple juice, paddy water, and paddy soil. Furthermore, the high stability, sensitivity, and biocompatibility of the nanomachine enabled monitoring of the malathion contamination in living cells and bioaccumulation in lettuce without additional purification. Consequently, with these excellent performances, it is strongly anticipated that the DNA walking machine has tremendous potential to be extended to general platforms against pesticides to avoid malathion-contaminated agricultural production for environmental safety and human health.

Recent advances in catalytic hairpin assembly signal amplification-based sensing strategies for microRNA detection

Accumulative evidences have indicated that abnormal expression of microRNAs (miRNAs) is closely associated with many health disorders, making them be regarded as potentialbiomarkers for early clinical diagnosis. Therefore, it is extremely necessary to develop a highly sensitive, specific and reliable approach for miRNA analysis. Catalytic hairpin assembly (CHA) signal amplification is an enzyme-free toehold-mediated strand displacement method, exhibiting significant potential in improving the sensitivity of miRNA detection strategies. In this review, we first describe the potential of miRNAs as disease biomarkers and therapeutics, and summarize the latest advances in CHA signal amplification-based sensing strategies for miRNA monitoring. We describe the characteristics and mechanism of CHA signal amplification and classify the CHA-based miRNA sensing strategies into several categories based on the "signal conversion substance", including fluorophores, enzymes, nanomaterials, and nucleotide sequences. Sensing performance, limit of detection, merits and disadvantages of these miRNA sensing strategies are discussed. Moreover, the current challenges and prospects are also presented.

Recent advances of functional nucleic acids-based electrochemiluminescent sensing

Electroluminescence (ECL) has been used in extensive applications ranging from bioanalysis to clinical diagnosis owing to its simple device requirement, low background, high sensitivity, and wide dynamic range. Nucleic acid is a significant theme in ECL bioanalysis. The inherent versatile selective molecular recognition of nucleic acids and their programmable self-assembly make it desirable for the robust construction of nanostructures. Benefiting from their unique structures and physiochemical properties, ECL biosensing based on nucleic acids has experienced rapid growth. This review focuses on recent applications of nucleic acids in ECL sensing systems, particularly concerning the employment of nucleic acids as molecular recognition elements, signal amplification units, and sensing interface schemes. In the end, an outlook of nucleic acid-based ECL biosensing will be provided for future developments and directions. We envision that nucleic acids, which act as an essential component for both bioanalysis and clinical diagnosis, will provide a new thinking model and driving force for developing next-generation sensing systems.

Novel preparation method of bipedal DNA walker based on hybridization chain reaction for ultrasensitive DNA biosensing

In this work, a novel strategy for preparation of bipedal DNA walker (BDW) based on hybridization chain reaction (HCR) with the assistance of Exonuclease III (Exo III) was proposed. Based on this strategy, an electrochemical biosensor was constructed to achieve sensitive detection of CYFRA 21-1 DNA. Firstly, target recognition and circulation were achieved through a one-step catalytic hairpin assembly (CHA) reaction. For further amplification, hybridization chain reaction (HCR) was employed to form duplex-stranded DNA (dsDNA) nanostructure in homogeneous solution. In particular, the elongated single strand of the hairpin DNA for HCR was designed as the Mg²⁺ DNAzyme sequence. With the assistance of Exo III, dsDNA nanostructure can be digested and transformed into large amounts of BDW. These BDW can cleave the signal probe driven by Mg²⁺, which was modified on the electrode surface and thus achieved "signal-off" detection of target. This BDW preparation method based on HCR with the digestion of Exo III converted one target input into large amount of BDW. Coupled with the walking cleavage of BDW, a series of cascade amplification endowed high sensitivity with this biosensor and realized ultrasensitive detection of target DNA with the detection limit as low as 3.01 aM.

Size-selective DNA nanocage-based activatable CRISPR-Cas12a for sensitive and accurate detection of mature microRNA

The sensitive and accurate detection of mature miRNA without the signal interference by pre-miRNAs is highly important. Herein, a size-selective DNA nanocage-based activatable CRISPR/Cas12a system was developed to achieve this goal.

FeII 4L4 Tetrahedron-Assisted Three-Way Junction Probe for Multiple miRNA Detection

MicroRNAs (miRNAs) modulate a variety of cellular signaling pathways and play a vital role in cell-to-cell communication. The overlapped expression of a certain miRNA is commonly reported to be related to cancers. Therefore, combined detection of multiple miRNAs is of great significance for cancer diagnosis. Herein, we developed a Fe^II ₄L₄ tetrahedron-assisted three-way junction (3WJ) probe, which exhibited a higher stability than the normal 3WJ probe, for multiple miRNA detection. In this method, the simultaneous existence of miRNA-21 and miRNA-144 triggers the release of the Y3 sequence in the Fe^II ₄L₄ tetrahedron-assisted 3WJ probe, which in turn triggers subsequent CRISPR-Cas12a-assisted rolling circle amplification. Based on this, simultaneous detection of miRNA-21 and miRNA-144 was achieved. Furthermore, we also applied this method to the detection of miRNAs in clinical samples and achieved good agreement with quantitative real-time polymerase chain reaction (qRT-PCR), indicating its significant potentials in early diagnosis and treatment of cancer.

A CHA-based DNA stochastic walker that traverses on cell membranes

DNA walkers, imitating protein motors, are a class of nucleic acid nanodevice that can move along a precisely defined "track". With a promising future in materials and biotechnology, DNA walkers have gained extensive attention among researchers. Here, we introduce a catalytic hairpin assembly (CHA)-based DNA walker on cell membranes. We designed hairpin strand (H1) modified cells as tracks. Driven by DNA strand exchange, catalytic strands move on cell membranes and other hairpin strands (H2) in the solution are loaded on cells. Additionally, we also introduce a CHA-based DNA motor and use the motor for cell membrane target sensing.

An integrated fluorescence biosensor for microRNA detection based on exponential amplification reaction-triggered three-dimensional bipedal DNA walkers

Sensitive and specific miRNA detection is essential for the early cancer diagnosis. In this work, we design a fluorescent microRNA biosensor based on exponential amplification reaction (EXPAR) and nicking endonuclease-powered three-dimensional (3-D) bipedal DNA walkers (BDW). Target microRNA initiates EXPAR with the help of polymerase and nicking endonuclease to generate the large number of BDW in solution. The newly generated BDW can be continuously assembled onto polystyrene microsphere track co-modified with fluorescence-labeled DNA strand. Thus, in the presence of nicking endonuclease, the walking machine is activated to produce enhanced fluorescent signal in the supernatant. Besides, we prove that BDW holds the faster walking speed than single-legged DNA walker (SDW) based on comparative study. Under optimal conditions, the proposed amplification method owns a wide linear range from 10 fM to 5 nM with a detection limit down to 5.2 fM. The reaction time of the assay takes about 70 min. The combination of enzyme-assisted EXPAR in solution and enzyme-powered BDW on particle significantly increases the signal amplification efficiency and improves the detection sensitivity. Therefore, our method has enormous potential for the application of BDW-related biosensors.

Simple Tripedal DNA Walker Prepared by Target-Triggered Catalytic Hairpin Assembly for Ultrasensitive Electrochemiluminescence Detection of MicroRNA

In contrast to common DNA walkers, multipedal DNA walkers exhibit larger walking area and faster walking kinetics and provide increased amplification efficiency. Consequently, they have received a considerable amount of attention in biosensing. However, most of them are synthesized by immobilizing multiple DNA walking strands on the surface of Au nanoparticles, which is tedious and time-consuming. Simple preparation of multipedal DNA walkers remains a challenge. Herein, we adopted a simple enzyme-free target-triggered catalytic hairpin assembly (CHA) circuit to synthesize a tripedal DNA walker. By walking on a DNA track-functionalized electrode, a sensitive electrochemiluminescence DNA nanomachine biosensor was constructed for sensing miRNA-21. The DNA walker was powered by toehold-mediated strand displacement; the whole process did not need the assistance of enzymes, thus avoiding tedious procedures and enzyme degradation under unfavorable environmental conditions. Specifically, a superior detection limit of 4 aM and a broad linear range of 10 aM to 1 pM were achieved. This CHA-tripedal DNA walker biosensor was then applied for the detection of miRNA-21 in human serum and showed high selectivity and excellent reproducibility, demonstrating its practical application in bioanalysis. In particular, the Y-shaped tripedal DNA walker comes from the DNA circuit, which makes the approach ideally suited for biosensing of small nucleic acid targets.