An Autonomous Self-Cleavage DNAzyme Walker for Live Cell MicroRNA Imaging

DNA nanosensor based on bipedal 3D DNA walker-driven proximal catalytic hairpin assembly for sensitive and fast TK1 mRNA detection

Hyperproliferative  diseases are the first step for tumor formation; thymidine kinase 1 (TK1) mRNA is closely related to cell proliferation. Therefore, the risk of malignant proliferation can be identified by sensitively detecting the variance in TK1 mRNA concentration, which can be used for tumor auxiliary diagnosis and monitoring tumor treatment. Owing to the low abundance and instability of TK1 mRNA in real samples, the development of a sensitive and fast mRNA detection method is necessary. A DNA nanosensor that can be used for detecting TK1 mRNA based on bipedal 3D DNA walker-driven proximal catalytic hairpin assembly (P-CHA) was developed. P-CHA hairpins were hybridized to a linker DNA strand coupled with magnetic nanoparticles to increase their local concentrations. The bipedal DNA walking on the surface of NPs accelerates reaction kinetics using the proximity effect. Taking advantage of the signal amplification of P-CHA as well as the rapid reaction rate of the DNA walker in 80 min, the proposed sensor detects TK1 mRNA with a low detection limit of 14 pM and may then be applied to clinical diagnosis.

Sensitive detection of microRNA by dynamic light scattering based on DNAzyme walker-mediated AuNPs self-assembly

As an important biomarker, microRNAs (miRNAs) play an important role in gene expression, and their detection has attracted increasing attention. In this study, a DNAzyme walker that could provide power to perform autonomous movement was designed. Based on the continuous mechanical motion characteristics of DNAzyme walker, a miRNA detection strategy for the self-assembly of AuNPs induced by the hairpin probe-guided DNAzyme walker "enzyme cleavage and walk" was established. In this strategy, DNAzyme walker continuously cleaved and walked on the hairpin probe on the surface of AuNPs to induce the continuous shedding of some segments of the hairpin probe. The remaining hairpin sequences on the surface of the AuNP pair with each other, causing the nanoparticles to self-assemble. This strategy uses the autonomous movement mechanism of DNAzyme walker to improve reaction efficiency and avoid the problem of using expensive and easily degradable proteases. Secondly, using dynamic light scattering technology as the signal output system, ultra-sensitive detection with a detection limit of 3.6 fM is achieved. In addition, this strategy has been successfully used to analyze target miRNAs in cancer cell samples.

Localization of multiple DNAzymes as a branchedzyme-powered nanodevice for the immunoassay of tumor biomarkers

Traditional immunoassay methods often face challenges due to the labeling procedure of protein enzymes, the use of multiple antibodies, and severe conditions. To address these limitations, we propose the concept of incorporating branchedzyme-powered nanodevices into immunoassays. In this strategy, multiple DNAzymes are localized onto gold nanoparticles (AuNPs) along with substrates. The localization format facilitates intramolecular reactions between DNAzymes and substrates, leading to accelerated kinetics of the nanodevice. Upon the formation of an immunocomplex with an antibody on a 96-well plate, the branchedzyme-powered nanodevice catalytically releases multiple fluorescent signals under ambient temperature, eliminating the need for secondary antibodies. The branched DNAzymes exhibit catalytic properties similar to those of protein enzymes, thus simplifying the assay procedure and achieving isothermal detection. Furthermore, the detection process can be controlled by the addition or deletion of cofactors. Additionally, the affinity ligand can be easily modified to construct nanodevices specific to different targets without requiring extensive redesign. This strategy has demonstrated successful quantification of tumor biomarkers such as alpha-fetoprotein (AFP) and prostate-specific antigen (PSA) at subpicomolar concentrations, showcasing its suitability for clinical applications. Consequently, the branchedzyme-powered nanodevice represents a valuable addition to the immunoassay toolbox, opening new possibilities for clinical diagnostics.

Advances and Trends in miRNA Analysis Using DNAzyme-Based Biosensors

miRNAs are endogenous small, non-coding RNA molecules that function in post-transcriptional regulation of gene expression. Because miRNA plays a pivotal role in maintaining the intracellular environment, and abnormal expression has been found in many cancer diseases, detection of miRNA as a biomarker is important for early diagnosis of disease and study of miRNA function. However, because miRNA is present in extremely low concentrations in cells and many types of miRNAs with similar sequences are mixed, traditional gene detection methods are not suitable for miRNA detection. Therefore, in order to overcome this limitation, a signal amplification process is essential for high sensitivity. In particular, enzyme-free signal amplification systems such as DNAzyme systems have been developed for miRNA analysis with high specificity. DNAzymes have the advantage of being more stable in the physiological environment than enzymes, easy to chemically synthesize, and biocompatible. In this review, we summarize and introduce the methods using DNAzyme-based biosensors, especially with regard to various signal amplification methods for high sensitivity and strategies for improving detection specificity. We also discuss the current challenges and trends of these DNAzyme-based biosensors.

A self-powered and reagent-less electrochemical aptasensor based on a DNA walker and tetraferrocene for the detection of aflatoxin B1

We constructed a self-powered and reagent-less electrochemical aptamer sensor for sensitive detection of aflatoxin B1 (AFB1). Here, the metal ion Mn²⁺ required for the DNAzyme to drive a DNA walker is wrapped in UIO-66(Zr)-(COOH)₂ and AFB1 triggers the DNAzyme walking strands to automatically and continuously cut the tetraferrocene-labeled substrate strands, which results in a significant decrease in the electrochemical signal. Under the optimal conditions, the concentration dependence of AFB1 is linear in the concentration range of 0.1 pg mL^-1 to 0.195 μg mL^-1, and the limit of detection is as low as 4.8 fg mL^-1. The sensor displayed good performance even for samples with a complex matrix, such as a peanut sample. The recoveries of AFB1 obtained ranged from 95.5 to 106.8%. The developed sensing platform is reagent-less, self-powered, and highly sensitive. It holds great potential for detection of AFB1 in environmental and food samples.

Multivalent self-assembled nano string lights for tumor-targeted delivery and accelerated biomarker imaging in living cells and in vivo

Multivalent self-assembled nano string lights for tumor-targeted delivery with high efficiency and accelerated biomarker imaging in living cells and in vivo.

DNA Tetrahedron-Based MNAzyme for Sensitive Detection of microRNA with Elemental Tagging

Heterogeneous immunoassay based on magnetic separation is commonly used in inductively coupled plasma-mass spectrometry (ICP-MS)-based biomedical analysis with elemental labeling. However, the functionalized magnetic beads (MBs) often suffer from non-specific adsorption and random distribution of the functional probes. To overcome these problems, DNA tetrahedron (DT)-functionalized MBs were designed and further conjugated with substrate modified Au NPs (Sub-AuNP). Based on the prepared MB-DT-AuNP probes, an MB-DT based multicomponent nucleic acid enzyme (MNAzyme) system involving Au NPs as the elemental tags was proposed for highly sensitive quantification of miRNA-155 by ICP-MS. Target miRNA would trigger the assembly of MNAzyme, and Sub-AuNP would be cleaved from the MB-DT-AuNP probe, resulting in a cyclic amplification. Single-stranded DNA-functionalized MB (MB-ssDNA)-AuNP probes were prepared as well. Comparatively, the amount of Au NPs grafted onto MB-ssDNA-AuNP probes was higher than that grafted onto MB-DT-AuNP probes. Meanwhile, a higher signal-to-noise ratio was obtained by using MB-DT-AuNP probes over MB-ssDNA-AuNP probes in the MNAzyme system. Under the optimal experimental conditions, the limit of detection for target miRNA obtained by using MB-DT-AuNP probes was 1.15 pmol L^-1, improved by 23 times over that obtained by the use of MB-ssDNA-AuNP probes. The proposed MB-DT-MNAzyme-ICP-MS method was applied to the analysis of miRNA-155 in serum samples, and recoveries of 86.7-94.6% were obtained. This method is featured with high sensitivity, good specificity, and simple operation, showing a great application potential in biomedical analysis.

Endogenous miRNA-Activated DNA Nanomachine for Intracellular miRNA Imaging and Gene Silencing

The development of multifunctional nanoplatforms that integrate both diagnostic and therapeutic functions has always been extremely desirable and challenging in the cancer combat. Here, we report an endogenous miRNA-activated DNA nanomachine (EMDN) in living cells for concurrent sensitive miRNA imaging and activatable gene silencing. EMDN is constructed by interval hybridization of two functional DNA monomers (R/HP and F) to a DNA nanowire generated by hybridization chain reaction. After the target cell-specific transportation of EMDN, intracellular let-7a miRNA initiates the DNA nanomachine by DNA strand displacement cascades, resulting in an amplified fluorescence resonance energy-transfer signal and the release of many free HP sequences. The restoration of HP hairpin structures further activates the split-DNAzyme to identify and cleave the EGR-1 mRNA to realize gene silencing therapy. The proposed EMDN shows efficient cell internalization, good biological stability, rapid reaction kinetics, and the ability to avoid false-positive signals, thus ensuring reliable miRNA imaging in living cells. Meanwhile, the controlled activation of the split-DNAzyme activity regulated by the intracellular specific miRNA may be promising in the precise treatment of cancer. Collectively, this strategy provides a valuable nanoplatform for early clinical diagnosis and activatable gene therapy of tumors.

Stimuli-Responsive Autonomous-Motion Molecular Machine for Sensitive Simultaneous Fluorescence Imaging of Intracellular MicroRNAs

DNAzymes with enzymatic activity identified from random DNA pools by in vitro selection have recently attracted considerable attention. In this work, a DNAzyme-based autonomous-motion (AM) molecular machine is demonstrated for sensitive simultaneous imaging of different intracellular microRNAs (miRNAs). The AM molecular machine consists of two basic elements, one of which is a target-analogue-embedded double-stem hairpin substrate (TDHS) and the other is a locking-strand-silenced DNAzyme (LSDz). LSDz can be activated by target miRNA and catalytically cleave TDHS, generating Clv-TDHS and releasing free target analogue capable of triggering the next round of cleavage reaction. As such, the molecular machine can exert sustainable autonomous operation, producing an enhanced signal. Because the active target analogue comes from the machine itself and offers cyclical stimulation in a feedback manner, this target-induced autonomous cleavage circuit is termed a self-feedback circuit (SFC). The SFC-based molecular machine can be used to quantify miRNA-21 down to 10 pM without interference from nontarget miRNAs, indicating a substantial improvement in assay performance compared with its counterpart system without an SFC effect. Moreover, due to the enzyme-free process, the AM molecular machine is suitable for miRNA imaging in living cells, and the quantitative results are consistent with the gold standard PCR assay. More interestingly, the AM molecular machine can be used for the simultaneous fluorescence imaging of several intracellular miRNAs, enabling the accurate discrimination of cancerous cells (e.g., HeLa and MCF-7) from healthy cells. The SFC-based autonomous-motion machine is expected to be a promising tool for the research of molecular biology and early diagnosis of human diseases.

Development of a neuron model based on DNAzyme regulation

Neural networks based on DNA molecular circuits play an important role in molecular information processing and artificial intelligence systems. In fact, some DNA molecular systems can become dynamic units with the assistance of DNAzymes. The complex DNA circuits can spontaneously induce corresponding feedback behaviors when their inputs changed. However, most of the reported DNA neural networks have been implemented by the toehold-mediated strand displacement (TMSD) method. Therefore, it was important to develop a method to build a neural network utilizing the TMSD mechanism and adding a mechanism to account for modulation by DNAzymes. In this study, we designed a model of a DNA neuron controlled by DNAzymes. We proposed an approach based on the DNAzyme modulation of neuronal function, combing two reaction mechanisms: DNAzyme digestion and TMSD. Using the DNAzyme adjustment, each component simulating the characteristics of neurons was constructed. By altering the input and weight of the neuron model, we verified the correctness of the computational function of the neurons. Furthermore, in order to verify the application potential of the neurons in specific functions, a voting machine was successfully implemented. The proposed neuron model regulated by DNAzymes was simple to construct and possesses strong scalability, having great potential for use in the construction of large neural networks.