Temperature-Robust DNAzyme Biosensors Confirming Ultralow Background Detection

Visualized lateral flow assay for logic determination of co-existing viral RNA fragments

Different types of pathogenic viruses that have common transmission path can be co-infected, inducing distinct disease procession in comparison to that infection of one. Also, in the post COVID-19 time, more types of respiratory infectious virus are becoming prevalent and are concurrent. Those bring an urgent need for detection of co-existing viruses. Here, we propose a visualized lateral flow assay for logic determination of co-existing viral RNA fragments. In the presence of specific viral RNA inputs, DNAzyme is de-blocked according to defined logic, and catalyzes the hydrolysis of hairpin-structural substrate. One of cleaved substrates contains DNAzyme domain to realize dual signal amplification, which obtains copious of the other cleaved substrates. The cleaved substrates act as linking strands for bridging DNA-modified gold nanoparticles onto lateral flow strip to induce coloration on test line. "AND", "OR" and "INHIBIT" controlled lateral flow assays are respectively demonstrated for co-existing viral RNA detection, and the visual results can be obtained by the same kind of prepared strip, without need of re-fabricating strips according to logic systems. The work provides a flexible, convenient, visual and logic-processing strategy for simultaneous analysis of co-existing viruses.

Ultralow background one-pot detection of Lead(II) using a non-enzymatic double-cycle system mediated by a hairpin-involved DNAzyme

A double-cycle system has been developed for specifically detecting trace amounts of Pb2+ by significantly decreasing the background signal. The detection involves two types of RNA cleavage reactions: one using a Pb2+-specific GR5 DNAzyme (PbDz) and the other utilizing a newly constructed 10-23 DNAzyme with two hairpins embedded in its catalytic center (hpDz). The ring-structured hpDz (c-hpDz) exhibits significantly lower activity compared to the circular 10-23 DNAzyme without hairpin structures, which plays a crucial role in reducing the background signal. When Pb2+ is present, PbDz cleaves c-hpDz to its active form, which then disconnects the molecular beacon to emit the fluorescent signal. The method allows for rapid and sensitive Pb2+ detection within 40 min for 10 fM of Pb2+ and even as short as 10 min for 100 nM of Pb2+. Additionally, visual detection is possible through the non-crosslinking assembly of Au nanoparticles. The entire process can be performed in one pot and even one step, making it highly versatile and suitable for a wide range of applications, including food safety testing and environmental monitoring.

Advances in Cas12a-Based Amplification-Free Nucleic Acid Detection

In biomedicine, rapid and sensitive nucleic acid detection technology plays an important role in the early detection of infectious diseases. However, most traditional nucleic acid detection methods require the amplification of nucleic acids, resulting in problems such as long detection time, complex operation, and false-positive results. In recent years, clustered regularly interspaced short palindromic repeats (CRISPR) systems have been widely used in nucleic acid detection, especially the CRISPR-Cas12a system, which can trans cleave single-stranded DNA and can realize the detection of DNA targets. But, amplification of nucleic acids is still required to further improve detection sensitivity, which makes Cas12a-based amplification-free nucleic acid detection methods a great challenge. This article reviews the recent progress of Cas12a-based amplification-free detection methods for nucleic acids. These detection methods apply electrochemical detection methods, fluorescence detection methods, noble metal nanomaterial detection methods, and lateral flow assay. Under various optimization strategies, unamplified nucleic acids have the same sensitivity as amplified nucleic acids. At the same time, the article discusses the advantages and disadvantages of each method and further discusses the current challenges such as off-target effects and the ability to achieve high-throughput detection. Amplification-free nucleic acid detection technology based on CRISPR-Cas12a has great potential in the biomedical field.

DNAzyme-templated exponential isothermal amplification for sensitive detection of lead pollution and high-throughput screening of microbial biosorbents

Very low concentrations of lead (Pb²⁺) pollution can have far-reaching adverse impacts on human health, due to the cumulative toxicity of Pb²⁺. Herein, we report a DNAzyme-templated exponential isothermal amplification strategy (termed DNAzymee) for the ultrasensitive detection of Pb²⁺ pollution and the high-throughput screening of microbial biosorbents to remove Pb²⁺ pollution. DNAzyme can specifically recognize Pb²⁺, and this recognition event can be amplified by the subsequent exponential isothermal amplification reaction (EXPAR) and monitored by a G-quadruplex specific dye. The proposed design showed a low limit of detection (95 pM) and could identify Pb²⁺ pollution in different real samples with high precision. In particular, the proposed assay was used to screen Pb²⁺ biosorbents, and the results showed that Leuconostoc mesenteroides is a promising microbial biosorbent for removing Pb²⁺ pollution. Thus, the DNAzymee assay can serve as a platform to monitor lead pollution in the environment and screen efficient biosorbents for the control of lead pollution.

Nanozyme-catalysed CRISPR-Cas12a system for the preamplification-free colorimetric detection of lead ion

CRISPR-based detection was often based on the target preamplification to realize the high sensitivity. Here, we prepared a CRISPR-Cas12a system for the colorimetric detection of lead ion (Pb²⁺) based on the assistance of DNAzyme and nanozyme instead of preamplification. The recognition between GR-5 DNAzyme and Pb²⁺ could trigger the CRISPR-Cas12a system. MnO₂ nanozymes connected with magnetic beads through single stranded DNA were prepared as the colorimetric signal probes and catalyst of CRISPR-Cas12a system for the strong oxidase-like activity inducing the color change of 3,3',5,5'-tetramethylbenzidine. The nanozyme-catalysed CRISPR-Cas12a system could be used to detect Pb²⁺ through the color change with high specificity and sensitivity. The linear range of this approach was 0.8 nM-2500 nM, with a limit of detection of 0.54 nM. This method was applied for the detection of the Pb²⁺ in food samples indicating good accuracy and anti-interference ability.

Platform Formed from ZIF-8 and DNAzyme: "Turn-On" Fluorescence Assay for Simple, High-Sensitivity, and High-Selectivity Detection of Pb2

Lead contamination has posed a potential threat to the environment and food safety, arousing extensive concern. In this work, we fabricated a novel fluorescent sensing platform based on zeolitic imidazolate framework-8 (ZIF-8) and DNAzyme for monitoring Pb²⁺ in water and fish samples. ZIF-8 was proposed as a fluorescence quencher with the advantages of simple synthesis, low cost, and high quenching efficiency. The Pb²⁺-dependent GR5 DNAzyme containing the large ssDNA loop can be adsorbed onto ZIF-8 accompanied by fluorescence quenching. Upon binding with Pb²⁺, GR5 DNAzyme was activated and cleaved, leading to the release of FAM-labeled 5-base ssDNA, which restored the fluorescence. The "turn-on" assay can detect Pb²⁺ through the one-pot procedure in the range of 0.01-10.0 nM with a detection limit of 7.1 pM. The platform is promising for on-site monitoring of Pb²⁺ owing to the excellent performance of high sensitivity, low background, strong anti-interference ability, and simple operation.

Amplification of the Fluorescence Signal with Clustered Regularly Interspaced Short Palindromic Repeats-Cas12a Based on Au Nanoparticle-DNAzyme Probe and On-Site Detection of Pb2+ Via the Photonic Crystal Chip

Although great headway has been made in DNAzyme-based detection of Pb²⁺, its adaptability, sensitivity, and accessibility in complex media still need to be improved. For this, we introduce new ways to surmount these hurdles. First, a spherical nucleic acid (SNA) fluorescence probe (Au nanoparticles-DNAzyme probe) is utilized to specifically identify Pb²⁺ and its suitability for precise detection of Pb²⁺ in complex samples due to its excellent nuclease resistance. Second, the sensitivity of Pb²⁺ detection is greatly enhanced via the use of a clustered regularly interspaced short palindromic repeats-Cas12a with target recognition accuracy to amplify the fluorescent signal upon the trans cleavage of the SNA (signal probe), and the limit of detection reaches as low as 86 fM. Third, we boost the fluorescence on photonic crystal chips with a bionic periodic arrangement by employing a straightforward detection device (smartphone and portable UV lamp) to achieve on-site detection of Pb²⁺ with the limit of detection as low as 24 pM. Based on the abovementioned efforts, the modified Pb²⁺ fluorescence sensor has the advantages of higher sensitivity, better specificity, accessibility, less sample consumption, and so forth. Moreover, it can be applied to accurately detect Pb²⁺ in complex biological or environmental samples, which is of great promise for widespread applications.

DNAzyme-based cascade signal amplification strategy for highly sensitive detection of lead ions in the environment

Lead ions are one of many common environmental pollutants, that can cause posing a serious threat to people's health, thus, their efficient and sensitive detection is important. We propose a cascade signal amplification sensor using a DNAzyme-based strand displacement amplification (SDA) and hybridization chain reaction (HCR) for the high-sensitivity detection of Pb²⁺. In the demonstrated sensor system, the target metal ion can activate DNAzyme to cause a strand displacement reaction. Under the synergistic action of polymerase and nickase, large numbers of DNA strands are generated that can initiate HCR. The subsequent HCR can restore the fluorescence intensity of the FAM quenched for the fluorescence resonance energy transfer effect, which exhibits a strong fluorescence signal. The DNAzyme-based sensor allowed the detection of Pb²⁺ down to 16.8 pM and resulted in a good dynamic line relationship ranging from 50 pM to 500 nM, and the biosensor also showed good selectivity. Furthermore, we confirmed that the proposed sensor can still detect lead ions in complex environments such as lake water, milk, and serum. We believe these findings will provide new ideas for the detection of toxic elements ions in the environment and food.

A novel strategy for programmable DNA tile self-assembly with a DNAzyme-mediated DNA cross circuit

The proposed strategy promotes the controllability and modularization of trigger elements, realizes programmable molecular self-assembly, and has broad applications for the construction of DNA nanodevices.

"Repaired and Activated" DNAzyme Enables the Monitoring of DNA Alkylation Repair in Live Cells

Direct measurement of DNA repair is critical for the annotation of their clinical relevance and the discovery of drugs for cancer therapy. Here we reported a "repaired and activated" DNAzyme (RADzyme) by incorporating a single methyl lesion (O⁶ MeG, 3MeC, or 1MeA) at designated positions through systematic screening. We found that the catalytic activity of the RADzyme was remarkably suppressed and could be restored via enzyme-mediated DNA repair. Benefit from these findings, a fluorogenic RADzyme sensor was developed for the monitoring of MGMT-mediated repair of O⁶ MeG lesion. Importantly, the sensor allowed the evaluation of MGMT repair activity in different cells and under drugs treatment. Furthermore, another RADzyme sensor was engineered for the monitoring of ALKBH2-mediated repair of 3MeC lesion. This strategy provides a simple and versatile tool for the study of the basic biology of DNA repair, clinical diagnosis and therapeutic assessment.

Temperature-robust and ratiometric G-quadruplex proximate DNAzyme assay for robustly monitoring of uranium pollution and its microbial biosorbents screening

Uranium pollution in environment and food chain is a serious threat to public security and human health. Herein, we proposed a temperature-robust, ratiometric, and label-free bioassay based on G-quadruplex proximate DNAzyme (G4DNAzyme), accommodating us to precisely monitor uranium pollution and biosorption. The proximity of split G-quadruplex probes was proposed to sense UO₂²⁺-activated DNAzyme activity, thus eliminating the use of chemically labeled nucleic acid probes. And the simultaneous monitoring of G-quadruplex and double-stranded structures of DNAzyme probes contributed to a ratiometric and robust detection of UO₂²⁺. Particularly, the separation of enzymatic digestion and fluorescence monitoring endued a robust and highly responsive detection of UO₂²⁺ upon the temperature of enzymatic digestion process ranged from 18° to 41 °C. Consequently, G4DNAzyme assay allowed a robust, label-free and ratiometric quantification of uranium. We demonstrated the feasibility of G4DNAzyme assay for estimating uranium pollution in water and aquatic product samples. Ultimately, G4DNAzyme assay was adopted to serve as the platform to screen bacterial species and conditions for uranium biosorption, promising its roles in uranium associated biosafety control.

Orthogonal Demethylase-Activated Deoxyribozyme for Intracellular Imaging and Gene Regulation

The epigenetic modification of nucleic acids represents a versatile approach for achieving high-efficient control over gene expression and transcription and could dramatically expand their biosensing and therapeutic applications. Demethylase-involved removal of N6-methyladenine (m⁶A) represents one of the vital epigenetic reprogramming events, yet its direct intracellular evaluation and as-guided gene regulation are extremely rare. The endonuclease-mimicking deoxyribozyme (DNAzyme) is a catalytically active DNA that enables the site-specific cleavage of the RNA substrate, and several strategies have imparted the magnificent responsiveness to DNAzyme by using chemical and light stimuli. However, the epigenetic regulation of DNAzyme has remained largely unexplored, leaving a significant gap in responsive DNA nanotechnology. Herein, we reported an epigenetically responsive DNAzyme system through the in vitro selection of an exquisite m⁶A-caged DNAzyme that could be specifically activated by FTO (fat mass and obesity-associated protein) demethylation for precise intracellular imaging-directed gene regulation. Based on a systematic investigation, the active DNAzyme configuration was potently disrupted by the site-specific incorporation of m⁶A modification and subsequently restored into the intact DNAzyme structure via the tunable FTO-specific removal of m⁶A-caging groups under a variety of conditions. This orthogonal demethylase-activated DNAzyme amplifier enables the robust and accurate monitoring of FTO and its inhibitors in live cells. Moreover, the simple demethylase-activated DNAzyme facilitates the assembly of an intelligent self-adaptive gene regulation platform for knocking down demethylase with the ultimate apoptosis of tumor cells. As a straightforward and scarless m⁶A removal strategy, the demethylase-activated DNAzyme system offers a versatile toolbox for programmable gene regulation in synthetic biology.

Label-free DNAzyme assays for dually amplified and one-pot detection of lead pollution

Lead pollution in water and soil often transfers to food, advocating tools for on-site detection of lead pollution to ensure both environmental and food safety. We proposed a label-free, dually amplified and homogeneous DNAzyme assay for sensitive and one-pot detection of lead pollution. Instead of using chemically modified DNA substrate, a structure-response digestion process was introduced to monitor Pb²⁺ presence-induced cleavage process of unlabeled substrate, further amplifying the response signals and eliminating the use of labeled DNA probes. The DNAzyme assay allowed to detect Pb²⁺ as low as 0.12 nM and endued a dynamic range from 0.1 nM to 30 nM. In addition, it can specifically identify Pb²⁺ among other metal ions. We demonstrated that the DNAzyme assay can precisely detect Pb²⁺ in tap water, milk and fish. Thus, the DNAzyme assay is promising for on-site monitoring lead pollution risk and ensuring environmental and food safety.

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.

Aptamer biorecognition-triggered hairpin switch and nicking enzyme assisted signal amplification for ultrasensitive colorimetric bioassay of kanamycin in milk

A colorimetric aptasensing strategy for detection of kanamycin was designed based on aptamer biorecognition and signal amplification assisted by nicking enzyme. The aptamer of kanamycin was designed to be contained in the metastable state hairpin DNA. The target DNA as recycling DNA was located in the loop of hairpin DNA. The presence of kanamycin stimulates the continuous actions, including specific recognition of the aptamer to kanamycin, the hybridization between target DNA and signal probe, the cleavage function of nicking enzyme. The actions induced accumulation of numerous free short sequences modified by platinum nanoparticles (PtNPs), which can catalyze the oxidation of 3,3',5,5'-tetramethylbenzidine (TMB)-H₂O₂ to produce a colorimetric response. The aptasensor exhibited good selectivity and sensitivity for kanamycin in milk with a detection limit as low as 0.2 pg·mL^-1. In addition, the proposed assay is potentially to be extended for other antibiotics detection in foods by adapting the corresponding aptamer sequence.

Colorimetric detection of class A soybean saponins by coupling DNAzyme with the gap ligase chain reaction

Class A saponins are responsible for the taste of soybean products, and the rapid identification of class A saponins from soybean food is essential for both food safety and cultivar screening. In this study, we propose a colorimetric assay based on the coupling of gap ligase chain reaction (Gap-LCR) with DNAzyme to detect the target GmSg-1 genes of class A soybean saponins with the naked eye, without the involvement of expensive instruments. The limits of detection (LODs) for the GmSg-1a and GmSg-1b genes were determined to be 0.1618 and 0.1625 μM, respectively, with a linear range of 0.2-1.2 μM. The DNAzyme-based Gap LCR assay was successfully employed to identify the target genes from different soybean cultivars, providing a simple means for monitoring the quality of soybean products.

An intelligent nanodevice based on the synergistic effect of telomerase-triggered photodynamic therapy and gene-silencing for precise cancer cell therapy

The development of intelligent and precise cancer therapy systems that enable accurate diagnosis and specific elimination of cancer cells while protecting normal cells to improve the safety and effectiveness of the treatment is still a challenge. Herein, we report a novel activatable nanodevice for precise cancer therapy. The nanodevice is constructed by adsorbing a DNA duplex probe onto MnO2 nanosheets. After cellular uptake, the DNA duplex probe undergoes telomerase-triggered conformation switching, resulting in a Ce6 "turn-on" signal for the identification of cancer cells. Furthermore, Deoxyribozyme (DNAzyme) is activated to catalyse the cleavage of survivin mRNA, actualizing a precise synergistic therapy in cancer cells involving photodynamic therapy and gene-silencing. The MnO2 nanosheets provide Mn2+ for the DNAzyme and relieve hypoxia to improve the efficiency of the photodynamic therapy. Live cell studies reveal that this nanodevice can diagnose cancer cells and specifically eliminate them without harming normal cells, so making the treatment safer and more effective. The developed DNA-MnO2 nanodevice provides a valuable and general platform for precise cancer therapy.

A photocontrolled and self-powered bipedal DNA walking machine for intracellular microRNA imaging

A photocontrolled and self-powered bipedal DNA walking machine for intracellular microRNA imaging has been reported.

Constructing Controllable Logic Circuits Based on DNAzyme Activity

Recently, DNA molecules have been widely used to construct advanced logic devices due to their unique properties, such as a simple structure and predictable behavior. In fact, there are still many challenges in the process of building logic circuits. Among them, the scalability of the logic circuit and the elimination of the crosstalk of the cascade circuit have become the focus of research. Inspired by biological allosteric regulation, we developed a controllable molecular logic circuit strategy based on the activity of DNAzyme. The E6 DNAzyme sequence was temporarily blocked by hairpin DNA and activated under appropriate input trigger conditions. Using a substrate with ribonucleobase (rA) modification as the detection strand, a series of binary basic logic gates (YES, AND, and INHIBIT) were implemented on the computational component platform. At the same time, we demonstrate a parallel demultiplexer and two multi-level cascade circuits (YES-YES and YES-Three input AND (YES-TAND)). In addition, the leakage of the cascade process was reduced by exploring factors such as concentration and DNA structure. The proposed DNAzyme activity regulation strategy provides great potential for the expansion of logic circuits in the future.