A CRISPR/Cas12a-based DNAzyme visualization system for rapid, non-electrically dependent detection of Bacillus anthracis

As next-generation pathogen detection methods, CRISPR-Cas-based detection methods can perform single-nucleotide polymorphism (SNP) level detection with high sensitivity and good specificity. They do not require any particular equipment, which opens up new possibilities for the accurate detection and identification of Bacillus anthracis. In this study, we developed a complete detection system for B. anthracis based on Cas12a. We used two chromosomally located SNP targets and two plasmid targets to identify B. anthracis with high accuracy. The CR5 target is completely new. The entire detection process can be completed within 90 min without electrical power and with single-copy level sensitivity. We also developed an unaided-eye visualization system based on G4-DNAzyme for use with our CRISPR-Cas12a detection system. This visualization system has good prospects for deployment in field-based point-of-care detection. We used the antisense nucleic acid CatG4R as the detection probe, which showed stronger resistance to interference from components of the solution. CatG4R can also be designed as an RNA molecule for adaptation to Cas13a detection, thereby broadening the scope of the detection system.

A Lateral Flow Test for Staphylococcus aureus in Nasal Mucus Using a New DNAzyme as the Recognition Element

Detection of pathogenic bacteria in complex biological matrices remains a major challenge. Herein, we report the selection and optimization of a new DNAzyme for Staphylococcus aureus (SA) and the use of the DNAzyme to develop a simple lateral flow device (LFD) for detection of SA in nasal mucus. The DNAzyme was generated by in vitro selection using a crude extra/intracellular mixture derived from SA, which could be used directly for simple solution or paper-based fluorescence assays for SA. The DNAzyme was further modified to produce a DNA cleavage fragment that acted as a bridging element to bind DNA-modified gold nanoparticles to the test line of a LFD, producing a simple colorimetric dipstick test. The LFD was evaluated with nasal mucus samples spiked with SA, and demonstrated that SA detection was possible in minutes with minimal sample processing.

Recent Progress and Perspectives on Cell Surface Modification

The cell membrane is a biological interface consisting of phospholipid bilayer, saccharides and proteins that maintains a stable metabolic intracellular environment as well as regulating and controlling the exchange of substances inside and outside the cell. Cell membranes provide a highly complex biological surface carrying a variety of essential surfaces ligands and receptors for cells to receive various stimuli of external signals, thereby inducing corresponding cell responses regulating the life activities of the cell. These surface receptors can be manipulated via cell surface modification to regulate cellular functions and behaviors Thus, cell surface modification has attracted considerable attention due to its significance in cell fate control, cell engineering and cell therapy. In this minireview, we describe the recent developments and advances of cell surface modification, and summarize the main modification methods with corresponding functions and applications. Finally, the prospect for the future development of the modification of the living cell membrane is discussed.

DNAzyme-Amplified Label-Free Biosensor for the Simple and Sensitive Detection of Pyrophosphatase

The level of pyrophosphatase (PPase) expression has been suggested as a potential biomarker of various cancers, and its prognostic value has been evaluated in patients suffering from lung cancer, colorectal cancer, and hyperthyroidism. However, the detection of PPase usually needs specific materials that require complicated, time-consuming reactions with restricted linear range and sensitivity, limiting their application in early clinical diagnosis. Herein, we developed a DNAzyme-based biosensor for the detection of PPase. In the presence of PPase, pyrophosphate (PPi) and Cu2+ ions released from the PPi-Cu2+-PPi complex induce the cleavage of the DNAzyme and the corresponding substrate. An apurinic/apyrimidinic (AP) site was elaborately designed within substrates that could encase the fluorophore 2-amino-5,6,7-trimethyl-1,8-naphthyridine (ATMND). The fluorescence of ATMND was initially quenched but restored when the DNAzyme/substrate complex was hydrolyzed with the release of ATMND. In this way, the PPase activity can be estimated by detecting the increased fluorescence of the released ATMND. Under optimized conditions, the activity of PPase could be analyzed at concentrations from 0.5 to 1000 mU, with the lowest detectable concentration being 0.5 mU. This work lays a foundation for developing a DNAzyme-amplified fluorescent biosensor with a high sensitivity, a wide linear range, and single-step operation for use as an easy diagnostic for PPase analysis.

Portable, quantitative, and sequential monitoring of copper ions and pyrophosphate based on a DNAzyme-Fe3O4 nanosystem and glucometer readout

In this report, portable, quantitative, and sequential monitoring of copper ions and pyrophosphate (PPi) with a single sensor based on a DNAzyme-Fe₃O₄ system and glucometer readout was performed. Initially, streptavidin was functionalized on the surface of magnetic Fe₃O₄ spheres through glutaraldehyde. Then, an invertase-modified DNA Cu substrate was connected to the magnetic Fe₃O₄ spheres by a specific reaction between streptavidin and biotin. The sensing system was formed by a hybridization reaction between the Cu substrate and Cu enzyme. In the presence of Cu²⁺, Cu²⁺ will recognize the Cu DNA substrate and form an “off-on” signal switch, thereby resulting in the separation of invertase from the Fe₃O₄ nanospheres. PPi recognizes Cu²⁺ to form a Cu²⁺-PPi complex, resulting in an “on-off” signal switch. Under optimized conditions, linear detection ranges for Cu²⁺ and PPi of 0.01–5 and 0.5–10 μM, and detection limits for Cu²⁺ and PPi of 10 nM and 500 nM, respectively, were obtained. Good selectivity was achieved for the analysis of Cu²⁺ and PPi. Satisfactory results were achieved for this biosensor during the determination of Cu²⁺ in real tap samples and PPi in human urine samples. This verified that the sensor is portable and low cost, and can be applied to the sequential monitoring of multiple analytes with a single point-of-care biosensor.

DNAzyme-based colorimetric assay and its application for lipopolysaccharide analysis assisted by oxime chemistry

Herein, for the first time, we propose that the cleavage activity of DNAzyme is accompanied by the release of hydroxyl ions, which can be used for colorimetric assay. Subsequently, we further construct a colorimetric strategy for lipopolysaccharide (LPS) analysis by using this property. Detailly, DNAzyme is split into two fragments separately modified with aldehyde group and hydroxylamine group, which can be linked together through oxime chemistry and the presence of LPS can prevent the formation of oxime bond. The formed whole DNAzyme can mediate the release of hydroxyl ions serving for colorimetric signal output. Taking LPS as model targets, DNAzyme-based colorimetric assay has been successfully constructed. This work not only provides a colorimetric strategy to analyze DNAzyme activity, but also gives a new insight to enrich the versatility of DNAzymes and to enhance their multifunctionality.

Development of a DNAzyme-based colorimetric biosensor assay for dual detection of Cd2+ and Hg2

A colorimetric biosensor assay has been developed for Cd²⁺ and Hg²⁺ detection based on Cd²⁺-dependent DNAzyme cleavage and Hg²⁺-binding-induced conformational switching of the G-quadruplex fragment. Two types of multifunctional magnetic beads (Cd-MBs and Hg-MBs) were synthesized by immobilizing two functionalized DNA sequences on magnetic beads via avidin-biotin chemistry. For Cd²⁺ detection, Cd-MBs are used as recognition probes, which are modified with a single phosphorothioate ribonucleobase (rA) substrate (PS substrate) and a Cd²⁺-specific DNAzyme (Cdzyme). In the presence of Cd²⁺, the PS substrate is cleaved by Cdzyme, and single-stranded DNA is released as the signal transduction sequence. After molecular assembly with the other two oligonucleotides, duplex DNA is produced, and it can be recognized and cleaved by FokI endonuclease. Thus, a signal output component consisting of a G-quadruplex fragment is released, which catalyzes the oxidation of ABTS with the addition of hemin and H₂O₂, inducing a remarkably amplified colorimetric signal. To rule out false-positive results and reduce interference signals, Hg-MBs modified with poly-T fragments were used as Hg²⁺ accumulation probes during the course of Cd²⁺ detection. On the other hand, Hg-MBs can perform their second function in Hg²⁺ detection by changing the catalytic activity of the G-quadruplex/hemin DNAzyme. In the presence of Hg²⁺, the G-quadruplex structure in Hg-MBs is disrupted upon Hg²⁺ binding. In the absence of Hg²⁺, an intensified color change can be observed by the naked eye for the formation of intact G-quadruplex/hemin DNAzymes. The biosensor assay exhibits excellent selectivity and high sensitivity. The detection limits for Cd²⁺ and Hg²⁺ are 1.9 nM and 19.5 nM, respectively. Moreover, the constructed sensors were used to detect environmental water samples, and the results indicate that the detection system is reliable and could be further used in environmental monitoring. The design strategy reported in this study could broadly extend the application of metal ion-specific DNAzyme-based biosensors.

DNAzyme-Based Biosensors: Immobilization Strategies, Applications, and Future Prospective

Since their discovery almost three decades ago, DNAzymes have been used extensively in biosensing. Depending on the type of DNAzyme being used, these functional oligonucleotides can act as molecular recognition elements within biosensors, offering high specificity to their target analyte, or as reporters capable of transducing a detectable signal. Several parameters need to be considered when designing a DNAzyme-based biosensor. In particular, given that many of these biosensors immobilize DNAzymes onto a sensing surface, selecting an appropriate immobilization strategy is vital. Suboptimal immobilization can result in both DNAzyme detachment and poor accessibility toward the target, leading to low sensing accuracy and sensitivity. Various approaches have been employed for DNAzyme immobilization within biosensors, ranging from amine and thiol-based covalent attachment to non-covalent strategies involving biotin-streptavidin interactions, DNA hybridization, electrostatic interactions, and physical entrapment. While the properties of each strategy inform its applicability within a proposed sensor, the selection of an appropriate strategy is largely dependent on the desired application. This is especially true given the diverse use of DNAzyme-based biosensors for the detection of pathogens, metal ions, and clinical biomarkers. In an effort to make the development of such sensors easier to navigate, this paper provides a comprehensive review of existing immobilization strategies, with a focus on their respective advantages, drawbacks, and optimal conditions for use. Next, common applications of existing DNAzyme-based biosensors are discussed. Last, emerging and future trends in the development of DNAzyme-based biosensors are discussed, and gaps in existing research worthy of exploration are identified.

Exo III-Catalyzed Release of a Zn2+-Ligation DNAzyme to Drive the Strand Displacement Reaction and Gold Aggregation for the Homogeneous Bioassay of Kanamycin Antibiotics

Herein, we combine the exonuclease III (Exo III)-catalyzed release of a Zn²⁺-dependent ligation DNAzyme with the DNAzyme-driven strand displacement reaction (SDR) to develop a novel homogeneous colorimetric bioassay method for kanamycin (Kana) antibiotic detection. Upon the biorecognition reaction between Kana and a designed hairpin DNA, the DNAzyme-containing strand can be catalytically released by Exo III. Then, this DNAzyme will catalyze the ligation of two oligonucleotides to cause a SDR and the aggregation of gold nanoparticles (Au NPs) labeled by two linker DNA strands. Due to the aggregation of Au NPs for colorimetric signal transduction and the Exo III and SDR-assisted dual signal amplification, this method shows a wide linear range of 5 orders of magnitude and a very low detection limit down to 8.1 fg mL^-1. Together with its excellent selectivity, repeatability, reliability, and convenient manipulation, the proposed method shows a great potential for the food quality monitoring application.

Femtomolar Detection of Thrombin in Serum and Cerebrospinal Fluid via Direct Electrocatalysis of Oxygen Reduction by the Covalent G4-Hemin-Aptamer Complex

Thrombin, a serine protease playing a central role in the coagulation cascade reactions and a potent neurotoxin produced by injured brain endothelial cells, is a recognized cardiac biomarker and a critical biomarker for Alzheimer's disease development. Both in vivo and in vitro, its low physiological concentrations and nonspecific binding of other components of physiological fluids complicate electroanalysis of thrombin. Here, femtomolar levels of thrombin in serum and an artificial cerebrospinal fluid (CSF) were detected by the indicator-free electrochemical methodology exploiting the O₂ reduction reaction directly, with no electron transfer mediators, electrocatalyzed by the covalent G4-hemin DNAzyme complex naturally self-assembling upon thrombin binding to the hemin-modified 29-mer DNA aptamer sequence tethered to gold via an alkanethiol linker. Coadsorbed PEG inhibited nonspecific protein binding and allowed the sought signal resolution. The proposed assay exploiting the "oxidase" activity of G4-hemin DNAzyme does not require any coreactants necessary for the traditional peroxidase activity-based assays with this DNAzyme, such as H₂O₂ and redox mediators, or solution deaeration and allows fast, overall 30 min analysis of thrombin in aerated buffer, CSF, and 1% human serum solutions. This pioneer approach exploiting the oxidase activity G4-hemin DNAzyme is simple, sensitive, and selective and represents a new tool for ultrasensitive electrocatalytic assays based on simple and efficient O₂-dependent DNAzyme labels.

A GATA3 Targeting Nucleic Acid Nanocapsule for In Vivo Gene Regulation in Asthma

Allergic asthma is one of the leading chronic lung diseases of both children and adults worldwide, resulting in significant morbidity and mortality in affected individuals. Many patients have severe asthma, which is refractory to treatment, illustrating the need for the development of new therapeutics for this disease. Herein, we describe the use of a peptide cross-linked nucleic acid nanocapsule (NAN) for the delivery of a GATA3-specific DNAzyme to immune cells, with demonstration of modulated transcriptional activity and behavior of those cells. The NAN, built from peptide cross-linked surfactants, is chemically designed to degrade under inflammation conditions releasing individual DNAzyme-surfactant conjugates in response to proteolytic enzymes. Using the NAN, GATA3 DNAzymes were delivered efficiently to human peripheral blood mononuclear cells, with clear evidence of uptake by CD4+ helper T cells without the need for harsh transfection agents. Knockdown of GATA3 was achieved in vitro using human Jurkat T cells, which express GATA3 under homeostatic conditions. Additionally, mice treated with DNAzyme-NANs during house dust mite (HDM)-induced asthma developed less severe allergic lung inflammation than HDM-only control mice, as measured by pulmonary eosinophilia. This study suggests that peptide cross-linked GATA3 DNAzyme-NANs may have the potential to decrease the severity of asthma symptoms in human patients, and development of this technology for human use warrants further investigation.

Thrombin-Binding Aptamer with Inversion of Polarity Sites (IPS): Effect on DNAzyme Activity and Anticoagulant Properties

In this work we examined the properties of thrombin-binding aptamer (TBA) modified by the introduction of inversion of polarity sites (IPS) in order to assess the effect of modification on the activation of TBA to serve as DNAzyme with peroxidase-like activity. Two oligonucleotides were designed to possess one (IPS1) or three (IPS2) inversion sites. TBA typically forms antiparallel G-quadruplexes with two G-tetrads, which exhibits very low DNAzyme peroxidise activity. DNAzyme activity is generally attributed to parallel G-quadruplexes. Hence, inversion of polarity was introduced in the TBA molecule to force the change of G-quadruplex topology. All oligonucleotides were characterized using circular dichroism and UV-Vis melting profiles. Next, the activity of the DNAzymes formed by studied oligonucleotides and hemin was investigated. The enhancement of peroxidase activity was observed when inversion of polarity was introduced. DNAzyme based on IPS2 showed the highest peroxidase activity in the presence of K⁺ or NH₄⁺ ions. This proves that inversion of polarity can be used to convert a low-activity DNAzyme into a DNAzyme with high activity. Since TBA is known for its anticoagulant properties, the relevant experiments with IPS1 and IPS2 oligonucleotides were performed. Both IPS1 and IPS2 retain some anticoagulant activity in comparison to TBA in the reaction with fibrinogen. Additionally, the introduction of inversion of polarity makes these oligonucleotides more resistant to nucleases.

G-quadruplex DNAzyme as peroxidase mimetic in a colorimetric biosensor for ultrasensitive and selective detection of trace tetracyclines in foods

The colorimetric method can determine the initial results even by the naked eyes, but its main challenge for antibiotics detection in food at present is the relatively low sensitivity. Herein, an ultrasensitive colorimetric biosensor based on G-quadruplex DNAzyme was firstly proposed for the rapid detection of trace tetracycline antibiotics like tetracycline, oxytetracycline, chlortetracycline and doxycycline. DNAzyme composed of hemin and G-quadruplex has peroxidase-like activity, and tetracyclines can combine with hemin to form a stable complex and reduce catalytic activity, making the color of solution changes from yellow to green. The limits of detection (LOD) of the proposed colorimetric biosensor for tetracyclines is determined as low as 3.1 nM, which is lower than most of the other colorimetric methods for antibiotics detection. Moreover, the average recovery range of tetracyclines in actual samples is from 89% to 99%, indicating that such strategy may has bright application prospects for tetracyclines detection in foods.

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.

DNAzyme Cleavage of CAG Repeat RNA in Polyglutamine Diseases

CAG repeat expansion is the genetic cause of nine incurable polyglutamine (polyQ) diseases with neurodegenerative features. Silencing repeat RNA holds great therapeutic value. Here, we developed a repeat-based RNA-cleaving DNAzyme that catalyzes the destruction of expanded CAG repeat RNA of six polyQ diseases with high potency. DNAzyme preferentially cleaved the expanded allele in spinocerebellar ataxia type 1 (SCA1) cells. While cleavage was non-allele-specific for spinocerebellar ataxia type 3 (SCA3) cells, treatment of DNAzyme leads to improved cell viability without affecting mitochondrial metabolism or p62-dependent aggresome formation. DNAzyme appears to be stable in mouse brain for at least 1 month, and an intermediate dosage of DNAzyme in a SCA3 mouse model leads to a significant reduction of high molecular weight ATXN3 proteins. Our data suggest that DNAzyme is an effective RNA silencing molecule for potential treatment of multiple polyQ diseases.

Rapid detection of Pseudomonas aeruginosa using a DNAzyme-based sensor

In the present study, a DNAzyme was screened in vitro through the use of a DNA library and crude extracellular mixture (CEM) of Pseudomonas aeruginosa. Following eight rounds of selection, a DNAzyme termed PAE-1 was obtained, which displayed high rates of cleavage with strong specificity. A fluorescent biosensor was designed for the detection of P. aeruginosa in combination with the DNAzyme. A detection limit as low as 1.2 cfu/ml was observed. Using proteases and filtration, it was determined that the target was a protein with a molecular weight of 10 kDa-50 kDa. The DNAzyme was combined with a polystyrene board to construct a simple indicator plate sensor which produced a color that identified the target within 10 min. The results were reliable when tap water and food samples were tested. The present study provides a novel experimental strategy for the development of sensors based on a DNAzyme to rapidly detect P. aeruginosa in the field.

DNAzyme-Catalyzed Cellular Oxidative Stress Amplification for Pro-protein Activation in Living Cells

The conditional control of protein function in response to the physiological change of cells is of great interest for studying protein function in biological settings and developing protein therapeutics. We report herein that catalase (CAT) DNAzyme can potentiate the generation of reactive oxygen species (ROS) in living cells by knocking down catalase expression, which could further activate a reactive oxygen species (ROS)-responsive pro-protein, RNase A-NBC, in situ. Using an optimized lipid nanoparticle delivery system to simultaneously introduce CAT DNAzyme and RNase A-NBC into cells, we show that the pro-protein, RNase A-NBC, could be activated in a significantly enhanced manner to prohibit tumor cell growth in different types of cancer cells. We believe the methodology of regulating pro-protein activity using DNAzyme biocatalysis to differentiate intracellular environment could further be extended to other functional proteins, and even fundamental investigations in living systems to develop pro-protein therapeutics.

DNA-only bioassay for simultaneous detection of proteins and nucleic acids

Testing multiple biomarkers, as opposed to one, has become a preferred approach for diagnosing many heterogeneous diseases, such as cancer and infectious diseases. However, numerous technologies, including gold standard ELISA and PCR, can detect only one type of biomarker, either protein or nucleic acid (NA), respectively. In this work, we report for the first time simultaneous detection of proteins and NAs in the same solution, using solely functional NA (FNA) molecules. In particular, we combined the thrombin binding aptamer (TBA) and the 10-23 RNA-cleaving DNA enzyme (DNAzyme) in a single aptazyme molecule (Aptazyme_1.15-3'), followed by extensive optimization of buffer composition, sequences and component ratios, to establish a competitive bioassay. Subsequently, to establish a multiplex bioassay, we designed a new aptazyme (Aptazyme_2.20-5') by replacing the target recognition and substrate sequences within Aptazyme_1.15-3'. This designing process included an in silico study, revealing the impact of the target recognition sequence on the aptazyme secondary structure and its catalytic activity. After proving the functionality of the new aptazyme in a singleplex bioassay, we demonstrated the capability of the two aptazymes to simultaneously detect thrombin and NA target, or two NA targets in a multiplex bioassay. High specificity in target detection was achieved with the limits of detection in the low nanomolar range, comparable to the singleplex bioassays. The presented results deepen the barely explored features of FNA for diagnosing multiple targets of different origins, adding an extra functionality to their catalogue.

A Synergistic DNA-polydopamine-MnO2 Nanocomplex for Near-Infrared-Light-Powered DNAzyme-Mediated Gene Therapy

DNAzyme is emerging for gene therapy. The administration of the in vivo catalytic activity of DNAzyme has proven important but challenging for clinical applications. Herein, we report a synergistic DNA-polydopamine-MnO₂ nanocomplex, which enables near-infrared (NIR)-light-powered catalytic activity of DNAzyme in vivo. The nanocomplex has a hierarchical structure: a DNA nanoframework as the scaffold and polydopamine-MnO₂ (PM) as the coating layer. The DNA nanoframework contains repeated DNAzyme sequences. PM assembles on the surface of the DNA nanoframework. When the nanocomplex accumulates at tumor sites, upon NIR-light radiation, polydopamine induces a temperature elevation at tumor sites via photothermal conversion; meanwhile, glutathione triggers decomposition of PM to release Mn²⁺ to activate DNAzyme in the cytoplasm for gene regulation. In vitro and in vivo experiments show that the PM-induced temperature elevation enhances the Egr-1 mRNA cleavage activity of DNAzyme, promoting downregulation of the Egr-1 protein in tumor cells. In addition, the temperature elevation induces heat stress, achieving a synergistic tumor ablation effect.

Diagnosing Antibiotic Resistance Using Nucleic Acid Enzymes and Gold Nanoparticles

The rapid and accurate detection of antimicrobial resistance is critical to limiting the spread of infections and delivering effective treatments. Here, we developed a rapid, sensitive, and simple colorimetric nanodiagnostic platform to identify disease-causing pathogens and their associated antibiotic resistance genes within 2 h. The platform can detect bacteria from different biological samples (i.e., blood, wound swabs) with or without culturing. We validated the multicomponent nucleic acid enzyme-gold nanoparticle (MNAzyme-GNP) platform by screening patients with central line associated bloodstream infections and achieved a clinical sensitivity and specificity of 86% and 100%, respectively. We detected antibiotic resistance in methicillin-resistant Staphylococcus aureus (MRSA) in patient swabs with 90% clinical sensitivity and 95% clinical specificity. Finally, we identified mecA resistance genes in uncultured nasal, groin, axilla, and wound swabs from patients with 90% clinical sensitivity and 95% clinical specificity. The simplicity and versatility for detecting bacteria and antibiotic resistance markers make our platform attractive for the broad screening of microbial pathogens.

Detection of Vibrio vulnificus in Seafood With a DNAzyme-Based Biosensor

Vibrio vulnificus is an important pathogenic bacterium that is often associated with seafood-borne illnesses. Therefore, to detect this pathogen in aquatic products, a DNAzyme-based fluorescent sensor was developed for the in vitro detection of V. vulnificus. After screening and mutation, a DNAzyme that we denominated “RFD-VV-M2” exhibited the highest activity, specificity, and sensitivity. The limit of detection was 2.2 × 10³ CFU/ml, and results could be obtained within 5–10 min. Our findings suggested that the target of DNAzyme RFD-VV-M2 was a protein with a molecular weight between 50 and 100 kDa. The proposed biosensor exhibited an excellent capacity to detect marine products contaminated with V. vulnificus. Therefore, our study established a rapid, simple, sensitive, and highly specific detection method for V. vulnificus in aquatic products.

DNAzyme-based sensing probe protected by DNA tetrahedron from nuclease degradation for the detection of lead ions

Lead poisoning endangers soil, plants and human health due to its toxic effect. It is urgent to develop ideal tool for the in vivo detection of Pb²⁺.In this study, tetrahedron-based Pb²⁺-sensitive DNAzyme sensor (TPS) is constructed by taking advantages of a classic Pb²⁺-dependent GR-5 DNAzyme and DNA tetrahedral structure, where the cleavage substrate and DNAzyme are modified with fluorophore FAM and quencher BHQ-1, respectively. DNA tetrahedron is arranged at the terminus of substrate/DNAzyme duplex to offer the protective shield against the nuclease attack. In the absence of Pb²⁺, FAM and BHQ-1 are kept close and FAM fluorescence is efficiently quenched. However, in the presence of Pb²⁺ cofactor, the DNAzyme exhibits the catalytic activity and cleaves the substrate strands, spatially separating the FAM away from BHQ-1 and releasing fluorescence. Utilizing the sensing probe, the Pb²⁺ can be quantitatively detected down to 1 nM without the interference from nontarget metal ions. Even if incubating in the human serum solution for 12 h, no substantial nuclease degradation is detected. In different complex biological milieu, the TPS can preserve the 85% of fluorescence signal, indicating that the developed TPS is a promising tool for the future application in the in vivo detection of Pb²⁺.

Ratiometric fluorescent detection and imaging of microRNA in living cells with manganese dioxide nanosheet-active DNAzyme

MicroRNAs (miRNAs) play an important role in multiple biological processes and can be used as biomarkers for clinical disease diagnosis, so their detection is of great importance. Here, manganese dioxide (MnO₂) nanosheet acts as carrier to deliver DNAzyme probes into cells through endocytosis, where intracellular glutathione (GSH) reduces the MnO₂ nanosheet to manganese ions (Mn²⁺) and releases the probes. The generated Mn²⁺ can be further used as an effective cofactor to activate the DNAzyme probe, and cleave the DNA strand into two fragments. Then, the miRNA-155 in the cells can hybridize with the cleaved fragment to cause the fluorescence signal change of the probe. The proposed proportional fluorescent method has been applied to the imaging of miRNA-155 in HeLa cells and HepG2 cells with the estimated detection limit (LOD) as 1.6 × 10^-12 M. The new method can provide great help for cancer diagnosis and biological research related to miRNA.

Portable microfluidic device with thermometer-like display for real-time visual quantitation of Cadmium(II) contamination in drinking water

Cadmium (Cd²⁺) is a toxic metal ion widely existing in water, soil and food. Conventional water quality control heavily relies on expensive, bulky and sophisticated instrument such as spectrometry, which is time-consuming and incompatible with on-site, real-time detection. Here, a portable microfluidic device with thermometer-like visual readouts is developed for real-time quantitation of cadmium (II) contamination in drinking water. We use Cd²⁺-dependent DNAzyme (Cd16), which is cleaved when Cd²⁺ is present, creating a single strand DNA which triggers catalytic hairpin assembly (CHA) with two hairpins H1 and H2 as the building blocks. Plenty of H1H2 complex, the product after the Cd²⁺-mediated CHA, are generated, which can connect magnetic microparticles (MMPs) and polystyrene microparticles (PMPs), forming "MMPs-H1H2-PMPs" sandwich structure. To provide visual readout to quantitate the particle connection, the particle solution is loaded into a portable microfluidic chip. A magnetic separator first removes MMPs and the connected PMPs, while free PMPs can continue flowing until accumulating into a bar at the particle dam. Shown as a thermometer-like display, the accumulating length is inversely proportional to the concentration of Cd²⁺, enabling quantitative detection of Cd²⁺ by the naked eye. The proposed device exhibits a limit of detection of 11.3 nM of Cd²⁺, selectivity >200-fold against other metal ions, high tolerance to the interferents present in drinking water and high recovery rate in tap water. With high analytical performance without any sample preparation step, this portable device is highly promising in real-time monitoring in urban drinking water at sites.

A Fluorescence Sensor for Pb2+ Detection Based on Liquid Crystals and Aggregation-Induced Emission Luminogens

Heavy metals, such as lead ions, are regarded as the main environmental contaminants and have a negative impact on human bodies, making detection technologies of lead ions critical. However, most existing detection methods suffer from time consumption, complicated sample pretreatment, and expensive equipment, which hinder their broad use in real-time detection. Herein, we show a new fluorescence sensor for detecting lead ions derived from liquid crystals doped with an aggregation-induced emission luminogen. The mechanism is based on the variation of fluorescence intensity caused by the disturbance of an ordered liquid crystal configuration in the presence of Pb²⁺, induced by DNAzyme and its catalytic cleavage. The proposed fluorescence sensor exhibits a low detection limit of 0.65 nM, which is 2 orders of magnitude lower than that previously reported in an optical sensor based on liquid crystals. The detection range of the Pb²⁺ fluorescence sensor is broad, from 20 nM to 100 μM, and it also selects lead ions from numerous metal ions exactly, resulting in a highly sensitive, highly selective, simple, and low-cost detection strategy of Pb²⁺ with potential applications in chemical and biological fields. This approach to designing a liquid crystal fluorescence sensor offers an inspiring stage for detecting biomacromolecules or other heavy metal ions by varying decorated molecules.

Self-Assembly of Copper-DNAzyme Nanohybrids for Dual-Catalytic Tumor Therapy

Despite the great efforts of using DNAzyme for gene therapy, its clinical success is limited by the lack of simple delivery systems and limited anticancer efficacy. Here, we develop a simple approach for the synthesis of hybrid nanostructures that exclusively consist of DNAzyme and Cu²⁺ with ultra-high loading capacity. The Cu-DNAzyme nanohybrids allow to effectively co-deliver DNAzyme and Cu²⁺ into cancer cells for combinational catalytic therapy. The released Cu²⁺ can be reduced to Cu⁺ by glutathione and then catalyze endogenous H₂ O₂ to form cytotoxic hydroxyl radicals for chemodynamic therapy (CDT), while the 10-23 DNAzyme enables the catalytic cleavage of VEGFR2 mRNA and activates gene silencing for gene therapy. We demonstrate that the system can efficiently accumulate in the tumor and exhibit amplified cascade antitumor effects with negligible systemic toxicity. Our work paves an extremely simple way to integrate DNAzyme with CDT for the dual-catalytic tumor treatment.

Microfluidic particle accumulation for visual quantitation of copper ions

A portable biosensor has been developed based on microfluidic particle accumulation for visual quantification of copper ions. A copper-dependent DNAzyme is used to connect magnetic microparticles (MMPs) and polystyrene microparticles (PMPs), forming "MMPs-DNAzyme-PMPs." When copper ions are present, the DNAzyme is cleaved, allowing free PMPs to be released from the MMPs-DNAzyme-PMP complex. Using a capillary-flow-based microfluidic device, the MMPs-DNAzyme-PMPs are first separated by a magnetic chamber, allowing the free PMPs to continue flowing until being trapped at a particle dam with a narrowing nozzle. Therefore, as a thermometer-like display, the copper level can be visually quantified by the accumulation length of the free PMPs in the trapping microchannel. The limit of detection (LOD) is 33 nM determined by the linear range of 25-100 nM, which is 900 times lower than the prevalent standard (~30 μM) in Hong Kong. The system shows excellent selectivity (> 1000-folds) against other heavy metal ions and abilities to adapt to multiple water environmental conditions. Tests on tap water samples and three local natural water sources in Hong Kong manifest that the device can effectively monitor the quality of freshwater with >70% recovery and 26.16% RSD.

A Bimetallic Metal-Organic Framework Encapsulated with DNAzyme for Intracellular Drug Synthesis and Self-Sufficient Gene Therapy

Although chemotherapy is one of the most widely used cancer treatments, there are serious side effects, drug resistance, and secondary metastasis. To address these problems, herein we designed a bimetallic metal-organic framework (MOF) encapsulated with DNAzyme for co-triggered in situ cancer drug synthesis and DNAzyme-based gene therapy. Once in cancer cells, MOFs would disassemble and liberate copper ions, zinc ions, and DNAzyme under the acidic environment of lysosomes. Copper ions can catalyze the synthesis of the chemotherapeutic drug through copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction after being reduced to Cu^I ; zinc ions act as the cofactor to activate the cleavage activity of DNAzyme. The anticancer drug is synthesized intracellularly and can kill cancer cells on site to minimize side effects to normal organisms. The activated DNAzyme starts gene therapy to inhibit tumor proliferation and metastasis by targeting and cleaving oncogene substrates.

DNAzyme-Triggered Sol-Gel-Sol Transition of a Hydrogel Allows Target Cell Enrichment

Enrichment of rare cancer cells from various cell mixtures for subsequent analysis or culture is essential for understanding cancer formation and progression. In particular, maintaining the viability of captured cancer cells and gently releasing them for relevant applications remain challenging for many reported methods. Here, a physically cross-linked deoxyribozyme (DNAzyme)-based hydrogel strategy was developed for the specific envelopment and release of targeted cancer cells, allowing the aptamer-guided capture, 3D envelopment, and Zn²⁺-dependent release of viable cancer cells. The DNAzyme hydrogel is constructed through the intertwinement and hybridization of two complementary DNAzyme strands located on two rolling circle amplification-synthesized ultralong DNA chains. The enveloping and separation of target cells were achieved during the formation of the DNAzyme hydrogel (sol-gel transition). Triggered by Zn²⁺, the encapsulated cells can be gently released from the dissociated DNAzyme hydrogel with high viability (gel-sol transition). Successful isolations of target cells from cancer cell mixtures and peripheral blood mononuclear cells (PBMC) were demonstrated. This method offers an attractive approach for the separation of target cancer cells for various downstream applications that require viable cells.

SERS-Microfluidic Approach for the Quantitative Detection of miRNA Using DNAzyme-Mediated Reciprocal Signal Amplification

MicroRNAs (miRNAs) play important roles in biological processes. Designing a sensitive, selective, and rapid method of miRNA detection is crucial for biological research. Here, with a reciprocal signal amplification (RSA) probe, this work established a novel surface-enhanced Raman scattering (SERS)-microfluidic approach for the quantitative analysis of miRNA. First, via a DNAzyme self-assemble cycle reaction, two types of SERS signals produce amplified reciprocal changes. The sum of the absolute signal value is first adopted for the quantitative analysis of miRNA, which results in an enhanced response and a reduced blank value. Furthermore, the assay is integrated in an electric drive microfluidic mixing reactor that enables physical mixing and enriching of the reactants for more rapid and enhanced detection sensitivity. The protocol owns the merits of the SERS technology, amplified reciprocal signals, and a microfluidic chip, with a detection limit of 2.92 fM for miR-141 in 40 min. In addition, successful determination of miRNA in a variety of cells proved the practicability of the assay. Compared with the reported strategies for miRNA analysis, this work avoids a complex and time-consuming procedure and enhances the sensitivity and specificity. The method opens a promising way for biomolecular chip detection and research.

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.

A responsive pure DNA hydrogel for label-free detection of lead ion

It is of great significance to develop facile and economical strategies for on-site detection and treatment of toxic metal ions. Stimulus-responsive DNA hydrogel materials have been increasingly used for convenient detection of metal ions due to their advantages such as simplicity, portability, and ease of storage. However, these methods still require encapsulation of signal tags by labeling or embedding. In this paper, a one-step preparation of Pb²⁺-responsive pure DNA hydrogel material was designed to realize a new label-free strategy for Pb²⁺ biosensing. The Pb²⁺-dependent DNAzyme strand and substrate strand were introduced to fabricate the DNA hydrogel. The presence of Pb²⁺ in the sample activates the enzyme strand in the hydrogel skeleton and triggers the cleavage of the substrate, thereby destroy the hydrogel structure. DNA fragments released by the collapsed hydrogel were readily measured as signal output for quantifying Pb²⁺ concentrations with a minimum detection limit of 7.7 nM. We successfully eliminated the need for embedding or labeling of signal molecules by using the DNA molecules that construct hydrogels as the signal output. And the newly developed method for label-free detection of Pb²⁺ based on pure DNA hydrogel is simple, easy readout, and cost-effective. By adjusting the DNAzyme and substrate sequences, label-free analysis of other metal ions can also be achieved. We expect that our strategy can be applied to the field detection of toxic metal ions.

Rational Control of the Activity of a Cu2+-Dependent DNAzyme by Re-engineering Purely Entropic Intrinsically Disordered Domains

The function and activity of many proteins is finely controlled by the modulation of the entropic contribution of intrinsically disordered domains that are not directly involved in any recognition event. Inspired by this mechanism, we demonstrate here that we could finely regulate the catalytic activity of a model DNAzyme (i.e., a synthetic DNA sequence with enzyme-like properties) by rationally introducing intrinsically disordered nucleic acid portions in its original sequence. More specifically, we have re-engineered here the well-characterized Cu²⁺-dependent DNAzyme that catalyzes a self-cleavage reaction by introducing a poly(T) linker domain in its sequence. The linker is not directly involved in the recognition event and connects the two domains that fold to form the catalytic core. We demonstrate that the enzyme-like activity of this re-engineered DNAzyme can be modulated in a predictable and fine way by changing the length, and thus entropy, of such a linker domain. Given these attributes, the rational design of intrinsically disordered domains could expand the available toolbox to achieve a control of the activity of DNAzymes and, in analogy, ribozymes through a purely entropic contribution.

An amplifying DNA circuit coupled with Mg2+-dependent DNAzyme for bisphenol A detection in milk samples

As bisphenol A (BPA) is harmful to human health, it is of great significance to develop a new method for BPA detection. Herein, we designed a BPA biosensor by integrating an amplifying DNA circuit with Mg²⁺-dependent DNAzyme into the sensing system. The BPA-aptamer binding activated a DNA circuit for signal amplification based on toehold-mediated strand displacement. A catalytic Mg²⁺-dependent DNAzyme was formed through synergistically DNA hybridization, which can cleave the dual-labeled substrate DNA into two segments. The separation of the fluorophore and quencher produces a high fluorescence response for BPA detection. This biosensor exhibited a superior sensitivity with a detection limit of 50 fM. The method is selective and robust, which can work even in milk samples with satisfactory accuracy. The biosensor analytical results were also verified by liquid chromatography coupled with mass spectrometry (LC-MS) and no obvious difference existed between the two methods.

Target-initiated autonomous synthesis of metal-ion dependent DNAzymes for label-free and amplified fluorescence detection of kanamycin in milk samples

Accurate and sensitive monitoring of the abused antibiotics is vital because excessive antibiotics in human body can cause toxicity to kidney or lead to potential loss of hearing. In this work, we described a label-free and highly sensitive fluorescent aptasensing platform for detecting kanamycin in milk samples based on the synchronization signal amplification of primer exchange reaction (PER) and metal-ion dependent DNAzyme. The target kanamycin binds the aptamer sequence hybridized on a hairpin template and initiates PER for autonomous synthesis of Mg²⁺-dependent DNAzyme sequences with aid of Bst-DNA polymerase at isothermal conditions. Such a synthesis process can be repeated many times to produce lots of DNAzymes to cyclically cleave the rA site in the signal hairpin substrates under the assistance of Mg²⁺ cofactor to liberate numerous free G-quadruplex fragments. The organic dye thioflavin T (ThT) further associates with these G-quadruplex fragments to yield substantially intensified fluorescence for sensitive detection of kanamycin with a low detection limit of 0.36 nM. In addition, the developed aptamer sensing method also shows a good selectivity for kanamycin against other interfering antibiotics, and can realize the monitoring of kanamycin added in milk samples, highlighting its potential for sensitive monitoring of trace amount of kanamycin for food safety applications.

Functional Nucleic Acid-Based Live-Cell Fluorescence Imaging

Cell is the structural and functional unit of organism. It serves as a key research object in various biological processes, such as growth, ontogeny, metabolism and stress. Studying the spatiotemporal distribution and functional activity of specific biological molecules in living cells is crucial for exploring the mechanism governing life. It also facilitates the elucidation of pathogenesis, clinical prevention and disease theranostics. In recent years, the fluorescence imaging technique has been greatly exploited for live-cell imaging. However, the development of molecular probes has lagged far behind. Functional nucleic acids (FNAs), for example, aptamer and DNAzyme, possess special chemical and/or biological functions, hence severing as promising molecular tools for cellular imaging. The current mini review focuses on the applications of FNAs in live-cell fluorescence imaging.

Ultrasensitive ratiometric detection of Pb2+ using DNA tetrahedron-mediated hyperbranched hybridization chain reaction

A fluorescent sensing strategy was developed for rapid, highly sensitive and specific detection of lead (II) ion (Pb²⁺) on the basis of Pb²⁺ DNAzyme-controlled tetrahedral DNA nanostructure (TDN)-mediated hyper-branched hybridization chain reaction (hHCR). In this strategy, DNA hairpins used for HCR amplification are modified on the four vertexes of TDN, which are then used to perform rapid TDN-hHCR in the presence of an initiator strand, producing large-sized cross-linked reaction products and thus giving greatly improved fluorescence resonance energy transfer (FRET) signal output. Pb²⁺ DNAzyme catalyzes the cleavage of the initiator strand, inhibiting the initiation of TDN-hHCR and giving decreased FRET signal. Synergetic signal amplification of Pb²⁺ DNAzyme-catalyzed cleavage reaction and subsequent TDN-hHCR confers the sensing platform with ultrahigh sensitivity. As low as 0.25 pM Pb²⁺ can be detected by using either signal "turn-on" or "turn-off" mode. The whole detection process can be finished within 20 min. Strong anti-interference capacity of FRET-based ratiometric detection and high specificity of Pb²⁺ DNAzyme endow the sensing platform with great practical application potential, which was demonstrated by the accurate detection of Pb²⁺ in real river water, fruit, vegetable and grain samples.

Visual Detection of SARS-CoV-2 RNA by Conventional PCR-Induced Generation of DNAzyme Sensor

The gold standard for the diagnosis of SARS-CoV-2, the causative agent of COVID-19, is real-time polymerase chain reaction (PCR), which is labor-intensive, expensive, and not widely available in resource-poor settings. Therefore, it is imperative to develop novel, accurate, affordable, and easily accessible assays/sensors to diagnose and isolate COVID-19 cases. To address this unmet need, we utilized the catalytic potential of peroxidase-like DNAzyme and developed a simple visual detection assay for SARS-CoV-2 RNA using a conventional thermal cycler by the PCR-induced generation of DNAzyme sensor. The performance of RT-PCR DNAzyme-based sensor was comparable to that of real-time PCR. The pilot scale validation of RT-PCR DNAzyme-based sensor has shown ~100% sensitivity and specificity in clinical specimens (nasopharyngeal swab, n = 34), with a good correlation (Spearman r = 0.799) with the Ct-value of fluorescence probe-based real-time PCR. These findings clearly indicate the potential of this inexpensive, sensitive, and specific molecular diagnostic test to extend our testing capabilities for the detection of SARS-CoV-2 to curtail COVID-19 transmission.

Liquid crystal-based sensing platform for detection of Pb2+ assisted by DNAzyme and rolling circle amplification

Lead ions (Pb²⁺) are one of the most widespread heavy metal contaminants that pose detrimental impact on environment and human health. We demonstrate a highly sensitive and specific liquid crystal (LC)-based sensing platform for detecting Pb²⁺ assisted by DNAzyme and rolling circle amplification (RCA). Magnetic beads (MBs) are functionalized with DNA duplexes of the catalytic strands (DNAzymes) and the substrate strands. In the presence of Pb²⁺, the substrate strands are disassembled due to activation of the DNAzyme, which allows initiation of DNA RCA on MBs. The amplified DNA strands can disrupt arrangement of octadecy trimethyl ammonium bromide monolayers (OTAB), thereby inducing planar orientation of LC molecules at the interface of aqueous and LCs. Thus, LCs exhibit bright appearance. In contrast, RCA cannot be triggered in the absence of Pb²⁺. Therefore, LC molecules adopt perpendicular orientation at the interface, which induces the dark morphology of LCs. The limit of detection reaches as low as 16.7 pM. It is an improvement of more than two orders of magnitude compared to that of previously reported LC-based sensing approaches. This approach also shows excellent performance in monitoring Pb²⁺ in tap water and lake water.

Core-Shell Nanosystems for Self-Activated Drug-Gene Combinations against Triple-Negative Breast Cancer

The combination of gene therapy with chemotherapeutics provides an efficacious strategy for enhanced tumor therapy. RNA-cleaving DNAzyme has been recognized as a promising gene-silencing tool, while its combination with chemotherapeutic drugs has been limited by the lack of an effective codelivery system to allow sufficient intracellular DNAzyme activation, which requires specific metal ions as a cofactor. Here, a self-activatable DNAzyme/drug core-shell codelivery system is fabricated to combat triple-negative breast cancer (TNBC). The hydrophobic chemotherapeutic, rapamycin (RAP), is self-assembled into the pure drug nanocore, and the metal-organic framework (MOF) shell based on coordination between Mn²⁺ and tannic acid (TA) is coated on the surface to coload an autophagy-inhibiting DNAzyme. The nanosystem efficiently delivers the payloads into tumor cells, and upon endocytosis, the MOF shell is disintegrated to release the therapeutics in response to an acidic endo/lysosome environment and intracellular glutathione (GSH). Notably, the coreleased Mn²⁺ serves as the cofactor of DNAzyme for effective self-activation, which suppresses the expression of Beclin 1 protein, the key initiator of autophagy, resulting in a significantly strengthened antitumor effect of RAP. Using tumor-bearing mouse models, the nanosystem could passively accumulate into the tumor tissue, impose potent gene-silencing efficacy, and thus sensitize chemotherapy to inhibit tumor growth upon intravenous administration, providing opportunities for combined gene-drug TNBC therapy.

Light-Induced Oxidase Activity of DNAzyme-Modified Quantum Dots

Here, we report the synthesis of a quantum dot (QD)-DNA covalent conjugate to be used as an H₂O₂-free DNAzyme system with oxidase activity. Amino-coupling conjugation was carried out between amino-modified oligonucleotides (CatG4-NH₂) and carboxylated quantum dots (CdTe@COOH QDs). The obtained products were characterized by spectroscopic methods (UV-Vis, fluorescence, circular dichroizm (CD), and IR) and the transmission electron microscopy (TEM) technique. A QD-DNA system with a low polydispersity and high stability in aqueous solutions was successfully obtained. The catalytic activity of the QD-DNA conjugate was examined with Amplex Red and ABTS (2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonate)) indicators using reactive oxygen species (ROS) generated by visible light irradiation. The synthesized QD-DNAzyme exhibited enhanced catalytic activity compared with the reference system (a mixture of QDs and DNAzyme). This proved the assumption that the covalent attachment of DNAzyme to the surface of QD resulted in a beneficial effect on its catalytic activity. The results proved that the QD-DNAzyme system can be used for generation of the signal by light irradiation. The light-induced oxidase activity of the conjugate was demonstrated, proving that the QD-DNAzyme system can be useful for the development of new cellular bioassays, e.g., for the determination of oxygen radical scavengers.

DNAzyme-Metal-Organic Framework Two-Photon Nanoprobe for In situ Monitoring of Apoptosis-Associated Zn2+ in Living Cells and Tissues

Monitoring Zn²⁺ in living cells is critical for fully elucidating the biological process of apoptosis. However, the quantitative intracellular sensing of Zn²⁺ using DNAzyme remains challenging because of issues related to penetration of the signal through tissue, targeted cellular uptake and activation, and susceptibility toward enzymatic degradation. In this study, we developed a novel phosphate ion-activated DNAzyme-metal-organic frameworks (MOFs) nanoprobe for two-photon imaging of Zn²⁺ in living cells and tissues. The design of this nanoprobe involved the loading of a Zn²⁺-specific, RNA-cleaving DNAzyme onto the MOFs through strong coordination between the phosphonate O atoms of the DNAzyme backbone and Zr atoms in the MOFs. This coordination restrained the extracellular activity of DNAzyme; however, after cell entry, the DNAzyme was released from the MOFs through a competitive binding by the phosphate ions present at a high intracellular concentration. Following their release, the two-photon (TP) fluorophore-labeled substrate strands of DNAzyme were cleaved with the aid of Zn²⁺, which resulted in a strong fluorescence signal. The incorporation of a TP fluorophore into the nanoprobe facilitated near-infrared excitation, which allowed the highly sensitive and specific imaging of Zn²⁺ in living cells and tissues at greater depths than possible previously. The TP-DNAzyme-MOFs nanoprobe achieved a low detection limit of 3.53 nM, extraordinary selectivity toward Zn²⁺, and a tissue signal penetration of 120 μm. More importantly, this nanoprobe was successfully used to monitor cell apoptosis, and this application of the DNAzyme-MOFs probe holds great potential for future use in biological studies and medical diagnostics.

DNAzyme Sensor for the Detection of Ca2+ Using Resistive Pulse Sensing

DNAzymes are DNA oligonucleotides that can undergo a specific chemical reaction in the presence of a cofactor. Ribonucleases are a specific form of DNAzymes where a tertiary structure undergoes cleavage at a single ribonuclease site. The cleavage is highly specificity to co-factors, which makes them excellent sensor recognition elements. Monitoring the change in structure upon cleavage has given rise to many sensing strategies; here we present a simple and rapid method of following the reaction using resistive pulse sensors, RPS. To demonstrate this methodology, we present a sensor for Ca²⁺ ions in solution. A nanoparticle was functionalised with a Ca²⁺ DNAzyme, and it was possible to follow the cleavage and rearrangement of the DNA as the particles translocate the RPS. The binding of Ca²⁺ caused a conformation change in the DNAzyme, which was monitored as a change in translocation speed. A 30 min assay produced a linear response for Ca²⁺ between 1–9 μm, and extending the incubation time to 60 min allowed for a concentration as low as 0.3 μm. We demonstrate that the signal is specific to Ca²⁺ in the presence of other metal ions, and we can quantify Ca²⁺ in tap and pond water samples.

Environmental and intercellular Pb2+ ions determination based on encapsulated DNAzyme in nanoscale metal-organic frameworks

With the merits of low cost, simple synthesis procedure, and high affinity for metal ions, deoxyribozyme (DNAzyme) have played important roles in metal ions detection. However, the intracellular applications of DNAzyme are limited because of enzymatic degradation and inefficient cellular uptake. To address these problems, GR-5 as model DNAzyme was encapsulated into zeolitic imidazolate frameworks-8 (ZIF-8) nanoparticles by biomimetic mineralization. The positively charged ZIF-8 with high DNAzyme loading capacity retained their ability to enter cells. Compared with free DNAzyme, the biomimetic mineralization synthesis method has greatly improved the stability of pristine DNAzyme. The as-synthesized DNAzyme@ZIF-8 composite exhibited good stability resisting DNase I, and was used as a sensitive fluorescent nanoprobe for Pb²⁺ determination and successfully achieved selective and sensitive determination for Pb²⁺ at λ_ex/λ_em = 494/522 nm in real samples. The linear range for the determination of Pb²⁺ is 50 to 500 nM. Moreover, the highly active DNAzyme delivered by ZIF-8 allows noninvasive imaging of Pb²⁺ measurement in living cells. This strategy will extend the suitability of functional nucleic acids for in vitro and in vivo bioanalysis and bioimaging. Graphical abstract.

Characterization of a DNA-hydrolyzing DNAzyme for generation of PCR strands of unequal length

I-R3 DNAzyme is a small, highly active catalytic DNA for DNA hydrolysis. In here, we designed two cis-structure DNAzymes (I-R3N and I-R3S) based on the different locates of the joint linker between I-R3 and its substrate. Data demonstrated that both DNAzymes were highly dependent on Zn²⁺, and worked at a narrow range around pH 7.0. They exhibited strong anti-interference with Mg²⁺ and Ca²⁺, but inhibited by Na⁺ and K⁺. Moreover, single and multiple-site mutations were generated within the catalytic core to carry out a comprehensive mutational study of I-R3 motif, in which most nucleotides were highly conserved and the nucleotides A5, T11 and T8 were identified as the mutational hotspots. Furthermore, an efficient variant A5G was obtained and its reaction condition was optimized. Finally, we constructed A5G to the 3' end of a single-stranded DNA (ssDNA) and applied it for asymmetrical PCR amplification to produce a single and double-stranded DNA mixture, in which A5G within ssDNA can self-cleave to generate a shorter desired ssDNA by denaturing gel separation. This would provide a new non-chemical modification approach for preparation of the expected ssDNA for in vitro selection of DNAzymes.

DNAzyme and rGO based fluorescence assay for Fpg activity analysis, drug screening, and bacterial imaging

Due to the significant role of formamidopyrimidine DNA glycosylase (Fpg) in physiological processes and DNA oxidative damage-related diseases, it is essential to establish sensitive methods for monitoring the Fpg activity in vitro and in vivo so as to illustrate its concrete role in these events. In this work, a sensitive, simple and reliable fluorescence assay was developed by taking the advantages of DNAzyme assisted cascade signal amplification and ultra-high fluorescence quenching efficiency of reduced graphene oxide (rGO). This detection system consisted of DNAzyme, rGO and fluorescence probe allows the activity of Fpg to be detected in a linear range from 0 to 80 U/mL with a detection limit of 0.66 U/mL. With the help of this method, 11 natural compounds were screened, and 7 compounds were identified as activators of Fpg. More importantly, the developed assay was used to monitor the activity of Fpg through fluorescence imaging in living Escherichia coli for the first time. The imaging results visually demonstrated the dynamic activation effect of natural compound Ginsenoside Re on the Fpg of Escherichia coli. In summary, these results indicated that this DNAzyme and rGO based fluorescence assay provides a potent strategy for Fpg quantitative assay in vitro and real-time monitoring in living bacteria, which holds great potential for applying on biological study and Fpg-targeted drug screening.

Suppressing the background activity of hemin for boosting the sensitivity of DNAzyme-based biosensors by SYBR Green I

Peroxidase-like DNAzymes have been extensively used to replace horseradish peroxidase (HRP) for developing biosensors for signal amplification. However, the background activity from the cofactor (i.e., free hemin) has limited the sensitivity of such sensors. Herein, we aim to find an inhibitor for hemin to suppress the background signal, and a classic split DNAzyme-based sensor was used to detect a complementary DNA oligonucleotide. After screening a series of dyes, SYBR Green I (SG, one of the DNA stanning dyes) was selected for suppressing the background. Simply by adding 0.84 μM SG, the background from 50 nM hemin was suppressed over 30-fold. The suppression was caused by the interaction between SG and hemin. In the presence of the target DNA, the formed duplex region and G-quadruplex structure can better bind SG and hemin respectively, thus preventing the interaction between them and showing a high activity of the DNAzyme. The optimized sensor showed a detection limit of 3.8 pM for the target DNA (p53 gene). In addition, the backgrounds from chemiluminescence, colorimetric and fluorescence sensing modes can all be reduced by adding SG to the split DNAzyme system. The suppression of the background of peroxidase DNAzymes is a critical step towards practical use of related biosensors.

Application of solid-phase DNA probe method with cleavage by deoxyribozyme for analysis of long non-coding RNAs

The solid-phase DNA probe method is a well-established technique for tRNA purification. We have applied this method for purification and analysis of other non-coding RNAs. Three columns for purification of tRNAPhe, transfer-messenger RNA (tmRNA) and 16S rRNA from Thermus thermophilus were connected in tandem and purifications were performed. From each column, tRNAPhe, tmRNA and 16S rRNA could be purified in a single step. This is the first report of purification of native tmRNA from T. thermophilus and the purification demonstrates that the solid-phase DNA probe method is applicable to non-coding RNA, which is present in lower amounts than tRNA. Furthermore, if a long non-coding RNA is cleaved site-specifically and the fragment can be purified by the solid-phase DNA probe method, modified nucleosides in the long non-coding RNA can be analysed. Therefore, we designed a deoxyribozyme (DNAzyme) to perform site-specific cleavage of 16S rRNA, examined optimum conditions and purified the resulting RNA fragment. Sequencing of complimentary DNA and mass spectrometric analysis revealed that the purified RNA corresponded to the targeted fragment of 16S rRNA. Thus, the combination of DNAzyme cleavage and purification using solid-phase DNA probe methodology can be a useful technique for analysis of modified nucleosides in long non-coding RNAs.

A label-free lead(II) ion sensor based on surface plasmon resonance and DNAzyme-gold nanoparticle conjugates

Detection of lead(II) (Pb²⁺) ions in water is important for the protection of human health and environment. The growing demand for onsite detection still faces challenges for sensitive and easy-to-use methods. In this work, a novel surface plasmon resonance (SPR) biosensor based on GR-5 DNAzyme and gold nanoparticles (AuNPs) was developed. Thiolated DNAzyme was immobilized on the gold surface of the sensor chip followed by anchoring the substrate-functionalized AuNPs through the DNAzyme-substrate hybridization. The coupling between the localized surface plasmon (LSP) of AuNPs and the surface plasmon polaritons (SPP) on the gold sensor surface was used to improve the sensitivity. The substrate cleavage in the presence of Pb²⁺ ions was catalyzed by DNAzyme, leading to the removal of AuNPs and the diminished LSP-SPP coupling. The optimal detection limit was 80 pM for the sensor fabricated with 1 μM DNAzyme, corresponding to two or three orders of magnitude lower than the toxicity levels of Pb²⁺ in drinking water defined by WHO and USEPA. By tuning the surface coverage of DNAzyme, the sensitivity and dynamic range could be controlled. This sensor also featured high selectivity to Pb²⁺ ions and simple detection procedure. Successful detection of Pb²⁺ ions in groundwater indicates that this method has the prospect in the onsite detection of Pb²⁺ ions in water. Given the variety of AuNPs and metal-specific DNAzymes, this detection strategy would lead to the development of more sensitive and versatile heavy metal sensors. Graphical abstract.

Effect of Distance from Catalytic Synergy Group to Iron Porphyrin Center on Activity of G-Quadruplex/Hemin DNAzyme

G-quadruplex/Hemin (G4/Hemin) complex has been widely used in biocatalysis and analytical applications. Meanwhile, compared with natural proteinous enzyme, its low catalytic activity is still limiting its applications. Even though several methods have been developed to enhance the peroxidation efficiency, the important core of the G4 design based enhancement mechanism is still indistinct. Here, we focus the mechanism study on the two most important microdomains: the iron porphyrin center and the catalytic synergy group within the 3' flanking. These microdomains not only provide the pocket for the combination of substrate, but also offer the axial coordination for the accelerated formation of Compound I (catalytic intermediate). In order to obtain a more suitable space layout to further accelerate the catalytic process, we have used the bases within the 3' flanking to precisely regulate the distance between microdomains. Finally, the position-dependent effect on catalytic enhancement is observed. When dC is positioned at the second-position of 3' flanking, the newly obtained DNAzyme achieves an order of magnitude improvement compared to parent G4/Hemin in catalytic activity. The results highlight the influence of the distance between the catalytic synergy group and iron porphyrin center on the activity of DNAzyme, and provide insightful information for the design of highly active DNAzymes.