Selection of a metal ligand modified DNAzyme for detecting Ni2

Sequence-Defined DNA Polymers: New Tools for DNA Nanotechnology and Nucleic Acid Therapy

Structural DNA nanotechnology offers a unique self-assembly toolbox to construct soft materials of arbitrary complexity, through bottom-up approaches including DNA origami, brick, wireframe, and tile-based assemblies. This toolbox can be expanded by incorporating interactions orthogonal to DNA base-pairing such as metal coordination, small molecule hydrogen bonding, π-stacking, fluorophilic interactions, or the hydrophobic effect. These interactions allow for hierarchical and long-range organization in DNA supramolecular assemblies through a DNA-minimal approach: the use of fewer unique DNA sequences to make complex structures. Here we describe our research group's work to integrate these orthogonal interactions into DNA and its supramolecular assemblies. Using automated solid phase techniques, we synthesized sequence-defined DNA polymers (SDPs) featuring a wide range of functional groups, achieving high yields in the process. These SDPs can assemble into not only isotropic spherical morphologies─such as spherical nucleic acids (SNAs)─but also into anisotropic nanostructures such as 1D nanofibers and 2D nanosheets. Our structural and molecular modeling studies revealed new insights into intermolecular chain packing and intramolecular chain folding, influenced by phosphodiester positioning and SDP sequence. Using these new self-assembly paradigms, we created hierarchical, anisotropic assemblies and developed systems exhibiting polymorphism and chiroptical behavior dependent on the SDP sequence. We could also precisely control the size of our nanofiber assemblies via nucleation-growth supramolecular polymerization and create compartmentalized nanostructures capable of precise surface functionalization.The exquisite control over sequence, composition, and length allowed us to combine our SDPs with nanostructures including DNA wireframe assemblies such as prisms, nanotubes, and cubes to create hybrid, stimuli-responsive assemblies exhibiting emergent structural and functional modes. The spatial control of our assemblies enabled their use as nanoreactors for chemical transformations in several ways: via hybridization chain reaction within SNA coronas, through chemical conjugation within SNA cores, and through a molecular "printing" approach within wireframe assemblies for nanoscale information transfer and the creation of anisotropic "DNA-printed" polymer particles.We have also employed our SDP nanostructures toward biological and therapeutic applications. We demonstrated that our SNAs could serve as both extrinsic and intrinsic therapeutic platforms, with improved cellular internalization and biodistribution profiles, and excellent gene silencing activities. Using SDPs incorporating hydrophobic dendrons, high-affinity and highly specific oligonucleotide binding to human serum albumin was demonstrated. These structures showed an increased stability to nuclease degradation, reduced nonspecific cellular uptake, no toxicity even at high concentrations, and excellent biodistribution beyond the liver, resulting in unprecedented gene silencing activity in various tissues.Control over the sequence has thus presented us with a unique polymeric building block in the form of the SDP, which combines the chemical and structural diversity of polymers with the programmability of DNA. By linking these orthogonal assembly languages, we have discovered new self-assembly rules, created DNA-minimal nanostructures, and demonstrated their utility through a range of applications. Developing this work further will open new avenues in the fields of DNA nanomaterials, nucleic acid therapeutics, as well as block copolymer self-assembly.

On-Site Portable Lithium Detection in Mining and Recycling Industries Based on a DNAzyme Fluorescent Sensor

The global demand for lithium has soared in recent years due to the wide use of lithium batteries. To meet this demand, we herein report developing novel on-site sample preparation methods for the extraction of Li+ from relevant materials, including brine water, spodumene rock, as well as lithium-ion battery electrodes, and a DNAzyme-based fluorescent sensor for sensitive and robust detection of Li+ in these samples down to 1.4 mM (10 ppm) using a portable fluorometer. The system can distinguish key threshold lithium levels that indicate economic value across several industries, including 200 ppm Li+ for brine mining, 6 % Li2O or SC6 for rock mining, and Li+-specific aging in LIBs. The methods developed and demonstrated in this work will allow highly selective, on-site, portable detection of lithium in both environmental samples to identify new lithium resources and in battery electrodes to guide recycling strategies in order to meet the global demand for lithium.

Colorimetric detection of furin based on enhanced catalytic activity of G-quadruplex/hemin DNAzyme

BACKGROUND

Rapid and sensitive colorimetric detection methods are crucial for diseases diagnosis, particularly those involving proteases like furin, which are implicated in various conditions, including cancer. Traditional detection methods for furin suffer from limitations in sensitivity and practicality for on-site detection, motivating the development of novel detection strategies. Therefore, developing a simple, enzyme-free, and rapid colorimetric analysis method with high sensitivity for furin detection is imperative.

RESULTS

Herein, we have proposed a colorimetric method in this work for the first time to detect furin, leveraging the assembly of G-quadruplex/hemin DNAzyme with enhanced catalytic activity. Specifically, a peptide-DNA conjugate (PDC) comprising a furin-recognition peptide and flanking DNA sequences for signal amplification is designed to facilitate the DNAzyme assembly. Upon furin treatment, PDC cleavage triggers a cyclic catalytic hairpin assembly reaction to form the complementary double-stranded structures by hairpin 1 (HP1) and hairpin 2 (HP2), bringing the G-quadruplex sequence in HP1 closer to hemin on HP2. Moreover, the resulting G-quadruplex/hemin DNAzymes exhibit robust peroxidase-like activity, enabling the catalysis of the colorimetric reaction of ABTS2- for furin detection. Our method demonstrates high sensitivity, rapid response, and compatibility with complex sample matrices, achieving a detection limit as low as 1.1 pM.

SIGNIFICANCE

The DNAzyme reported in this work exhibits robust catalytic activity, enabling high sensitivity and good efficiency for the detection. By eliminating the requirement for exogenous enzymes, our approach enables visual furin detection without expensive instrumentation and reagents, promising significant utility in biomedical and clinical diagnostic applications. Given the various design of peptide sequence and the programmability of DNA, it can be readily applied to analyzing other useful tumor biomarkers.

In-vitro Clinical Diagnostics using RNA-Cleaving DNAzymes

Over the last three decades, significant advancements have been made in the development of biosensors and bioassays that use RNA-cleaving DNAzymes (RCDs) as molecular recognition elements. While early examples of RCDs were primarily responsive to metal ions, the past decade has seen numerous RCDs reported for more clinically relevant targets such as bacteria, cancer cells, small metabolites, and protein biomarkers. Over the past 5 years several RCD-based biosensors have also been evaluated using either spiked biological matrixes or patient samples, including blood, serum, saliva, nasal mucus, sputum, urine, and faeces, which is a critical step toward regulatory approval and commercialization of such sensors. In this review, an overview of the methods used to generate RCDs and the properties of key RCDs that have been utilized for in vitro testing is first provided. Examples of RCD-based assays and sensors that have been used to test either spiked biological samples or patient samples are then presented, highlighting assay performance in different biological matrixes. A summary of current prospects and challenges for development of in vitro diagnostic tests incorporating RCDs and an overview of future directions of the field is also provided.

Engineered Electrochemiluminescence Biosensors for Monitoring Heavy Metal Ions: Current Status and Prospects

Metal ion contamination has serious impacts on environmental and biological health, so it is crucial to effectively monitor the levels of these metal ions. With the continuous progression of optoelectronic nanotechnology and biometrics, the emerging electrochemiluminescence (ECL) biosensing technology has not only proven its simplicity, but also showcased its utility and remarkable sensitivity in engineered monitoring of residual heavy metal contaminants. This comprehensive review begins by introducing the composition, advantages, and detection principles of ECL biosensors, and delving into the engineered aspects. Furthermore, it explores two signal amplification methods: biometric element-based strategies (e.g., HCR, RCA, EDC, and CRISPR/Cas) and nanomaterial (NM)-based amplification, including quantum dots, metal nanoclusters, carbon-based nanomaterials, and porous nanomaterials. Ultimately, this review envisions future research trends and engineered technological enhancements of ECL biosensors to meet the surging demand for metal ion monitoring.

Poly(3-amino-carbazole) derivatives containing 1,10-phenanthroline and 8-hydroxyquinoline ligands: Synthesis, properties and application as ion sensors

As we know, excessive metal ions can even damage human health. Herein, two novel kinds of fluorescent sensing materials Poly(3-amino-carbazole) derivatives containing 1,10-phenanthroline and 8-hydroxyquinoline were synthesized and further applied to fluorescence detection for ions. The results show that Ni²⁺, Cu²⁺, and Pd²⁺ have excellent quenching effects on the fluorescence of Poly[9-(1,10-phenanthroline-2-yl)-9H-carbazol-3-amine] (PPNC), the LOD for these ions reaches 5.2 nM, 12.7 nM, 33.5 nM respectively. In the process of ion response, there is no shift of UV absorption peak, combined with IR spectra and theoretical calculation simulation, the quenching is considered to be caused by the coordination between metal ions and the second amine (-NH-) or 1,10-phenanthroline ligand of PPNC, which leads to the charge transfer from ligands to metal ions. In addition, an acid test was done for PPNC to verify and detect the presence of secondary amine (-NH-), and the results show that PPNC has good acid sensing ability which also supports the secondary amine (-NH-) structure. Finally, the paper test was performed on PPNC, indicating that PPNC has the potential for visual application.

A triple amplification strategy using GR-5 DNAzyme as a signal medium for ultrasensitive detection of trace Pb2+ based on CRISPR/Cas12a empowered electrochemical biosensor

Lead ions (Pb²⁺) are a well-known toxic heavy metal that poses a significant threat to human health. Therefore, the development of a simple and ultrasensitive technique for detecting Pb²⁺ is essential. With their trans-cleavage properties, the newly discovered CRISPR-V effectors have become a potential high-precision biometric tool. In this regard, a CRISPR/Cas12a-based electrochemical biosensor (E-CRISPR) has been developed, which is combined with the GR-5 DNAzyme that can specifically recognize Pb²⁺. In this strategy, the GR-5 DNAzyme acts as a signal-mediated intermediary, which can convert Pb²⁺ into nucleic acid signals, thereby becoming single-stranded DNA that triggers strand displacement amplification (SDA) reaction. This is coupled with following activated CRISPR/Cas12a cleavage of the electrochemical signal probe, enabling cooperative signal amplification for ultrasensitive Pb²⁺ detection. The proposed method has a detection limit as low as 0.02 pM. Therefore, we have developed an E-CRISPR detection platform with GR-5 DNAzyme as a signal medium (called SM-E-CRISPR biosensor). This provides a method for the CRISPR system to specifically detect non-nucleic substances by converting the signal using a medium.

An efficient DNAzyme for the fluorescence detection of Vibrio cholerae

Vibrio cholerae (Vc) causes cholera disease. Vc contamination is widely found in water and aquatic products, and therefore is a serious food safety concern, especially for the seafood industry. In this paper, we attempted the rapid detection of V. cholerae. Nine rounds of in vitro selection using an unmodified DNA library were successfully performed to find specific DNAzymes of Vc. Their activity was evaluated based on a fluorescence assay and gel electrophoresis. Finally, a DNAzyme (named DVc1) with good activity and specificity with a detection limit of 7.2 × 103 CFU/mL of Vc was selected. A simple biosensor was constructed by immobilizing DVc1 and its substrate in shallow circular wells of a 96-well plate using pullulan polysaccharide and trehalose. When the crude extracellular mixture of Vc was added to the detection wells, the fluorescent signal was observed within 20 min. The sensor effectively detected Vc in aquatic products indicating its simplicity and efficiency. This sensitive DNAzyme sensor can be a rapid onsite Vc detection tool.

Development of a Fluorescent Biosensor Based on DNAzyme for Tracing the Release of Zinc in Maize Leaves

A fluorescent biosensor for real-time monitoring the release of Zn²⁺ in plants was constructed through immobilization of DNAzyme-containing hairpin DNA on nanofertilizer ZnO@Au nanoparticles (ZnO@Au NPs). A specially designed hairpin DNA containing both DNAzyme and its substrate sequence, which was also labeled with 5'-FAM and 3'-SH groups, was modified on ZnO@Au NPs through the Au-S bond. The fluorescent signal of FAM was initially quenched by AuNPs. When Zn²⁺ was released from ZnO@Au NPs, DNAzyme was activated and the substrate sequence in hairpin DNA was cleaved. The restored fluorescent signal in Tris-HCl buffer (pH 6.5) was correlated with the concentration of the released Zn²⁺. The performance of the biosensor was first demonstrated in the solution. The linear detection range was from 50 nM to 1.5 μM, with a detection limit of 30 nM. The biosensor system can penetrate into maize leaves with ZnO@Au NPs. With the release of Zn²⁺ in leaves, the restored fluorescence can be imaged by a confocal laser scanning microscope and used for monitoring the release and distribution of Zn²⁺. This work may provide a novel strategy for tracing and understanding the mechanism of nanofertilizers in organisms.

Visible light-driven i-motif-based DNAzymes

DNA foldings provide variant possibilities to develop DNAzymes with remarkable catalytic performance. In spite of fruitful reports on G-quadruplex DNAzymes, four-stranded cytosine-rich i-motifs have not been explored as the potential skeletons of DNAzymes. In this work, we developed a visible light-driven DNAzyme based on human telomeric i-motifs using a natural photosensitizer of hypericin (Hyp) as the cofactor and dissolved oxygen as the oxidant source. The i-motif folding in acidic solution caused the distal thymine overhangs at the 3' and 5' ends to approach each other to provide a favorable binding site for Hyp via an interaction of fully complementary hydrogen bonding. However, the i-motifs without the distal overhangs or with the inappropriate overhang length and the base identity exhibited no binding with Hyp. The binding event converted Hyp from the fully dark state to the emissive state under visible light illumination. Subsequently, the excited Hyp had an opportunity to transfer energy to dissolved oxygen. Resultantly, singlet oxygen (¹O₂) was generated to initiate the substrate oxidation. The catalytic performance of the DNAzyme can be improved using a long-lived mediator. Our developed i-motif-based DNAzyme can be driven by almost the whole range of visible lights, suggesting broad applications in the photocatalytic fields, for example, as an alternative strategy in developing biodevices.

DNA-based enzymatic systems and their applications

DNA strands with unique secondary structures can catalyze various chemical reactions and mimic natural enzymes with the assistance of cofactors, which have attracted much research attention. At the same time, the emerging DNA nanotechnology provides an efficient platform to organize functional components of the enzymatic systems and regulate their catalytic performances. In this review, we summarize the recent progress of DNA-based enzymatic systems. First, DNAzymes (Dzs) are introduced, and their versatile utilities are summarized. Then, G-quadruplex/hemin (G4/hemin) Dzs with unique oxidase/peroxidase-mimicking activities and representative examples where these Dzs served as biosensors are explicitly elaborated. Next, the DNA-based enzymatic cascade systems fabricated by the structural DNA nanotechnology are depicted. In addition, the applications of catalytic DNA nanostructures in biosensing and biomedicine are included. At last, the challenges and the perspectives of the DNA-based enzymatic systems for practical applications are also discussed.

Recent Advances on DNAzyme-Based Sensing

DNAzymes are functional nucleic acid with catalytic activity. Owing to the high sensitivity, excellent programmability, and flexible obtainment through in vitro selection, RNA-cleaving DNAzymes have attracted increasing interest in developing DNAzyme-based sensors. In this review, we summarize the recent advances on DNAzyme-based sensing applications. We initially conclude two general strategies to expand the library of DNAzymes, in vitro selection to discover new DNAzymes towards different targets of interest and chemical modifications to endue the existing DNAzymes with new function or properties. We then discuss the recent applications of DNAzyme-based sensors for the detection of a variety of important biomolecules both in vitro and in vivo . Finally, perspectives on the challenges and future directions in the development of DNAzyme-based sensors are provided.

Development of the DNA-based biosensors for high performance in detection of molecular biomarkers: More rapid, sensitive, and universal

The molecular biomarkers are molecules that are closely related to specific physiological states. Numerous molecular biomarkers have been identified as targets for disease diagnosis and biological research. To date, developing highly efficient probes for the precise detection of biomarkers has become an attractive research field which is very important for biological and biochemical studies. During the past decades, not only the small chemical probe molecules but also the biomacromolecules such as enzymes, antibodies, and nucleic acids have been introduced to construct of biosensor platform to achieve the detection of biomarkers in a highly specific and highly efficient way. Nevertheless, improving the performance of the biosensors, especially in clinical applications, is still in urgent demand in this field. A noteworthy example is the Corona Virus Disease 2019 (COVID-19) that breaks out globally in a short time in 2020. The COVID-19 was caused by the virus called SARS-CoV-2. Early diagnosis is very important to block the infection of the virus. Therefore, during these months scientists have developed dozens of methods to achieve rapid and sensitive detection of the virus. Nowadays some of these new methods have been applied for producing the commercial detection kit and help people against the disease worldwide. DNA-based biosensors are useful tools that have been widely applied in the detection of molecular biomarkers. The good stability, high specificity, and excellent biocompatibility make the DNA-based biosensors versatile in application both in vitro and in vivo. In this paper, we will review the major methods that emerged in recent years on the design of DNA-based biosensors and their applications. Moreover, we will also briefly discuss the possible future direction of DNA-based biosensors design. We believe this is helpful for people interested in not only the biosensor field but also in the field of analytical chemistry, DNA nanotechnology, biology, and disease diagnosis.

DNAzyme-Amplified Electrochemical Biosensor Coupled with pH Meter for Ca2+ Determination at Variable pH Environments

For more than 50% of multiparous cows, it is difficult to adapt to the sudden increase in calcium demand for milk production, which is highly likely to cause hypocalcemia. An electrochemical biosensor is a portable and efficient method to sense Ca²⁺ concentrations, but biomaterial is easily affected by the pH of the analyte solution. Here, an electrochemical biosensor was fabricated using a glassy carbon electrode (GCE) and single-walled carbon nanotube (SWNT), which amplified the impedance signal by changing the structure and length of the DNAzyme. Aiming at the interference of the pH, the electrochemical biosensor (GCE/SWNT/DNAzyme) was coupled with a pH meter to form an electrochemical device. It was used to collect data at different Ca²⁺ concentrations and pH values, and then was processed using different mathematical models, of which GPR showed higher detecting accuracy. After optimizing the detecting parameters, the electrochemical device could determine the Ca²⁺ concentration ranging from 5 μM to 25 mM, with a detection limit of 4.2 μM at pH values ranging from 4.0 to 7.5. Finally, the electrochemical device was used to determine the Ca²⁺ concentrations in different blood and milk samples, which can overcome the influence of the pH.

Small DNAs that Bind Nickel(II) Specifically and Tightly

Metal recognition by nucleic acids provides an intriguing route for biosensing of metal. Toward this goal, a key prerequisite is the acquisition of nucleic acids that can selectively respond to specific metals. Herein, we report for the first time the discovery of two small DNAs that can specifically bind Ni²⁺ and discriminate against similar ions, particularly, Co²⁺. Their minimal effective constructs are 60-70 nucleotides (nt) in length with Ni²⁺ binding even at harsh denaturing conditions of 8 M urea and 50 mM EDTA. Using isothermal titration calorimetry (ITC), we estimated the dissociation constant (K_D) of a representative DNA to be 24.0 ± 4.5 μM, with a 9:1 stoichiometry of Ni²⁺ bound to DNA. As being engineered into nanosized particles, these DNAs can act like nanosponges to specifically adsorb Ni²⁺ from artificial wastewater, demonstrating their potential as a novel molecular tool for high-quality nickel enrichment and detection.

Rapid heavy metal sensing platform: A case of triple signal amplification strategy for the sensitive detection of serum copper

Heavy metals are considered as hazardous substances to human because of their toxicity, persistence and bioaccumulation, and the level in serum is an important factor to evaluate the caused health risk, which depends on efficient and sensitive analytical methods. Here, a triple signal-amplified electrochemical sensing platform based on metal-dependent DNAzymes was fabricated for sensitive determination of heavy metals in serum (copper as a model target). Under the optimized conditions, the proposed method showed good sensitivity (limit of detection, 0.33 fM for Cu²⁺) with excellent selectivity and stability, which is ascribed to: (i) tetrahedral DNA nanostructures (TDNs) that was used as a promising scaffold to adjust the selective transformation between heterogeneous and homogeneous reactions, preventing the nonspecific binding of electrodes surface and DNA probes; (ii) the magnetic beads (MBs) used which led to signal amplification and decreased background owing to its excellent properties of extracting equivalent targets from the complex samples; (iii) two signal amplification strategy of catalytic hairpin assembly (CHA) and hybridization chain reaction (HCR). In addition, the proposed sensing platform displayed satisfactory accuracy through the validation with inductively coupled plasma-mass spectrometry (ICP-MS) and a spike-recovery analysis (recoveries, 87.92-111.61%; RSD, 4.89-8.85%), indicating the great potential for rapid and sensitive detection of Cu²⁺ or other metal ions.

Biosensing with DNAzymes

This article provides a comprehensive review of biosensing with DNAzymes, providing an overview of different sensing applications while highlighting major progress and seminal contributions to the field of portable biosensor devices and point-of-care diagnostics. Specifically, the field of functional nucleic acids is introduced, with a specific focus on DNAzymes. The incorporation of DNAzymes into bioassays is then described, followed by a detailed overview of recent advances in the development of in vivo sensing platforms and portable sensors incorporating DNAzymes for molecular recognition. Finally, a critical perspective on the field, and a summary of where DNAzyme-based devices may make the biggest impact are provided.

High Catalytic Activity of Fluorophore-Labeled Y-Shaped DNAzyme/3D MOF-MoS2NBs as a Versatile Biosensing Platform for the Simultaneous Detection of Hg2+, Ni2+, and Ag+ Ions

In this study, we have designed a three-fluorophore-labeled Y-shaped DNAzyme with a high catalytic cleavage activity and a three-dimensional (3D) MOF-MoS₂NB (metal-organic framework fused with molybdenum disulfide nanobox), which was synthesized as an efficient quencher of the fluorescent biosensor. The synthesized porous 3D MOF-MoS₂NBs and Y-shaped DNAzyme exhibited a good analytical response toward the simultaneous multiple detections of Hg²⁺, Ni²⁺, and Ag⁺ ions over the other coexisting metal ions. More specifically, the three kinds of enzyme aptamer and substrate aptamer (SA) were hybridized and annealed to form the Y-shaped DNAzyme structure and labeled with three different fluorophores such as FAM, TAMRA, and ROX over the 3'-end of SA. When the targets were induced, the DNAzyme was triggered to cleave the fluorophore-labeled SAs. Then, the cleaved SAs (FAM-SA, TAMRA-SA, and ROX-SA) were adsorbed on the 3D MOF-MoS₂NB surface to quench the fluorescence signal due to a noncovalent interaction (van der Waals and π-π stacking interaction), which transmuted the fluorescence on-state to off-state. As a result, the fluorescence assay confiscated the high selectivity and sensitivity for the target analytes of Hg²⁺, Ni²⁺, and Ag⁺ ions achieved for the detection limits of 0.11 nM, 7.8 μM, and 0.25 nM, respectively. Accordingly, the sensitivity of the developed sensor was explored with a better lower detection limit than the previously reported biosensors. The utility of the designed Y-shaped DNAzyme may find a broad field of application in real water sample analysis with interfering contaminants.

Development of DNA Biosensors Based on DNAzymes and Nucleases

DNA biosensors play important roles in environmental, medical, industrial and agricultural analysis. Many DNA biosensors have been designed based on the enzyme catalytic reaction. Because of the importance of enzymes in biosensors, we present a review on this topic. In this review, the enzymes were divided into DNAzymes and nucleases according to their chemical nature. Firstly, we introduced the DNAzymes with different function inducing cleavage, metalation, peroxidase, ligation and allosterism. In this section, the G-quadruplex DNAzyme, as a hot topic in recent years, was described in detail. Then, the nucleases-assisted signal amplification method was also reviewed in three categories including exonucleases, endonucleases and other nucleases according to the digestion sites in DNA substrates. In exonucleases section, the Exo I and Exo III were selected as examples. Then, the DNase I, BamH I, nicking endonuclease, S1 nuclease, the duplex specific nuclease (DSN) and RNases were chosen to illustrate the application of endonucleases. In other nucleases section, DNA polymerases and DNA ligases were detailed. Last, the challenges and future perspectives in the field were discussed.

UV-fluorescence probe for detection Ni2+ with colorimetric/spectral dual-mode analysis method and its practical application

Fluorescence probe combines with fluorescence imaging technology has become the most powerful analytical method with their great advantages of high sensitivity and selectivity and real-time monitoring. Ni²⁺ is widely distributed in food, environment and living animals, thereof, it is of great significance for detection Ni²⁺ with high selectivity. Herein, a simple strategy is proposed to design and synthesiz a small molecule fluorescent probe Y1 by using "one-pot" method. The spectroscopic behaviors including UV-Vis absorption and fluorescence emission spectrum have been used to verify the feasibility of probe towards Ni²⁺ in water/EtOH (v/v = 2:8) mixtures under neutral condition. As expected, Y1 offers high selectivity and sensitivity for detection Ni²⁺ in aqueous solution with a good linear relationship and low detection limit within Ni²⁺ concentration variation from 0 to 13 μM (DOL = 0.0038 μM, R² = 0.9983). It is remarkable that Y1 can be applied for real-time visualization Ni²⁺ change in sprouted potato and zebrafish with great photo-stability, highlighting that the practicability and feasibility of Y1 to detect and monitor Ni²⁺ in the field of food industry and biomedical field.

Wavelength-Selective Activation of Photocaged DNAzymes for Metal Ion Sensing in Live Cells

RNA-cleaving DNAzymes are widely applied as sensors for detecting metal ions in environmental samples owing to their high sensitivity and selectivity, but their use for sensing biological metal ions in live cells is challenging because constitutive sensors fail to report the spatiotemporal heterogeneity of biological processes. Photocaged DNAzymes can be activated by light for sensing purposes that need spatial and temporal resolution. Studying complex biological processes requires logic photocontrol, but unfortunately all the literature-reported photocaged DNAzymes working in live cells cannot be selectively controlled by light irradiation at different wavelengths. In this work, we developed photocaged DNAzymes responsive to UV and visible light using a general synthetic method based on phosphorothioate chemistry. Taking the Zn²⁺-dependent DNAzyme sensor as a model, we achieved wavelength-selective activation of photocaged DNAzymes in live human cells by UV and visible light, laying the groundwork for the logic activation of DNAzyme-based sensors in biological systems.

Construction of DNA Biosensors for Mercury (II) Ion Detection Based on Enzyme-Driven Signal Amplification Strategy

Mercury ion (Hg²⁺) is a well-known toxic heavy metal ion. It is harmful for human health even at low concentrations in the environment. Therefore, it is very important to measure the level of Hg²⁺. Many methods, reviewed in several papers, have been established on DNA biosensors for detecting Hg²⁺. However, few reviews on the strategy of enzyme-driven signal amplification have been reported. In this paper, we reviewed this topic by dividing the enzymes into nucleases and DNAzymes according to their chemical nature. Initially, we introduce the nucleases including Exo III, Exo I, Nickase, DSN, and DNase I. In this section, the Exo III-driven signal amplification strategy was described in detail. Because Hg²⁺ can help ssDNA fold into dsDNA by T-Hg-T, and the substrate of Exo III is dsDNA, Exo III can be used to design Hg²⁺ biosensor very flexibly. Then, the DNAzyme-assisted signal amplification strategies were reviewed in three categories, including UO₂²⁺-specific DNAzymes, Cu²⁺-specific DNAzymes and Mg²⁺-specific DNAzymes. In this section, the Mg²⁺-specific DNAzyme was introduced in detail, because this DNAzyme has highly catalytic activity, and Mg²⁺ is very common ion which is not harmful to the environment. Finally, the challenges and future perspectives were discussed.

Recent Developments in Fluorescent Materials for Heavy Metal Ions Analysis From the Perspective of Forensic Chemistry

Forensic chemistry deals with the analysis of various types of physical evidences related to crime, corresponding to the detection of target substances or elements in complex matrices. There is a vital need for highly selective, rapid, and sensitive biosensing technologies in heavy metal ions analysis especially those from living persons, autopsy, food, water, soil, and other identified substances at very preliminary stages. Fluorescent materials-based method for heavy metal ions detection is one of the most important analytical methods, resulting in the ability to measure analytes in complex matrices with unsurpassed selectivity and sensitivity. In this mini review, different fluorescent materials-based analytical methods aiming at several heavy metal ions detection are exclusively reviewed through a comprehensive literature survey. In addition, current challenges to achieve integrated evidence analysis process are briefly discussed to provide an outlook for heavy metal ions detection based on fluorescent analytical methods in the forensic chemistry field.

Zn2+ -Dependent DNAzymes: From Solution Chemistry to Analytical, Materials and Therapeutic Applications

Since 1994, deoxyribozymes or DNAzymes have been in vitro selected to catalyze various types of reactions. Metal ions play a critical role in DNAzyme catalysis, and Zn²⁺ is a very important one among them. Zn²⁺ has good biocompatibility and can be used for intracellular applications. Chemically, Zn²⁺ is a Lewis acid and it can bind to both the phosphate backbone and the nucleobases of DNA. Zn²⁺ undergoes hydrolysis even at neutral pH, and the partially hydrolyzed polynuclear complexes can affect the interactions with DNA. These features have made Zn²⁺ a unique cofactor for DNAzyme reactions. This review summarizes Zn²⁺ -dependent DNAzymes with an emphasis on RNA-/DNA-cleaving reactions. A key feature is the sharp Zn²⁺ concentration and pH-dependent activity for many of the DNAzymes. The applications of these DNAzymes as biosensors for Zn²⁺ , as therapeutic agents to cleave intracellular RNA, and as chemical biology tools to manipulate DNA are discussed. Future studies can focus on the selection of new DNAzymes with improved performance and detailed biochemical characterizations to understand the role of Zn²⁺ , which can facilitate practical applications of Zn²⁺ -dependent DNAzymes.

In vitro Selection of Chemically Modified DNAzymes

DNAzymes are in vitro selected DNA oligonucleotides with catalytic activities. RNA cleavage is one of the most extensively studied DNAzyme reactions. To expand the chemical functionality of DNA, various chemical modifications have been made during and after selection. In this review, we summarize examples of RNA-cleaving DNAzymes and focus on those modifications introduced during in vitro selection. By incorporating various modified nucleotides via polymerase chain reaction (PCR) or primer extension, a few DNAzymes were obtained that can be specifically activated by metal ions such as Zn2+ and Hg2+. In addition, some modifications were introduced to mimic RNase A that can cleave RNA substrates in the absence of divalent metal ions. In addition, single modifications at the fixed regions of DNA libraries, especially at the cleavage junctions, have been tested, and examples of DNAzymes with phosphorothioate and histidine-glycine modified tertiary amine were successfully obtained specific for Cu2+, Cd2+, Zn2+, and Ni2+. Labeling fluorophore/quencher pair right next to the cleavage junction was also used to obtain signaling DNAzymes for detecting various metal ions and cells. Furthermore, we reviewed work on the cleavage of 2'-5' linked RNA and L-RNA substrates. Finally, applications of these modified DNAzymes as biosensors, RNases, and biochemical probes are briefly described with a few future research opportunities outlined at the end.

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.