In Vitro Selection of Chromium-Dependent DNAzymes for Sensing Chromium(III) and Chromium(VI)

Fingerprinting DNAzyme Cross-Reactivity for Pattern-Based Detection of Heavy Metals

Heavy metal contamination in food and water is a major public health concern because heavy metals are toxic in minute amounts. DNAzyme sensors are emerging as a promising tool for rapid onsite detection of heavy metals, which can aid in minimizing exposure. However, DNAzyme activity toward its target metal is not absolute and has cross-reactivity with similar metals, which is a major challenge in the wide-scale application of DNAzyme sensors for environmental monitoring. To address this, we constructed a four DNAzyme array (17E, GR-5, EtNA, and NaA43) and used a pattern-based readout to improve sensor accuracy. We measured cross-reactivity between three metal cofactors (Pb2+, Ca2+, and Na+) and common interferents (Mg2+, Zn2+, Mn2+, UO22+, Li+, K+, and Ag+) and then used t-SNE analysis to identify and quantify the metal ion. We further showed that this method can be used for distinguishing mixtures of metals and detecting Pb2+ in environmental soil samples at micromolar concentrations.

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.

Tris buffer-accelerated ligand exchange rate for instant fluorescence detection of trivalent chromium ion

Functional nucleic acids (FNAs) have attracted a lot of attention for the rapid detection of metal ions. Cr3+ is one of the major heavy metal ions in natural waters. Due to the slow ligand exchange rate of Cr3+, the FNA-based Cr3+ sensors require long assay times, limiting the on-site applications. In this study, we report that the good's buffers containing amino and polyhydroxy groups greatly increase the ligand exchange rate of Cr3+. Using EDTA as a model coordinate ligand, the Tris buffer (100 mM, pH 7.0) showed the best acceleration effect among the eight buffers. It improved the rate constant ∼20-fold, shorten the half-time 19-fold, and lowered the activation energy ∼70% at 40 °C. The Tris buffer was then applied for sensor based on the Cr3+-binding induced fluorescence quenching of fluorescein (FAM)-labeled and single-stranded DNA (ssDNA), which shortened the assay time from 1 h to 1 min. The Tris buffer also ∼100% enhanced the fluorescence intensity of FAM, achieving the 11.4-fold lower limit of detection (LOD = 6.97 nM, S/N = 3). By the combination use of the Tris buffer and ascorbic acid, the strong interference from Cu2+, Pb2+, and Fe3+ suffered in many previous reported Cr3+ sensors was avoided. The practical application of the sensor for the detection of Cr3+ spiked in the real water samples were demonstrated with high recovery percentages. The Tris buffer could be applied for other metal ions with slow ligand exchange rate (such as V2+, Co3+ and Fe2+) to solve diverse issues such as long assay time and low synthesis yield of metal complexes, without the need of heating treatment.

Hybrid Nanoparticle/DNAzyme Electrochemical Biosensor for the Detection of Divalent Heavy Metal Ions and Cr3

A hybrid noble nanoparticle/DNAzyme electrochemical biosensor is proposed for the detection of Pb2+, Cd2+, and Cr3+. The sensor takes advantage of a well-studied material that is known for its selective interaction with heavy metal ions (i.e., DNAzymes), which is combined with metallic nanoparticles. The double-helix structure of DNAzymes is known to dissociate into smaller fragments in the presence of specific heavy metal ions; this results in a measurable change in device resistance due to the collapse of conductive inter-nanoparticle DNAzyme bridging. The paper discusses the effect of DNAzyme anchoring groups (i.e., thiol and amino functionalization groups) on device performance and reports on the successful detection of all three target ions in concentrations that are well below their maximum permitted levels in tap water. While the use of DNAzymes for the detection of lead in particular and, to some extent, cadmium has been studied extensively, this is one of the few reports on the successful detection of chromium (III) via a sensor incorporating DNAzymes. The sensor showed great potential for its future integration in autonomous and remote sensing systems due to its low power characteristics, simple and cost-effective fabrication, and easy automation and measurement.

Ratiometric Detection of Zn2+ Using DNAzyme-Based Bioluminescence Resonance Energy Transfer Sensors

While fluorescent sensors have been developed for monitoring metal ions in health and diseases, they are limited by the requirement of an excitation light source that can lead to photobleaching and a high autofluorescence background. To address these issues, bioluminescence resonance energy transfer (BRET)-based protein or small molecule sensors have been developed; however, most of them are not highly selective nor generalizable to different metal ions. Taking advantage of the high selectivity and generalizability of DNAzymes, we report herein DNAzyme-based ratiometric sensors for Zn2+ based on BRET. The 8-17 DNAzyme was labeled with luciferase and Cy3. The proximity between luciferase and Cy3 permiQed BRET when coelenterazine, the substrate for luciferase, was introduced. Adding samples containing Zn2+ resulted in a cleavage of the substrate strand, causing dehybridization of the DNAzyme construct, thus increasing the distance between Cy3 and luciferase and changing the BRET signals. Using these sensors, we detected Zn2+ in serum samples and achieved Zn2+ detection with a smartphone camera. Moreover, since the BRET pair is not the component that determines the selectivity of the sensors, this sensing platform has the potential to be adapted for the detection of other metal ions with other metal-dependent DNAzymes.

A Highly Selective Mn(II)-Specific DNAzyme and Its Application in Intracellular Sensing

Manganese is an essential trace element in the human body that acts as a cofactor in many enzymes and metabolisms. It is important to develop methods to detect Mn²⁺ in living cells. While fluorescent sensors have been very effective in detecting other metal ions, Mn²⁺-specific fluorescent sensors are rarely reported due to nonspecific fluorescence quenching by the paramagnetism of Mn²⁺ and poor selectivity against other metal ions such as Ca²⁺ and Mg²⁺. To address these issues, we herein report in vitro selection of an RNA-cleaving DNAzyme with exceptionally high selectivity for Mn²⁺. Through converting it into a fluorescent sensor using a catalytic beacon approach, Mn²⁺ sensing in immune cells and tumor cells has been achieved. The sensor is also used to monitor degradation of manganese-based nanomaterials such as MnOx in tumor cells. Therefore, this work provides an excellent tool to detect Mn²⁺ in biological systems and monitor the Mn²⁺-involved immune response and antitumor therapy.

Simultaneous Fe2+/Fe3+ imaging shows Fe3+ over Fe2+ enrichment in Alzheimer's disease mouse brain

Visualizing redox-active metal ions, such as Fe²⁺ and Fe³⁺ ions, are essential for understanding their roles in biological processes and human diseases. Despite the development of imaging probes and techniques, imaging both Fe²⁺ and Fe³⁺ simultaneously in living cells with high selectivity and sensitivity has not been reported. Here, we selected and developed DNAzyme-based fluorescent turn-on sensors that are selective for either Fe²⁺ or Fe³⁺, revealing a decreased Fe³⁺/Fe²⁺ ratio during ferroptosis and an increased Fe³⁺/Fe²⁺ ratio in Alzheimer's disease mouse brain. The elevated Fe³⁺/Fe²⁺ ratio was mainly observed in amyloid plaque regions, suggesting a correlation between amyloid plaques and the accumulation of Fe³⁺ and/or conversion of Fe²⁺ to Fe³⁺. Our sensors can provide deep insights into the biological roles of labile iron redox cycling.

Ecological effects, remediation, distribution, and sensing techniques of chromium

Chromium is detected in most ecosystems due to the increased anthropogenic activities in addition to that developed from natural pollution. Chromium contamination in the food chain results due to its persistent and non-degradable nature. The release of chromium in the ecosystem accretes and thereafter impacts different life forms, including humans, aquatic and terrestrial organisms. Leaching of chromium into the ground and surface water triggers several health ailments, such as dermatitis, eczematous skin, allergic reactions, mucous and skin membrane ulcerations, allergic asthmatic reactions, bronchial carcinoma and gastroenteritis. Physiological and biological treatments for the removal of chromium have been discussed in depth in the present communication. Adsorption and biological treatment methods are proven to be alternatives to chemical removal techniques in terms of cost-effectiveness and low sludge formation. Chromium sensing is an alternative approach for regular monitoring of chromium in different water bodies. This review intended to explore different classes of sensors for chromium monitoring. However, the spectrochemical methods are more sensitive in chromium ions sensing than electrochemical methods. Future study should focus on miniaturization for portability and on-site measurements without requiring a large instrument provides a good aspect for future research.

Overcoming Major Barriers to Developing Successful Sensors for Practical Applications Using Functional Nucleic Acids

For many years, numerous efforts have been focused on the development of sensitive, selective, and practical sensors for environmental monitoring, food safety, and medical diagnostic applications. However, the transition from innovative research to commercial success is relatively sparse. In this review, we identify four scientific barriers and one technical barrier to developing successful sensors for practical applications, including the lack of general methods to (a) generate receptors for a wide range of targets, (b) improve sensor selectivity to overcome interferences, (c) transduce the selective binding to different optical, electrochemical, and other signals, and (d) tune dynamic range to match thresholds of detection required for different targets; and the costly development of a new device. We then summarize solutions to overcome these barriers using sensors based on functional nucleic acids that include DNAzymes, aptamers, and aptazymes and how these sensors are coupled to widely available measurement devices to expand their capabilities and lower the barrier for their practical applications in the field and point-of-care settings.

Electrochemiluminescent sensor based on an aggregation-induced emission probe for bioanalytical detection

In recent years, with the rapid development of electrochemiluminescence (ECL) sensors, more luminophores have been designed to achieve high-throughput and reliable analysis. Impressively, after the proposed fantastic concept of "aggregation-induced electrochemiluminescence (AIECL)" by Cola, the application of AIECL emitters provides more abundant choices for the further improvement of ECL sensors. In this review, we briefly report the phenomenon, principle and representative applications of aggregation-induced emission (AIE) and AIECL emitters. Moreover, it is noteworthy that the cases of AIECL sensors for bioanalytical detection are summarized in detail, from 2017 to now. Finally, inspired by the applications of AIECL emitters, relevant prospects and challenges for AIECL sensors are proposed, which is of great significance for exploring more advanced bioanalytical detection technology.

Molecularly imprinted polymers via reversible addition-fragmentation chain-transfer synthesis in sensing and environmental applications

Molecularly imprinted polymers (MIP) have shown their potential as artificial and selective receptors for environmental monitoring. These materials can be tailor-made to achieve a specific binding event with a template through a chosen mechanism. They are capable of emulating the recognition capacity of biological receptors with superior stability and versatility of integration in sensing platforms. Commonly, these polymers are produced by traditional free radical bulk polymerization (FRP) which may not be the most suitable for enhancing the intended properties due to the poor imprinting performance. To improve the imprinting technique and the polymer capabilities, controlled/living radical polymerization (CRP) has been used to overcome the main drawbacks of FRP. Combining CRP techniques such as RAFT (reversible addition-fragmentation chain transfer) with MIP has achieved higher selectivity, sensitivity, and sorption capacity of these polymers when implemented as the transductor element in sensors. The present work focuses on RAFT-MIP design and synthesis strategies to enhance the binding affinities and their implementation in environmental contaminant sensing applications.

Recent Advances on Functional Nucleic-Acid Biosensors

In the past few decades, biosensors have been gradually developed for the rapid detection and monitoring of human diseases. Recently, functional nucleic-acid (FNA) biosensors have attracted the attention of scholars due to a series of advantages such as high stability and strong specificity, as well as the significant progress they have made in terms of biomedical applications. However, there are few reports that systematically and comprehensively summarize its working principles, classification and application. In this review, we primarily introduce functional modes of biosensors that combine functional nucleic acids with different signal output modes. In addition, the mechanisms of action of several media of the FNA biosensor are introduced. Finally, the practical application and existing problems of FNA sensors are discussed, and the future development directions and application prospects of functional nucleic acid sensors are prospected.

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.

Nucleic Acid Tests for Clinical Translation

Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are natural biopolymers composed of nucleotides that store, transmit, and express genetic information. Overexpressed or underexpressed as well as mutated nucleic acids have been implicated in many diseases. Therefore, nucleic acid tests (NATs) are extremely important. Inspired by intracellular DNA replication and RNA transcription, in vitro NATs have been extensively developed to improve the detection specificity, sensitivity, and simplicity. The principles of NATs can be in general classified into three categories: nucleic acid hybridization, thermal-cycle or isothermal amplification, and signal amplification. Driven by pressing needs in clinical diagnosis and prevention of infectious diseases, NATs have evolved to be a rapidly advancing field. During the past ten years, an explosive increase of research interest in both basic research and clinical translation has been witnessed. In this review, we aim to provide comprehensive coverage of the progress to analyze nucleic acids, use nucleic acids as recognition probes, construct detection devices based on nucleic acids, and utilize nucleic acids in clinical diagnosis and other important fields. We also discuss the new frontiers in the field and the challenges to be addressed.

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.

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.

One-Step Synthesis of Water-Soluble CdS Quantum Dots for Silver-Ion Detection

To realize fast synthesis of cadmium sulfide (CdS) quantum dots with a low-toxic material, a one-step synthesis method is investigated and conducted. Potato extract is used as a stabilizer and modifier, by which aqueous CdS quantum dots can be prepared at a lower temperature with a shorter time. Through systematic characterization and analysis, a green and fast synthesis mechanism is demonstrated in detail. And the nanoscale CdS quantum dots are uniform in size and dispersity. With low cost and high sensitivity, the prepared CdS quantum dots show promising application in silver-ion detection. This method shows great significance for an environmentally friendly and facile synthesis of CdS quantum dots.

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.

Allosteric Regulation of DNAzyme Activities through Intrastrand Transformation Induced by Cu(II)-Mediated Artificial Base Pairing

Allosteric regulation is gaining increasing attention as a basis for the production of stimuli-responsive materials in many research areas including DNA nanotechnology. We expected that metal-mediated artificial base pairs, consisting of ligand-type nucleotides and a bridging metal ion, could serve as allosteric units that regulate the function of DNA molecules. In this study, we established a rational design strategy for developing Cu^II-responsive allosteric DNAzymes by incorporating artificial hydroxypyridone ligand-type nucleotides (H) that form a Cu^II-mediated base pair (H-Cu^II-H). We devised a new enzymatic method using a standard DNA polymerase and a ligase to prepare DNA strands containing H nucleotides. Previously reported DNAzymes were modified by introducing a H-H pair into the stem region, and the stem-loop sequences were altered so that the structure becomes catalytically inactive in the absence of Cu^II ions. The formation of a H-Cu^II-H base pair triggers intrastrand transformation from the inactive to the active structure, enabling allosteric regulation of the DNAzyme activity in response to Cu^II ions. The activity of the H-modified DNAzyme was reversibly switched by the addition and removal of Cu^II ions under isothermal conditions. Similarly, by incorporating a H-Cu^II-H pair into an in vitro-selected Ag^I-dependent DNAzyme, we have developed a DNAzyme that exhibits an AND logic-gate response to Cu^II and Ag^I ions. The rational design strategy and the easy enzymatic synthetic method presented here provide a versatile way to develop a variety of metal-responsive allosteric DNA materials, including molecular machines and logic circuits, based on metal-mediated artificial base pairing.

Light-Emitting Multifunctional Maleic Acid-co-2-(N-(hydroxymethyl)acrylamido)succinic Acid-co-N-(hydroxymethyl)acrylamide for Fe(III) Sensing, Removal, and Cell Imaging

The intrinsically fluorescent highly hydrophilic multifunctional aliphatic terpolymer, maleic acid (MA)-co-2-(N-(hydroxymethyl)acrylamido)succinic acid (NHASA)-co-N-(hydroxymethyl)acrylamide (NHMA), that is, 1, was designed and synthesized via C-C/N-C-coupled in situ allocation of a fluorophore monomer, that is, NHASA, composed of amido and carboxylic acid functionalities in the polymerization of two nonemissive MA and NHMA. The scalable and reusable intrinsically fluorescent biocompatible 1 was suitable for sensing and high-performance adsorptive exclusion of Fe(III), along with the imaging of Madin-Darby canine kidney cells. The structure of 1, in situ fluorophore monomer, aggregation-induced enhanced emission, cell-imaging ability, and superadsorption mechanism were studied via microstructural analyses using 1H/13C NMR, X-ray photoelectron spectroscopy, Fourier transform infrared spectroscopy, atomic absorption spectroscopy, ultraviolet-visible spectroscopy, thermogravimetric analysis, dynamic light scattering, high-resolution transmission electron microscopy, solid-state fluorescence, fluorescence lifetime, and fluorescence imaging, along with measuring kinetics, isotherms, and thermodynamic parameters. The location, electronic structures, and geometries of the fluorophore and absorption and emission properties of 1 were investigated using density functional theory and natural transition orbital analyses. The limit of detection and the maximum adsorption capacity were 2.45 × 10-7 M and 542.81 mg g-1, respectively.

DNAzyme–gold nanoparticle-based probes for biosensing and bioimaging

The design and applications of DNAzyme–gold nanoparticle-based probes in biosensing and bioimaging are summarized here.

DNAzymes as Activity-Based Sensors for Metal Ions: Recent Applications, Demonstrated Advantages, Current Challenges, and Future Directions

Metal ions can be beneficial or toxic depending on their identity, oxidation state, and concentration. Therefore, the ability to detect and quantify different types of metal ions using portable sensors or in situ imaging agents is important for better environmental monitoring, in vitro medical diagnostics, and imaging of biological systems. While numerous metal ions in different oxidation states are present in the environment and biological systems, only a limited number of them can be detected effectively using current methods. In this Account, we summarize research results from our group that overcome this limitation by the development of a novel class of activity-based sensors based on metal-dependent DNAzymes, which are DNA molecules with enzymatic activity. First, we have developed an in vitro selection method to obtain DNAzymes from a large DNA library of up to 1015 sequences that can carry out cleavage of an oligonucleotide substrate only in the presence of a specific metal ion with high selectivity. Negative selection steps can further be used to improve the selectivity against potentially competing targets by removing sequences that recognize the competing metal ions. Second, we have developed a patented catalytic beacon method to transform the metal-dependent DNAzyme cleavage reaction into a turn-on fluorescent signal by attaching a fluorophore and quenchers to the DNAzyme complex. Because of the difference in the melting temperatures of DNA hybridization before and after metal-ion-dependent cleavage of the DNAzyme substrate, the fluorophore on the DNA cleavage product can be released from its quenchers to create a turn-on fluorescent signal. Because DNAzymes are easy to conjugate with other signaling moieties, such as gold nanoparticles, lanthanide-doped upconversion nanoparticles, electrochemical agents, and gadolinium complexes, these DNAzymes can also readily be converted into colorimetric sensors, upconversion luminescence sensors, electrochemical sensors, or magnetic resonance contrast agents. In addition to describing recent progress in developing and applying these metal ion sensors for environmental monitoring, point-of-care diagnostics, cellular imaging, and in vivo imaging in zebrafish, we summarize major advantages of this class of activity-based sensors. In addition to advantages common to most activity-based sensors, such as enzymatic turnovers that allow for signal amplification and the use of initial rates instead of absolute signals for quantification to avoid interferences from sample matrices, the DNAzyme-based sensors allow for in vitro selection to expand the method to almost any metal ion under a variety of conditions, negative selection to improve the selectivity against competing targets, and reselection of DNAzymes and combination of active and inactive variants to fine-tune the dynamic range of detection. The use of melting temperature differences to separate target binding from signaling moieties in the catalytic beacon method allows the use of different fluorophores and nanomaterials to extend the versatility and modularity of this sensing platform. Furthermore, sensing and imaging artifacts can be minimized by using an inactive mutant DNAzyme as a negative control, while spatiotemporal control of sensing/imaging can be achieved using optical, photothermal, and endogenous orthogonal caging methods. Finally, current challenges, opportunities, and future perspectives for DNAzymes as activity-based sensors are also discussed.

From general base to general acid catalysis in a sodium-specific DNAzyme by a guanine-to-adenine mutation

Recently, a few Na+-specific RNA-cleaving DNAzymes were reported, where nucleobases are likely to play critical roles in catalysis. The NaA43 and NaH1 DNAzymes share the same 16-nt Na+-binding motif, but differ in one or two nucleotides in a small catalytic loop. Nevertheless, they display an opposite pH-dependency, implicating distinct catalytic mechanisms. In this work, rational mutation studies locate a catalytic adenine residue, A22, in NaH1, while previous studies found a guanine (G23) to be important for the catalysis of NaA43. Mutation with pKa-perturbed analogs, such as 2-aminopurine (∼3.8), 2,6-diaminopurine (∼5.6) and hypoxanthine (∼8.7) affected the overall reaction rate. Therefore, we propose that the N1 position of G23 (pKa ∼6.6) in NaA43 functions as a general base, while that of A22 (pKa ∼6.3) in NaH1 as a general acid. Further experiments with base analogs and a phosphorothioate-modified substrate suggest that the exocyclic amine in A22 and both of the non-bridging oxygens at the scissile phosphate are important for catalysis for NaH1. This is an interesting example where single point mutations can change the mechanism of cleavage from general base to general acid, and it can also explain this Na+-dependent DNAzyme scaffold being sensitive to a broad range of metal ions and molecules.

Fluorescent Terpolymers via In Situ Allocation of Aliphatic Fluorophore Monomers: Fe(III) Sensor, High-Performance Removals, and Bioimaging

Herein, purely aliphatic intrinsically fluorescent terpolymers, i.e., 1 and 2, are synthesized through one-pot solution polymerization via N-H functionalized and multi C-C/C-N coupled in situ protrusion of fluorescent monomers using two nonemissive monomers. These scalable terpolymers are suitable for highly selective Fe(III) sensing, high-performance exclusion of Fe(III), logic function and the imaging of normal mammalian Madin-Darby canine kidney and human osteosarcoma cancer cell lines. The structures of terpolymers, in situ attachment of fluorescent monomers, clusteroluminescence, adsorption-mechanism, and cell-imaging abilities are understood via unadsorbed and/or adsorbed microstructural analyses using ¹ H/¹³ C NMR, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, UV-vis spectroscopy, atomic absorption spectroscopy, thermogravimetric analysis, high-resolution transmission electron microscopy, dynamic light scattering, fluorescence imaging, and fluorescence lifetime. The geometries, electronic structures, location of fluorophores, and singlet-singlet absorption and emission of terpolymers are examined using density functional theory (DFT) and time-dependent DFT. For the precise identification of fluorophores, transition from occupied natural transition orbitals (NTOs) to unoccupied NTOs is computed. For 1/2, limit of detection (LOD) values and adsorption capacities are 6.0 × 10^-7 /8.0 × 10^-7 m and 147.82/120.56 mg g^-1 at pH_i = 7.0 and 303 K, respectively. The overall properties of 1 are more advantageous compared to 2 in sensing, cell imaging, and adsorptive exclusion of Fe(III).

Metal-Dependent DNAzymes for the Quantitative Detection of Metal Ions in Living Cells: Recent Progress, Current Challenges, and Latest Results on FRET Ratiometric Sensors

Many different metal ions are involved in various biological functions including metallomics and trafficking, and yet there are currently effective sensors for only a few metal ions, despite the first report of metal sensors for calcium more than 40 years ago. To expand upon the number of metal ions that can be probed in biological systems, we and other laboratories employ the in vitro selection method to obtain metal-specific DNAzymes with high specificity for a metal ion and then convert these DNAzymes into fluorescent sensors for these metal ions using a catalytic beacon approach. In this Forum Article, we summarize recent progress made in developing these DNAzyme sensors to probe metal ions in living cells and in vivo, including several challenges that we were able to overcome for this application, such as DNAzyme delivery, spatiotemporal control, and signal amplification. Furthermore, we have identified a key remaining challenge for the quantitative detection of metal ions in living cells and present a new design and the results of a Förster resonance energy transfer (FRET)-based DNAzyme sensor for the ratiometric quantification of Zn2+ in HeLa cells. By converting existing DNAzyme sensors into a ratiometric readout without compromising the fundamental catalytic function of the DNAzymes, this FRET-based ratiometric DNAzyme design can readily be applied to other DNAzyme sensors as a major advance in the field to develop much more quantitative metal-ion probes for biological systems.

Orthogonal Activation of RNA-Cleaving DNAzymes in Live Cells by Reactive Oxygen Species

RNA-cleaving DNAzymes are useful tools for intracellular metal-ion sensing and gene regulation. Incorporating stimuli-responsive modifications into these DNAzymes enables their activities to be spatiotemporally and chemically controlled for more precise applications. Despite the successful development of many caged DNAzymes for light-induced activation, DNAzymes that can be intracellularly activated by chemical inputs of biological importance, such as reactive oxygen species (ROS), are still scarce. ROS like hydrogen peroxide (H₂ O₂ ) and hypochlorite (HClO) are critical mediators of oxidative stress-related cell signaling and dysregulation including activation of immune system as well as progression of diseases and aging. Herein, we report ROS-activable DNAzymes by introducing phenylboronate and phosphorothioate modifications to the Zn²⁺ -dependent 8-17 DNAzyme. These ROS-activable DNAzymes were orthogonally activated by H₂ O₂ and HClO inside live human and mouse cells.

Application of the Monte Carlo Library Least-Squares (MCLLS) approach for chromium quantitative analysis in aqueous solution

In the present work, a new in-situ prompt gamma-ray neutron activation analysis (PGNAA) setup was developed for the quantitative measurement of chromium (Cr) in aqueous solutions which consists of a 4" × 4″ inch Bismuth Germanate detector and a 300 mCi ²⁴¹Americium-beryllium neutron source. A series of standard samples were prepared by dissolving Cr compounds in deionized water of analytical pure grade and measured using the in situ PGNAA setup. Quantitative spectrum analysis was conducted using Monte Carlo Library Least-Squares approach (MCLLS). Simulates of elemental library spectra were in silico modeled using the CEARCPG code, which was developed by Prof. Robin Gardner research group in North Carolina State University. The fitted spectra presented were in excellent agreement with the total experimental spectrum, and the correlation coefficients were all nearly 1. After applying the MCLLS approach, the minimum detectable concentration of Cr was 301.5 mg/L, better than that obtained with other setups, and the relative deviation of the Cr quantitative analysis accuracy was less than 4.09%.

Optical Control of Metal Ion Probes in Cells and Zebrafish Using Highly Selective DNAzymes Conjugated to Upconversion Nanoparticles

Spatial and temporal distributions of metal ions in vitro and in vivo are crucial in our understanding of the roles of metal ions in biological systems, and yet there is a very limited number of methods to probe metal ions with high space and time resolution, especially in vivo. To overcome this limitation, we report a Zn²⁺-specific near-infrared (NIR) DNAzyme nanoprobe for real-time metal ion tracking with spatiotemporal control in early embryos and larvae of zebrafish. By conjugating photocaged DNAzymes onto lanthanide-doped upconversion nanoparticles (UCNPs), we have achieved upconversion of a deep tissue penetrating NIR 980 nm light into 365 nm emission. The UV photon then efficiently photodecages a substrate strand containing a nitrobenzyl group at the 2'-OH of adenosine ribonucleotide, allowing enzymatic cleavage by a complementary DNA strand containing a Zn²⁺-selective DNAzyme. The product containing a visible FAM fluorophore that is initially quenched by BHQ1 and Dabcyl quenchers is released after cleavage, resulting in higher fluorescent signals. The DNAzyme-UCNP probe enables Zn²⁺ sensing by exciting in the NIR biological imaging window in both living cells and zebrafish embryos and detecting in the visible region. In this study, we introduce a platform that can be used to understand the Zn²⁺ distribution with spatiotemporal control, thereby giving insights into the dynamical Zn²⁺ ion distribution in intracellular and in vivo models.

Instantaneous Iodine-Assisted DNAzyme Cleavage of Phosphorothioate RNA

Metal ions play a critical role in the RNA-cleavage reaction by interacting with the scissile phosphate and stabilizing the highly negatively charged transition state. Many metal-dependent DNAzymes have been selected for RNA cleavage. Herein, we report that the Ce13d DNAzyme can use nonmetallic iodine (I₂) to cleave a phosphorothioate (PS)-modified substrate. The cleavage yield exceeded 60% for both the R_p and S_p stereoisomers in 10 s, while the yield without the enzyme strand was only ∼10%. The Ce13d cleavage with I₂ also required Na⁺, consistent with the property of Ce13d and confirming the similar role of I₂ as a metal ion. Ce13d had the highest yield among eight tested DNAzymes, with the second highest DNAzyme showing only 20% cleavage. The incomplete cleavage was due to competition from desulfurization and isomerization reactions. This DNAzyme was engineered for fluorescence-based I₂ detection. With EDTA for masking metal ions, I₂ was selectively detected down to 4.7 nM. Oxidation of I^- with Fe³⁺ produced I₂ in situ, allowing detection of Fe³⁺ down to 78 nM. By harnessing nonelectrostatic interactions, such as the I₂/sulfur interaction observed here, more nonmetal species might be discovered to assist DNAzyme-based RNA cleavage.

An in Vitro-Selected DNAzyme Mutant Highly Specific for Na+ under Slightly Acidic Conditions

Sodium is one of the most common metal ions in biology; however, DNA-based sodium probes have only been reported recently. A Na⁺ -specific RNA-cleaving DNAzyme named NaA43 is active with Na⁺ alone. In this work, we were using Co(NH₃ )₆ ³⁺ as the intended metal cofactor for in vitro selection, but obtained a mutant of the NaA43 DNAzyme. The mutant was named NaH1, and differs from NaA43 by only two nucleotides. NaA43 has an optimal pH of 7.0, whereas the optimal pH for NaH1 is 6.0. This difference might be due to our selection having been performed at pH 6.0. NaH1 also displays an excellent selectivity for sodium relative to other competing monovalent ions, as well as a fast catalytic rate of (0.11±0.01) min^-1 with 50 mm Na⁺ . At low Na⁺ concentrations, the selected DNAzyme exhibited a higher cleavage rate than NaA43 and thus a tighter apparent K_d of (12.0±1.6) mm Na⁺ . Furthermore, the NaH1 DNAzyme was engineered into a fluorescent Na⁺ biosensor by attaching a fluorophore/quencher pair to the DNAzyme with a detection limit of 223 μm Na⁺ . Preliminary work on detection of Na⁺ in serum was demonstrated as well. This study provides a useful mutant that works in a slightly acidic environment, which might be useful for sensing Na⁺ in acidic in vivo environments.

Biocomputing for Portable, Resettable, and Quantitative Point-of-Care Diagnostics: Making the Glucose Meter a Logic-Gate Responsive Device for Measuring Many Clinically Relevant Targets

It is recognized that biocomputing can provide intelligent solutions to complex biosensing projects. However, it remains challenging to transform biomolecular logic gates into convenient, portable, resettable and quantitative sensing systems for point-of-care (POC) diagnostics in a low-resource setting. To overcome these limitations, the first design of biocomputing on personal glucose meters (PGMs) is reported, which utilizes glucose and the reduced form of nicotinamide adenine dinucleotide as signal outputs, DNAzymes and protein enzymes as building blocks, and demonstrates a general platform for installing logic-gate responses (YES, NOT, INHIBIT, NOR, NAND, and OR) to a variety of biological species, such as cations (Na+ ), anions (citrate), organic metabolites (adenosine diphosphate and adenosine triphosphate) and enzymes (pyruvate kinase, alkaline phosphatase, and alcohol dehydrogenases). A concatenated logical gate platform that is resettable is also demonstrated. The system is highly modular and can be generally applied to POC diagnostics of many diseases, such as hyponatremia, hypernatremia, and hemolytic anemia. In addition to broadening the clinical applications of the PGM, the method reported opens a new avenue in biomolecular logic gates for the development of intelligent POC devices for on-site applications.

How to Construct DNA Hydrogels for Environmental Applications: Advanced Water Treatment and Environmental Analysis

With high binding affinity, porous structures, safety, green, programmability, etc., DNA hydrogels have gained increasing recognition in the environmental field, i.e., advanced treatment technology of water and analysis of specific pollutants. DNA hydrogels have been demonstrated as versatile potential adsorbents, immobilization carriers of bioactive molecules, catalysts, sensors, etc. Moreover, altering components or choosing appropriate functional DNA optimizes environment-oriented hydrogels. However, the lack of comprehensive information hinders the continued optimization. The principle used to fabricate the most suitable hydrogels in terms of the requirements is the focus of this Review. First, different fabrication strategies are introduced and the ideal characteristic for environmental applications is in focus. Subsequently, recent environmental applications and the development of diverse DNA hydrogels regarding their synthesis mechanism are summarized. Finally, the Review provides an insight into the remaining challenging and future perspectives in environmental applications.

Rational design of sequestered DNAzyme beacons to enable flexible control of catalytic activities

DNAzymes as functional units play increasingly important roles for DNA nanotechnology, and fine control of the catalytic activities of DNAzymes is a crucial element in the design and construction of functional and dynamic devices. So far, attempts to control cleavage kinetics can be mainly achieved through varying the concentrations of the specific metal ions. Here we present a facile sequestered DNAzyme beacon strategy based on precisely blocking the catalytic core of the DNAzyme, which can flexibly regulate the DNAzyme cleavage kinetics without changing the concentrations of metal ions. This strategy can be extended to couple with a large number of other RNA-cleaving DNAzymes and was successfully applied in designing a dual stem-loop structure probe for arbitrary sequence biosensing, which provides the possibility of scaling up versatile and dynamic DNA devices that use DNAzymes as functional modules.

We present a sequestered DNAzyme beacon strategy based on precisely blocking the catalytic core for flexible regulation of DNAzyme kinetics.

Two Completely Different Mechanisms for Highly Specific Na+ Recognition by DNAzymes

Our view of the interaction between Na⁺ and nucleic acids was changed by a few recently discovered Na⁺ -specific RNA-cleaving DNAzymes. In addition to nonspecific electrostatic interactions, highly specific recognition is also possible. Herein, two such DNAzymes, named EtNa and Ce13d, are compared to elucidate their mechanisms of Na⁺ binding. Mutation studies indicate that they have different sequence requirements. Phosphorothioate (PS) substitution at the scissile phosphate drops the activity of EtNa 140-fold, and it cannot be rescued by thiophilic Cd²⁺ or Mn²⁺ , whereas the activity of PS-modified Ce13d can be rescued. Na⁺ -dependent activity assays indicate that two Na⁺ ions bind cooperatively in EtNa, and each Na⁺ likely interacts with a nonbridging oxygen atom in the scissile phosphate, whereas Ce13d binds only one Na⁺ ion in a well-defined Na⁺ aptamer, and this Na⁺ ion does not directly interact with the scissile phosphate. Both DNAzymes display a normal pH-rate profile, with a single deprotonation reaction required for catalysis. For EtNa, Na⁺ fails to protect the conserved nucleotides from dimethyl sulfate attack, and no specific Na⁺ binding is detected by 2-aminopurine fluorescence, both of which are different from those observed for Ce13d. This work suggests that EtNa binds Na⁺ mainly through its scissile phosphate without significant involvement of the nucleotides in the enzyme strand, whereas Ce13d has a well-defined aptamer for Na⁺ binding. Therefore, DNA has at least two distinct ways to achieve highly selective Na⁺ binding.

Kinetic Discrimination of Metal Ions Using DNA for Highly Sensitive and Selective Cr3+ Detection

Most metal sensors are designed for a strong binding affinity toward target metal ions, and the underlying principle relies on binding thermodynamics. The kinetic aspect of binding, however, was rarely explored for sensing. In this work, the binding kinetics of 19 common or toxic metal ions are compared based on a fluorescence quenching assay using DNA oligonucleotides as ligands. Among these metals, Cr³⁺ shows uniquely slow fluorescence quenching kinetics, and the quenched fluorescence cannot be recovered by EDTA or sulfide. Most other metals quenched fluorescence instantaneously and can be fully recovered by these metal chelators. Various factors such as DNA sequence and length, chelating agent, pH, and fluorophore type were studied to understand the binding mechanism, leading to a unique two-stage binding model for Cr³⁺. This system has a wide dynamic range of up to 50 μM Cr³⁺ and a low limit of detection of 80 nM. It is also useful for measuring Cr³⁺ in lake water. This work proposes a new metal sensor design by monitoring binding kinetics with Cr³⁺ being a primary example.

DNAzyme sensors for detection of metal ions in the environment and imaging them in living cells

The on-site and real-time detection of metal ions is important for environmental monitoring and for understanding the impact of metal ions on human health. However, developing sensors selective for a wide range of metal ions that can work in the complex matrices of untreated samples and cells presents significant challenges. To meet these challenges, DNAzymes, an emerging class of metal ion-dependent enzymes selective for almost any metal ion, have been functionalized with fluorophores, nanoparticles and other imaging agents and incorporated into sensors for the detection of metal ions in environmental samples and for imaging metal ions in living cells. Herein, we highlight the recent developments of DNAzyme-based fluorescent, colorimetric, SERS, electrochemical and electrochemiluminscent sensors for metal ions for these applications.

The Triple Roles of Glutathione for a DNA-Cleaving DNAzyme and Development of a Fluorescent Glutathione/Cu2+-Dependent DNAzyme Sensor for Detection of Cu2+ in Drinking Water

Pistol-like DNAzyme (PLDz) is an oxidative DNA-cleaving catalytic DNA with ascorbic acid as cofactor. Herein, glutathione was induced into the reaction system to maintain reduced ascorbic acid levels for higher efficient cleavage. However, data indicated that glutathione played triple roles in PLDz-catalyzed reactions. Glutathione alone had no effect on PLDz, and showed inhibitory effect on ascorbic acid-induced PLDz catalysis, but exhibited stimulating effect on Cu²⁺-promoted self-cleavage of PLDz. Further analysis of the effect of glutathione/Cu²⁺ on PLDz indicated that H₂O₂ played a key role in PLDz catalysis. Finally, we developed a fluorescent Cu²⁺ sensor (PL-Cu 1.0) based on the relationship between glutathione/Cu²⁺ and catalytic activity of PLDz. The fluorescent intensity showed a linear response toward the logarithm concentration of Cu²⁺ over the range from 80 nM to 30 μM, with a detection limit of 21.1 nM. PL-Cu 1.0 provided only detection of Cu²⁺ over other divalent metal ions. Ca²⁺ and Mg²⁺ could not interfere with Cu²⁺ detection even at a 1000-fold concentration. We further applied PL-Cu 1.0 for Cu²⁺ detection in tap and bottled water. Water stored in copper taps overnight had relatively high Cu²⁺ concentrations, with a maximum 22.3 μM. Trace Cu²⁺ (52.2 nM) in deep spring was detected among the tested bottled water. Therefore, PL-Cu 1.0 is feasible to detect Cu²⁺ in drinking water, with a practical application.