Biochemical characterization of a uranyl ion-specific DNAzyme

Designing biomimetic two-dimensional channels for uranium separation from seawater

Efficient separation of uranium from seawater stands as a pivotal challenge. This study unveils an approach focusing on the ingenious design of biomimetic two-dimensional (2D) membranes tailored explicitly for this purpose. Leveraging the unique interplay of DNA strands housing U aptamers, pH-responsive i-motifs, and poly A(10) segments ingeniously embedded within graphene oxide membranes, a distinctive biomimetic 2D channel is engineered. The strategic integration of these bio-inspired elements enables dynamic adjustment of interlayer spacing, augmenting both the permeability of the membrane and the selectivity of the aptamer for uranyl ions. During the separation process, the encounter between uranyl ions and the enhanced aptamer within the interlayers initiates a crucial interaction, triggering a specific concentration polarization mechanism. This mechanism stands as the cornerstone for achieving a highly selective separation of uranyl ions from the vast and complex matrix of seawater. The membrane exhibits excellent performance in real seawater, with a rejection rate of uranyl ions of ≈100% and sustained selectivity of uranyl ions over ten cycles. Importantly, the selectivity of uranium and vanadium can reach 14.66. The significance of this research lies not only in the effective separation of uranyl ions but also in showcasing the broader applicability of 2D membrane design in chemical engineering.

Improving the Sensitivity of a Mn(II)-Specific DNAzyme for Cellular Imaging Sensor through Sequence Mutations

Detection of Mn2+ in living cells is important in understanding the roles of Mn2+ in cellular processes and investigating its potential implications in various diseases and disorders. Toward this goal, we have previously selected a Mn2+-specific 11-5 DNAzyme through an in vitro selection method and converted it into a fluorescence sensor for intracellular Mn2+ sensing. Despite the progress, the nucleotides responsible for the activity are unclear, and the performance of the DNAzyme needs to be improved in order for more effective applications in biological systems. To address these issues, we herein report site-specific mutations within the catalytic domain of the selected 11-5 DNAzyme. As a result, we successfully identified a variant DNAzyme, designated as Mn5V, which exhibited a twofold increase in activity compared to the original 11-5 DNAzyme. Importantly, Mn5V DNAzyme maintained its high selectivity for Mn2+ over other competing metal ions. Upon the addition of Mn2+, Mn5V DNAzyme exhibited a higher fluorescence signal within the tumor cells compared to that of the 11-5 DNAzyme. This study therefore provides a better understanding of how the DNAzyme functions and a more sensitive probe for investigating Mn2+ in biological systems.

Heavy Metal-Induced Assembly of DNA Network Biosensor from Double-Loop Hairpin Probes for Ultrasensitive Detection of UO22+ in Water and Soil Samples

The uranyl ion (UO22+) is the most stable form of uranium, which exhibits high toxicity and bioavailability posing a severe risk to human health. The construction of ultrasensitive, reliable, and robust sensing techniques for UO22+ detection in water and soil samples remains a challenge. Herein, a DNA network biosensor was fabricated for UO22+ detection using DNAzyme as the heavy metal recognition element and double-loop hairpin probes as DNA assembly materials. UO22+-activated specific cleavage of the DNAzyme will liberate the triggered DNA fragment, which can be utilized to launch a double-loop hairpin probe assembly among Hab, Hbc, and Hca. Through multiple cyclic cross-hybridization reactions, hexagonal DNA duplex nanostructures (n[Hab•Hbc•Hca]) were formed. This DNA network sensing system generates a high fluorescence response for UO22+ monitoring. The biosensor is ultrasensitive, with a detection limit of 2 pM. This sensing system also displays an excellent selectivity and robustness, enabling the DNA network biosensor to work even in complex water and soil samples with excellent accuracy and reliability. With the advantages of enzyme-free operation, outstanding specificity, and high sensitivity, our proposed DNA network biosensor provides a reliable, simple, and robust method for trace levels of UO22+ detection in environmental samples.

Solar-powered simultaneous highly efficient seawater desalination and highly specific target extraction with smart DNA hydrogels

Obtaining freshwater and important minerals from seawater with solar power facilitates the sustainable development of human society. Hydrogels have demonstrated great solar-powered water evaporation potential, but highly efficient and specific target extraction remains to be expanded. Here, we report the simultaneous highly efficient seawater desalination and specific extraction of uranium with smart DNA hydrogels. The DNA hydrogel greatly promoted the evaporation of water, with the water evaporation rate reached a high level of 3.54 kilograms per square meter per hour (1 kilowatt per square meter). Simultaneously, uranyl-specific DNA hydrogel exhibited a high capture capacity of 5.7 milligrams per gram for uranium from natural seawater due to the rapid ion transport driven by the solar powered interfacial evaporation and the high selectivity (10.4 times over vanadium). With programmable functions and easy-to-use devices, the system is expected to play a role in future seawater treatment.

Single-Molecule Study of DNAzyme Reveals Its Intrinsic Conformational Dynamics

DNAzyme is a class of DNA molecules that can perform catalytic functions with high selectivity towards specific metal ions. Due to its potential applications for biosensors and medical therapeutics, DNAzyme has been extensively studied to characterize the relationships between its biochemical properties and functions. Similar to protein enzymes and ribozymes, DNAzymes have been found to undergo conformational changes in a metal-ion-dependent manner for catalysis. Despite the important role the conformation plays in the catalysis process, such structural and dynamic information might not be revealed by conventional approaches. Here, by using the single-molecule fluorescence resonance energy transfer (smFRET) technique, we were able to investigate the detailed conformational dynamics of a uranyl-specific DNAzyme 39E. We observed conformation switches of 39E to a folded state with the addition of Mg²⁺ and to an extended state with the addition of UO₂²⁺. Furthermore, 39E can switch to a more compact configuration with or without divalent metal ions. Our findings reveal that 39E can undergo conformational changes spontaneously between different configurations.

Smart DNA-gold nanoparticle hybrid hydrogel film based portable, cost-effective and storable biosensing system for the colorimetric detection of lead (II) and uranyl ions

A portable, cost-effective and storable DNA-gold nanoparticle (AuNP) hybrid hydrogel film based biosensing system was developed, with AuNPs serving as both the crosslinking units of the film and the signaling units. Using a layer-by-layer assembly method, hydrogel film composed of three-dimensional hydrophilic network of densely packed AuNPs interconnected by responsive DNA structures was constructed onto a glass slide. By programming the sequence of DNA structures, target-responsive hybrid films were constructed. As a proof of concept, the sequence of a substrate DNA which can be identified and cleaved by Pb²⁺-dependent DNAzyme was encoded to construct Pb²⁺-responsive DNA-AuNP hybrid hydrogel film. The high-density packing of AuNPs as signal substances significantly improved the sensitivity of the ultrathin film biosensing system while reduced the cost of expensive DNA materials. A hydrogel film composed of 10 layers of assembled DNA-AuNP structures generated sufficient visual colorimetric signals for Pb²⁺ detection, with a detection limit of 2.6 nM. By introducing UO₂²⁺-dependent DNAzyme, the system could be further applied in the sensitive and selective detection of UO₂²⁺, with a detection limit of 10.3 nM. Compared with bulk-sized DNA hydrogel biosensing systems, the DNA-AuNP hydrogel film biosensing system exhibited faster response thanks to the sub-micrometer ultrathin film structures. Moreover, the protection of fragile non-covalently crosslinked DNA films with solid slides also facilitated the portable application and long-term storage of the resulting biosensing system, with 95% of the response signal retained after three months of storage. The DNA-AuNPs hydrogel film biosensing system is highly promising for future rapid on-site detection applications.

Selection of M2+-independent RNA-cleaving DNAzymes with Sidechains Mimicking Arginine and Lysine

Sequence-specific cleavage of RNA by nucleic acid catalysts in the absence of a divalent metal cation (M 2+ ) has remained an important goal in biomimicry with potential therapeutic applications. Given the lack of functional group diversity in canonical nucleotides, modified nucleotides with amino acid-like side chains were used to enhance self-cleavage rates at a single embedded ribonucleoside site. Previous works relied on three functional groups: an amine, a guanidine and an imidazole ensconced on three different nucleosides. However, to date, few studies have systematically addressed the necessity of all three modifications, as the value of any single modified nucleoside is contextualized at the outset of selection. Herein, we report on the use of only two modified dNTPs, excluding an imidazole, i.e. 5-(3-guanidinoallyl)-2'-dUTP (dU ga TP) and 5-aminoallyl-2'-dCTP (dC aa TP), to select in-vitro self-cleaving DNAzymes that cleave in the absence of M 2+ in a pH-independent fashion. Cleavage shows biphasic kinetics with rate constants that are significantly higher than in unmodified DNAzymes and compare favorably to certain DNAzymes involving an imidazole. This work is the first report of a M2+-independent DNAzyme with two cationic modifications; as such it shows appreciable self-cleaving activity in the absence of an imidazole modification.

X-ray photoemission studies of the interaction of metals and metal ions with DNA

X-ray Photoelectron Spectroscopy (XPS) has been used to study the interactions of heavy metal ions with DNA with some success. Surface sensitivity and selectivity of XPS are advantageous for identifying and characterizing the chemical and elemental structure of the DNA to metal interaction. This review summarizes the status of what amounts to a large part of the photoemission investigations of biomolecule interactions with metals and offers insight into the mechanism for heavy metal-bio interface interactions. Specifically, it is seen that metal interaction with DNA results in conformational changes in the DNA structure.

DEOXYRIBOZYMES IN DETECTION OF PATHOGENIC BACTERIA

Aim. The purpose of the review was to analyze the use of DNAzyme biosensors for the detection of pathogens. In the recent years, deoxyribozymes (DNAzymes) have a significant impact as biosensors in diverse fields, from detection of metal ions in the environment to theranostic applications and detection of microorganisms. Although routinely used sophisticated instrumental methods are available to detect pathogenic bacterial contamination, they involve time-consuming, complicated sample pre-treatment and expensive instruments. As an alternative, pathogen-specific DNAzymes have demonstrated a series of advantages: a non-destructive rapid analysis technique with in situ and real-time detection of bacteria with high sensitivity and selectivity. A wide range of pathogen-specific DNAzymes has been developed using colorimetric and fluorescence-based detections for pathogenic bacterial contamination in various samples. The current review summarizes the in vitro selection of pathogen-specific DNAzymes, various strategies utilized in the sensor designs, and their potential use in theranostic applications.

Ultrafast high-capacity capture and release of uranium by a light-switchable nanotextured surface

Nuclear power is growing in demand as a promising sustainable energy source, its most prevalent source being uranium salts. The resulting processing and transportation of uranium raise concerns regarding the environmental impact and risks for human health. Close proximity to uranium mines puts populations at higher risk for exposure due to elevated uranium concentrations. As the main form of uranium in aqueous solutions, uranyl (UO₂ ²⁺) has been the focus of many methods of uranium sieving; most fall short by being time-consuming or lacking a retrieval mechanism for the captured uranium. Here, we demonstrate the ultrafast and selective uranyl-capturing properties of aptamer-modified branched silicon nanopillar (BSiNP) arrays. Our nanostructured surfaces demonstrate an ultrahigh surface area modified with a uranyl-specific DNA aptamer, allowing for high uranyl-capturing capacity, reaching up to 550 mg g^-1. Uranyl capture is followed by the activation of a covalently bonded photoacid, causing a light-triggerable, ultrafast release. This capture-and-release cycle results in the collection of over 70% of the uranium found in the original samples within less than one hour.

Biological, biomolecular, and bio-inspired strategies for detection, extraction, and separations of lanthanides and actinides

Lanthanides and actinides are elements of ever-increasing technological importance in the modern world. However, the similar chemical and physical properties within these groups make purification of individual elements a challenge. Current industrial standards for the extraction, separation, and purification of these metals from natural sources, recycled materials, and industrial waste are inefficient, relying upon harsh conditions, repetitive steps, and ligands with only modest selectivity. Biological, biomolecular, and bio-inspired strategies towards improving these separations and making them more environmentally sustainable have been researched for many years; however, these methods often have insufficient selectivity for practical application. Recent developments in the understanding of how lanthanides are selectively acquired and used by certain bacteria offer the opportunity for a newer, more efficient take on these designs, as well as the possibility for fundamentally new designs and strategies. Herein, we review current cell-based and biomolecular (primarily small-molecule and protein-based) methods for detection, extraction, and separations of f-block elements. We discuss how the increasing knowledge regarding the selective recognition, uptake, trafficking, and storage of these elements in biological systems has informed and will continue to promote development of novel approaches to achieve these ends.

Direct Detection of Uranyl in Urine by Dissociation from Aptamer-Modified Nanosensor Arrays

An ever-growing demand for uranium in various industries raises concern for human health of both occupationally exposed personnel and the general population. Toxicological effects related to uranium (natural, enriched, or depleted uranium) intake involve renal, pulmonary, neurological, skeletal, and hepatic damage. Absorbed uranium is filtered by the kidneys and excreted in the urine, thus making uranium detection in urine a primary indication for exposure and body burden assessment. Therefore, the detection of uranium contamination in bio-samples (urine, blood, saliva, etc.,) is of crucial importance in the field of occupational exposure and human health-related applications, as well as in nuclear forensics. However, the direct determination of uranium in bio-samples is challenging because of "ultra-low" concentrations of uranium, inherent matrix complexity, and sample diversity, which pose a great analytical challenge to existing detection methods. Here, we report on the direct, real-time, sensitive, and selective detection of uranyl ions in unprocessed and undiluted urine samples using a uranyl-binding aptamer-modified silicon nanowire-based field-effect transistor (SiNW-FET) biosensor, with a detection limit in the picomolar concentration range. The aptamer-modified SiNW-FET presented in this work enables the simple and sensitive detection of uranyl in urine samples. The experimental approach has a straight-forward implementation to other metals and toxic elements, given the availability of target-specific aptamers. Combining the high surface-to-volume ratio of SiNWs, the high affinity and selectivity of the uranyl-binding aptamer, and the distinctive sensing methodology gives rise to a practical platform, offering simple and straightforward sensing of uranyl levels in urine, suitable for field deployment and point-of-care applications.

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.

Molecular Features and Metal Ions That Influence 10-23 DNAzyme Activity

Deoxyribozymes (DNAzymes) with RNA hydrolysis activity have a tremendous potential as gene suppression agents for therapeutic applications. The most extensively studied representative is the 10-23 DNAzyme consisting of a catalytic loop and two substrate binding arms that can be designed to bind and cleave the RNA sequence of interest. The RNA substrate is cleaved between central purine and pyrimidine nucleotides. The activity of this DNAzyme in vitro is considerably higher than in vivo, which was suggested to be related to its divalent cation dependency. Understanding the mechanism of DNAzyme catalysis is hindered by the absence of structural information. Numerous biological studies, however, provide comprehensive insights into the role of particular deoxynucleotides and functional groups in DNAzymes. Here we provide an overview of the thermodynamic properties, the impact of nucleobase modifications within the catalytic loop, and the role of different metal ions in catalysis. We point out features that will be helpful in developing novel strategies for structure determination and to understand the mechanism of the 10-23 DNAzyme. Consideration of these features will enable to develop improved strategies for structure determination and to understand the mechanism of the 10-23 DNAzyme. These insights provide the basis for improving activity in cells and pave the way for developing DNAzyme applications.

Uranyl Binding to Proteins and Structural-Functional Impacts

The widespread use of uranium for civilian purposes causes a worldwide concern of its threat to human health due to the long-lived radioactivity of uranium and the high toxicity of uranyl ion (UO₂²⁺). Although uranyl–protein/DNA interactions have been known for decades, fewer advances are made in understanding their structural-functional impacts. Instead of focusing only on the structural information, this article aims to review the recent advances in understanding the binding of uranyl to proteins in either potential, native, or artificial metal-binding sites, and the structural-functional impacts of uranyl–protein interactions, such as inducing conformational changes and disrupting protein-protein/DNA/ligand interactions. Photo-induced protein/DNA cleavages, as well as other impacts, are also highlighted. These advances shed light on the structure-function relationship of proteins, especially for metalloproteins, as impacted by uranyl–protein interactions. It is desired to seek approaches for biological remediation of uranyl ions, and ultimately make a full use of the double-edged sword of uranium.

Sensitivity of a classic DNAzyme for Pb2+ modulated by cations, anions and buffers

Both cations and anions in salt strongly affect the activity of a classic Pb²⁺ specific DNAzyme, which in turn can affect the sensitivity of related biosensors.

An investigation of solid-state nanopores on label-free metal-ion signalling via the transition of RNA-cleavage DNAzyme and the hybridization chain reaction

Recent advances have proven solid-state nanopores as a powerful analysis platform that enables label-free and separation-free single-molecule analysis. However, the relatively low resolution still limits its application because many chemicals or targets with small sizes could not be recognized in a label-free condition. In this paper, we provide a possible solution that uses solid-state nanopores for small species signaling via the transition of huge DNA assembly products. DNAzyme responding to metal ions and the hybridization chain reaction (HCR) generating nanopore-detectable dsDNA concatamers are used as the transition model set. By the two-step DNAzyme-HCR transition, Pb2+ that was too tiny to be sensed was successfully recognized by the nanopore. The whole process happened in a completely homogeneous solution without any chemical modification. During condition optimization, we also discussed one possible application challenge that may affect the HCR signal-background distinction. Solid-state nanopores provide a potential solution to this challenge due to its ability to profile product length or even 3D structure information.

Enhancing Catalytic Activity of Uranyl-Dependent DNAzyme by Flexible Linker Insertion for More Sensitive Detection of Uranyl Ion

The uranyl-dependent DNAzyme 39E cleaves its nucleic acid substrate in the presence of uranyl ion (UO₂²⁺). It has been widely utilized in many sensor designs for selective and sensitive detection of UO₂²⁺ in the environment and inside live cells. In this work, by inserting a flexible linker (C3 Spacer) into one critical site (A₂₀) of the 39E catalytic core, we successfully enhanced the original catalytic activity of 39E up to 8.1-fold at low UO₂²⁺ concentrations. Applying such a modified DNAzyme (39E-A₂₀-C3) in a label-free fluorescent sensor for UO₂²⁺ detection achieved more than 1 order of magnitude sensitivity enhancement over using native 39E, with the UO₂²⁺ detection limit improved from 2.6 nM (0.63 ppb) to 0.19 nM (0.047 ppb), while the high selectivity to UO₂²⁺ over other metal ions was fully preserved. The method was also successfully applied for the detection of UO₂²⁺-spiked environmental water samples to demonstrate its practical usefulness.

A review on nanomaterial-based electrochemical, optical, photoacoustic and magnetoelastic methods for determination of uranyl cation

This review (with 177 refs) gives an overview on nanomaterial-based methods for the determination of uranyl ion (UO₂²⁺) by different types of transducers. Following an introduction into the field, a first large section covers the fundamentals of selective recognition of uranyl ion by receptors such as antibodies, aptamers, DNAzymes, peptides, microorganisms, organic ionophores (such as salophens, catechols, phenanthrolines, annulenes, benzo-substituted macrocyclic diamides, organophosphorus receptors, calixarenes, crown ethers, cryptands and β-diketones), by ion imprinted polymers, and by functionalized nanomaterials. A second large section covers the various kinds of nanomaterials (NMs) used, specifically on NMs for electrochemical signal amplification, on NMs acting as signal tags or carriers for signal tags, on fluorescent NMs, on NMs for colorimetric assays, on light scattering NMs, on NMs for surface enhanced Raman scattering (SERS)-based assays and wireless magnetoelastic detection systems. We then discuss detection strategies, with subsections on electrochemical methods (including ion-selective and potentiometric systems, voltammetric systems and impedimetric systems). Further sections treat colorimetric, fluorometric, resonance light scattering-based, SERS-based and photoacoustic methods, and wireless magnetoelastic detection. The current state of the art is summarized, and current challenges are discussed at the end. Graphical abstract An overview is given on nanomaterial-based methods for the detection of uranyl ion by different types of transducers (such as electrochemical, optical, photoacoustic, magnetoelastic, etc) along with a critical discussion of their limitations, benefits and application to real samples.

A quencher-free DNAzyme beacon for fluorescently sensing uranyl ions via embedding 2-aminopurine

DNAzyme-based fluorescent probes have provided valuable protocols for detecting uranium, one of the most common radioactive contaminants in the environment, with ultra-high selectivity and sensitivity. Designing novel DNAzyme beacons to update the mode of fluorescence reporting and/or quenching will continuously enhance "turn-on" sensing performance as well as promote actual application of the biological probes. In this work, we developed a novel quencher-free DNAzyme beacon by embedding fluorescent 2-aminopurine for rapid detection of uranyl ion. 2-aminopurine is able to substitute adenine and keep strong fluorescence in single-stranded DNA whereas being quenched in the hybridized double-stranded DNA by the base-stacking interaction. The combination of such trait of 2-aminopurine and cleavage reaction of DNAzyme in the presence of target co-factors possesses two main advantages for ion sensing: simplicity for avoidance of extra quencher groups and high performance because of superiority of DNAzyme essence. The experimental conditions including embedding site, pH and salt concentration of buffer solutions, and the amount ratio of enzyme strand to substrate strand used to form DNAzymes were systematically optimized to inspire the highest performance of the biological beacon. Thus, a detection limit of 9.6 nM, a wide linear range from 5 nM to 400 nM (R² = 0.997), and selectivity of more than 400 000-fold over other metal ions were achieved by the novel DNAzyme probes. The highly sensitive, selective and quencher-free DNAzyme probes accommodated a simple and cost-efficient alternative to current fluorescent counterparts, holding a great potential for further application in practical ion assay.

A simple mix-and-read bacteria detection system based on a DNAzyme and a molecular beacon

A simple improved mix-and-read method for the detection of bacteria is developed based on a DNAzyme and a molecular beacon.

Colorimetric Detection of Uranyl Using a Litmus Test

Ingestion of water containing toxic contaminants above levels deemed safe for human consumption can occur unknowingly since numerous common contaminants in drinking water are colorless and odorless. Uranyl is particularly problematic as it has been found at dangerous levels in sources of drinking water. Detection of this heavy metal-ion species in drinking water currently requires sending a sample to a laboratory where trained personnel use equipment to perform the analysis and turn-around times can be long. A pH-responsive colorimetric biosensor was developed to enable detection of uranyl in water which coupled the uranyl-specific 39E DNAzyme as a recognition element, and an enzyme capable of producing a pH change as the reporter element. The rapid colorimetric assay presented herein can detect uranyl in lake and well water at concentrations relevant for environmental monitoring, as demonstrated by the detection of uranyl at levels below the limits set for drinking water by major regulatory agencies including the World Health Organization (30 μg/L). This simple and inexpensive DNAzyme-based assay enabled equipment-free visual detection of 15 μg/L uranyl, using both solution-based and paper-based pH-dependent visualization strategies.

Multi-metal-dependent nucleic acid enzymes

Nucleic acid enzymes require metal ions for activity, and many recently discovered enzymes can use multiple metals, either binding to the scissile phosphate or also playing an allosteric role.

Determination of trace uranium by resonance fluorescence method coupled with photo-catalytic technology and dual cloud point extraction

In this paper, two kinds of salophens (Sal) with different solubilities, Sal1 and Sal2, have been respectively synthesized, and they all can combine with uranyl to form stable complexes: [UO2(2+)-Sal1] and [UO2(2+)-Sal2]. Among them, [UO2(2+)-Sal1] was used as ligand to extract uranium in complex samples by dual cloud point extraction (dCPE), and [UO2(2+)-Sal2] was used as catalyst for the determination of uranium by photocatalytic resonance fluorescence (RF) method. The photocatalytic characteristic of [UO2(2+)-Sal2] on the oxidized pyronine Y (PRY) by potassium bromate which leads to the decrease of RF intensity of PRY were studied. The reduced value of RF intensity of reaction system (ΔF) is in proportional to the concentration of uranium (c), and a novel photo-catalytic RF method was developed for the determination of trace uranium (VI) after dCPE. The combination of photo-catalytic RF techniques and dCPE procedure endows the presented methods with enhanced sensitivity and selectivity. Under optimal conditions, the linear calibration curves range for 0.067 to 6.57ngmL(-1), the linear regression equation was ΔF=438.0 c (ngmL(-1))+175.6 with the correlation coefficient r=0.9981. The limit of detection was 0.066ngmL(-1). The proposed method was successfully applied for the separation and determination of uranium in real samples with the recoveries of 95.0-103.5%. The mechanisms of the indicator reaction and dCPE are discussed.

Transforming the blood glucose meter into a general healthcare meter for in vitro diagnostics in mobile health

Recent advances in mobile network and smartphones have provided an enormous opportunity for transforming in vitro diagnostics (IVD) from central labs to home or other points of care (POC). A major challenge to achieving the goal is a long time and high costs associated with developing POC IVD devices in mobile Health (mHealth). Instead of developing a new POC device for every new IVD target, we and others are taking advantage of decades of research, development, engineering and continuous improvement of the blood glucose meter (BGM), including those already integrated with smartphones, and transforming the BGM into a general healthcare meter for POC IVDs of a wide range of biomarkers, therapeutic drugs and other analytical targets. In this review, we summarize methods to transduce and amplify selective binding of targets by antibodies, DNA/RNA aptamers, DNAzyme/ribozymes and protein enzymes into signals such as glucose or NADH that can be measured by commercially available BGM, making it possible to adapt many clinical assays performed in central labs, such as immunoassays, aptamer/DNAzyme assays, molecular diagnostic assays, and enzymatic activity assays onto BGM platform for quantification of non-glucose targets for a wide variety of IVDs in mHealth.

Biochemical and Biophysical Understanding of Metal Ion Selectivity of DNAzymes

This review summarizes research into the metal-binding properties of catalytic DNAzymes, towards the goal of understanding the structural properties leading to metal ion specificity. Progress made and insight gained from a range of biochemical and biophysical techniques are covered, and promising directions for future investigations are discussed.

Precisely Determining Ultralow level UO2(2+) in Natural Water with Plasmonic Nanowire Interstice Sensor

Uranium is an essential raw material in nuclear energy generation; however, its use raises concerns about the possibility of severe damage to human health and the natural environment. In this work, we report an ultrasensitive uranyl ion (UO₂²⁺) detection method in natural water that uses a plasmonic nanowire interstice (PNI) sensor combined with a DNAzyme-cleaved reaction. UO₂²⁺ induces the cleavage of DNAzymes into enzyme strands and released strands, which include Raman-active molecules. A PNI sensor can capture the released strands, providing strong surface-enhanced Raman scattering signal. The combination of a PNI sensor and a DNAzyme-cleaved reaction significantly improves the UO₂²⁺ detection performance, resulting in a detection limit of 1 pM and high selectivity. More importantly, the PNI sensor operates perfectly, even in UO₂²⁺-contaminated natural water samples. This suggests the potential usefulness of a PNI sensor in practical UO₂²⁺-sensing applications. We anticipate that diverse toxic metal ions can be detected by applying various ion-specific DNA-based ligands to PNI sensors.

In vitro selection of deoxyribozymes active with Cd(2+) ions resulting in variants of DNAzyme 8-17

In vitro selection was performed to search for RNA-cleaving DNAzymes catalytically active with Cd(2+) ions from the oligonucleotide combinatorial library with a 23-nucleotide random region. All the selected, catalytically active variants turned out to belong to the 8-17 type DNAzyme. Three DNAzymes were prepared in shortened, cis-acting versions which were subjected to a detailed study of the kinetic properties and metal ion preferences. Although the selection protocol was designed for Cd(2+)-dependent DNAzymes, the variants showed broader metal ion specificity. They preferred Cd(2+) but were also active with Mn(2+) and Zn(2+), suggesting that binding of the catalytic ion does not require an extremely specific coordination pattern. The unexpected decrease of the catalytic activity of the variants along with the temperature increase suggested that some changes occurred in their structures or the rate-limiting step of the reaction was changed. Two elements of the catalytic core of DNAzyme 1/VIIWS, the nucleotide at position 12 and the three-base-pair hairpin motif, were mutated. The presence of a purine residue at position 12 was crucial for the catalytic activity but the changes at that position had a relatively small influence on the metal ion preferences of this variant. The middle base pair of the three-base-pair hairpin was changed from A-T to C-G interaction. The catalytic activity of the mutated variant was increased with Zn(2+), decreased with Mn(2+), and was not changed in the presence of Cd(2+) ions. Clearly, this base pair was important for defining the metal ion preferences of the DNAzyme 1/VIIWS.

Ultrasensitive electrochemical detection of UO22+ based on DNAzyme and isothermal enzyme-free amplification

A novel enzyme-free amplification biosensor for uranyl detection was developed based on UO₂²⁺-specific DNAzyme and a hybridization chain reaction.

Exonuclease III-assisted substrate fragment recycling amplification strategy for ultrasensitive detection of uranyl by a multipurpose DNAzyme

Substrate fragment cleaved by UO₂²⁺ hybridizes with SSP6 to form dsDNA, triggering substrate fragment recycling amplification by Exo III.

Poly-adenine-based programmable engineering of gold nanoparticles for highly regulated spherical DNAzymes

Enzyme complexes are assembled at the two-dimensional lipid membrane or prearranged on three-dimensional scaffolding proteins to regulate their catalytic activity in cells. Inspired by nature, we have developed gold nanoparticle-based spherical DNAzymes (SNAzymes) with programmably engineered activities by exploiting poly-adenine (polyA)-Au interactions. In a SNAzyme, AuNPs serve as the metal core, which is decorated with a functional shell of DNAzymes. Conventional thiolated DNAzyme-based assembly leads to disordered structures with suppressed activity. In contrast, by using an anchoring block of polyA tails, we find that the activity of SNAzymes can be programmably regulated. By using a polyA30 tail, SNAzymes demonstrated remarkably enhanced binding affinity compared to the thiolated DNAzyme-based assembly (∼75-fold) or individual DNAzymes in the solution phase (∼10-fold). More significantly, this increased affinity is directly translated to the sensitivity improvement in the SNAzyme-based lead sensor. Hence, this design of SNAzymes may provide new opportunities for developing biosensors and bioimaging probes for theranostic applications.

Searching for a DNAzyme Version of the Leadzyme

The leadzyme refers to a small ribozyme that cleaves a RNA substrate in the presence of Pb(2+). In an optimized form, the enzyme strand contains only two unpaired nucleotides. Most RNA-cleaving DNAzymes are much longer. Two classical Pb(2+)-dependent DNAzymes, 8-17 and GR5, both contain around 15 nucleotides in the enzyme loop. This is also the size of most RNA-cleaving DNAzymes that use other metal ions for their activity. Such large enzyme loops make spectroscopic characterization difficult and so far no high-resolution structural information is available for active DNAzymes. The goal of this work is to search for DNAzymes with smaller enzyme loops. A simple replacement of the ribonucleotides in the leadzyme by deoxyribonucleotides failed to produce an active enzyme. A Pb(2+)-dependent in vitro selection combined with deep sequencing was then performed. After sequence alignment and DNA folding, a new DNAzyme named PbE22 was identified, which contains only 5 nucleotides in the enzyme catalytic loop. The biochemical characteristics of PbE22 were compared with those of the leadzyme and the two classical Pb(2+)-dependent DNAzymes. The rate of PbE22 rises with increase in Pb(2+) concentration, being 1.7 h(-1) in the presence of 100 μM Pb(2+) and reaching 3.5 h(-1) at 500 µM Pb(2+). The log of PbE22 rate rises linearly in a pH-dependent fashion (20 µM Pb(2+)) with a slope of 0.74. In addition, many other abundant sequences in the final library were studied. These sequences are quite varied in length and nucleotide composition, but some contain a few conserved nucleotides consistent with the GR5 structure. Interestingly, some sequences are active with Pb(2+) but none of them were active with even 50 mM Mg(2+), which is reminiscent of the difference between the GR5 and 8-17 DNAzymes.

Desulfurization Activated Phosphorothioate DNAzyme for the Detection of Thallium

Thallium (Tl) is a highly toxic heavy metal situated between mercury and lead in the periodic table. While its neighbors have been thoroughly studied for DNA-based sensing, little is known about thallium detection. In this work, in vitro selection of RNA-cleaving DNAzymes is carried out using Tl(3+) as the target metal cofactor. Both normal DNA and phosphorothioate (PS)-modified DNA are tested for this purpose. While no Tl(3+)-dependent DNAzymes are obtained, a DNA oligonucleotide containing a single PS-modified RNA nucleotide is found to cleave by ∼7% by Tl(3+) at the RNA position. The remaining 93% are desulfurized. By hybridization of this PS-modified oligonucleotide with the Tm7 DNAzyme, the cleavage yield increases to ∼40% in the presence of Tl(3+) and Er(3+). Tm7 is an Er(3+)-dependent RNA-cleaving DNAzyme. It cleaves only the normal substrate but is completely inactive using the PS-modified substrate. Tl(3+) desulfurizes the PS substrate to the normal substrate to be cleaved by Tm7 and Er(3+). This system is engineered into a catalytic beacon for Tl(3+) with a detection limit of 1.5 nM, which is below its maximal contamination limit defined by the U.S. Environmental Protection Agency (10 nM).

A turn-off fluorescent biosensor for the rapid and sensitive detection of uranyl ion based on molybdenum disulfide nanosheets and specific DNAzyme

A novel fluorescent biosensor for detecting uranyl ion (UO2(2+)) in aqueous environment has been developed based on the specific recognition of DNAzyme and the fluorescence quenching ability of molybdenum disulfide (MoS2) nanosheets. The DNAzyme contains a DNA enzyme strand and a 6-carboxylfluorescein (FAM)-labeled DNA substrate strand. We demonstrated that MoS2 nanosheets have low affinity to the substrate-enzyme complex DNAzyme. Whereas, in the presence of UO2(2+), UO2(2+) can specifically cleave DNAzyme to release FAM-labeled single-strand DNA and the released FAM-labeled single-strand DNA can be firmly adsorbed on the surface of MoS2 nanosheets, which resulted in an obvious decrease of fluorescence intensity. This provided a sensing platform for the rapid, simple and sensitive fluorescent detection of UO2(2+). By using the sensing platform, a sensitive and selective fluorescent method for the rapid detection of UO2(2+) has been developed. In comparison with previous biosensor, the proposed method has obvious analytical advantage such as relatively high sensitivity and good stability, short analytical time and low cost. It can be used to detect as low as 2.14 nM of UO2(2+) in aqueous environment with a recovery of 96-102% and a RSD<5% (n=6). The success of this study provides a promising alternative for the rapid and on-site detection of UO2(2+) in environmental monitoring.

Programmed DNAzyme-Triggered Dissolution of DNA-Based Hydrogels: Means for Controlled Release of Biocatalysts and for the Activation of Enzyme Cascades

Acrylamide/acrylamide-modified nucleic acid copolymer chains provide building units for the construction of acrylamide-DNA hydrogels. Three different hydrogels are prepared by the cross-linking of the acrylamide-DNA chains with metal ion-dependent DNAzyme sequences and their substrates. The metal ion-dependent DNAzyme sequences used in the study include the Cu(2+)-, Mg(2+)-, and Zn(2+)-dependent DNAzymes. In the presence of the respective metal ions, the substrates of the respective DNAzymes are cleaved, leading to the separation of the cross-linking units and to the dissolution of the hydrogel. The different hydrogels were loaded with a fluorophore-modified dextran or with a fluorophore-functionalized glucose oxidase. Treatment of the different hydrogels with the respective ions led to the release of the loaded dextran or the enzyme, and the rates of releasing of the loaded macromolecules followed the order of Cu(2+) > Mg(2+) > Zn(2+). Also, the different hydrogels were loaded with the enzymes β-galactosidase (β-Gal), glucose oxidase (GOx), or horseradish peroxidase (HRP). In the presence of the appropriate metal ions, the respective hydrogels were dissolved, resulting in the activation of the β-Gal/GOx or GOx/HRP bienzyme cascades and of the β-Gal/GOx/HRP trienzyme cascade.

Application of a tailor-made polymer as a selective and sensitive colorimetric sensor for reliable detection of trace levels of uranyl ions in complex matrices

In this study, a new colorimetric chemosensor based on ion imprinted polymer nanoparticles was designed for quantitative detection of uranyl ions at trace levels in environmental water samples.

Sensing parts-per-trillion Cd(2+), Hg(2+), and Pb(2+) collectively and individually using phosphorothioate DNAzymes

Cadmium, mercury, and lead are collectively banned by many countries and regions in electronic devices due to their extremely high toxicity. To date, no sensing method can detect them as a group and also individually with sufficient sensitivity and selectivity. An RNA-cleaving DNAzyme (Ce13d) was recently reported to be active with trivalent lanthanides, which are hard Lewis acids. In this work, phosphorothioate (PS) modifications were systematically made on Ce13d. A single PS modification at the substrate cleavage site shifts the activity from being dependent on lanthanides to soft thiophilic metals. By incorporating the PS modification to another DNAzyme, a sensor array was prepared to detect each metal. Individual sensors have excellent sensitivity (limit of detection = 4.8 nM Cd(2+), 2.0 nM Hg(2+), and 0.1 nM Pb(2+)). This study provides a new route to obtain metal-specific DNAzymes by atomic replacement and also offers important mechanistic insights into metal binding and DNAzyme catalysis.

DNA as sensors and imaging agents for metal ions

Increasing interest in detecting metal ions in many chemical and biomedical fields has created demands for developing sensors and imaging agents for metal ions with high sensitivity and selectivity. This review covers recent progress in DNA-based sensors and imaging agents for metal ions. Through both combinatorial selection and rational design, a number of metal-ion-dependent DNAzymes and metal-ion-binding DNA structures that can selectively recognize specific metal ions have been obtained. By attachment of these DNA molecules with signal reporters such as fluorophores, chromophores, electrochemical tags, and Raman tags, a number of DNA-based sensors for both diamagnetic and paramagnetic metal ions have been developed for fluorescent, colorimetric, electrochemical, and surface Raman detection. These sensors are highly sensitive (with a detection limit down to 11 ppt) and selective (with selectivity up to millions-fold) toward specific metal ions. In addition, through further development to simplify the operation, such as the use of "dipstick tests", portable fluorometers, computer-readable disks, and widely available glucose meters, these sensors have been applied for on-site and real-time environmental monitoring and point-of-care medical diagnostics. The use of these sensors for in situ cellular imaging has also been reported. The generality of the combinatorial selection to obtain DNAzymes for almost any metal ion in any oxidation state and the ease of modification of the DNA with different signal reporters make DNA an emerging and promising class of molecules for metal-ion sensing and imaging in many fields of applications.

Surfactant-free nanoparticle–DNA complexes with ultrahigh stability against salt for environmental and biological sensing

A AuNP–DNA complex highly stable in extremely high ionic strength media, such as seawater, was obtained by inserting a few thymine bases into the DNA strands.