Metal-ion-dependent folding of a uranyl-specific DNAzyme: insight into function from fluorescence resonance energy transfer studies

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

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

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.

A novel sensitive DNAzyme-based optical fiber evanescent wave biosensor for rapid detection of Pb2+ in human serum

We describe here a portable DNAzyme-based optical fiber evanescent wave biosensor (OFEWB) for the rapid and sensitive detection of Pb²⁺ in human serum. Unlike other biosensors, the OFEWB dispensed with the complicated process of attaching biometric elements to the optical fiber, and the optical fiber directly acted as a transducer to transmit the excitation light and simultaneously collected the fluorescence, which could simplify the detection process, avoid the susceptibility to interference from complex environments and strengthen the reusability of the biosensor. The fluorescence (Cy3) labelled substrate sequence (GR-5S-Cy3) could be cleaved under the catalysis of the GR-5 DNAzyme sequence (GR-5E-BHQ2) in the presence of Pb²⁺; then the released fluorescence labelled fragments could be directly excited and detected by the OFEWB due to the high transmission efficiency of the excitation light and fluorescence in the OFEWB. Several key factors affecting Pb²⁺ detection were investigated in detail and optimized. Under the optimal conditions, the LOD of Pb²⁺ in human serum was 9.34 nM (equivalent to 93.4 nM in whole serum) with a detection range of 0-120 nM. The possible matrix interference was evaluated with different spiked human serum samples, and the recovery of Pb²⁺ ranged from 74.4% to 112.5% with RSD < 14.8%, implying this method had excellent practicability and could be potentially used in analyzing some biomedical samples.

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

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

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.

Terpyridine-based complex nanofibers with Eu3+ as a highly selective chemical probes for UO22

Uranyl is a radioactive, toxic pollutant commonly found in the waste remaining after nuclear fuel reprocessing, and it poses several types of risks to human health; therefore, developing absorbents and chemical probes for this compound is crucial to overcoming these issues. This study examined the sensing abilities of terpyridine-appended benzenetricarboxyamide (T-BTA) as a chromogenic probe for detecting uranyl ions (UO₂²⁺). The complex with Eu³⁺ (1-Eu) spontaneously formed nanostructured fibers in H₂O owing to the triamide groups of T-BTA, which induced intermolecular hydrogen-bonding interactions. The strong blue emission of these nanofibers in H₂O was quenched upon adding UO₂²⁺ but not upon adding any other metal ion. This high selectivity was probably because of the interactions between the nitrigen atoms of the terpyridine moieties of 1 and UO₂²⁺. Furthermore, the 1-Eu nanofibers assumed spherical morphologies when UO₂²⁺ was added. To develop a convenient UO₂²⁺ sensor, an electrospun film incorporating 1-Eu (ESF-1-Eu) was manufactured, and it exhibited high selectivity for UO₂²⁺ over a variety of rival metal ions. The plot for luminescence change of ESF-1-Eu vs UO₂²⁺ concentrations in seawater samples showed a good linearty. Thus, the ESF-1-Eu shows potential as a useful sensor for detecting and removing UO₂²⁺ in H₂O.

Misfolding of a DNAzyme for ultrahigh sodium selectivity over potassium

Herein, the excellent Na+ selectivity of a few RNA-cleaving DNAzymes was exploited, where Na+ can be around 3000-fold more effective than K+ for promoting catalysis. By using a double mutant based on the Ce13d DNAzyme, and by lowering the temperature, increased 2-aminopurine (2AP) fluorescence was observed with addition of both Na+ and K+. The fluorescence increase was similar for these two metals at below 10 mM, after which K+ took a different pathway. Since 2AP probes its local base stacking environment, K+ can be considered to induce misfolding. Binding of both Na+ and K+ was specific, since single base mutations could fully inhibit 2AP fluorescence for both metals. The binding thermodynamics was measured by temperature-dependent experiments revealing enthalpy-driven binding for both metals and less coordination sites compared to G-quadruplex DNA. Cleavage activity assays indicated a moderate cleavage activity with 10 mM K+, while further increase of K+ inhibited the activity, also supporting its misfolding of the DNAzyme. For comparison, a G-quadruplex DNA was also studied using the same system, where Na+ and K+ led to the same final state with only around 8-fold difference in Kd. This study provides interesting insights into strategies for discriminating Na+ and K+.

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.

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.

Splitting a DNAzyme enables a Na+-dependent FRET signal from the embedded aptamer

Recently, a few Na⁺-specific RNA-cleaving DNAzymes have been reported, and a Na⁺ aptamer was identified from the NaA43 and Ce13d DNAzymes. These DNAzymes and the embedded aptamer have been used for Na⁺ detection. In this work, we studied the Na⁺-dependent folding of the Ce13d DNAzyme using fluorescence resonance energy transfer (FRET). When a FRET donor and an acceptor were respectively labeled at the ends of the DNAzyme, Na⁺ failed to induce an obvious end-to-end distance change, suggesting a rigid global structure. To relax this rigidity, the Ce13d DNAzyme was systematically split at various sites on both the enzyme and the substrate strands. The Na⁺ binding activity of the split structures was characterized by 2-aminopurine fluorescence, enzymatic activity, Tb³⁺-sensitized luminescence, and DMS footprinting. Among the various constructs, the only one that retained Na⁺ binding was the split at the cleavage site, and this construct was further labeled with two dyes near the split site. This FRET result showed Na⁺-dependent folding with a K_d of 26 mM Na⁺. This study provides important structural information related to Na⁺ binding to this new aptamer, which might also be useful for future work in biosensor design.

Folding of the silver aptamer in a DNAzyme probed by 2-aminopurine fluorescence

The RNA-cleaving Ag10c DNAzyme was recently isolated via in vitro selection and it can bind two Ag⁺ ions for activity. The Ag10c contains a well-defined Ag⁺ binding aptamer as indicated by DMS footprinting. Since aptamer binding is often accompanied with conformational changes, we herein used 2-aminopurine (2AP) to probe its folding in the presence of Ag⁺. The Ag10c was respectively labeled with 2AP at three different positions, both in the substrate strand and in the enzyme strand, one at a time. Ag⁺-induced folding was observed at the substrate cleavage junction and the A9 position of the enzyme strand, consistent with aptamer binding. The measured K_d at the A9 position was 18 μM Ag⁺ with a Hill coefficient of 2.17, similar to those obtained from the previous cleavage activity based assays. However, labeling a 2AP at the A2 position inhibited the activity and folding. Compared to other metal ions, Ag⁺ has a unique sigmoidal folding profile indicative of multiple silver binding cooperatively. This suggests that Ag⁺ can induce a local folding in the enzyme loop and this folding is important for activity. This study provides important biophysical insights into this new DNAzyme, suggesting the possibility of designing folding-based biosensors for Ag⁺.

A highly specific sodium aptamer probed by 2-aminopurine for robust Na+ sensing

Sodium is one of the most abundant metals in the environment and in biology, playing critical ecological and physiological roles. Na⁺ is also the most common buffer salt for nucleic acids research, while its specific interaction with DNA has yet to be fully studied. Herein, we probe a highly selective and robust Na⁺ aptamer using 2-aminopurine (2AP), a fluorescent adenine analog. This aptamer has two DNA strands derived from the Ce13d DNAzyme. By introducing a 2AP at the cleavage site of the substrate strand, Na⁺ induces ∼40% fluorescence increase. The signaling is improved by a series of rational mutations, reaching >600% with the C₁₀A₂₀ double mutant. This fluorescence enhancement suggests relaxed base stacking near the 2AP label upon Na⁺ binding. By replacing a non-conserved adenine in the enzyme strand by 2AP, Na⁺-dependent fluorescence quenching is observed, suggesting that the enzyme loop folds into a more compact structure upon Na⁺ binding. The fluorescence changes allow for Na⁺ detection. With an optimized sequence, a detection limit of 0.4 mM Na⁺ is achieved, reaching saturated signal in less than 10 s. The sensor response is insensitive to ionic strength, which is critical for Na⁺ detection.

Fluorescent nanoprobes for sensing and imaging of metal ions: recent advances and future perspectives

Recent advances in nanoscale science and technology have generated nanomaterials with unique optical properties. Over the past decade, numerous fluorescent nanoprobes have been developed for highly sensitive and selective sensing and imaging of metal ions, both in vitro and in vivo. In this review, we provide an overview of the recent development of the design and optical properties of the different classes of fluorescent nanoprobes based on noble metal nanomaterials, upconversion nanoparticles, semiconductor quantum dots, and carbon-based nanomaterials. We further detail their application in the detection and quantification of metal ions for environmental monitoring, food safety, medical diagnostics, as well as their use in biomedical imaging in living cells and animals.

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.

Functional nucleic acid-based sensors for heavy metal ion assays

Heavy metal contaminants such as lead ions (Pb(2+)), mercury ions (Hg(2+)) and silver ions (Ag(+)) can cause significant harm to humans and generate enduring bioaccumulation in ecological systems. Even though a variety of methods have been developed for Pb(2+), Hg(2+) and Ag(+) assays, most of them are usually laborious and time-consuming with poor sensitivity. Due to their unique advantages of excellent catalytic properties and high affinity for heavy metal ions, functional nucleic acids such as DNAzymes and aptamers show great promise in the development of novel sensors for heavy metal ion assays. In this review, we summarize the development of functional nucleic acid-based sensors for the detection of Pb(2+), Hg(2+) and Ag(+), and especially focus on two categories including the direct assay and the amplification-based assay. We highlight the emerging trends in the development of sensitive and selective sensors for heavy metal ion assays as well.

Applications of synchrotron-based spectroscopic techniques in studying nucleic acids and nucleic acid-functionalized nanomaterials

In this review, we summarize recent progress in the application of synchrotron-based spectroscopic techniques for nucleic acid research that takes advantage of high-flux and high-brilliance electromagnetic radiation from synchrotron sources. The first section of the review focuses on the characterization of the structure and folding processes of nucleic acids using different types of synchrotron-based spectroscopies, such as X-ray absorption spectroscopy, X-ray emission spectroscopy, X-ray photoelectron spectroscopy, synchrotron radiation circular dichroism, X-ray footprinting and small-angle X-ray scattering. In the second section, the characterization of nucleic acid-based nanostructures, nucleic acid-functionalized nanomaterials and nucleic acid-lipid interactions using these spectroscopic techniques is summarized. Insights gained from these studies are described and future directions of this field are also discussed.

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.

Metal ion as both a cofactor and a probe of metal-binding sites in a uranyl-specific DNAzyme: a uranyl photocleavage study

DNAzymes are known to bind metal ions specifically to carry out catalytic functions. Despite many studies since DNAzymes were discovered nearly two decades ago, the metal-binding sites in DNAzymes are not fully understood. Herein, we adopt uranyl photocleavage to probe specific uranyl-binding sites in the 39E DNAzyme with catalytically relevant concentrations of uranyl. The results indicate that uranyl binds between T23 and C25 in the bulge loop, G11 and T12 in the stem loop of the enzyme strand, as well as between T2.4 and G3 close to the cleavage site in the substrate strand. Control experiments using two 39E DNAzyme mutants revealed a different cleavage pattern of the mutated region. Another DNAzyme, the 8–17 DNAzyme, which has a similar secondary structure but shows no activity in the presence of uranyl, indicated a different uranyl-dependent photocleavage as well. In addition, a close correlation between the concentration-dependent photocleavage and enzymatic activities is also demonstrated. Together, these experiments suggest that uranyl photocleavage has been successfully used to probe catalytically relevant uranyl-binding sites in the 39E DNAzyme. As uranyl is the cofactor of the 39E DNAzyme as well as the probe, specific uranyl binding has now been identified without disruption of the structure.

Investigating the interactions between cations, peroxidation substrates and G-quadruplex topology in DNAzyme peroxidation reactions using statistical testing

Cations affect the topology and enzymatic proficiency of most macromolecular catalysts but the role of cations in DNAzyme peroxidation reactions remains unresolved. Herein, we use statistical methods (ANOVA, t-test and Wilcoxon Mann-Whitney non-parametric test) to demonstrate that there are strong associations between cations, DNAzyme topology, peroxidation substrate and peroxidation rates of G-quadruplex peroxidises. Ammonium cation was found to be superior to all tested cations, including potassium. A t-test indicated that NH(4)(+) was better than K(+) with a p-value=0.05. Interestingly, the nature of the peroxidation substrate employed affected the dependence of peroxidation rate on the cation present and of the three substrates tested, 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid (ABTS), tyramine and 3,3',5,5'-tetramethylbenzidine (TMB), ABTS was the most sensitive to the nature of cation present.