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

Field Detection of Uranyl in Coastal Water of China Using a Portable Device via DNA Photocleavage

The urgent need for field detection of uranium in seawater is 2-fold: to provide prompt guidance for uranium extraction and to prevent human exposure to nuclear radiation. However, current methods for this purpose are largely hindered by bulky instrumentation, high costs of developed materials, and severe matrix interferences, which limit their further application in the field. Herein, we demonstrated a portable and label-free strategy for the field detection of uranyl in seawater based on the efficient photocleavage of DNA. Further experiments confirmed the generation of ultraviolet (UV) light-induced reactive oxygen species (ROS), such as O2•- and •OH, which fragmented oligomeric DNA in the presence of uranyl and UV light. Detailed studies showed that DNA significantly enhances uranyl absorption in the UV-visible region, leading to the generation of more ROS. A fluorescence system for the selective detection of uranyl in seawater was established by immobilizing two complementary oligonucleotides with the fluorescent dye SYBR Green I. The strategy of UV-induced photocleavage offers high selectivity, excellent interference immunity, and high sensitivity for uranyl, with a detection limit of 6.8 nM. Additionally, the fluorescence can be visually detected using a 3D-printed miniaturized device integrated with a smartphone. This method has been successfully applied to the on-site detection of uranyl in seawater in 18 Chinese coastal cities and along the coast of Hainan Island within 3 min for a single sample. The sample testing and field analysis results indicate that this strategy has promising potential for real-time monitoring of trace uranyl in China's coastal waters. It is expected to be utilized for the rapid assessment of nuclear contamination and nuclear engineering construction.

A close-looped DNAzyme walker with an available catalytic domain for electrochemiluminescent detection of acetamiprid

Traditional DNA walkers face enormous challenges due to limited biostability and reaction kinetics. Herein, we designed a self-driven close-looped DNAzyme walker (cl-DW) with high structural biostability and catalytic activity that enabled rapid electrochemiluminescence (ECL) detection of pesticide residue acetamiprid. Specifically, cl-DW exhibited increasing ability to resist nuclease degradation with a 570-fold longer half-degradation time than that of the single-stranded DNAzyme walker (ss-DW) due to the protected DNA terminal. Furthermore, cl-DW achieved high catalytic activity with a 4.3-fold faster reaction kinetic than that of ss-DW due to the circularized nanostructure of an available catalytic domain. Consequently, we utilized cl-DW as a signal amplifier and tin-based sulfide (SnS2) nanoflowers as ECL emitters to construct an ECL aptasensor, which realized the sensitive detection of acetamiprid with a limit of detection of 0.85 nM. This work provides a reliable approach to exploring DNA walkers with high catalytic activity and better biostability for molecular monitoring.

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.

Construction and bioanalytical applications of poly-adenine-mediated gold nanoparticle-based spherical nucleic acids

Owing to the versatile photophysical and chemical properties, spherical nucleic acids (SNAs) have been widely used in biosensing. However, traditional SNAs are formed by self-assembly of thiolated DNA on the surface of a gold nanoparticle (AuNP), where it is challenging to precisely control the orientation and surface density of DNA. As a new SNA, a polyadenine (polyA)-mediated SNA using the high binding affinity of consecutive adenines to AuNPs shows controllable surface density and configuration of DNA, which can be used to improve the performance of a biosensor. Herein, we first introduce the properties of polyA-mediated SNAs and fundamental principles regarding the polyA-AuNP interaction. Then, we provide an overview of current representative synthesis methods of polyA-mediated SNAs and their advantages and disadvantages. After that, we summarize the application of polyA-mediated SNAs in biosensing based on fluorescence and colorimetric methods, followed by discussion and an outlook of future challenges in this field.

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.

Recent Advances on DNAzyme-Based Biosensors for Detection of Uranyl

Nuclear facilities are widely used in fields such as national defense, industry, scientific research, and medicine, which play a huge role in military and civilian use. However, in the process of widespread application of nuclear technology, uranium and its compounds with high carcinogenic and biologically toxic cause a lot of environmental problems, such as pollutions of water, atmosphere, soil, or ecosystem. Bioensors with sensitivity and specificity for the detection of uranium are highly demand. Nucleic acid enzymes (DNAzyme) with merits of high sensitivity and selectivity for targets as excellent molecular recognition elements are commonly used for uranium sensor development. In this perspective review, we summarize DNAzyme-based biosensors for the quantitative detection of uranyl ions by integrating with diverse signal outputting strategies, such as fluorescent, colorimetry, surface-enhanced Raman scattering, and electrochemistry. Different design methods, limit of detection, and practical applications are fully discussed. Finally, the challenges, potential solutions, and future prospects of such DNAzyme-based sensors are also presented.

Interpenetrating porous photonic crystal balls for rapid naked eye detection of uranyl ions

We developed a label-free interpenetrating porous photonic crystal ball sensor with amidoxime groups and carboxyl groups by two-step activation for rapid detection of UO22+ with the naked eye without an angle dependence.

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

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

Molecular Structure of the Surface-Immobilized Super Uranyl Binding Protein

Recently, a super uranyl binding protein (SUP) was developed, which exhibits excellent sensitivity/selectivity to bind uranyl ions. It can be immobilized onto a surface in sensing devices to detect uranyl ions. Here, sum frequency generation (SFG) vibrational spectroscopy was applied to probe the interfacial structures of surface-immobilized SUP. The collected SFG spectra were compared to the calculated orientation-dependent SUP SFG spectra using a one-excitonic Hamiltonian approach based on the SUP crystal structures to deduce the most likely surface-immobilized SUP orientation(s). Furthermore, discrete molecular dynamics (DMD) simulation was applied to refine the surface-immobilized SUP conformations and orientations. The immobilized SUP structures calculated from DMD simulations confirmed the SUP orientations obtained from SFG data analyzed based on the crystal structures and were then used for a new round of SFG orientation analysis to more accurately determine the interfacial orientations and conformations of immobilized SUP before and after uranyl ion binding, providing an in-depth understanding of molecular interactions between SUP and the surface and the effect of uranyl ion binding on the SUP interfacial structures. We believe that the developed method of combining SFG measurements, DMD simulation, and Hamiltonian data analysis approach is widely applicable to study biomolecules at solid/liquid interfaces.

Temperature-robust and ratiometric G-quadruplex proximate DNAzyme assay for robustly monitoring of uranium pollution and its microbial biosorbents screening

Uranium pollution in environment and food chain is a serious threat to public security and human health. Herein, we proposed a temperature-robust, ratiometric, and label-free bioassay based on G-quadruplex proximate DNAzyme (G4DNAzyme), accommodating us to precisely monitor uranium pollution and biosorption. The proximity of split G-quadruplex probes was proposed to sense UO₂²⁺-activated DNAzyme activity, thus eliminating the use of chemically labeled nucleic acid probes. And the simultaneous monitoring of G-quadruplex and double-stranded structures of DNAzyme probes contributed to a ratiometric and robust detection of UO₂²⁺. Particularly, the separation of enzymatic digestion and fluorescence monitoring endued a robust and highly responsive detection of UO₂²⁺ upon the temperature of enzymatic digestion process ranged from 18° to 41 °C. Consequently, G4DNAzyme assay allowed a robust, label-free and ratiometric quantification of uranium. We demonstrated the feasibility of G4DNAzyme assay for estimating uranium pollution in water and aquatic product samples. Ultimately, G4DNAzyme assay was adopted to serve as the platform to screen bacterial species and conditions for uranium biosorption, promising its roles in uranium associated biosafety control.

Detection and Quantification of Tightly Bound Zn2+ in Blood Serum Using a Photocaged Chelator and a DNAzyme Fluorescent Sensor

DNAzymes have emerged as a powerful class of sensors for metal ions due to their high selectivity over a wide range of metal ions, allowing for on-site and real-time detection. Despite much progress made in this area, detecting and quantifying tightly bound metal ions, such as those in the blood serum, remain a challenge because the DNAzyme sensors reported so far can detect only mobile metal ions that are accessible to bind the DNAzymes. To overcome this major limitation, we report the use of a photocaged chelator, XDPAdeCage to extract the Zn²⁺ from the blood serum and then release the chelated Zn²⁺ into a buffer using 365 nm light for quantification by an 8-17 DNAzyme sensor. Protocols to chelate, uncage, extract, and detect metal ions in the serum have been developed and optimized. Because DNAzyme sensors for other metal ions have already been reported and more DNAzyme sensors can be obtained using in vitro selection, the method reported in this work will significantly expand the applications of the DNAzyme sensors from sensing metal ions that are not only free but also bound to other biomolecules in biological and environmental samples.

Amplified electrochemical determination of UO22+ based on the cleavage of the DNAzyme and DNA-modified gold nanoparticle network structure

A superior electrochemical biosensor was designed for the determination of UO₂²⁺ in aqueous solution by integration of DNAzyme and DNA-modified gold nanoparticle (DNA-AuNP) network structure. Key features of this method include UO₂²⁺ inducing the cleavage of the DNAzyme and signal amplification of DNA-AuNP network structure. In this electrochemical method, the DNA-AuNP network structure can be effectively modified on the surface of gold electrode and then employed as an ideal signal amplification unit to generate amplified electrochemical response by inserting a large amount of electrochemically active indicator methylene blue (MB). In the presence of UO₂²⁺, the specific sites on DNA-AuNP network structure can be cleaved by UO₂²⁺, releasing the DNA-AuNP network structure with detectable reduction of electrochemical response intensity. The electrochemical response intensity is related to the concentration of UO₂²⁺. The logarithm of electrochemical response intensity and UO₂²⁺ concentration showed a wide linear range of 10~100 pM, and the detection limit reached 8.1 pM (S/N = 3). This method is successfully used for determination of UO₂²⁺ in water samples. Graphical abstract Fabricated DNAzyme network structure for enhanced electrical signal. Numerical experiments show that the current signal decreases as the concentration of UO₂²⁺ increases. It can be seen that the biosensors could be used to detect UO₂²⁺ in aqueous solution effectively.

Flexible DNA Hydrogel SERS Active Biofilms for Conformal Ultrasensitive Detection of Uranyl Ions from Aquatic Products

It is of great significance to sensitively and conveniently detect trace UO₂²⁺ ions in biological and environmental samples due to severe health risks. However, such suitable sensors are still scarce. In this work, DNAzyme-based hydrogels modified on Ag NP-grafted PAN nanorods array as flexible SERS biosensor have been developed for ultrasensitive UO₂²⁺ ion detection. They were first formed by the substrate strand and enzyme strand comprising the main cleavage-reaction stem-loop complex. Then, a UO₂²⁺ ions responsive smart hydrogel capsule was achieved by DNAzyme complex hybridized with DNA polyacrylamide chains. Raman reporter RhB was introduced and intentionally trapped inside the hydrogel. In the absence of UO₂²⁺ ions, a tiny Raman signal was presented because RhB was trapped inside the hydrogel and far away from SERS substrates. Conversely, the responsive hydrogel could be specifically attacked by UO₂²⁺ ions to release RhB, leading to a strong Raman signal. With the amplified signal procedure, this flexible SERS biofilm accomplished sensitive and selective detection of UO₂²⁺ ions with a wide linear range from 1 pM to 0.1 μM and a low detection limit of 0.838 pM. This result is nearly five orders below the EPA-defined maximum contaminant level (180 nM). Furthermore, this biofilm gives full play to the advantages of a flexible biosensor. It can directly detect the aquatic products (such as fish and kelp) polluted by UO₂²⁺ ions, demonstrating that this flexible SERS biofilm has promising potential for applications in a rapid environmental safety inspection.

A simple and programmed DNA tweezer probes for one-step and amplified detection of UO22

A simple DNA tweezer was proposed for one-step and amplified detection of UO₂²⁺ based on DNAzyme catalytic cleavage. The two arms of DNA tweezers are close in the original form. Thus, the fluorescent signal of fluorophore at the end of arm is dramatically quenched. However, the structure of DNA tweezers can be changed from "close" to "open" in the presence of UO₂²⁺, resulting the strong fluorescent signal. The linear range was obtained in the range of 0.1 nM to 60 nM and the limit of detection was 25 pM with the amplification of DNAzyme catalytic cleavage reaction. Importantly, the whole detection process is very simple and only one operation step is required. In addition, it shows great potential and promising prospects for uranyl detection in practical application.