Improving Fluorescent DNAzyme Biosensors by Combining Inter- and Intramolecular Quenchers

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.

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.

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.

DNA-Based Biosensors for the Biochemical Analysis: A Review

In recent years, DNA-based biosensors have shown great potential as the candidate of the next generation biomedical detection device due to their robust chemical properties and customizable biosensing functions. Compared with the conventional biosensors, the DNA-based biosensors have advantages such as wider detection targets, more durable lifetime, and lower production cost. Additionally, the ingenious DNA structures can control the signal conduction near the biosensor surface, which could significantly improve the performance of biosensors. In order to show a big picture of the DNA biosensor's advantages, this article reviews the background knowledge and recent advances of DNA-based biosensors, including the functional DNA strands-based biosensors, DNA hybridization-based biosensors, and DNA templated biosensors. Then, the challenges and future directions of DNA-based biosensors are discussed and proposed.

Fluorescence-Based Kinetic Measurements for RNA-Cleaving DNAzymes

Studying the catalytic behavior of biocatalysts under different conditions including temperature, buffer conditions, and cofactor concentrations is an important tool to understand their reaction mechanism. We describe two protocols that allow for the investigation of the catalysis of RNA-cleaving DNAzymes. The techniques include the use of FRET-labeled RNA substrates for studying the RNA-cleavage reaction in real-time under high throughput as well as RNA substrates labeled with a fluorescein molecule at the 5' end for gel-based assays. Both methods allow for an accurate determination of rate constants given a reaction model.

DNAzyme-Based Lithium-Selective Imaging Reveals Higher Lithium Accumulation in Bipolar Disorder Patient-Derived Neurons

Lithium has been a drug for bipolar disorders (BD) for over 70 years; however, its usage has been limited by its narrow therapeutic window (between 0.6 and 1.2 mM). Understanding the cellular distribution of lithium ions (Li+) in patient cells will offer deep insight into this limitation, but selective imaging of Li+ in living cells under biomedically relevant concentration ranges has not been achieved. Herein, we report in vitro selection and development of a Li+-specific DNAzyme fluorescent sensor with >100-fold selectivity over other biorelevant metal ions. This sensor allows comparative Li+ visualization in HeLa cells, human neuronal progenitor cells (NPCs), and neurons derived from BD patients and healthy controls. Strikingly, we detected enhanced accumulation of Li+ in cells derived from BD patients compared with healthy controls in differentiated neurons but not NPCs. These results establish the DNAzyme-based sensor as a novel platform for biomedical research into BD and related areas using lithium drugs.

Advances in the Functional Nucleic Acid Biosensors for Detection of Lead Ions

Lead ions (Pb²⁺) are destructive to the natural environment and public health, so the efficient detection of Pb²⁺ is particularly important. Although the instrumental analysis methods have high accuracy, they require high cost and precise operation, which limits their wide application. Therefore, many strategies have been extensively studied for detecting Pb²⁺ by biosensors. Functional nucleic acids have become an efficient tool in this field. This review focuses on the recent biosensors of detecting Pb²⁺ based on functional nucleic acids from 2010 to 2020, in which DNAzyme, DNA G-quadruplex and aptamer will be introduced. The biosensors are divided into three categories that colorimetric, fluorometric and electrochemical biosensors according to the different reported signals. The action mechanism and detection effect of each biosensor are explained. Finally, the present situation of nucleic acid biosensor for the detection of Pb²⁺ is summarized and the future research direction is prospected.

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-based sensing probe protected by DNA tetrahedron from nuclease degradation for the detection of lead ions

Lead poisoning endangers soil, plants and human health due to its toxic effect. It is urgent to develop ideal tool for the in vivo detection of Pb²⁺.In this study, tetrahedron-based Pb²⁺-sensitive DNAzyme sensor (TPS) is constructed by taking advantages of a classic Pb²⁺-dependent GR-5 DNAzyme and DNA tetrahedral structure, where the cleavage substrate and DNAzyme are modified with fluorophore FAM and quencher BHQ-1, respectively. DNA tetrahedron is arranged at the terminus of substrate/DNAzyme duplex to offer the protective shield against the nuclease attack. In the absence of Pb²⁺, FAM and BHQ-1 are kept close and FAM fluorescence is efficiently quenched. However, in the presence of Pb²⁺ cofactor, the DNAzyme exhibits the catalytic activity and cleaves the substrate strands, spatially separating the FAM away from BHQ-1 and releasing fluorescence. Utilizing the sensing probe, the Pb²⁺ can be quantitatively detected down to 1 nM without the interference from nontarget metal ions. Even if incubating in the human serum solution for 12 h, no substantial nuclease degradation is detected. In different complex biological milieu, the TPS can preserve the 85% of fluorescence signal, indicating that the developed TPS is a promising tool for the future application in the in vivo detection of Pb²⁺.

Ionophore-Based Ion-Selective Nanospheres Based on Monomer-Dimer Conversion in the Near-Infrared Region

Here, we report ion-selective nanospheres with readout in the near-infrared (NIR) region in both fluorescence and absorbance modes. The nanospheres rely on an ionophore-mediated monomer-dimer conversion of an NIR transducer, DTTC. The DTTC monomer in the nanospheres emits fluorescence around 820 nm, while the dimer in the aqueous environment generates strong blue-shifted emission around 660 nm. With a lead ionophore, an unprecedented lower detection limit of 3 pM for Pb²⁺ was achieved, allowing us to determine Pb²⁺ levels in river water without diluting the sample. Also, the Cu²⁺-selective nanospheres showed a detection limit of 5 nM. Taking advantage of the biologically desired NIR window, blood potassium concentrations were also determined without a complicated sample pretreatment. The sensing process was explained with a theoretical model. The detection range was found finely adjustable by the amount of nanospheres used. Therefore, the nanospheres formed a highly selective, sensitive, versatile, and rapid analytical platform for metal-ion sensing.

Label-free DNAzyme assays for dually amplified and one-pot detection of lead pollution

Lead pollution in water and soil often transfers to food, advocating tools for on-site detection of lead pollution to ensure both environmental and food safety. We proposed a label-free, dually amplified and homogeneous DNAzyme assay for sensitive and one-pot detection of lead pollution. Instead of using chemically modified DNA substrate, a structure-response digestion process was introduced to monitor Pb²⁺ presence-induced cleavage process of unlabeled substrate, further amplifying the response signals and eliminating the use of labeled DNA probes. The DNAzyme assay allowed to detect Pb²⁺ as low as 0.12 nM and endued a dynamic range from 0.1 nM to 30 nM. In addition, it can specifically identify Pb²⁺ among other metal ions. We demonstrated that the DNAzyme assay can precisely detect Pb²⁺ in tap water, milk and fish. Thus, the DNAzyme assay is promising for on-site monitoring lead pollution risk and ensuring environmental and food safety.

Ultrasensitive ratiometric detection of Pb2+ using DNA tetrahedron-mediated hyperbranched hybridization chain reaction

A fluorescent sensing strategy was developed for rapid, highly sensitive and specific detection of lead (II) ion (Pb²⁺) on the basis of Pb²⁺ DNAzyme-controlled tetrahedral DNA nanostructure (TDN)-mediated hyper-branched hybridization chain reaction (hHCR). In this strategy, DNA hairpins used for HCR amplification are modified on the four vertexes of TDN, which are then used to perform rapid TDN-hHCR in the presence of an initiator strand, producing large-sized cross-linked reaction products and thus giving greatly improved fluorescence resonance energy transfer (FRET) signal output. Pb²⁺ DNAzyme catalyzes the cleavage of the initiator strand, inhibiting the initiation of TDN-hHCR and giving decreased FRET signal. Synergetic signal amplification of Pb²⁺ DNAzyme-catalyzed cleavage reaction and subsequent TDN-hHCR confers the sensing platform with ultrahigh sensitivity. As low as 0.25 pM Pb²⁺ can be detected by using either signal "turn-on" or "turn-off" mode. The whole detection process can be finished within 20 min. Strong anti-interference capacity of FRET-based ratiometric detection and high specificity of Pb²⁺ DNAzyme endow the sensing platform with great practical application potential, which was demonstrated by the accurate detection of Pb²⁺ in real river water, fruit, vegetable and grain samples.

Nanopore detection of metal ions: Current status and future directions

In this review, we highlight recent research efforts that aimed at developing nanopore sensors for detection of metal ions, which play a crucial role in environmental safety and human health. Protein pores use three stochastic sensing-based strategies for metal ion detection. The first strategy is to construct engineered nanopores with metal ion binding sites, so that the interaction between the target analytes and the nanopore can slow the movement of metal ions in the nano-channel. Second, large molecules such as nucleic acids and especially peptides could be utilized as external selective molecular probes to detect metal ions based on the conformational change of the ligand molecules induced by the metal ion-ligand chelation / coordination interaction. Third, enzymatic reactions can also be used as an alternative to the molecule probe strategy in the situation that a sensitive and selective probe molecule for the target analyte is difficult to obtain. On the other hand, by taking advantage of steady-state analysis, synthetic nanopores mainly use two strategies (modification and modification-free) to detect metals. Given the advantages of high sensitivity & selectivity, and label-free detection, nanopore-based metal ion sensors should find useful application in many fields, including environmental monitoring, medical diagnosis, and so on.

In vitro Selection of Chemically Modified DNAzymes

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

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.

Enzyme-Mediated Endogenous and Bioorthogonal Control of a DNAzyme Fluorescent Sensor for Imaging Metal Ions in Living Cells

Bioorthogonal control of metal-ion sensors for imaging metal ions in living cells is important for understanding the distribution and fluctuation of metal ions. Reported here is the endogenous and bioorthogonal activation of a DNAzyme fluorescent sensor containing an 18-base pair recognition site of a homing endonuclease (I-SceI), which is found by chance only once in 7×1010  bp of genomic sequences, and can thus form a near bioorthogonal pair with I-SceI for DNAzyme activation with minimal effect on living cells. Once I-SceI is expressed inside cells, it cleaves at the recognition site, allowing the DNAzyme to adopt its active conformation. The activated DNAzyme sensor is then able to specifically catalyze cleavage of a substrate strand in the presence of Mg2+ to release the fluorophore-labeled DNA fragment and produce a fluorescent turn-on signal for Mg2+ . Thus I-SceI bioorthogonally activates the 10-23 DNAzyme for imaging of Mg2+ in HeLa cells.

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.

DNAzyme-Functionalized R-Phycoerythrin as a Cost-Effective and Environment-Friendly Fluorescent Biosensor for Aqueous Pb2+ Detection

The sensitive detection of Pb²⁺ is of significant importance for food safety, environmental monitoring, and human health care. To this end, a novel fluorescent biosensor, DNAzyme-functionalized R-phycoerythrin (DNAzyme-R-PE), was presented for Pb²⁺ analysis. The biosensor was prepared via the immobilization of Iowa Black^® FQ-modified DNAzyme–substrate complex onto the surface of SPDP-functionalized R-PE. The biosensor produced a minimal fluorescence signal in the absence of Pb²⁺. However, Pb²⁺ recognition can induce the cleavage of substrate, resulting in a fluorescence restoration of R-PE. The fluorescence changes were used to measure sensitively Pb²⁺ and the limit of detection was 0.16 nM with a linear range from 0.5–75 nM. Furthermore, the proposed biosensor showed excellent selectivity towards Pb²⁺ even in the presence of other metal ions interferences and was demonstrated to successfully determine Pb²⁺ in spiked lake water 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.

Real-Time FO-SPR Monitoring of Solid-Phase DNAzyme Cleavage Activity for Cutting-Edge Biosensing

DNA nanotechnology has a great potential in biosensor design including nanostructuring of the biosensor surface through DNA origami, target recognition by means of aptamers, and DNA-based signal amplification strategies. In this paper, we use DNA nanotechnology to describe for the first time the concept of real-time solid-phase monitoring of DNAzyme cleavage activity for the detection of specific single-stranded DNA (ssDNA) with a fiber optic surface plasmon resonance (FO-SPR) biosensor. Hereto, we first developed a robust ligation strategy for the functionalization of the FO-SPR biosensing surface with ssDNA-tethered gold nanoparticles, serving as the substrate for the DNAzyme. Next, we established a relation between the SPR signal change, due to the cleavage activity of the 10-23 DNAzyme, and the concentration of the DNAzyme, showing faster cleavage kinetics for higher DNAzyme concentrations. Finally, we implemented this generic concept for biosensing of ssDNA target in solution. Hereto, we designed a DNAzyme-inhibitor complex, consisting of an internal loop structure complementary to the ssDNA target, that releases active DNAzyme molecules in a controlled way as a function of the target concentration. We demonstrated reproducible target detection with a theoretical limit of detection of 1.4 nM, proving that the presented ligation strategy is key to a universal DNAzyme-based FO-SPR biosensing concept with promising applications in the medical and agrofood sector.

Fluorescence Based Investigation of Temperature-Dependent Pb2+-Specific 8-17E DNAzyme Catalytic Sensor

The 8-17E DNAzyme is a temperature-dependent DNA metalloenzyme catalyzing RNA trans esterification in the presence of Pb²⁺ metal ions. Labeling the stems of the substrate and DNAzyme with the Cy3 and Cy5 respectively, the considered DNAzyme was studied by the fluorescence spectroscopy. The temperature-dependent variability of the Pb²⁺-specific 8-17E DNAzyme catalytic sensor was investigated trough a number of successive temperature fluctuations from 4 to 25 °C to obtain information. Investigating underlined biochemical system reveals that in this sensor, free single strands Enzyme (Cy5-E) and Substrate (Cy3-S) have higher fluorescence intensities than hybridized forms, suggesting that the fluorophores are in a contact quenched. Increasing the temperature has three effects: 1) Fluorescence intensities for the free fluorophores were reduced, 2) stability of the hybridized form was reduced and cleavage of substrate in presence of Pb²⁺was occurred, and 3) conformation of ES hybridized form was changed (before cleavage). As a result of conformation changes in ES, S was more affected than E in the ES. Pb²⁺ ion shows quenching effect on both fluorophores and in the absence of N₂(g) purge the effect was more considerable. A main goal that we had in mind was to find if significantly lower concentrations of Pb²⁺ and ES, compared to previous reports, can generate any observable cleavage in substrate. Analysis of the cleavage reaction for 50 nM ES indicates that S is cleaved at 25 °C in presence of N₂(g) and 0.5 μM Pb²⁺, while in same condition no apparent change occurs in the 4 or 10 °C. The rapid, sensitive and low cost strategy presented here can be applicable to study temperature-dependent behavior of other nucleic acid-based biosensors.

Rapid Quantitative Fluorescence Detection of Copper Ions with Disposable Microcapsule Arrays Utilizing Functional Nucleic Acid Strategy

In this work, an economical and easy-to-use microcapsule array fabricated by ice printing technique has been realized for ultrasensitive fluorescence quantification of copper ions employing functional nucleic acid strategy. With ice printing, the detection reagents are sealed by polystyrene (PS) film isolation and photopolymer, which guarantees a stable and contamination-free environment for functional nucleic acid reaction. Our microcapsule arrays have shown long-term stability (20 days) under -20 °C storage in frozen form before use. During the Cu²⁺ on-site detection, 1 μL sample is simply injected into the thawy microcapsule by a microliter syringe under room temperature, and after 20 minutes the fluorescence result can be obtained by an LED transilluminator. This method can realize the detection limit to 100 nM (100 fmol/μL) with high specificity.

Temperature-Robust DNAzyme Biosensors Confirming Ultralow Background Detection

Catalytic DNA/RNA, such as DNAzyme, has been widely adopted to construct biosensors, especially for metal ion analysis. However, traditional DNAzyme biosensors still suffer from fluctuating and relatively high background. Herein, we proposed a temperature-robust DNAzyme, conferring ultralow background in various temperatures, thus leading to highly sensitive and robust detection of metal ions. Instead of labeling substrate to directly output fluorescence signal, our proposed DNAzyme biosensor utilized a sequential detection process with a couple of proximity fluorescent probes, confirming very low background regardless of the conditions of cleavage reaction. This sequential DNAzyme biosensor conferred a signal to background ratio over 20 when the temperature of the catalytic reaction ranged from 20 to 41 °C. Benefitting from its ultralow background, it could confer a detection limit of 0.22 nM, which ranked as one of the highest sensitivity levels among DNAzyme-based fluorescent biosensors. This DNAzyme biosensor was over 6000 times more selective for Pb²⁺ against the most active interfering metal ions, Zn²⁺. Further, it has been successfully applied for analyzing lead pollution in tap water and eggs, with total recoveries ranging from 87% to 114%. This facile, simple, and effective design strategy would significantly improve the detection performance of DNAzyme biosensors, thus facilitating its practical applications for both food safety analysis and environment monitoring.

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.

The Optimization and Characterization of an RNA-Cleaving Fluorogenic DNAzyme Probe for MDA-MB-231 Cell Detection

Breast cancer is one of the most frequently diagnosed cancers in females worldwide and lacks specific biomarkers for early detection. In a previous study, we obtained a selective RNA-cleaving Fluorogenic DNAzyme (RFD) probe against MDA-MB-231 cells, typical breast cancer cells, through the systematic evolution of ligands by exponential process (SELEX). To improve the performance of this probe for actual application, we carried out a series of optimization experiments on the pH value of a reaction buffer, the type and concentration of cofactor ions, and sequence minimization. The length of the active domain of the probe reduced to 25 nt from 40 nt after optimization, which was synthesized more easily and economically. The detection limit of the optimized assay system was 2000 MDA-MB-231 cells in 30 min, which is more sensitive than the previous one (almost 5000 cells). The DNAzyme probe was also capable of distinguishing MDA-MB-231 cell specifically from 3 normal cells and 10 other tumor cells. This probe with high sensitivity, selectivity, and economic efficiency enhances the feasibility for further clinical application in breast cancer diagnosis. Herein, we developed an optimization system to produce a general strategy to establish an easy-to-use DNAzyme-based assay for other targets.

A sensitive biosensor with a DNAzyme for lead(II) detection based on fluorescence turn-on

In this paper, we described a new DNAzyme-based fluorescent biosensor for the detection of Pb(2+). In the biosensor, the bulged structure is formed between the substrate labeled with fluorescein amidite (FAM) and DNAzyme after being annealed. Ethidium bromide (EB), the DNA intercalator, then intercalates into the double-stranded DNA section. Once FAM is excited, the FRET takes place from FAM to EB, which leads to the fluorescence of FAM decreasing greatly. In the presence of Pb(2+), the substrate is cleaved by DNAzyme, which breaks the bulged structure. Then EB is released and the FRET from FAM to EB is inhibited. In this case, the fluorescence of FAM increases dramatically. Thus, the Pb(2+) ions can be detected by measuring the fluorescence enhancement of FAM. Under optimal conditions, the increased fluorescence intensity ratio of FAM is dependent on the lead level in the sample, and exhibits a linear response over a Pb(2+) concentration range of 0-100 nM with a detection limit of 530 pM. The sensor showed high selectivity in the presence of a number of interference ions. The river water samples were also tested with satisfying results by using the new method. This sensor is highly sensitive and simple without any additional treatments, which provides a platform for other biosensors based on DNAzyme.

Colorimetric detection of lead(ii) ions based on accelerating surface etching of gold nanorods to nanospheres: the effect of sodium thiosulfate

The lead ion-participated etching of gold nanorods leads to qualitative spectral change from double bands to single band LSPR, which results in a distinct irreversible color change of the gold colloid from blue to red.

DNAzyme-based biosensors and nanodevices

DNAzymes, screened through in vitro selection, have shown great promise as molecular tools in the design of biosensors and nanodevices. The catalytic activities of DNAzymes depend specifically on cofactors and show multiple enzymatic turnover properties, which make DNAzymes both versatile recognition elements and outstanding signal amplifiers. Combining nanomaterials with unique optical, magnetic and electronic properties, DNAzymes may yield novel fluorescent, colorimetric, surface-enhanced Raman scattering (SERS), electrochemical and chemiluminescent biosensors. Moreover, some DNAzymes have been utilized as functional components to perform arithmetic operations or as "walkers" to move along DNA tracks. DNAzymes can also function as promising therapeutics, when designed to complement target mRNAs or viral RNAs, and consequently lead to down-regulation of protein expression. This feature article focuses on the most significant achievements in using DNAzymes as recognition elements and signal amplifiers for biosensors, and highlights the applications of DNAzymes in logic gates, DNA walkers and nanotherapeutics.

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.

Highly sensitive and selective detection of Pb2+ ions using a novel and simple DNAzyme-based quartz crystal microbalance with dissipation biosensor

A novel, label-free DNAzyme-based quartz crystal microbalance with dissipation monitoring (QCM-D) biosensor was developed for the highly sensitive and specific detection of Pb(2+) ions. To enhance the performance of the sensor, oligonucleotide-functionalized gold nanoparticles were used for both frequency and dissipation amplification. This sensor was developed by immobilizing Pb(2+)-specific DNAzymes onto the QCM-D sensor surface and allowing them to hybridize with substrate-functionalized AuNPs. The DNAzyme catalyzed the cleavage of the substrate in the presence of Pb(2+) ions, causing the cleaved substrate-functionalized AuNPs to be removed from the sensor surface. Thus, Pb(2+) ions can be determined on-line by monitoring the change in frequency and dissipation signals. The results revealed that the sensor showed a sensitive response to Pb(2+) ions with detection limits of 14 nM and 20 nM for frequency and dissipation, respectively. This QCM-D biosensor also exhibited excellent selectivity toward Pb(2+) ions in the presence of other divalent metal ions. In addition, the approach was able to detect Pb(2+) in tap water, demonstrating its great potential for monitoring drinking water quality. The proposed sensor system described here represents a new class of lead ion sensor. Its simple detection strategy makes it feasible for 'pollution-free' detection; thus, the approach could have applications in on-line water quality monitoring.

Cleavage-based hybridization chain reaction for electrochemical detection of thrombin

In the present work, we constructed a new label-free "inter-sandwich" electrochemical aptasensor for thrombin (TB) detection by employing a cleavage-based hybridization chain reaction (HCR). The designed single-stranded DNA (defined as binding DNA), which contained the thrombin aptamer binding sequence, a DNAzyme cleavage site and a signal reporter sequence, was first immobilized on the electrode. In the absence of a target TB, the designed DNAzymes could combine with the thrombin aptamer binding sequence via complementary base pairing, and then Cu(2+) could cleave the binding DNA. In the presence of a target TB, TB could combine with the thrombin aptamer binding sequence to predominantly form an aptamer-protein complex, which blocked the DNAzyme cleavage site and prevented the binding DNA from being cleaved by Cu(2+)-dependent DNAzyme. As a result, the signal reporter sequence could leave the electrode surface to trigger HCR with the help of two auxiliary DNA single-strands, A1 and A2. Then, the electron mediator hexaammineruthenium (III) chloride ([Ru(NH3)6](3+)) was embedded into the double-stranded DNA (dsDNA) to produce a strong electrochemical signal for the quantitative measurement of TB. For further amplification of the electrochemical signal, graphene reduced by dopamine (PDA-rGO) was introduced as a platform in this work. With this strategy, the aptasensor displayed a wide linearity in the range of 0.0001 nM to 50 nM with a low detection limit of 0.05 pM. Moreover, the resulting aptasensor exhibited good specificity and acceptable reproducibility and stability. Because of these factors, the fabrication protocol proposed in this work may be extended to clinical application.

A High-Throughput Kinetic Assay for RNA-Cleaving Deoxyribozymes

Determining kinetic constants is important in the field of RNA-cleaving deoxyribozymes (DNAzymes). Using todays conventional gel assays for DNAzyme assays is time-consuming and laborious. There have been previous attempts at producing new and improved assays; however these have drawbacks such as incompatibility with structured DNAzymes, enzyme or substrate modifications and increased cost. Here we present a new method for determining single-turnover kinetics of RNA-cleaving DNAzymes in real-time and in a high-throughput fashion. The assay is based on an intercalating fluorescent dye, PicoGreen, with high specificity for double-stranded DNA and heteroduplex DNA-RNA in this case formed between the DNAzyme and the target RNA. The fluorescence decreases as substrate is converted to product and is released from the enzyme. Using a Flexstation II multimode plate reader with built in liquid handling we could automate parts of the assay. This assay gives the possibility to determine single-turnover kinetics for up to 48 DNAzymes simultaneously. As the fluorescent probe is extrinsic there is no need for enzyme or substrate modifications, making this method less costly compared to other methods. The main novelty of this assay is the possibility of using full-length mRNA as the DNAzyme target.

In vitro selection of a sodium-specific DNAzyme and its application in intracellular sensing

Over the past two decades, enormous progress has been made in designing fluorescent sensors or probes for divalent metal ions. In contrast, the development of fluorescent sensors for monovalent metal ions, such as sodium (Na(+)), has remained underdeveloped, even though Na(+) is one the most abundant metal ions in biological systems and plays a critical role in many biological processes. Here, we report the in vitro selection of the first (to our knowledge) Na(+)-specific, RNA-cleaving deoxyribozyme (DNAzyme) with a fast catalytic rate [observed rate constant (ko(bs)) ∼ 0.1 min(-1)], and the transformation of this DNAzyme into a fluorescent sensor for Na(+) by labeling the enzyme strand with a quencher at the 3' end, and the DNA substrate strand with a fluorophore and a quencher at the 5' and 3' ends, respectively. The presence of Na(+) catalyzed cleavage of the substrate strand at an internal ribonucleotide adenosine (rA) site, resulting in release of the fluorophore from its quenchers and thus a significant increase in fluorescence signal. The sensor displays a remarkable selectivity (>10,000-fold) for Na(+) over competing metal ions and has a detection limit of 135 µM (3.1 ppm). Furthermore, we demonstrate that this DNAzyme-based sensor can readily enter cells with the aid of α-helical cationic polypeptides. Finally, by protecting the cleavage site of the Na(+)-specific DNAzyme with a photolabile o-nitrobenzyl group, we achieved controlled activation of the sensor after DNAzyme delivery into cells. Together, these results demonstrate that such a DNAzyme-based sensor provides a promising platform for detection and quantification of Na(+) in living cells.

Addressing, amplifying and switching DNAzyme functions by electrochemically-triggered release of metal ions

The addressable potential-controlled release of metal ions into electrolyte solutions containing mixtures of nucleic acids leads to the metal ion-guided generation of different DNAzymes and to the activation of DNA cascades.

The design of artificial cells, which mimic the functions of native cells, is an ongoing scientific goal. The development of stimuli-responsive chemical systems that stimulate cascaded catalytic transformations, trigger chemical networks, and control vectorial branched transformations and dose-controlled processes, are the minimum requirements for mimicking cell functions. We have studied the electrochemical programmed release of ions from electrodes, which trigger selective DNAzyme-driven chemical reactions, cascaded reactions that self-assemble catalytic DNAzyme polymers, and the ON–OFF switching and dose-controlled operation of catalytic reactions. The addressable and potential-controlled release of Pb²⁺ or Ag⁺ ions into an electrolyte that includes a mixture of nucleic acids, results in the metal ion-guided selection of nucleic acids yielding the formation of specific DNAzymes, which stimulate orthogonal reactions or activate DNAzyme cascades.