DNAzyme catalytic beacon sensors that resist temperature-dependent variations

Recent Advances on Functional Nucleic-Acid Biosensors

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

Biosensing with DNAzymes

This article provides a comprehensive review of biosensing with DNAzymes, providing an overview of different sensing applications while highlighting major progress and seminal contributions to the field of portable biosensor devices and point-of-care diagnostics. Specifically, the field of functional nucleic acids is introduced, with a specific focus on DNAzymes. The incorporation of DNAzymes into bioassays is then described, followed by a detailed overview of recent advances in the development of in vivo sensing platforms and portable sensors incorporating DNAzymes for molecular recognition. Finally, a critical perspective on the field, and a summary of where DNAzyme-based devices may make the biggest impact are provided.

A label-free fluorescent biosensor based on a catalyzed hairpin assembly for HIV DNA and lead detection

Herein, a label-free fluorescent signal amplification system based on a catalyzed hairpin assembly (CHA) is reported. In this system, two hairpin probes, H1 and H2, were well-designed in which G-quadruplex sequences were integrated into H2. The CHA reaction was triggered by target/trigger DNA and G-quadruplex sequences were released, which can bind the fluorescent amyloid dye thioflavin T (ThT) to provide fluorescence signals. At the same time, target/trigger DNA was released from the product of the CHA reaction (H1-H2), which continued to initiate the next CHA cycle, and the signal was eventually amplified. This signal amplification approach has been successfully used to develop a label-free fluorescent sensing platform for sensitive detection of human immunodeficiency virus (HIV) DNA and Pb²⁺.

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.

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.

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.

Re-engineering 10-23 core DNA- and MNAzymes for applications at standard room temperature

DNA- and MNAzymes are nucleic acid-based enzymes (NAzymes), which infiltrated the otherwise protein-rich field of enzymology three decades ago. The 10-23 core NAzymes are one of the most widely used and well-characterized NAzymes, but often require elevated working temperatures or additional complex modifications for implementation at standard room temperatures. Here, we present a generally applicable method, based on thermodynamic principles governing hybridization, to re-engineer the existing 10-23 core NAzymes for use at 23 °C. To establish this, we first assessed the activity of conventional NAzymes in the presence of cleavable and non-cleavable substrate at 23 °C as well as over a temperature gradient. These tests pointed towards a non-catalytic mechanism of signal generation at 23 °C, suggesting that conventional NAzymes are not suited for use at this temperature. Following this, several novel NAzyme-substrate complexes were re-engineered from the conventional ones and screened for their performance at 23 °C. The complex with substrate and substrate-binding arms of the NAzymes shortened by four nucleotides on each terminus demonstrated efficient catalytic activity at 23 °C. This has been further validated over a dilution of enzymes or enzyme components, revealing their superior performance at 23 °C compared to the conventional 10-23 core NAzymes at their standard operating temperature of 55 °C. Finally, the proposed approach was applied to successfully re-engineer three other new MNAzymes for activity at 23 °C. As such, these re-engineered NAzymes present a remarkable addition to the field by further widening the diverse repertoire of NAzyme applications.

Biochemical and Biophysical Understanding of Metal Ion Selectivity of DNAzymes

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

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.

A label-free biosensor for selective detection of DNA and Pb2+ based on a G-quadruplex

Schematic representation of the DNA and Pb²⁺ detection method.

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.

Lanthanide-dependent RNA-cleaving DNAzymes as metal biosensors

Lanthanides represent a group of very important but challenging analytes for biosensor development. These 15 elements are very similar in their chemical properties. So far, limited success has been realized using the rational ligand design approach. My laboratory has successfully accomplished the task of carrying out combinatorial selection to isolate lanthanide-dependent RNA-cleaving DNAzymes. We report two new DNAzymes, each discovered in a different selection condition and both are highly specific to lanthanides. When both DNAzymes are used together, it is possible to identify the last few heavy lanthanides. Upon introducing a phosphorothioate modification, one of the abovementioned DNAzymes becomes highly active with many toxic heavy metals. With the selection of more DNAzymes with different activity patterns cross the lanthanide series, a sensor array might be produced for identifying each ion. This article is a minireview of the current developments on this topic and some of the historical aspects. It reflects the main content of the Fred Beamish Award presentation delivered at the 2014 Canadian Society for Chemistry Conference in Vancouver. Future directions in this area are also discussed.

Sensitive fluorescence “turn-on” detection of bleomycin based on a superquenched perylene–DNA complex

We introduced a superquenched perylene–DNA complex based method for sensitive fluorescence “turn-on” detection of bleomycin.

Functionalization of cationic poly(p-phenylene ethynylene) with dendritic polyethylene enables efficient DNAzyme delivery for imaging Pb2+ in living cells

We report here an effective Pb²⁺-dependent DNAzyme (8-17 DNAzyme) delivery system based on the water-soluble dendritic polyethylene-cationic poly(p-phenylene ethynylene) for successfully imaging Pb²⁺ in living cells. For utilizing the 8-17 DNAzyme and its unique ability to catalyze a phosphodiester bond cleavage reaction in the presence of Pb²⁺, the distinctive conjugated polymer-based polyvalent nanocarrier design manages to load and transport 8-17 DNAzyme across cell membranes, and to realize the fluorescence imaging of Pb²⁺ in living cells. As shown by the confocal microscopy and flow cytometry observations, the fluorescence of Cy5.5 is obviously activated under the conditions of incubation with Pb²⁺, compared with the absence of Pb²⁺. Taken together, the study demonstrates the combination of the molecular-wire effect with "dendrimer effects" on their effective DNAzyme delivery and their cellular imaging Pb²⁺.

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.

Peroxidase mimicking DNA-gold nanoparticles for fluorescence detection of the lead ions in blood

Oligonucleotide (T30695) modified gold nanoparticles (T30695-Au NPs) have been prepared and employed for quantification of lead ions (Pb(2+)) in blood. The detection of Pb(2+) ions is through the formation of Au-Pb alloys and oligonucleotide-Pb(2+) complexes that catalyze the H(2)O(2)-mediated oxidation of non-fluorescent Amplex UltraRed (AUR) to form a highly fluorescent oxidized AUR product. Surface-assisted laser desorption/ionization time-of-flight mass spectrometry (SALDI-TOF MS) and inductively coupled plasma mass spectrometry (ICP-MS) revealed the formation of Au-Pb alloys on the surfaces of the 40T30695-Au NPs (i.e., the system featuring 40 molecules of T30695 per Au NP) in the presence of Pb(2+) ions, leading to increased catalytic activity for the H(2)O(2)-mediated oxidation of AUR. The fluorescence intensity (excitation/emission maxima: ca. 540/584 nm) of the oxidized AUR product is proportional to the concentration of Pb(2+) ions over the range 0.1-100 nM, with a linear correlation (R(2) = 0.99). The 40T30695-Au NP/AUR probe is highly selective toward Pb(2+) ions (by at least 200-fold over other tested metal ions). The 40T30695-Au NPs/AUR probe provided limits of detection (LOD, at a signal-to-noise ratio 3) for Pb(2+) ions of 0.05 and 0.1 nM, in Tris-acetate solution (5 mM, pH 8.0) without and with salt (150 mM NaCl, 5 mM KCl, 1 mM MgCl(2), and 1 mM CaCl(2)), respectively. Without conducting tedious sample pretreatment, the approach allows detection of Pb(2+) ions in blood samples, showing the potential of the 40T30695-Au NPs/AUR assay for on-site and real-time detection of Pb(2+) ions in biological samples.

Single-stranded DNAzyme-based Pb2+ fluorescent sensor that can work well over a wide temperature range

DNAzymes have become an excellent choice for sensing applications. Based on DNAzymes, three generations of Pb(2+) fluorescent sensors have been reported. In these sensors, two oligonucleotide strands (substrate strand and enzyme strand) were used, which not only increased the complexity of the detection system, but also brought some difficulties for the use of the sensors at elevated temperatures. To overcome this problem, a single-stranded DNAzyme-based Pb(2+) fluorescent sensor was designed by combining the substrate sequence and the enzyme sequence into one oligonucleotide strand. The intramolecular duplex structure of this single-stranded DNAzyme kept the fluorophore and the quencher, labeled at its two ends, in close proximity; thus the background fluorescence was significantly suppressed. Using this fluorescent sensor, Pb(2+) quantitation can be achieved with high sensitivity and high selectivity. In addition, the extraordinary stability of the intramolecular duplex structure could assure a low background fluorescence at high temperature, even if the number of complementary base pairs between the substrate sequence and the enzyme sequence was reduced, allowing the sensor to work well over a wide temperature range. Similar performances of the fluorescent sensor at 4, 25 and 37°C suggested that this sensor has a good ability to resist temperature fluctuations.

Metal ion sensors based on DNAzymes and related DNA molecules

Metal ion sensors are an important yet challenging field in analytical chemistry. Despite much effort, only a limited number of metal ion sensors are available for practical use because sensor design is often a trial-and-error-dependent process. DNAzyme-based sensors, in contrast, can be developed through a systematic selection that is generalizable for a wide range of metal ions. Here, we summarize recent progress in the design of DNAzyme-based fluorescent, colorimetric, and electrochemical sensors for metal ions, such as Pb(2+), Cu(2+), Hg(2+), and UO(2)(2+). In addition, we also describe metal ion sensors based on related DNA molecules, including T-T or C-C mismatches and G-quadruplexes.

Fluorescence detection of lead(II) ions through their induced catalytic activity of DNAzymes

We have developed a fluorescence approach for the highly selective and sensitive detection of Pb(2+) ions using AGRO100, a G-quadruplex DNAzyme. The sensing strategy is based on Pb(2+) ions inducing increased DNAzyme activity of AGRO100 in the presence of hemin, which acts as a cofactor to catalyze H(2)O(2)-mediated oxidation of Amplex UltraRed (AUR). A test of eight aptamers of various sequences for the detection of Pb(2+) ions revealed that AGRO100 performed the best in terms of sensitivity. The AGRO100-AUR probe exhibited high selectivity (>100-fold) toward Pb(2+) ions over other tested metal ions. The fluorescence intensity (excitation/emission maxima, ca. 561/592 nm) of the AUR product was proportional to the concentration of Pb(2+) ions over the range 0-1000 nM, with a linear correlation (R(2) = 0.98). For 5 mM Tris-acetate (pH 7.4) solutions in the presence and absence of 100 mM NaCl, the AGRO100-AUR probe provided limits of detection (signal-to-noise ratio = 3) for Pb(2+) ions of 1.0 and 0.4 nM, respectively. We validated the practicality of the use of the AGRO100-AUR probe for the determination of the concentrations of Pb(2+) ions in soil samples. This approach allows the determination of the concentrations of Pb(2+) ions with simplicity, selectivity, and sensitivity.

Label-free colorimetric biosensing of copper(II) ions with unimolecular self-cleaving deoxyribozymes and unmodified gold nanoparticle probes

Using unimolecular copper(II)-dependent self-cleaving deoxyribozymes (DNAzymes), a label-free colorimetric biosensor for copper(II) ions (Cu2+) has been developed based on the sequence-length-dependent adsorption of single-stranded deoxyribonucleic acid (ssDNA) on unmodified gold nanoparticles (AuNPs). In the presence of Cu2+, the Cu2+-dependent DNAzyme could be self-cleaved into short ssDNA fragments. The cleaved short ssDNA could adsorb rapidly onto the surface of the AuNPs. This enhanced the stability of the AuNPs against salt-induced aggregation, and thus the solution color remained red. In the absence of Cu2+, however, uncleaved long ssDNA adsorbed relatively slowly onto the AuNPs and upon the addition of salt, the electrostatic repulsion between the AuNPs was screened, resulting in aggregation of the AuNPs which produced a red-to-blue color change. Thus, Cu2+ detection could be realized by monitoring the color change of the AuNPs. The calibration curve showed that the absorption ratio values at 520 and 620 nm increased linearly over the Cu2+ concentration range of 0.625-15 microM, with a limit of detection of 290 nM. The other environmentally relevant metal ions did not interfere with the determination of Cu2+. Subsequently, the assay was employed to determine Cu2+ in several water samples, and the results were satisfactory. It is expected that the present colorimetric strategy will be possibly extended to the detection of cofactors of other in vitro-selected unimolecular self-cleaving DNAzymes, such as amino acids, nucleic acids, metal ions and small organic molecules.

A highly selective lead sensor based on a classic lead DNAzyme

A catalytic beacon sensor for Pb(2+) has been developed based on the first DNAzyme discovered in the field, and such a sensor has shown a much higher metal ion selectivity (40,000 times) than the previously reported Pb(2+) sensor based on 8-17 DNAzyme and thus is suitable for a wider range of practical applications.