Pb(2+)-introduced activation of horseradish peroxidase (HRP)-mimicking DNAzyme

Unraveling the Kinetics of the 10-23 RNA-Cleaving DNAzyme

DNA-based enzymes, or DNAzymes, are single-stranded DNA sequences with the ability to catalyze various chemical reactions, including the cleavage of the bond between two RNA nucleotides. Lately, an increasing interest has been observed in these RNA-cleaving DNAzymes in the biosensing and therapeutic fields for signal generation and the modulation of gene expression, respectively. Additionally, multiple efforts have been made to study the effects of the reaction environment and the sequence of the catalytic core on the conversion of the substrate into product. However, most of these studies have only reported alterations of the general reaction course, but only a few have focused on how each individual reaction step is affected. In this work, we present for the first time a mathematical model that describes and predicts the reaction of the 10-23 RNA-cleaving DNAzyme. Furthermore, the model has been employed to study the effect of temperature, magnesium cations and shorter substrate-binding arms of the DNAzyme on the different kinetic rate constants, broadening the range of conditions in which the model can be exploited. In conclusion, this work depicts the prospects of such mathematical models to study and anticipate the course of a reaction given a particular environment.

DNA-only bioassay for simultaneous detection of proteins and nucleic acids

Testing multiple biomarkers, as opposed to one, has become a preferred approach for diagnosing many heterogeneous diseases, such as cancer and infectious diseases. However, numerous technologies, including gold standard ELISA and PCR, can detect only one type of biomarker, either protein or nucleic acid (NA), respectively. In this work, we report for the first time simultaneous detection of proteins and NAs in the same solution, using solely functional NA (FNA) molecules. In particular, we combined the thrombin binding aptamer (TBA) and the 10-23 RNA-cleaving DNA enzyme (DNAzyme) in a single aptazyme molecule (Aptazyme1.15-3'), followed by extensive optimization of buffer composition, sequences and component ratios, to establish a competitive bioassay. Subsequently, to establish a multiplex bioassay, we designed a new aptazyme (Aptazyme2.20-5') by replacing the target recognition and substrate sequences within Aptazyme1.15-3'. This designing process included an in silico study, revealing the impact of the target recognition sequence on the aptazyme secondary structure and its catalytic activity. After proving the functionality of the new aptazyme in a singleplex bioassay, we demonstrated the capability of the two aptazymes to simultaneously detect thrombin and NA target, or two NA targets in a multiplex bioassay. High specificity in target detection was achieved with the limits of detection in the low nanomolar range, comparable to the singleplex bioassays. The presented results deepen the barely explored features of FNA for diagnosing multiple targets of different origins, adding an extra functionality to their catalogue.

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.

Advances in Optical Biosensors and Sensors Using Nanoporous Anodic Alumina

This review paper focuses on recent progress in optical biosensors using self-ordered nanoporous anodic alumina. We present the fabrication of self-ordered nanoporous anodic alumina, surface functionalization, and optical sensor applications. We show that self-ordered nanoporous anodic alumina has good potential for use in the fabrication of antibody-based (immunosensor), aptamer-based (aptasensor), gene-based (genosensor), peptide-based, and enzyme-based optical biosensors. The fabricated optical biosensors presented high sensitivity and selectivity. In addition, we also showed that the performance of the biosensors and the self-ordered nanoporous anodic alumina can be used for assessing biomolecules, heavy ions, and gas molecules.

Bioanalytical Application of Peroxidase-Mimicking DNAzymes: Status and Challenges

DNAzymes with peroxidase-mimicking activity are a new class of catalytically active DNA molecules. This system is formed as a complex of hemin and a G-quadruplex structure created by oligonucleotides rich in guanine. Considering catalytic activity, this DNAzyme mimics horseradish peroxidase, the enzyme most commonly used for signal generation in bioassays. Because DNAzymes exhibit many advantages over protein enzymes (thermal stability, easy and cheap synthesis and purification) they can successfully replace HRP in bioanalytical applications. HRP-like DNAzymes have been applied in the detection of several DNA sequences. Many amplification techniques have been conjugated with DNAzyme systems, resulting in ultrasensitive bioassays. On the other hand, the combination of aptamers and DNAzymes has led to the development of aptazymes for specific targets. An up-to-date summary of the most interesting DNAzyme-based assays is presented here. The elaborated systems can be used in medical diagnosis or chemical and biological studies.

Logic Catalytic Interconversion of G-Molecular Hydrogel

By incorporating hemin into G-quadruplex (G₄) during cation-templated self-assembly between guanosine and KB(OH)₄, we have constructed an artificial enzyme hydrogel (AEH)-based system for the highly sensitive and selective detection of Pb²⁺. The sensing strategy is based on a Pb²⁺-induced decrease in AEH activity. Because of the higher efficiency of Pb²⁺ for stabilizing G₄ compared with K⁺, the Pb²⁺ ions substitute K⁺ and trigger hemin release from G₄, thus giving rise to a conformational interconversion accompanied by the loss of enzyme activity. The Pb²⁺-induced catalytic interconversion endows the AEH-based system with high sensitivity and selectivity for detecting Pb²⁺. As a result, the AEH-based system shows an excellent response for Pb²⁺ in the range from 1 pM to 50 nM with a limit of detection of ∼0.32 pM, which is much lower than that of the previously reported G₄-DNAzyme. We also demonstrate that this AEH-based system exhibits high selectivity toward Pb²⁺ over other metal ions. Furthermore, two two-input INHIBIT logic gates have been constructed via switching of the catalytic interconversion induced by K⁺ and Pb²⁺ or K⁺ and pH. Given its versatility, this AEH-based system provides a novel platform for sensing and biomolecular computation.

Cerium Dioxide-Mediated Signal "On-Off" by Resonance Energy Transfer on a Lab-On-Paper Device for Ultrasensitive Detection of Lead Ions

In this report, a 3D microfluidic lab-on-paper device for ultrasensitive detection of lead cation was designed using phoenix tree fruit-shaped CeO₂ nanoparticles (PFCeO₂ NPs) as the catalyst and 50 nm silver NPs (Ag NPs) as the quencher. First, snowflake-like Ag NPs were grown on the paper working electrode through an in situ growth method and used as a matrix for DNAzymes that were specific for lead ions (Pb²⁺). After the addition of Ag NP-labeled substrate strands, the Ag NPs restrained the electrochemiluminescence (ECL) intensity of luminol greatly through the resonance energy transfer from luminol to Ag NPs. However, under the existence of Pb²⁺, the substrate strands were separated, and then PFCeO₂ NP-labeled signal strands were hybridized with the DNAzymes. The ECL signal was improved greatly under the fast catalytic reaction between PFCeO₂ NPs and H₂O₂, which converted the response from signal off to signal on state, resulting in sensitive detection of Pb²⁺. Under the optimal conditions, the ECL signal response exhibited a good linear relationship with the logarithm of lead cation in a wide linear range of 0.05-2000 nM and an ultralow detection limit of 0.016 nM. Meanwhile, a sensor featured with good specificity, acceptable stability, reproducibility, and low cost provides a promising portable, simple, and effective strategy for Pb²⁺ detection.

A resonance Rayleigh scattering sensor for detection of Pb2+ ions via cleavage-induced G-wire formation

A resonance Rayleigh scattering (RRS) aptasensor was fabricated for detection of Pb²⁺via hairpin-like label-free substrate and G-wire for signal amplification. A hairpin-like DNA substrate contains a sequence in the loop labeled with ribonucleobase A and c-myc sequence in the stem. When hybridized with 8-17 DNAzyme in the presence of Pb²⁺, the sequence in the loop was activated and cleaved. Hundreds of c-myc sequences departing from the 8-17 DNAzyme yield nanowires superstructure called G-wire in the presence of Mg²⁺. The polymer G-wire was demonstrated by the RRS spectrum, polyacrylamide gel electrophoresis, and AFM. The RRS intensity was enhanced by the product G-wires, and the RRS signal at 370nm was linear with the logarithm of Pb²⁺ concentration in the range of 2.0nM to 5.0μM. This method was selective for Pb²⁺ even coexisting with other metal ions at high concentrations and was successfully applied to the determination of Pb²⁺ in real samples. The aptasensor holds a great promise for universal RRS sensing platform for sensitive detection of various metal ions just by changing the sequence of the probe in the loop and DNAzyme.

DNA G-Quadruplex-Based Assay of Enzyme Activity

DNA G-quadruplexes are special three-dimensional (3D) DNA nanostructures formed by specific G-rich DNA sequences. These 3D DNA nanostructures can bind with hemin and significantly improve the intrinsic peroxidase activity of hemin. Besides this function, they also enhance the fluorescence intensity of some G-quadruplex-specific dyes. Owing to these features, G-quadruplexes possess several superiorities in the detection of enzymes involved in nucleic acid metabolism, including facile probe fabrication without labeling, simple detection process without washing or separation steps, rapid observation by naked eyes, and easy integration with nucleic acid amplification strategies to amplify signals. Herein, we describe two strategies for label-free detection of enzyme activity based on DNA G-quadruplexes. To increase sensitivity, template-dependent and template-independent DNA amplifications were introduced for the amplification of G-rich DNA sequences. DNA methyltransferase and terminal deoxynucleotidyl transferase were detected as two model analytes, respectively.

Insight into G-quadruplex-hemin DNAzyme/RNAzyme: adjacent adenine as the intramolecular species for remarkable enhancement of enzymatic activity

G-quadruplex (G4) with stacked G-tetrads structure is able to bind hemin (iron (III)-protoporphyrin IX) to form a unique type of DNAzyme/RNAzyme with peroxidase-mimicking activity, which has been widely employed in multidisciplinary fields. However, its further applications are hampered by its relatively weak activity compared with protein enzymes. Herein, we report a unique intramolecular enhancement effect of the adjacent adenine (EnEAA) at 3' end of G4 core sequences that significantly improves the activity of G4 DNAzymes. Through detailed investigations of the EnEAA, the added 3' adenine was proved to accelerate the compound I formation in catalytic cycle and thus improve the G4 DNAzyme activity. EnEAA was found to be highly dependent on the unprotonated state of the N1 of adenine, substantiating that adenine might function as a general acid-base catalyst. Further adenine analogs analysis supported that both N1 and exocyclic 6-amino groups in adenine played key role in the catalysis. Moreover, we proved that EnEAA was generally applicable for various parallel G-quadruplex structures and even G4 RNAzyme. Our studies implied that adenine might act analogously as the distal histidine in protein peroxidases, which shed light on the fundamental understanding and rational design of G4 DNAzyme/RNAzyme catalysts with enhanced functions.

Dual-modal light scattering and fluorometric detection of lead ion by stimuli-responsive aggregation of BSA-stabilized copper nanoclusters

A new and facilely prepared light scattering (LS) and fluorometric dual-mode sensor is developed for lead ion (Pb²⁺) detection with high sensitivity and selectivity by use of bovine serum albumin stabilized copper nanoclusters (BSA–Cu NCs).

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.

Simple and efficient method to purify DNA-protein conjugates and its sensing applications

DNA-protein conjugates are very useful in analytical chemistry for target recognition and signal amplification. While a number of methods for conjugating DNA with proteins are known, methods for purification of DNA-protein conjugates from reaction mixture containing unreacted proteins are much less investigated. In this work, a simple and efficient approach to purify DNA-invertase conjugates from reaction mixture via a biotin displacement strategy to release desthiobiotinylated DNA-invertase conjugates from streptavidin-coated magnetic beads was developed. The conjugates purified by this approach were utilized for quantitative detection of cocaine and DNA using a personal glucose meter through structure-switching DNA aptamer sensors and competitive DNA hybridization assays, respectively. In both cases, the purified DNA-invertase conjugates showed better performance compared to the same assays using unpurified conjugates. The approach demonstrated here can be further expanded to other DNA and proteins to generate purified DNA-protein conjugates for analytical and other applications.

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.

Label-free fluorescent sensor for lead ion detection based on lead(II)-stabilized G-quadruplex formation

A label-free fluorescent DNA sensor for the detection of lead ions (Pb(2+)) based on lead(II)-stabilized G-quadruplex formation is proposed in this article. A guanine (G)-rich oligonucleotide, T30695, was used as a recognition probe, and a DNA intercalator, SYBR Green I (SG), was used as a signal reporter. In the absence of Pb(2+), the SG intercalated with the single-stranded random-coil T30695 and emitted strong fluorescence. While in the presence of Pb(2+), the random-coil T30695 would fold into a G-quadruplex structure and the SG could barely show weak fluorescence, and the fluorescence intensity was inversely proportional to the involving amount of Pb(2+). Based on this, a selective lead ion sensor with a limit of detection of 3.79 ppb (parts per billion) and a detection range from 0 to 600 ppb was constructed. Because detection for real samples was also demonstrated to be reliable, this simple, low-cost, sensitive, and selective sensor holds good potential for Pb(2+) detection in real environmental samples.

A new colorimetric strategy for monitoring caspase 3 activity by HRP-mimicking DNAzyme–peptide conjugates

A new colorimetric method is designed for the detection of caspase 3 activity by HRP-mimicking DNAzyme–peptide conjugates.

Ultrasensitive detection of 3′-5′ exonuclease enzymatic activity using molecular beacons

An ultrasensitive and rapid fluorescence assay was developed for the detection of 3′-5′ exonuclease activity using molecular beacons.

Rapid and highly sensitive detection of lead ions in drinking water based on a strip immunosensor

In this study, we have first developed a rapid and sensitive strip immunosensor based on two heterogeneously-sized gold nanoparticles (Au NPs) probes for the detection of trace lead ions in drinking water. The sensitivity was 4-fold higher than that of the conventional LFA under the optimized conditions. The visual limit of detection (LOD) of the amplified method for qualitative detection lead ions was 2 ng/mL and the LOD for semi-quantitative detection could go down to 0.19 ng/mL using a scanning reader. The method suffered from no interference from other metal ions and could be used to detect trace lead ions in drinking water without sample enrichment. The recovery of the test samples ranged from 96% to 103%. As the detection method could be accomplished within 15 min, this method could be used as a potential tool for preliminary monitoring of lead contamination in drinking water.

Resonance Raman scattering of catalytic beacons for DNA detection

A novel method for analysing the catalytic action of a DNAzyme is reported. Resonance Raman scattering (RRS) is shown to successfully monitor the oxidation of two different peroxidase substrates and has been implemented in an assay for the detection of target DNA, providing a more sensitive method of analysis than current colorimetric techniques.

Deciphering the DNAzyme activity of multimeric quadruplexes: insights into their actual role in the telomerase activity evaluation assay

The end of human telomeres is comprised of a long G-rich single-stranded DNA (known as 3'-overhang) able to adopt an unusual three-dimensional "beads-on-the-string" organization made of consecutively stacked G-quadruplex units (so-called quadruplex multimers). It has been widely demonstrated that, upon interaction with hemin, discrete quadruplexes acquire peroxidase-mimicking properties, oxidizing several organic probes in H(2)O(2)-rich conditions; this property, known as DNAzyme, has found tens of applications in the last two decades. However, little is known about the DNAzyme activity of multimeric quadruplexes; this is an important question to address, especially in light of recent reports that exploit the DNAzyme process to optically assess the activity of an enzyme that elongates the telomeric overhang, the telomerase. Herein, we thoroughly investigate the DNAzyme activity of long telomeric fragments, with a particular focus on both the nature of the hemin/multimeric quadruplex interactions and the putative higher-order fold of the studied fragments; in light of our results, we also propose possible ways that may be followed to improve the use of DNAzyme to evaluate the telomerase activity.