Target‐stimulated DNAzyme Concatamers Released from Aptasensor for Highly Sensitive and Specific Detection of Progesterone

Aiming at the detection of ultralow concentration target progesterone (Pro), a novel electrochemical aptasensor based on DNAzyme concatamers signal amplification strategy was proposed. The strategy consists of target DNA strands (TDNAs), and two different hairpin DNA molecules (H1 and H2). The signal is amplified by the large amount of DNAzyme. The TDNAs modified on the electrode open H1 structures in sequence and propagate a reaction of hybridization events between two alternating hairpins (H1and H2) to obtain abundant DNAzyme concatamers. Upon target Pro introduction, a specific Pro‐TDNAs reaction was executed, thereby resulting in the release of DNAzyme concatamers from the electrode. Subsequent differential pulse voltammetry(DPV) detection of aminoazobenzene (DAP) resulting by DNAzyme catalyze the oxidation of o‐phenylenediamine (OPD) with the aid of hydrogen peroxide (H₂O₂). Likewise, a small amount of target Pro can efficiently induce the release of a large number of the DNAzyme from the electrode in the form of DNAzyme concatamer. Under optimal conditions, the the proposed assay presents good electrochemical responses for determination of target Pro in the range of 0.5 to 15 ng/mL with the detection limit of 0.36 ng/mL. In addition, the resulting sensor can successfully distinguish Pro from coexisting interfering substance and show good stability and high repeatability. What's more, the methodology has also been demonstrated by assaying Pro‐spiked samples in serum.     

Assistant deoxyribonucleic acid recycling with Zn and molecular beacon for electrochemical detection of deoxyribonucleic acid via target-triggered assembly of mutated DNAzyme

A novel enzyme-free amplification strategy was designed for sensitive electrochemical detection of deoxyribonucleic acid (DNA) based on Zn²⁺ assistant DNA recycling via target-triggered assembly of mutated DNAzyme. A gold electrode was used to immobilize molecular beacon (MB) as the recognition probe and perform the amplification procedure. In the presence of target DNA, the hairpin probe 1 was opened, and the DNAzyme was liberated from the caged structure. The activated DNAzyme first hybridized and then cleaved the MB in the presence of cofactor Zn²⁺. After cleavage, the MB was cleaved into two pieces and the ferrocene (Fc) labeled piece dissociated from the gold electrode, thus obviously decreasing the Fc signal and forming a free DNAzyme strand. Finally, each target-induced activated DNAzyme underwent many cycles to trigger the cleavage of many MB substrates. Therefore, the peak current of Fc dramatically decreased to approximately zero. The strategy showed a detection limit at 35 fM levels, which was about 2 orders of magnitude lower than that of the conventional hybridization without Zn²⁺-based amplification. The Zn²⁺ assistant DNA recycling offers a versatile platform for DNA detection in a cost-effective manner, and has a promising application in clinical diagnosis.     

Enzyme spheres as novel tracing tags coupled with target-induced DNAzyme assembly for ultrasensitive electrochemical microRNA assay

In this work, an ultrasensitive electrochemical microRNA detection strategy was developed based on porous palladium-modified horseradish peroxidase sphere (Pd@HRP) and target-induced assembly of DNAzyme. A highly loaded HRP sphere was prepared by covalent layer-by-layer assembly with CaCO₃ as sacrificial template for the first time, and was further modified with porous Pd. Notably, Pd@HRP composite showed a good redox activity of HRP and electrocatalytic activity toward H₂O₂. The utilization of Pd@HRP as electrochemical signal indicator and enhancer to fabricate biosensor could avoid the need for additional redox mediator and amplify the detection sensitivity. Moreover, target recycling amplification was achieved by Pb²⁺-induced cleavage of ternary “Y” structure, circumventing the use of labile nuclease. Subsequent DNA concatamer synthesized through rolling circle amplification (RCA) reaction with cleaved hairpin probe as primer, hybridized with plentiful Pd@HRP-DNA probes, which led to the increased loading of redox-active and electrocatalytic Pd@HRP for sensitivity improvement. So the proposed electrochemical biosensor detected miRNA-24 down to 0.2 fM (S/N = 3) with a wide linear range from 3 fM to 1 nM. With bifunctional Pd@HRP tag, DNAzyme-aided target recycle and programmable junction probe, this strategy possessed the advantages of high efficiency, high sensitivity, low cost and versatility, and thus held great promise for other low-abundance nucleic acids determination.     

Label-free and amplified electrochemical detection of cytokine based on hairpin aptamer and catalytic DNAzyme

In this work, by incorporating a specific DNAzyme sequence into a hairpin aptamer probe, we describe a label-free and sensitive method for electrochemical detection of cytokines using recombinant human IFN-γ as the model analyte. The hairpin aptamer probes are immobilized on a gold electrode through self-assembly. The presence of IFN-γ opens the hairpin structure and forms the hemin/G-quadruplex peroxidase-mimicking DNAzyme with subsequent addition of hemin. The peroxidase-mimicking DNAzyme catalyzes the electro-reduction of H(2)O(2) and amplifies the current response for IFN-γ detection, which enables the monitoring of IFN-γ at the sub-nanomolar level. The proposed sensor also shows high selectivity towards the target analyte. Our strategy thus opens new opportunities for label-free and amplified detection of different types of cytokines.     

Label-free fluorescent detection of thrombin using G-quadruplex-based DNAzyme as sensing platform

We report herein a label-free and sensitive fluorescent method for detection of thrombin using a G-quadruplex-based DNAzyme as the sensing platform. The thrombin-binding aptamer (TBA) is able to bind hemin to form the G-quadruplex-based DNAzyme, and thrombin can significantly enhance the activity of the G-quadruplex-based DNAzyme. The G-quadruplex-based DNAzyme is found to effectively catalyze the H(2)O(2)-mediated oxidation of thiamine, giving rise to fluorescence emission. This allows us to utilize the H(2)O(2)-thiamine fluorescent system for the quantitative analysis of thrombin. The assay shows a linear toward thrombin concentration in the range of 0.01-0.12 nM. The present limit of detection for thrombin is 1 pM, and the sensitivity for analyzing thrombin is improved by about 10,000-fold as compared with the reported colorimetric counterpart. The work also demonstrates that thiamine is an excellent substrate for the fluorescence assay using the G-quadruplex-based DNAzyme as the sensing platform.     

Zn(2+)-ligation DNAzyme-driven enzymatic and nonenzymatic cascades for the amplified detection of DNA

A generic fluorescence sensing platform for analyzing DNA by the Zn(2+)-dependent ligation DNAzyme as amplifying biocatalyst is presented. The platform is based on the target DNA induced ligation of two substrate subunits and the subsequent opening of a beacon hairpin probe by the ligated product. The strand displacement of the ligated product by the beacon hairpin is, however, of limited efficiency. Two strategies are implemented to overcome this limitation. By one method, a "helper" nucleic acid sequence is introduced into the system, and this hybridizes with the DNAzyme components and releases the ligated product for opening of the hairpin. By the second method, a nicking enzyme (Nt.BspQI) is added to the system, and this nicks the duplex between the beacon and ligated product while recycling the free ligation product. By combining the two coadded components ("helper" sequence and nicking enzyme), the sensitive detection of the analyte is demonstrated (detection limit, 20 pM). The enzyme-free amplified fluorescence detection of the target DNA is further presented by the Zn(2+)-dependent ligation DNAzyme-driven activation of the Mg(2+)-dependent DNAzyme. According to this method, the Mg(2+)-dependent DNAzyme subunits displace the ligated product, and the resulting assembled DNAzyme cleaves a fluorophore/quencher-modified substrate to yield fluorescence. The method enabled the detection of the target DNA with a detection limit corresponding to 10 pM. The different sensing platforms are implemented to detect the Tay-Sachs genetic disorder mutant.     

Amplified analysis of DNA by the autonomous assembly of polymers consisting of DNAzyme wires

A systematic study of the amplified optical detection of DNA by Mg(2+)-dependent DNAzyme subunits is described. The use of two DNAzyme subunits and the respective fluorophore/quencher-modified substrate allows the detection of the target DNA with a sensitivity corresponding to 1 × 10(-9) M. The use of two functional hairpin structures that include the DNAzyme subunits in a caged, inactive configuration leads, in the presence of the target DNA, to the opening of one of the hairpins and to the activation of an autonomous cross-opening process of the two hairpins, which affords polymer DNA wires consisting of the Mg(2+)-dependent DNAzyme subunits. This amplification paradigm leads to the analysis of the target DNA with a sensitivity corresponding to 1 × 10(-14) M. The amplification mixture composed of the two hairpins can be implemented as a versatile sensing platform for analyzing any gene in the presence of the appropriate hairpin probe. This is exemplified with the detection of the BRCA1 oncogene.     

A Competitor-switched Electrochemical Sensor for Detection of DNA

A competitor‐switched electrochemical sensor based on a generic displacement strategy was designed for DNA detection. In this strategy, an unmodified single‐stranded DNA (cDNA) completely complementary to the target DNA served as the molecular recognition element, while a hairpin DNA (hDNA) labeled with a ferrocene (Fc) and a thiol group at its terminals served as both the competitor element and the probe. This electrochemical sensor was fabricated by self‐assembling a dsDNA onto a gold electrode surface. The dsDNA was pre‐formed through the hybridization of Fc‐labeled hDNA and cDNA with their part complementary sequences. Initially, the labeled ferrocene in the dsDNA was far from surface of the electrode, the electrochemical sensor exhibited a "switch‐off" mode due to unfavorable electron transfer of Fc label. However, in the presence of target DNA, cDNA was released from hDNA by target DNA, the hairpin‐open hDNA restored its original hairpin structure and the ferrocene approached onto the electrode surface, thus the electrochemical sensor exhibited a "switch‐on" mode accompanying with a change in the current response. The experimental results showed that as low as 4.4×10⁻¹⁰ mol/L target DNA could be distinguishingly detected, and this method had obvious advantages such as facile operation, low cost and reagentless procedure.     

Hemin/G-quadruplex-based DNAzyme concatamers as electrocatalysts and biolabels for amplified electrochemical immunosensing of IgG1

Hemin/G-quadruplex-based DNAzyme concatamers were utilized as electrocatalysts and biolabels to construct a sandwich-type electrochemical immunosensor for sensitive detection of IgG1 (as a model analyte).     

Enzyme-free signal amplification in the DNAzyme sensor via target-catalyzed hairpin assembly

A simple, highly sensitive and enzyme-free DNAzyme sensor based on target-catalyzed hairpin assembly is developed, which permits detection of 0.1 pM target DNA. Furthermore, this DNAzyme sensor is capable of detecting target DNA in real samples because of its high selectivity.     

A new electrochemical method for DNA sequence detection with homogeneous hybridization based on host–guest recognition technology

This communication reports on a new electrochemical method to detect the hybridization specificity by using host–guest recognition technique. A hairpin DNA with dabcyl-labeled at its 3′ and NH₂ group at 5′ terminal was combined with CdS nanoparticle to construct a double-labeled probe (DLP), which could selectively hybridize with its target DNA in homogeneous solution. A β-CD modified Poly(N-acetylaniline) glassy carbon electrode was used for capturing the dabcyl label in DLP. When without binding with target DNA, the DLP kept its stem-loop structure which shielded the dabcyl molecule due to the loop of the hairpin DNA and CdS nanoparticle blocking dabcyl enter into the cavity of these β-CD molecules on the electrode. However, in present of complementary sequence, the target-binding DLP was incorporated into double stranded DNA, causing the DLP’s loop-stem structure opened and then the dabcyl was easily captured by the β-CD modified electrode. During electrochemical measurement, the signal from the dissolved Cd²⁺ was used for target DNA quantitative analysis.     

Dual Signal Amplification Electrochemical Biosensor for Lead Cation

Herein, a sensitive electrochemical Pb²⁺ sensor was developed which based on DNA‐functionalized Au nanoparticles(AuNPs) and nanocomposite modified electrode. The DNA‐functionalized AuNPs includes two types of DNA, namely a Pb²⁺‐mediated DNAzyme comprising a biotin labeled‐enzyme DNA and a substrate strand DNA with a typical stem‐loop structure, and a ferrocene‐labeled linear signal DNA. Without Pb²⁺, the hairpin loop impeded biotin binding to avidin on the electrode. However,when the goal Pb²⁺ exists, the substratum strand was divided into two fragments that lead to the enzyme strand was substratumed on the electrode and biotin was admited by avidin, bringing about DNA‐functionalized AuNP(AuNPs) deposition on the electrode surface.The differential pulse voltammetry (DPV) was used to measure electrochemical response signals connect to signal DNA.For the amplification characters of the DNA‐functionalized AuNPs and nanocomposite, the electrochemical detection signal of Pb²⁺ was greatly improved and revealed high specificity. Under optimum conditions, the resultant biosensor bringed out a high sensitivity and selectivity for the determination of Pb²⁺. The proposed method was able to detect as low as picomolar Pb²⁺ concentrations.     

A novel electrochemical aptasensor for highly sensitive detection of thrombin based on the autonomous assembly of hemin/G-quadruplex horseradish peroxidase-mimicking DNAzyme nanowires

In this work, a new signal amplified strategy was constructed based on isothermal exponential amplification reaction (EXPAR) and hybridization chain reaction (HCR) generating the hemin/G-quadruplex horseradish peroxidase-mimicking DNAzyme (HRP-mimicking DNAzyme) nanowires as signal output component for the sensitive detection of thrombin (TB). We employed EXPAR’s ultra-high amplification efficiency to produce a large amount of two hairpin helper DNAs within a minutes. And then the resultant two hairpin helper DNAs could autonomously assemble the hemin/G-quadruplex HRP-mimicking DNAzymes nanowires as the redox-active reporter units on the electrode surface via hybridization chain reaction (HCR). The hemin/G-quadruplex structures simultaneously served as electron transfer medium and electrocatalyst to amplify the signal in the presence of H₂O₂. Specifically, only when the EXPAR reaction process has occurred, the HCR could be achieved and the hemin/G-quadruplex complexes could be formed on the surface of an electrode to give a detectable signal. The proposed strategy combines the amplification power of the EXPAR, HCR, and the inherent high sensitivity of the electrochemical detection. With such design, the proposed assay showed a good linear relationship within the range of 0.1 pM–50 nM with a detection limit of 33 fM (defined as S/N = 3) for TB.     

Comparative Study of HRP,a Peroxidase‐Mimicking DNAzyme,and ALP as Enzyme Labels in Developing Electrochemical Genosensors for Pathogenic Bacteria

A comparative evaluation of an electrochemical sandwich genoassay for pathogenic bacteria based on immobilized hairpin DNA probes and three different enzyme labels (horseradish peroxidase, alkaline phosphatase and a biomimetic peroxidase‐like DNAzyme) is reported. The natural enzymes were used as streptavidin conjugates, coupled to the surface duplex by using a biotin‐labeled signaling probe, whereas the DNAzyme was directly incorporated to the sequence of the signaling probe. HRP provides enhanced sensitivity although the choice of a catalytic reporter DNA sequence could simplify the assay.     

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

A novel nucleic acid hairpin structure composed of Pb(2+)-dependent DNAzyme and HRP-mimicking DNAzyme was developed. This hairpin structure can be used as a sensor for the detection of Pb(2+) based on colorimetry.     

A sensitive electrochemical aptasensor for ATP detection based on exonuclease III-assisted signal amplification strategy

A target-induced structure-switching electrochemical aptasensor for sensitive detection of ATP was successfully constructed which was based on exonuclease III-catalyzed target recycling for signal amplification. With the existence of ATP, methylene blue (MB) labeled hairpin DNA formed G-quadruplex with ATP, which led to conformational changes of the hairpin DNA and created catalytic cleavage sites for exonuclease III (Exo III). Then the structure-switching DNA hybridized with capture DNA which made MB close to electrode surface. Meanwhile, Exo III selectively digested aptamer from its 3′-end, thus G-quadruplex structure was destroyed and ATP was released for target recycling. The Exo III-assisted target recycling amplified electrochemical signal significantly. Fluorescence experiment was performed to confirm the structure-switching process of the hairpin DNA. In fluorescence experiment, AuNPs–aptamer conjugates were synthesized, AuNPs quenched fluorescence of MB, the target-induced structure-switching made Exo III digested aptamer, which restored fluorescence. Under optimized conditions, the proposed aptasensor showed a linear range of 0.1–20 nM with a detection limit of 34 pM. In addition, the proposed aptasensor had good stability and selectivity, offered promising choice for the detection of other small molecules.     

DNAzyme based electrochemical sensors for trace uranium

We have developed a uranyl-specific DNAzyme that was immobilized on the surface of a gold electrode to give a highly sensitive and selective biosensor for uranyl ion. The typical DNAzyme system consisted of the RNA (rA) as the substrate (ADNA), and the other strand is the enzyme (TDNA) with a ferrocene (Fc). The presence of uranyl ion induces the cleavage of the DNA substrate strand at the rA position to form two fragments. The Fc unit thereby is released from the surface of the electrode, and this results in a decreased peak current. This electrochemical biosensor has a dynamic range from 2 nM to 14 nM of uranyl ion, with a detection limit at 1 nM. It exhibits high sensitivity and excellent selectivity over other metal ions, and thus represents a promising technique for simple, fast, on-site, and real-time electrochemical sensing of UO₂(II) ion. It also serves as a guide in choosing different methods for designing electrochemical sensors for other metal ions.

Molecular beacon mediated circular strand displacement strategy for constructing a ratiometric electrochemical deoxyribonucleic acid sensor

A novel ratiometric electrochemical sensor for sensitive and selective determination of deoxyribonucleic acid (DNA) had been developed based on signal-on and signal-off strategy. The target DNA hybridized with the loop portion of ferrocene (Fc) labeled hairpin probe immobilized on the gold electrode (GE), the Fc away from the surface of GE and the methylene blue (MB) was attached to an electrode surface by hybridization between hairpin probe and MB labeled primer. Such conformational changes resulted in the oxidation peak current of Fc decreased and that of MB increased, and the changes of dual signals are linear with the concentration of DNA. Furthermore, with the help of strand-displacement polymerization, polymerase catalyzed the extension of the primer and the sequential displacement of the target DNA, which led to the release of target and another polymerization cycle. Thus the circular strand displacement produced the multiplication of the MB confined near the GE surface and Fc got away from the GE surface. Therefore, the recognition of target DNA resulted in both the “signal-off” of Fc and the “signal-on” of MB for dual-signal electrochemical ratiometric readout. The dual signal strategy offered a dramatic enhancement of the stripping response. The dynamic range of the target DNA detection was from 10⁻¹³ to 10⁻⁸ mol L⁻¹ with a detection limit down to 28 fM level. Compared with the single signaling electrochemical sensor, the dual-signaling electrochemical sensing strategy developed in this paper was more selective. It would have important applications in the sensitive and selective electrochemical determination of other small molecules and proteins.     

An Electrochemical Sensor for the Detection of Cu2+ Based on Gold Nanoflowers‐modifed Electrode and DNAzyme Functionalized Au@MIL‐101 (Fe)

In this study, we developed an electrochemical sensor for sensitive detection of Cu²⁺ based on gold nanoflowers (AuNFs)‐modified electrode and DNAzyme functionalized Au@MIL‐101(Fe) (MIL: Materials of Institute Lavoisier). The AuNFs‐modified indium tin oxide modified conductive glass electrode(AuNFs/ITO) prepared via electrodeposition showed improved electronic transport properties and provided more active sites to adsorb large amounts of oligonucleotide substrate (DNA1) via thiol‐gold bonds. The stable Au@MIL‐101(Fe) could guarantee the sensitivity because of its intrinsic peroxidase mimic property, while the Cu²⁺‐dependent DNA‐cleaving DNAzyme linked to Au@MIL‐101(Fe) achieved the selectivity toward Cu²⁺. After the DNAzyme substrate strand (DNA2) was cleaved into two parts due to the presence of Cu²⁺, the oligonucleotide fragment linked to MIL‐101(Fe) was able to hybridize with DNA1 adsorbed onto the surface of AuNFs/ITO. Due to the peroxidase‐like catalytic activity of MIL‐101(Fe) and the affinity recognition property of DNAzyme toward Cu²⁺, the electrochemical biosensor showed a sensitive detection range from 0.001 to 100 μM, a detection limit of 0.457 nM and a high selectivity, demonstrating its potential for Cu²⁺ detection in real environmental samples.     

A pseudo triple-enzyme electrochemical aptasensor based on the amplification of Pt–Pd nanowires and hemin/G-quadruplex

Our present work aimed at developing a pseudo triple-enzyme cascade electrocatalytic electrochemical aptasensor for determination of thrombin with the amplification of alcohol dehydrogenase (ADH)-Pt–Pd nanowires bionanocomposite and hemin/G-quadruplex structure that simultaneously acted as NADH oxidase and HRP-mimicking DNAzyme. With the addition of ethanol to the electrolyte, the ADH immobilized on the Pt–Pd nanowires catalyzed ethanol to acetaldehyde accompanied by NAD⁺ being converted to NADH. Then the hemin/G-quadruplex firstly served as NADH oxidase, converting the produced NADH to NAD⁺ with the concomitant local formation of high concentration of H₂O₂. Subsequently, the hemin/G-quadruplex acted as HRP-mimicking DNAzyme, bioelectrocatalyzing the produced H₂O₂. At the same time, the Pt–Pd nanowires employed in our strategy not only provided a large surface area for immobilizing thrombin binding aptamer (TBA) and ADH, but also served as HRP-mimicking DNAzyme which rapidly bioelectrocatalyzed the reduction of the produced H₂O₂. Thus, such a pseudo triple-enzyme cascade electrochemical aptasensor could greatly promote the electron transfer of hemin and resulted in the dramatic enhancement of electrochemical signal. As a result, a wide dynamic concentration linear range from 0.2 pM to 20 nM with a low detection limit of 0.067 pM for thrombin (TB) determination was obtained. The excellent performance indicated that our strategy was a promising way for ultrasensitive assays in electrochemical aptasensors.