Hemin/G-quadruplex simultaneously acts as NADH oxidase and HRP-mimicking DNAzyme for simple, sensitive pseudobienzyme electrochemical detection of thrombin

The Recent Progress in DNAzymes-Based Aptasensors for Thrombin Detection

Thrombin (TB) is classified among human blood coagulation proteins with key functions in hemostasis of blood vessels, wound healing, atherosclerosis, tissue adhesion, etc. Moreover, TB is involved as the main enzyme in the conversion of the fibrinogen to fibrin. Given the importance of TB detection in the clinical area, the development of innovative methods can considerably improve TB detection. Newly, aptasensors or aptamer-based biosensors have received special attention for sensitive and facile TB detection. In addition, the aptamer/nanomaterial conjugates have presented new prospects in accurate TB detection as nanoaptasensors. DNA-based enzymes or DNAzymes, as new biocatalysts, have many advantages over protein enzymes and can be used in analytical tools. This article reviews a brief overview of significant progresses regarding the various types of DNAzymes-based aptasensors and nano aptasensors developed for thrombin detection. In the following, challenges and prospects of TB detection by DNAzymes-based aptasensors are discussed.

DNA-targeted formation and catalytic reactions of DNAzymes for label-free ratiometric electrochemiluminescence biosensing

A label-free ratiometric electrochemiluminescence (ECL) sensing strategy for the sensitive detection of target DNA (T-DNA) was proposed on the basis of G-quadruplex/hemin-regulated ECL emissions of CdS quantum dots (QDs) and luminol with their common coreactant of H₂O₂. The ECL biosensor was constructed through stepwise assemblies of CdS QDs and hairpin DNA (H-DNA) on a glassy carbon electrode, and subsequent introduction of T-DNA resulted in the development of G-quadruplex/hemin DNAzymes via the specific recognition of T-DNA and H-DNA in the presence of hemin and K⁺ ions. The formed DNAzymes not only prompted the catalytic oxidation of hydroquinone followed by deposition of insoluble oxidation oligomers on the electrode surface to attenuate the cathodic ECL emission of CdS QDs but also triggered the catalytic oxidation of luminol to enhance the anodic ECL emission. The label-free ratiometric ECL biosensor for the detection of T-DNA showed a wide response range from 1 to 10,000 fM (10^-15 M) with a low detection limit of 0.2 fM and exhibited excellent selectivity against mismatched base sequences. This work provides a reliable and sensitive sensing platform for the detection of targets in analytical community by means of rational design of DNA sequences.

An intensive and glow-type chemiluminescence of luminol-embedded, guanosine-derived hydrogel

In this paper, an intensive and glow-type chemiluminescence (CL) hydrogel was prepared by simultaneous incorporation of chemiluminescence reagent (luminol) and catalytic cofactor (hemin) into the scaffold of guanosine-derived hydrogel. The self-assembled hydrogel consisted of K⁺ stabilized hemin/G-quartet structures, showing significant enzyme-like activity to H₂O₂-mediated oxidation of luminol. After adding H₂O₂ into the hydrogel, blue light visible to naked eyes would come into being and last for over 8 h. The lasting-time CL emission of hydrogel was achieved due to a mechanism of slow-diffusion-controlled heterogeneous catalysis. Moreover, this self-assembled hydrogel performed a good response to H₂O₂ and the CL emission images could be recorded by smartphone. The hydrogel could remain excellent lifetime stability for months and the stable, enhanced and glow-type CL emission could improve the reliability and precision of CL detection, which has a promising application in cold light source and H₂O₂ detection of real biological samples.

Stochastic Collision Electrochemistry from Single G-Quadruplex/Hemin: Electrochemical Amplification and MicroRNA Sensing

Stochastic collision electrochemistry is a hot topic in single molecule/particle research, which provides an opportunity to investigate the details of the single molecule/particle reaction mechanism that is always masked in ensemble-averaged measurements. In this work, we develop an electrochemical amplification strategy to monitor the electrocatalytic behavior of single G-quadruplex/hemin (GQH) for the reaction between hydrogen peroxide and hydroquinone (HQ) through the collision upon a gold nanoelectrode. The intrinsic peroxidase activities of single GQH were investigated by stochastic collision electrochemical measurements, giving further insights into understanding biocatalytic processes. Based on the unique catalytic activity of GQH, we have also designed a hybridization chain reaction strategy to detect miRNA-15 with good selectivity and sensitivity. This work provided a meaningful strategy to investigate the electrochemical amplification and the broad application for nucleic acid sensing at the single molecule/particle level.

Platinum nanoparticle-deposited multi-walled carbon nanotubes as a NADH oxidase mimic: characterization and applications

The effective regeneration of bioactive NAD+ plays an important role in numerous dehydrogenase-dependent applications including biocatalysis and biosensing. However, this process usually suffers from high thermodynamic barrier, instability and high cost associated with natural enzymes. The emergence of nanomaterials with enzyme mimic characteristics has offered a potential alternative to many enzyme-catalyzed processes. Platinum nanoparticles (PtNPs), for example, have been extensively studied for their peroxidase- and oxidase-like activities. However, their behavior as a NADH oxidase mimic has barely been characterized in detail. Herein, we report a facile approach for preparing PtNP-deposited multi-walled carbon nanotubes (PtNPs@MWCNTs) as the nanozyme for NADH oxidation. Its enzymatic activity was investigated in depth, revealing that it is a NADH oxidase instead of a peroxidase and the catalytic process generates O2˙-, rather than OH˙ or 1O2, from dissolved O2. The recovery yield of bioactive NAD+ regeneration by the nanozyme could reach ∼100% with a total turnover number of ∼6000. Besides, it exhibited terrific electrochemical performance for NADH oxidation and sensing by greatly boosting the response and lowering the oxidation overpotential. It could also work on biomimetic cofactors with even higher activity. Finally, xylose dehydrogenase was immobilized with the nanozyme to constitute a hybrid bioelectrode for xylose sensing. The biosensor had a xylose detecting range of 5-400 μM with the limit of detection as low as 1 μM and can retain its performance after being reused several times. Our results suggest that the PtNPs@MWCNTs characterized as a NADH oxidase nanozyme hold great promise in the applications of biocatalysis and biosensing, which intensively deal with dehydrogenases and natural or biomimetic cofactors.

Ultrasensitive DNA Detection Based on Inorganic-Organic Nanocomposite Cosensitization and G-Quadruplex/Hemin Catalysis for Signal Amplification

A novel photoelectrochemical (PEC) aptasensor was fabricated for DNA detection based on the coupling of cosensitization and peroxidase-like catalytic activity. Specifically, the surfaces of branched-TiO₂ nanorods (B-TiO₂ NRs) were modified with Cd²⁺ and S²⁺ to obtain B-TiO₂ NRs/CdS hybrid structures, which were subsequently used as matrices to immobilize hairpin DNA (hDNA) probes. CdTe/TCPP (TCPP = meso-tetra(4-carboxyphenyl)-porphine) used for signal amplification was labeled on the terminal of the hDNA probe. Without the target DNA (tDNA) presence, the immobilized hDNA probe with CdTe/TCPP possessed a hairpin form and was located near the B-TiO₂ NRs/CdS electrode surface, forming a cosensitized structure formation and then generating strong photocurrent with H₂O₂ as the electron donor. During detection, the specific recognition of tDNA by the sensing hDNA probe triggered the formation of the G-quadruplex/hemin DNAzyme, which effectively catalyzed the decomposition of H₂O₂. Meanwhile, cosensitization disappeared when the hDNA probe hybridized with tDNA, further reducing the photocurrent. With a double-signal amplification strategy, the sensing platform designed in this work demonstrated a linear detection ability in the 0.5 fM-5 nM range with a detection limit equal to 0.14 fM. Notably, through encoding in the base sequences of the hDNA and marking it, a versatile PEC platform could be structured for the detection of various DNA targets, which could promise applications in point-of-care diagnostic fields.

A fluorometric assay of thrombin using magnetic nanoparticles and enzyme-free hybridization chain reaction

A fluorescence method based on functionalized magnetic nanoparticles (FMNPs) and hybridization chain reaction (HCR) is developed for the enzyme-free amplified determination of thrombin. In the proposed design, aptamer against thrombin was hybridized with the capture DNA-modified magnetic nanoparticles to yield the FMNPs. In the presence of thrombin, aptamers are released due to the specific and high-affinity binding between thrombin and its aptamer. The exposed capture DNA subsequently hybridized with the partial sequence of helper DNA, and the vacant sequence of helper DNA further hybridized with HCR products which is pre-formed by the alternate hybridization of single-stranded DNAs (H1 and H2). The immobilized HCR products were then labeled with YOYO-1 for fluorescence measurement. Fluorescence signal intensity of labeled YOYO-1 was measured at an emission wavelength of 519 nm (excitation under 488 nm) and used for calibration. By taking advantage of HCR amplification, this direct assay strategy showed a linear response in the 20- to 200-pM concentration range, and the limit of detection is 9.2 pM which is about 3-orders of magnitude lower than the serum thrombin concentration (10 nM) that triggers blood clotting. This developed method can efficiently differentiate the target protein from a protein matrix, and it is verified by determination of thrombin in spiked serum samples with recoveries in the range of 94.5-103.3%. Graphical abstract A fluorometry method for thrombin detection using magnetic nanoparticles and enzyme-free hybridization chain reaction.

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.

Imidazole-modified G-quadruplex DNA as metal-triggered peroxidase

Four imidazoles, serving as metalloprotein-inspired ligands for complexing a range of transition metal cations, were incorporated into tetramolecular G-quadruplex DNA structures. Modified quadruplexes were found to complex Cu(ii), Ni(ii), Zn(ii) and Co(ii) in a 1 : 1 ratio with unprecedented strong thermal stabilizations of up to ΔT _1/2 = +51 °C. Furthermore, addition of Cu(ii) was found to lead to extraordinarily fast G-quadruplex association rates with k _on values being ∼100 times higher compared to unmodified G-quadruplexes. This is ascribed to a template effect of Cu(ii), preorganizing the four single strands via coordination, followed by rapid formation of hydrogen-bonded G-quartets. Native electrospray ionization mass spectrometry (ESI), coupled with trapped ion-mobility spectrometry (timsTOF), supports the proposed 1 : 1 G-quadruplex-metal complexes and could further disclose their ability to bind the iron-porphyrin complex hemin in a 1 : 1 stoichiometry. DNA sequence design allowed us to equip this G-quadruplex-hemin complex, known to function as a horseradish peroxidase mimic, with a metal-dependent trigger. A competitive screen of transition metals revealed a high selectivity for Cu(ii), even in mixtures of several divalent metal cations. Once formed, the Cu(ii)-carrying DNAzyme was shown to be preserved in the presence of EDTA, attributed to its remarkable kinetic stability. Stimuli-responsive G-quadruplexes promise application in DNAzymes with switchable activity, adaptive sensors and dynamic DNA origami constructs.

A Label-free Resonance Rayleigh Scattering Sensor for Detection of Thrombin Based on Aptamer Recognizing

The interaction between thrombin binding aptamer (TBA) and thrombin (TB) was studied by resonance Rayleigh scattering (RRS). In neutral medium, TBA is present in a balanced form between a G-quadruplex structure and a random coil structure, and the TBA can be induced by metal ions to form a G-quadruplex structure. Upon addition of thrombin, the G-quadruplex selectively bound to TB, which resulted in enhanced resonance Rayleigh scattering. The scattering intensities increased proportionally with the concentration of TB from 10 to 50 nM. The method had very high sensitivity and good selectivity, and the detection limit (3δ/s) was 1 nM. In this work, the spectral characteristics of RRS, the optimum conditions of the reaction, and influencing factors for the RRS intensities were investigated. Furthermore, the structure of the TBA-TB complex and the sensing mechanism were explored. The TB sensor was applied to a diluted human serum sample with satisfactory results, indicating the potential of this method to be applied to biological samples. A selective and simple RRS sensor for the detection of trace amounts of TB is proposed based on conformational change of TBA.

Ce(III, IV)-MOF electrocatalyst as signal-amplifying tag for sensitive electrochemical aptasensing

Metal-organic frameworks (MOFs) as a new class of porous materials have attracted increasing attention in the field of biomimetic catalysis. This study firstly reports a mixed valence state Ce-MOF possessing intrinsic catalytic activity towards thionine (Thi), and its application in constructing an amplified electrochemical aptasensor for thrombin detection. As noticed, the novel catalytic process combines the advantages of 3D infinite extension of the Ce(III, IV)-MOF skeleton containing large amounts of catalytic sites and spontaneous recycling of the Ce(III)/Ce(IV) for electrochemical reduction of Thi, thereby presenting amplified electrochemical signals. To further improve the aptasensor performance, the high selectivity of proximity binding-induced DNA strand displacement and high efficiency of exonuclease III-assisted recycling amplification were incorporated into the assay. The aptasensor was employed to detect thrombin in complex serum samples, which shows high sensitivity, specificity, stability and reproducibility. This work offers an opportunity to develop MOF-based electrocatalyst as signal-amplifying tag for versatile bioassays and catalytic applications.

Electrochemical and AFM Characterization of G-Quadruplex Electrochemical Biosensors and Applications

Guanine-rich DNA sequences are able to form G-quadruplexes, being involved in important biological processes and representing smart self-assembling nanomaterials that are increasingly used in DNA nanotechnology and biosensor technology. G-quadruplex electrochemical biosensors have received particular attention, since the electrochemical response is particularly sensitive to the DNA structural changes from single-stranded, double-stranded, or hairpin into a G-quadruplex configuration. Furthermore, the development of an increased number of G-quadruplex aptamers that combine the G-quadruplex stiffness and self-assembling versatility with the aptamer high specificity of binding to a variety of molecular targets allowed the construction of biosensors with increased selectivity and sensitivity. This review discusses the recent advances on the electrochemical characterization, design, and applications of G-quadruplex electrochemical biosensors in the evaluation of metal ions, G-quadruplex ligands, and other small organic molecules, proteins, and cells. The electrochemical and atomic force microscopy characterization of G-quadruplexes is presented. The incubation time and cations concentration dependence in controlling the G-quadruplex folding, stability, and nanostructures formation at carbon electrodes are discussed. Different G-quadruplex electrochemical biosensors design strategies, based on the DNA folding into a G-quadruplex, the use of G-quadruplex aptamers, or the use of hemin/G-quadruplex DNAzymes, are revisited.

Highly sensitive electrochemical thrombin aptasensor based on peptide-enhanced electrocatalysis of hemin/G-quadruplex and nanocomposite as nanocarrier

In this work, we first conjugated a short peptide to thrombin binding aptamer (TBA) and bond hemin to the hybrid, effectively rendering hemin/G4-peptide more active over the original hemin/G4, so that a highly sensitive electrochemical thrombin (TB) aptasensor was developed based on it and PtNTs@rGO nanocomposite. It was the first report on the application of hemin/G4-peptide in electrochemical aptasensor. PtNTs@rGO with large surface area served as excellent nanocarrier for high loading of hemin/G4-peptide hybrids, resulting in the formation of hemin/G4-peptide-PtNTs@rGO bioconjugate as the secondary aptamer and further signal enhancement. The specific affinity of aptamer for target TB made the secondary aptamer go into the sensing interface, and then a noticeable current signal was obtained from hemin without additional redox mediators. Due to the collaborative electrocatalysis of hemin/G4-peptide and PtNTs toward H₂O₂, which was formed in situ during the process of hemin/G4-peptide-catalyzed oxidation of NADH with dissolved O₂, the current intensity increased dramatically. Such an electrochemical aptasensing system could be used to detect TB with a linear range of 0.05 pM-60nM and very lower detection limit of 15fM. Notably, this method exhibited a higher sensitivity than that of many hemin/G4-based electrochemical strategies for TB detection due to the improvement of the catalytic activity of hemin/G4-peptide. The present works opened a new way for expanding the application of hemin/G4 in biological detection. With the mediator-free, proteinous enzyme-free yet high-sensitivity advantages, this electrochemical aptasensor held great promise for other biomarker detections in clinical diagnostics.

A reusable aptasensor of thrombin based on DNA machine employing resonance light scattering technique

The design of molecular nanodevices attracted great interest in these years. Herein, a reusable, sensitive and specific aptasensor was constructed based on an extension-contraction movement of DNA interconversion for the application of human thrombin detection. The present biosensor was based on resonance light scattering (RLS) using magnetic nanoparticles (MNPs) as the RLS probe. MNPs coated with streptavidin can combine with biotin labeled thrombin aptamers. The combined nanoparticles composite is monodispersed in aqueous medium. When thrombin was added a sandwich structure can form on the surface of MNPs, which induced MNPs aggregation. RLS signal was therefore enhanced, and there is a linear relationship between RLS increment and thrombin concentration in the range of 60pM-6.0nM with a limit of detection at 3.5pM (3.29S_B/m, according to the recent recommendation of IUPAC). The present aptasensor can be repeatedly used for at least 6 cycling times by heat to transfer G-quadruplex conformation to single strand of DNA sequence and release thrombin. MNPs can be captured by applying the external magnetic field. Furthermore, the proposed biosensor was successfully applied to detect thrombin in human plasma.

Target-triggered catalytic hairpin assembly and TdT-catalyzed DNA polymerization for amplified electronic detection of thrombin in human serums

Specific and sensitive detection of protein biomarkers is of great importance in biomedical and bioanalytical applications. In this work, a dual amplified signal enhancement approach based on the integration of catalytic hairpin assembly (CHA) and terminal deoxynucleotidyl transferase (TdT)-mediated in situ DNA polymerization has been developed for highly sensitive and label-free electrochemical detection of thrombin in human serums. The presence of the target thrombin leads to the unfolding and capture of a significant number of hairpin signal probes with free 3'-OH termini on the sensor electrode. Subsequently, TdT can catalyze the elongation of the signal probes and formation of many G-quadruplex sequence replicates with the presence of dGTP and dATP at a molar ratio of 6:4. These G-quadruplex sequences bind hemin and generate drastically amplified current response for sensitive detection of thrombin in a completely label-free fashion. The sensor shows a linear range of 0.5pM-10.0nM and a detection limit of 0.12pM for thrombin. Moreover, the developed sensor can selectively discriminate the target thrombin against other non-target proteins and can be employed to monitor thrombin in human serum samples.

Aptazyme-Gold Nanoparticle Sensor for Amplified Molecular Probing in Living Cells

To date, a few of DNAzyme-based sensors have been successfully developed in living cells; however, the intracellular aptazyme sensor has remained underdeveloped. Here, the first aptazyme sensor for amplified molecular probing in living cells is developed. A gold nanoparticle (AuNP) is modified with substrate strands hybridized to aptazyme strands. Only the target molecule can activate the aptazyme and then cleave and release the fluorophore-labeled substrate strands from the AuNP, resulting in fluorescence enhancement. The process is repeated so that each copy of target can cleave multiplex fluorophore-labeled substrate strands, amplifying the fluorescence signal. Results show that the detection limit is about 200 nM, which is 2 or 3 orders of magnitude lower than that of the reported aptamer-based adenosine triphosphate (ATP) sensors used in living cells. Furthermore, it is demonstrated that the aptazyme sensor can readily enter living cells and realize intracellular target detection.

Hemin/G-quadruplex DNAzyme nanowires amplified luminol electrochemiluminescence system and its application in sensing silver ions

Herein, a DNA biosensor with a hemin/G-quadruplex DNAzyme amplified luminol electrochemiluminescence (ECL) system was constructed for sensing silver ions (Ag⁺).

Protein-templated cobaltous phosphate nanocomposites for the highly sensitive and selective detection of platelet-derived growth factor-BB

We synthesized novel Co3(PO4)2-based nanocomposites with 3D porous architectures via self-assembly; here, bovine serum albumin (BSA) and aptamer were used as organic phases to produce Co3(PO4)2@BSA and Co3(PO4)2@Apt nanocomposites, respectively. The formation mechanism of Co3(PO4)2-based nanocomposites was described based on characterizations of their physio-chemical performance, and the developed nanocomposites were applied as scaffold materials to construct a novel electrochemical aptasensor and detect platelet-derived growth factor-BB (PDGF-BB). The PDGF-BB targeting aptamer must be immobilized onto the Co3(PO4)2@BSA-modified electrode to detect PDGF-BB, whereas Co3(PO4)2@Apt-based aptasensor may be directly used to determine the target protein. Electrochemical impedance spectroscopy results showed that the developed Co3(PO4)2@BSA- and Co3(PO4)2@Apt-based aptasensors present highly sensitive detection ability toward PDGF-BB. Due to the special nanoflower structure, the Co3(PO4)2@BSA-based aptasensor features a detection limit of 3.7 pg mL(-1); while the limit of detection of the Co3(PO4)2@Apt-based aptasensor is 61.5 pg mL(-1), which is the possible bioactivity loss of the aptamer in Co3(PO4)2@Apt nanocomposite. The two detection limits obtained are still much lower than or comparable with those of previously reported aptasensors. The Co3(PO4)2@BSA- and Co3(PO4)2@Apt-based aptasensors showed high selectivity, stability, and applicability for detecting the desired protein. This finding indicates that the Co3(PO4)2-based nanocomposites could be used as an electrochemical biosensor for various detection procedures in the biomedical field.

Triplex DNA: A new platform for polymerase chain reaction-based biosensor

Non - specific PCR amplification and DNA contamination usually accompany with PCR process, to overcome these problems, here we establish a sensor for thrombin by sequence - specific recognition of the PCR product with molecular beacon through triplex formation. Probe A and probe B were designed for the sensor, upon addition of thrombin, two probes hybridized to each other and the probe B was extended in the presence of Klenow Fragment polymerase and dNTPs. The PCR amplification occurred with further addition of Taq DNA Polymerase and two primers, the PCR product was recognized by molecular beacon through triplex formation. The fluorescence intensity increased with the logarithm of the concentration of thrombin over the range from 1.0 × 10⁻¹² M to 1.0 × 10⁻⁷ M, with a detection limit of 261 fM. Moreover, the effect of DNA contamination and non - specific amplification could be ignored completely in the proposed strategy.

An electrochemiluminescent microRNA biosensor based on hybridization chain reaction coupled with hemin as the signal enhancer

In this study, a new universal biosensor based on luminol anodic electrochemiluminescence (ECL) for the detection of microRNA-155 was constructed by using hydrogen peroxide (H2O2) as a co-reactant and hemin as a catalyzer for signal amplification. The bare glassy carbon electrode (GCE) was first electrodeposited with Au nanoparticles (AuNPs). Then, helper DNA, which was partly complementary with the hairpin DNA chains, was assembled on the prepared GCE. Target microRNA-155 and the hairpin hybridization chains could create a formation of extended double-stranded DNA (dsDNA) polymers through the displacement of hybridization chains and the hybridization chain reaction (HCR). The HCR-generated dsDNA polymers give rise to the intercalation of a lot of hemin which could catalyze the oxidation of H2O2, leading to a remarkably amplified ECL signal output. The proposed biosensor showed a wide linear range from 5 fM to 50 pM with a relatively low detection limit of 1.67 fM for microRNA-155 detection. With excellent selectivity, good stability and high sensitivity, the proposed biosensor is promising in the development of a high-throughput assay of microRNA-155.

l-Cysteine induced hemin/G-quadruplex concatemers electrocatalytic amplification with Pt–Pd supported on fullerene as a nanocarrier for sensing the spore wall protein of Nosema bombycis

This work described an amplified immunosensor for sensing spore wall protein (SWP) ofN. bombycisbased on a novel electrocatalytic function of C₆₀@Pt–Pd loaded with hemin/G-quadruplex.

A sensitive electrochemical aptasensor based on the co-catalysis of hemin/G-quadruplex, platinum nanoparticles and flower-like MnO2 nanosphere functionalized multi-walled carbon nanotubes

A sensitive thrombin electrochemical aptasensor is developed based on the co-catalysis of hemin/G-quadruplex, platinum nanoparticles and flower-like MnO₂ nanosphere functionalized multi-walled carbon nanotubes.

Versatile biosensing platform for DNA detection based on a DNAzyme and restriction-endonuclease-assisted recycling

On the basis of a DNAzyme and a restriction-endonuclease-assisted target recycling strategy using Pd-Au alloy nanocrystals to immobilize probe DNA on an electrode and catalyze the reduction of H2O2 which amplified signal and promoted the detection sensitivity, a versatile biosensing platform for DNA detection was proposed. Using p53 and oral cancer genes as models, hemin/G-quadruplex simultaneously acted as a reduced nicotinamide adenine dinucleotide (NADH) oxidase and a horseradish peroxidase (HRP)-mimicking DNAzyme, and a versatile DNA biosensor was designed for the first time based on the good electrocatalytic activity of Pd-Au alloy nanocrystals. Hemin/G-quadruplex catalyzed the reduction of H2O2, which was generated from NADH in the presence of O2, to produce an electrochemical signal when thionine functioned as the electron mediator. Moreover, the nicking endonuclease N.BstNB I caused the target DNA to cycle for multiple rounds and further amplified the electrochemical response. This versatile DNA biosensor exhibited linear ranges for the detection of p53 and oral cancer genes from 0.1 fmol L(-1) to 0.1 nmol L(-1) and 0.1 fmol L(-1) to 1 nmol L(-1), respectively. The detection limits, established as 3σ, were estimated to be 0.03 and 0.06 fmol L(-1) for the p53 and oral cancer genes, respectively. The as-prepared biosensor could discriminate mismatched sequences, indicating a satisfactory selectivity and validating the feasibility of the proposed strategy. More importantly, simply by changing the helper DNA, this versatile DNA biosensor could detect different target DNA species, which could create a new avenue for the potential diagnosis of cancer.

An electrochemical aptasensor for thrombin detection based on the recycling of exonuclease III and double-stranded DNA-templated copper nanoparticles assisted signal amplification

In this paper, we report an improved electrochemical aptasensor based on exonuclease III and double-stranded DNA (dsDNA)-templated copper nanoparticles (CuNPs) assisted signal amplification. In this sensor, duplex DNA from the hybridization of ligated thrombin-binding aptamer (TBA) subunits and probe DNA can act as an effective template for the formation of CuNPs on the electrode surface, so copper ions released from acid-dissolution of CuNPs may catalyze the oxidation of ο-phenylenediamine to produce an amplified electrochemical response. In the presence of thrombin, a short duplex domain with four complementary base pairs can be stabilized by the binding of TBA subunits with thrombin, in which TBA subunit 2 can be partially digested from 3' terminal with the cycle of exonuclease III, so the ligation of TBA subunits and the subsequent formation of CuNPs can be inhibited. By electrochemical characterization of dsDNA-templated CuNPs on the electrode surface, our aptasensor can display excellent performances for the detection of thrombin in a broad linear range from 100 fM to 1 nM with a low detection limit of 20.3 fM, which can also specially distinguish thrombin in both PBS and serum samples. Therefore, our aptasensor might have great potential for clinical diagnosis of biomarkers in the future.

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.

Electrochemical impedance spectroscopy aptasensor for ultrasensitive detection of adenosine with dual backfillers

A highly sensitive and label-free electrochemical impedance spectroscopy (EIS) aptasensor for the detection of adenosine was fabricated by co-assembling thiolated aptamer, dithiothreitol (DTT) and 6-mercaptohexanol (MCH) on gold electrode surface, forming Au/aptamer-DTT/MCH. The interfacial electron transfer resistance (Ret) of the aptasensor using [Fe(CN)6](3-/4-) as the probe increased with adenosine concentration, and the change in Ret (∆Ret) against the logarithm of adenosine concentration was linear over the range from 0.05 pM to 17 pM with a detection limit of 0.02 pM. Compared to that of aptasensors fabricated with MCH or DTT alone as the backfiller, the detection limit was improved dramatically (LOD was 0.03 nM and 0.2 pM for Au/aptamer/MCH and Au/aptamer-DTT, respectively), which was attributed primarily to the coupling of the cyclic- and linear -configuration backfillers. The coupling showed remarkably higher resistance to nonspecific adsorption, leading to low background noise and high response signal. The aptasensor reported herein is applicable for the detection of other kinds of aptamer-binding chemicals and biomolecules.

An ultrasensitive electrochemical aptasensor with autonomous assembly of hemin-G-quadruplex DNAzyme nanowires for pseudo triple-enzyme cascade electrocatalytic amplification

We for the first time fabricate a pseudo triple-enzyme cascade electrocatalytic electrochemical aptasensor by using the alcohol dehydrogenase (ADH) as well as the autonomously assembled hemin-G-quadruplex that simultaneously acted as an NADH oxidase and HRP-mimicking DNAzyme.

Porous platinum nanotubes labeled with hemin/G-quadruplex based electrochemical aptasensor for sensitive thrombin analysis via the cascade signal amplification

For the first time, a sensitive electrochemical aptasensor for thrombin (TB) was developed by using porous platinum nanotubes (PtNTs) labeled with hemin/G-quadruplex and glucose dehydrogenase (GDH) as labels. Porous PtNTs with large surface area exhibited the peroxidase-like activity. Coupling with GDH and hemin/G-quadruplex as NADH oxidase and HRP-mimicking DNAzyme, the cascade signal amplification was achieved by the following ways: in the presence of glucose and NAD(+) in the working buffer, GDH electrocatalyzed the oxidation of glucose with the production of NADH. Then, hemin/G-quadruplex as NADH oxidase catalyzed the oxidation of NADH to in situ generate H2O2. Based on the corporate electrocatalysis of PtNTs and hemin/G-quadruplex toward H2O2, the electrochemical signal was significantly amplified, allowing the detection limit of TB down to 0.15 pM level. Moreover, the proposed strategy was simple because the intercalated hemin offered the readout signal, avoiding the adding of additional redox mediator as signal donator. Such an electrochemical aptasensor is highly promising for sensitive detection of other proteins in clinical diagnostics.