Colorimetric detection of genetically modified organisms based on exonuclease III-assisted target recycling and hemin/G-quadruplex DNAzyme amplification

An isothermal colorimetric method is described for amplified detection of the CaMV 35S promoter sequence in genetically modified organism (GMO). It is based on (a) target DNA-triggered unlabeled molecular beacon (UMB) termini binding, and (b) exonuclease III (Exo III)-assisted target recycling, and (c) hemin/G-quadruplex (DNAzyme) based signal amplification. The specific binding of target to the G-quadruplex sequence-locked UMB triggers the digestion of Exo III. This, in turn, releases an active G-quadruplex segment and target DNA for successive hybridization and cleavage. The Exo III impellent recycling of targets produces numerous G-quadruplex sequences. These further associate with hemin to form DNAzymes and hence will catalyze H₂O₂-mediated oxidation of the chromogenic enzyme substrate ABTS^2? causing the formation of a green colored product. This finding enables a sensitive colorimetric determination of GMO DNA (at an analytical wavelength of 420 nm) at concentrations as low as 0.23 nM. By taking advantage of isothermal incubation, this method does not require sophisticated equipment or complicated syntheses. Analyses can be performed within 90 min. The method also discriminates single base mismatches. In our perception, it has a wide scope in that it may be applied to the detection of many other GMOs.

Open image in new window

Graphical abstract An isothermal and sensitive colorimetric method is described for amplified detection of CaMV 35S promoter sequence in genetically modified organism (GMO). It is based on target DNA-triggered molecular beacon (UMB) termini-binding and exonuclease III assisted target recycling, and on hemin/G-quadruplex (DNAzyme) signal amplification.

     

Chemiluminescence immunoassay for cardiac troponin T by using silver nanoparticles functionalized with hemin/G-quadruplex DNAzyme on a glass chip array

The authors describe an array for chemiluminescence (CL) based determination of cardiac troponin T (cTnT), an important cardiovascular disease marker. The tracing tag consists of silver nanoparticles (AgNPs) loaded with guanine-rich DNA sequences and detection antibody in a high numerical ratio. The loaded AgNPs were then reacted with hemin to form a hemin/G-quadruplex DNAzyme. A disposable immunosensor array was fabricated by immobilizing capture antibody on corresponding sensing sites on a glass chip. Once a sandwich immunocomplex is formed on the array, the tracing tag catalyzes the CL reaction of the luminol-p-iodophenol and H₂O₂ system to produce a CL signal, which is collected by a CCD camera. An intuitive CL image is obtained containing all of the spots on the array. Under optimal conditions, the method shows a wide linear range over 4 orders of magnitude (from 0.003 to 270 ng·L^?1), a detection limit down to 84 fg·L^?1, and a throughput as high as 44 tests·h^?1. The results obtained with serum samples are in acceptable agreement with reference values. The AgNP-based tracing tag as well as the immunoassay method shows a promising potential for point-of-care testing for the early clinical diagnosis of cardiovascular disease.

Open image in new window

Graphical abstract Schematic presentation of silver nanoparticles (AgNPs) functionalized with hemin/G-quadruplex DNAzyme for highly sensitive chemiluminescence (CL) immunoassay of cardiac troponin T (cTnT) on a glass chip array.

     

A homogeneous hemin/G-quadruplex DNAzyme based turn-on chemiluminescence aptasensor for interferon-gamma detection via in-situ assembly of luminol functionalized gold nanoparticles,deoxyribonucleic acid,interferon-gamma and hemin

A homogeneous hemin/G-quadruplex DNAzyme (HGDNAzyme) based turn-on chemiluminescence aptasensor for interferon-gamma (IFN-γ) detection is developed, via dynamic in-situ assembly of luminol functionalized gold nanoparticles (lum-AuNPs), DNA, IFN-γ and hemin. The G-quadruplex oligomer of the HGDNAzyme was split into two halves, which was connected with the complementary sequence of P1 (IFN-γ-binding aptamer) to form the oligonucleotide P2. P2 hybridized with IFN-γ-binding aptamer and meanwhile assembled onto lum-AuNPs through biotin–streptavidin specific interaction. When IFN-γ was recognized by aptamer, P2 was released into the solution. The two lateral portions of P2 combined with hemin to yield the catalytic hemin/G-quadruplex DNAzyme, which amplified the luminol oxidation for a turn-on chemiluminescence signaling. Based on this strategy, the homogeneous aptasensor enables the facile detection of IFN-γ in a range of 0.5–100 nM. Moreover, the aptasensor showed high sensitivity (0.4 nM) and satisfactory specificity, pointing to great potential applications in clinical analysis.     

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.     

Sensitive pseudobienzyme electrocatalytic DNA biosensor for mercury(II) ion by using the autonomously assembled hemin/G-quadruplex DNAzyme nanowires for signal amplification

Herein, a novel sensitive pseudobienzyme electrocatalytic DNA biosensor was proposed for mercury ion (Hg²⁺) detection by using autonomously assembled hemin/G-quadruplex DNAzyme nanowires for signal amplification. Thiol functionalized capture DNA was firstly immobilized on a nano-Au modified glass carbon electrode (GCE). In presence of Hg²⁺, the specific coordination between Hg²⁺ and T could result in the assembly of primer DNA on the electrode, which successfully triggered the HCR to form the hemin/G-quadruplex DNAzyme nanowires with substantial redox probe thionine (Thi). In the electrolyte of PBS containing NADH, the hemin/G-quadruplex nanowires firstly acted as an NADH oxidase to assist the concomitant formation of H₂O₂ in the presence of dissolved O₂. Then, with the redox probe Thi as electron mediator, the hemin/G-quadruplex nanowires acted as an HRP-mimicking DNAzyme that quickly bioelectrocatalyzed the reduction of produced H₂O₂, which finally led to a dramatically amplified electrochemical signal. This method has demonstrated a high sensitivity of Hg²⁺ detection with the dynamic concentration range spanning from 1.0 ng L⁻¹ to 10 mg L⁻¹ Hg²⁺ and a detection limit of 0.5 ng L⁻¹ (2.5 pM) at the 3S_blank level, and it also demonstrated excellent selectivity against other interferential metal ions.     

Characterization of G-quadruplex/hemin peroxidase: substrate specificity and inactivation kinetics

Recently, G-quadruplex/hemin (G4/hemin) complexes have been found to exhibit peroxidase activity, and this feature has been extensively exploited for colorimetric detection of various targets. To further understand and characterize this important DNAzyme, its substrate specificity, inactivation mechanism, and kinetics have been examined by comparison with horseradish peroxidase (HRP). G4/hemin DNAzyme exhibits broader substrate specificity and much higher inactivation rate than HRP because of the exposure of the catalytic hemin center. The inactivation of G4/hemin DNAzyme is mainly attributed to the degradation of hemin by H(2)O(2) rather than the destruction of G4. Both the inactivation rate and catalytic oxidation rate of G4/hemin DNAzyme depend on the concentration of H(2)O(2), which suggests that active intermediates formed by G4/hemin and H(2)O(2) are the branch point of catalysis and inactivation. Reducing substrates greatly inhibit the inactivation of G4/hemin DNAzyme by rapidly reacting with the active intermediates. A possible catalytic and inactivation process of G4/hemin has been proposed. These results imply a potential cause for the hemin-mediated cellular injury and provide insightful information for the future application of G4/hemin DNAzyme.     

基于DNA酶催化增敏的微流控顺序注射化学发光法检测钾离子的研究

基于G-四联体/血红素形成的DNA酶催化增敏鲁米诺-H2O2发光反应原理,建立了微流控顺序注射化学发光检测K+的新方法。在K+的促进作用下,富含鸟嘌呤的寡核苷酸PS5.M折叠成G-四联体,并对血红素表现出较高的亲合力,形成DNA酶,显著地增强血红素的类辣根过氧化物酶活性,催化鲁米诺-H2O2化学发光反应。在优化的实验条件下,化学发光检测K+的线性范围为1.0~700μmol·L-1,检出限为0.54μmol·L-1,用100μmol·L-1的K+形成的DNA酶连续测定10次,相对标准偏差(RSD)为1.61%。常见的碱金属和碱土金属离子均无显著干扰。该方法可用于真实水样中K+的分析,测定结果与原子吸收法一致。     

Ultrasensitive immunoassay of microcystins-LR using G-quadruplex DNAzyme as an electrocatalyst

An electrochemical immunoassay for microcystin-LR (MC-LR) detection was developed using multi-labeled horseradish peroxidase-mimicking DNAzyme on carbon nanotubes (CNTs) as electrocatalyst for signal amplification. CNTs were covalently conjugated to multiple DNAzyme along with MC-LR for a competitive immunoassay. The as-prepared DNAzyme/CNTs/MC-LR biolabel was specifically captured on the electrode surface, and current responses were obtained upon the electro-catalytic reduction of hydrogen peroxide by the captured biolabels. Under optimal conditions, the electro-catalytic current decreased linearly with the increase amount of MC-LR in the range from 0.01 to 7.0 µg L^?1. The linear regression equation was I (µA) = 12.96 ? 1.48 X _[MC–LR] (µg L^?1), with a correlation coefficient of 0.989. The limit of detection of MC-LR was 2.31 ng L^?1. Application of the immunoassay method and LC/MS/MS method for MC-LR determination on spiked reservoir water gave recovery range of 91.7–105.2% and 94.0–105.0%, respectively. The resulting versatile immunoassay exhibited high sensitivity, good precision and satisfactory reproducibility, which could have vast potential in routine water quality monitoring for various environmental toxins.     

G-quadruplex based impedimetric 2-hydroxyfluorene biosensor using hemin as a peroxidase enzyme mimic

We describe a sensitive and selective biosensor for the environmental metabolite 2-hydroxyfluorene (2-HOFlu). It is based on electrochemical impedance spectroscopy and was obtained by assembling a thiolated single-stranded DNA on a gold electrode via S-Au covalent bonding. It is then transformed to a K⁺-stabilized G-quadruplex-hemin complex which exhibits peroxidase-like activity to catalyze the oxidation of 2-HOFlu by H₂O₂. This results in the formation of insoluble products that are precipitated on the gold electrode. As a result, the charge transfer resistance (R _CT) between the solution and the electrode surface is strongly increased within 10 min as demonstrated by using the ferro/ferricyanide system as a redox probe. The difference in the charge transfer resistances (ΔR _CT) before and after incubation of the DNA film with 2-HOFlu and H₂O₂ serves as the signal for the quantitation of 2-HOFlu with a 1.2. nM detection limit in water of pH 7.4. The assay is highly selective over other selected fluorene derivatives. It was exploited to determine 2-HOFlu in spiked lake water samples where it displayed a detection limit of 3.6 nM. Conceivably, this method has a wide scope in that it may be applied to other analytes for which respective G-quadruplexes are available.

A G-quadruplex DNAzyme based impedimetric biosensor for sensitive detection of 2-hydroxyfluorene using hemin as a peroxidase enzyme mimic was constructed with a detection limit of 1.2 nM in water and 3.6 nM in spiked lake water samples.

     

Quadruple signal amplification strategy based on hybridization chain reaction and an immunoelectrode modified with graphene sheets,a hemin/G-quadruplex DNAzyme concatamer,and alcohol dehydrogenase: ultrasensitive determination of influenza virus subtype H7N9

We report on a new amplification strategy for use in an immunoassay for influenza virus subtype H7N9. Graphene sheets were first placed on a glassy carbon electrode (GCE), and gold nanoparticles were then electrodeposited as a support for a layer of alcohol dehydrogenase (ADH) in a sol–gel containing thiol groups. Protein A was used to properly orientate immobilized antibody against H7N9 on the sol–gel, and this is shown to result in strongly improved specificity of the antigen-antibody binding. Thus, a sensitive and specific immunosensor was obtained in which a quadruple signal amplification strategy is employed, viz. (a) via the use of graphene sheets, (b) via a hybridization chain reaction, (c) the use of hemin/G-quadruplex DNAzyme concatamers, and (d) the use of ADH. The hemin/G-quadruplex is a typical DNAzyme, which simultaneously acts as NADH oxidase and HRP-mimicking DNAzyme. The hybridization chain reaction-based DNAzyme concatamers assembled on multi-walled carbon nanotubes (MWCNTs) and the ADH represent a triple electrocatalytic enzyme cascade system. Sandwich immunoreactions occurred between the capture antibody on the electrode and the secondary antibody labeled with MWCNTs. Positively charged Methylene Blue (MB) was then used as an intercalator to detect the DNAzyme concatamer formed. The differential pulse voltammetric signals for MB are related to the concentration of H7N9 in the range from 8 to 60 pg · mL⁻¹, and the detection limit is 0.81 pg · mL⁻¹ (at an S/N ratio of 3). This immunoassay is very sensitive, specific and robust.

An electrochemical sandwich immunosensor has been developed for sensitive and specific detection of influenza virus subtype H7N9. Protein A was used to properly orientate antibody. The hybridization chain reaction based DNAzyme concatamers assembled on multi-walled carbon nanotubes (MWCNTs) and the ADH represent a triple electrocatalytic enzyme cascade system.

     

G-quadruplex DNAzyme as the turn on switch for fluorimetric detection of genetically modified organisms

A novel fluorescent sensor for detection of genetically modified organisms was developed, and in the sensor G-quadruplex DNAzyme (G-quadruplex-hemin complex) was used as the turn on switch.     

Colorimetric detection of sodium ion in serum based on the G-quadruplex conformation related DNAzyme activity

There has been a big challenge in developing the Na⁺ sensor that can be practically used in the physiological system with the interference of large amounts of K⁺. In this research, a novel Na⁺ sensor has been designed based on the G-quadruplex-conformation related DNAzyme activity. The sensor exhibits high selectivity and sensitivity with the detection limit of 0.6 μM, which enables the sensor to be practically used in determination of the Na⁺ level in serum. The research not only provides a simple Na⁺ sensor but also opens a new way for developing the detection technology of Na⁺.     

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

For the first time, hemin/G-quadruplex was employed to simultaneously serve as NADH oxidase and an HRP-mimicking DNAzyme for constructing a simple and sensitive pseudobienzyme-amplifying electrochemical aptasensor for thrombin detection.     

A dual-amplification aptasensor for highly sensitive detection of thrombin based on the functionalized graphene-Pd nanoparticles composites and the hemin/G-quadruplex

In this work, an advanced sandwich-type electrochemical aptasensor for thrombin was proposed by integrating hemin/G-quadruplex with functionalized graphene-Pd nanoparticles composites (PdNPs-RGs). The hemin/G-quadruplex formed by intercalating hemin into thrombin binding aptamer (TBA), firstly acted as a NADH oxidase, assisting the oxidation of NADH to NAD⁺ accompanying with the generation of H₂O₂ in the presence of dissolved O₂. Subsequently, the hemin/G-quadruplex acted as HRP-mimicking DNAzyme that rapidly bioelectrocatalyze the reduction of the produced H₂O₂. At the same time, the Pd nanoparticles supported on p-iodoaniline functionalized graphene were also adopted to catalyze the reduction of H₂O₂. Thus, with the dual catalysis, a dramatically amplified electrochemical signal could be obtained. Besides, the avidin–biotin system for binding aptamer sequences on electrodes not only improved the sensitivity of thrombin analysis but also obtained an acceptable repeatability of the aptasensor. With several factors mentioned above, a wide linear ranged from 0.1 pM to 50 nM was acquired with a relatively low detection limit of 0.03 pM (defined as S/N = 3). These excellent performances provided our approach a promising way for ultrasensitive assay in electrochemical aptasensors.     

Synthesis and binding properties of a noncovalent molecularly imprinted testosterone-specific polymer

In this study, molecular imprinting was used to develop a method based on noncovalent interactions for synthesis of a testosterone-specific polymer. The effect of the different template–monomer ratios, the particle sizes of polymers, and chromatographic mobile phases on steroid–polymer interactions are discussed. The polymer obtained was found to interact specifically with testosterone, while other steroids under study were eluted close to the void volume in the HPLC experiments. Batch rebinding studies in acetonitrile were undertaken to quantitatively evaluate the affinity of the polymer for testosterone. During this experiment, the testosterone concentration was measured in two ways: spectrophotometrically and by HPLC on a column with testosterone-specific imprinted polymer synthesized by us. Both methods resulted in similar values of association constants and the number of binding sites. However, the second method has obvious advantages when the analyzed solution contains a mixture of optically dense compounds. The results obtained focus on the two-point binding nature of the imprinted polymer–testosterone interaction and the significant role of hydrogen bonds between the OH group of testosterone and carboxy group of methacrylic acid residues inside specific recognition sites of the imprinted polymer. © 1998 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 36: 1725–1732, 1998     

FRET study of a trifluorophore-labeled DNAzyme

A fluorescence resonance energy transfer (FRET) study of biomolecules typically employs two fluorophores. The increasing number of branches and complexity of biomolecules call for simultaneously monitoring structures and dynamics of several branches in a single system. Furthermore, despite recent studies that show DNAzymes can be a stable and cost-effective alternative to protein and ribozymes for pharmaceutical and biotechnological applications, no FRET study of DNAzymes has been reported. Here, we describe the FRET study of a trifluorophore-labeled "8-17" DNAzyme, in which each of the three branches is labeled with a different fluorophore. From the study, we found that the (ratio)(A) method that has been commonly used in dual-fluorophore-labeled systems is also applicable to trifluorophore-labeled systems. However, while both FRET efficiency and fluorophore-to-fluorophore distance can be used to measure FRET in dual-fluorophore-labeled systems, only the average distance should be used in trifluorophore-labeled systems. The ability to monitor all three branches in a single system allowed us to reveal new metal-ion-dependent conformational changes in the DNAzyme. The trifluorophore-labeled "8-17" DNAzyme has been found to adopt a two-step folding process in the presence of Zn(2+). Each step is induced by one Zn(2+) binding, with apparent dissociation constants of 19 microM and 260 microM for binding the first and second Zn(2+), respectively. The trifluorophore FRET results are verified by a dual-labeled control experiment. The results demonstrated that the trifluorophore-labeled system is simple and yet powerful in studying complicated biomolecular structure and dynamics and is capable of revealing new sophisticated structural changes that may have functional implications.     

The development of biocatalytic membrane electrodes

Recent developments and future prospects of biocatalytic membrane electrodes are examined in the light of past experience. The influences of scientific, economic and human factors on the course of development is evident.