Ligase-based ultrasensitive detection of DNAzyme cleavage product using molecular beacon

Detection for deoxyribozyme(DNAzyme) cleavage usually needs complex and time-consuming radial labeling,gel electrophoresis and autoradiography.A new approach was reported for detection DNAzyme cleavage product based on molecular beacon (MB).Part of the loop of MB was designed to complementary to DNAzyme cleavage product.MB was employed to monitor ligation process of RNA/DNA complex and to convert directly cleavage product information into fluorescence signal.Detection limit of the assay is 0.02 nmol/L.The cleavage product of 8 -17 DNAzyme against HCV-RNA was detected perfectly based on this assay.The method is fast,simple and ultrasensitive,which might hold great promise in DNAzyme reaction and DNAzyme gene therapy.     

Paper-based scanometric assay for lead ion detection using DNAzyme

A facile and simple paper-based scanometric assay was developed to detect Pb²⁺ using GR5-DNAzyme. Magnetic beads (MBs) and gold nanoparticles (AuNPs) were used as a signal collector and a signal indicator, respectively. They were linked together by GR5-DNAzyme, comprising an enzyme and a substrate strand pairing up with each other. In the presence of Pb²⁺, the substrate strand is cut into two pieces, resulting in the disassembly of AuNPs from the MBs. These AuNPs were spotted on predefined areas on a chromatography paper, where signal is amplified through silver reduction. This sensing platform exhibits high sensitivity and selectivity toward Pb²⁺, giving a detection limit of 0.3 nM and a linear fitting range from 0.1 to 1000 nM. Testing of this biosensor in river water and synthetic urine samples also showed satisfying results. Besides offering simultaneous and multi-sample analysis, this paper-based sensing platform presented here could be potentially applied and served as a general platform for on-site, naked eyes, and low-cost monitoring of other heavy metal ions in environmental and body fluid samples.     

Amplified electrochemical DNA sensor using peroxidase-like DNAzyme

A novel electrochemical DNA sensor was developed here by using peroxidase-like G-quadruplex-based DNAzyme as a biocatalytic label. A hairpin structure including the G-quadruplex-based DNAzyme in a caged configuration and the target DNA probe were immobilized on Au-electrode surface. Upon hybridization with the target, the hairpin structure was opened, and the G-quadruplex-based DNAzyme was generated on the electrode surface, triggering the electrochemical oxidization of hydroquinone by H₂O₂, which provide a quantitative measure for the detection of the target DNA. The DNA target was analyzed with a detection limit of 0.6 nM. This method is simple and easy to design without direct conjugation of redox-active element.     

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.     

Real-time monitoring of double-stranded DNA cleavage using molecular beacons

Traditional methods to assay enzymatic cleavage of DNA are discontinuous, time-consuming and laborious. Here, we report a new approach for real-time monitoring of double-stranded DNA cleavage by restriction endonuclease based on nucleic acid ligation using molecular beacon. Upon cleavage of DNA, the cleavage product can be ligated by DNA ligase, which results in a fluorescence enhancement of the molecular beacon. This method permits real-time monitoring of DNA cleavage and makes it easy to characterize the activity of restriction endonuclease and to study the cleavage reaction kinetics.     

Label-free fluorescent assay for real-time monitoring site-specific DNA cleavage by EcoRI endonuclease

DNA cleavage reaction catalyzed by nucleases is essential in many important biological processes and medicinal chemistry. Therefore, it is important to develop reliable and facile methods to assay nuclease activity. With this goal in mind, we report a fluorescent assay for label-free, facile, and real-time monitoring of DNA cleavage by EcoRI endonuclease using SYBR Green I (SGI) as a signal probe. The fluorescence of SGI dramatically increased when the free SGI was mixed with double-stranded DNA (dsDNA) substrate. Upon interacting with EcoRI, which cleaves the dsDNA into small fragments, the weakened interaction between SGI and the shortened DNA fragments caused a decrease in fluorescence of SGI. EcoRI-DNA interaction was real-time studied by monitoring fluorescence change with the prolonging of interaction time. The important kinetic parameters, including Michaelis-Menten constant (K(M)) and maximum initial velocity (V(max)), were accurately calculated, which is consistent with previously reported studies. Site-specific DNA cleavage by EcoRI endonuclease has also been verified by gel electrophoresis analysis, which indicated that this method is a simple and effective approach to assay DNA cleavage reaction. Specificity investigation demonstrated that EcoRI-DNA interactions can be studied with high selectivity. Compared with previously reported methods, this approach is selective, simple, convenient and cost-efficient without any labeling of the probe or of the target.     

Coupling hybridization chain reaction with DNAzyme recycling for enzyme-free and dual amplified sensitive fluorescent detection of methyltransferase activity

Aberrant DNA methylation originated from changes in DNA methyltransferase activity can lead to many genetic diseases and tumor types, and the monitoring of methyltransferase activity is thus of great importance in disease diagnosis and drug screening. In this work, by combing hybridization chain reaction (HCR) and metal ion-dependent DNAzyme recycling, we have developed a convenient enzyme-free signal amplification strategy for highly sensitive detection of DNA adenine methyltransferase (Dam MTase) activity and its inhibitors. The Dam MTase-induced methylation and subsequent cleavage of the methylated hairpin DNA probes by DpnI endonuclease lead to the release of ssDNA triggers for HCR formation of many Mg²⁺-dependent DNAzymes, in which the fluorescently quenched substrate sequences are catalytically and cyclically cleaved by Mg²⁺ to generate remarkably amplified fluorescent signals for highly sensitive detection of Dam MTase at 7.23 × 10⁻⁴ U/mL. In addition, the inhibition of different drugs to Dam MTase activity can also be evaluated with the developed method. With the advantages of simplicity and significant signal amplification over other common methods, the demonstrated biosensing approach thus offers great potential for highly sensitive detection of various methyltransferases and provides a convenient platform for drug screening for therapeutic applications.     

DNAzyme amplification of molecular beacon signal

This paper reports an improved catalytic molecular beacon. Addition of the target oligonucleotide activates a DNA enzyme (DNAzyme), which, in turn, activates multiple copies of molecular beacons (MB) and gives rise to a strong fluorescence signal. In a previous design, the activated DNAzyme could oligomerize, especially dimerize, and result in inactivation of the DNAzyme. The current design avoids this problem, upon activated by the target DNA, the DNAzyme will stay constantly active. With the improved method, a detection of 10 pM DNA has been demonstrated, which is 1000 times more sensitive than the method previously reported.     

基于DNAzyme的单链核酸酶活性研究

本文报道了一种基于DNAzyme的可视检测单链核酸酶活性的新方法.DNAzyme是一种具有类过氧化物酶活性的单链DNA分子,在H_2O_2存在下能够催化无色底物2,2′-连氮基-双-(3-乙基并二氢噻唑啉-6-磺酸)二价阴离子(ABTS~(2-))氧化成蓝绿色物质ABTS~-·5自由基.催化体系中单链核酸酶的加入能水解DNAzyme,导致被DNAzyme催化的ABTS~-·5减少,从而可以通过颜色变化和紫外-可见吸收光谱检测相应的单链核酸酶活性.以Dnase I和S1核酸酶作为单链核酸酶代表进行实验,实验结果表明对Dnase I检测的线性范围为0.5 ～5 U/mL,检出限为0.15 U/mL;对S1核酸酶检测的线性范围为1～10 U/mL,检出限为0.11 U/mL.该方法还能用于单链核酸酶抑制剂的检测,结果表明:Zn~(2+)对Dnase I的半数抑制浓度(Ic_(50))为56.4 mol/L,焦磷酸盐对S1核酸酶的Ic50为1.17 mmol/L.     

基于"分段"-"完整"转化的G-四链体脱氧核糖核酸酶传感器用于多聚核苷酸激酶的检测

采用"分段"转化为"完整"G-四链体脱氧核糖核酸酶的策略,构建了检测多聚核苷激酶(T4 PNK)的传感器.将形成G-四链体的富G序列PS5.M序列拆分成5 '和3'端均为羟基的两条链:链S1OH和链S2OH,即分别具有12个碱基的"分段"的PS5.M.在ATP存在下,T4 PNK酶可以将链S2OH的5 '端的羟基磷酸化,转化为S2P;在S1OH、S2P以及Helper链S—H存在下,T4 DNA连接酶(T4 DNA Ligase)将链S1OH和链S2P连接成"完整"的PS5.M序列.在体系中再加入核酸外切酶Ⅲ(ExoⅢ),从S—H的3'端剪切S-H,释放出PS5.M.在K+存在下,PS5.M与氯化血红素(Hemin)作用,形成具有类过氧化物酶活性的复合物,催化H2O2氧化2,2'-联氮-二(3-乙基-苯并噻唑-6-磺酸)二铵盐(ABTS)的反应,通过检测氧化产物在418 nm处的吸收值变化,实现对T4 PNK活性的定量检测.线性检测范围为0.02 ～ 3.0 U/mL,检出限为0.014 U/mL(S/N=3).对Hela细胞和HEK293细胞实际样本的T4 PNK活性进行了检测,平均回收率为95.6％～105.7％.     

A Rapid Sputum-based Lateral Flow Assay for Airway Eosinophilia using an RNA-cleaving DNAzyme Selected for Eosinophil Peroxidase

The first protein-binding allosteric RNA-cleaving DNAzyme (RCD) obtained by direct in vitro selection against eosinophil peroxidase (EPX), a validated marker for airway eosinophilia, is described. The RCD has nanomolar affinity for EPX, shows high selectivity against related peroxidases and other eosinophil proteins, and is resistant to degradation by mammalian nucleases. An optimized RCD was used to develop both fluorescence and lateral flow assays, which were evaluated using 38 minimally processed patient sputum samples (23 non-eosinophilic, 15 eosinophilic), producing a clinical sensitivity of 100 % and specificity of 96 %. This RCD-based lateral flow assay should allow for rapid evaluation of airway eosinophilia as an aid for guiding asthma therapy.     

基于脱氧核酶的无标记端粒酶检测新方法

设计了一种发卡型核酸探针,结合脱氧核酶(DNAzyme)与支点介导链置换技术建立了一种检测端粒酶的新方法.该发卡型探针通过阻碍G-四链体的形成来抑制DNAzyme的过氧化物酶活性.当体系中的端粒酶引物TS被催化延伸后,可以通过链置换反应破坏该发卡结构,从而释放出自由的DNAzyme以催化过氧化氢氧化ABTS2-,产生可被检测的吸收信号变化.实验结果表明,应用该方法可以检测低至500个Hela细胞等当量的端粒酶,且该方法操作简单、不需要荧光标记和复杂的表面修饰,有望在肿瘤细胞端粒酶活性分析中获得广泛应用.     

Real time monitoring uracil excision using uracil-containing molecular beacons

As a highly conserved damage repair protein, UDG excises uracil bases through its glycosylase activity. We report here an alternative fluorescence method for UDG assay with high accuracy and sensitivity by applying uracil-modified molecular beacons as substrates. The detection limit of UDG is 0.005 U mL⁻¹. The K_M and k_cat are 0.89 ± 0.1 μM and 210 ± 10 min⁻¹, respectively. The method is applied to screening inhibitors and the results indicate that both of the 5-FU and cisplatin can inhibit UDG activity with the IC₅₀ values of 6.1 ± 0.52 mM and 3.2 ± 0.24 mM, respectively. Furthermore, the combination of uracil-modified molecular beacons and nuclease inhibitor makes the new method possible to specifically detect UDG activity in cell-free extracts and serum. Taken together, the simple, rapid and sensitive method has potential relevance for a variety of applications, such as molecular diagnosis and screening of UDG inhibitors.     

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。     

Real-time monitoring of enzymatic cleavage of nucleic acids using a quartz crystal microbalance.

The use of quartz crystal microbalance (QCM) for monitoring in situ the enzymatic cleavage of surface-confined nucleic acids by nucleases is described. Such real-time monitoring of mass changes associated with the enzymatic digestion indicates that the activity and specificity of nucleases is preserved at the gold surface, and can be used for manipulating surface-confined DNAs and RNAs. These observations indicate great promise for using QCM for elucidating the interactions of nucleic acids with enzymes, and for enhancing the power of hybridization biosensors.     

Homogeneous Chemiluminescent Determination of Mercury(II) Using a Peroxidase-Mimicking DNAzyme Assay

Environmental pollution in manufacturing sectors is often accompanied by the release of diverse forms of pollutants including heavy metals. Mercury is one of the most toxic heavy metals. Here, we describe a homogeneous chemiluminescent method for Hg²⁺ detection based on allosteric activation of peroxidase-mimicking DNAzyme and formation of Hg²⁺-thymine bonds in DNA duplex with T–T mismatches in the presence of mercury. The formation of such duplex increased the activity of peroxidase-mimicking DNAzyme. The analysis conditions and structures of probes were optimized. Under the favorable conditions, the limit of detection and a linear range of the assay were 12 and 12–600?nM, respectively. The values of coefficient of variation measured within the working range varied from 0.7 to 3.0%. The study of cross-reactivity of Hg²⁺, Ag⁺, Pb²⁺, Ca²⁺, Zn²⁺, Bi³⁺, Ni²⁺, Co²⁺, Ba²⁺, Mn²⁺, Cd²⁺, Mg²⁺, and Cr³⁺ showed that only mercury in concentration nanoscale activates peroxidase-mimicking DNAzyme that indicates high specificity of the developed Hg²⁺ assay. Thus, an easy-to-use, specific, rapid, and sensitive method for Hg²⁺ detection was developed.     

Design of a High-Sensitivity Dimeric G-Quadruplex/Hemin DNAzyme Biosensor for Norovirus Detection

G-quadruplexes can bind with hemin to form peroxidase-like DNAzymes that are widely used in the design of biosensors. However, the catalytic activity of G-quadruplex/hemin DNAzyme is relatively low compared with natural peroxidase, which hampers its sensitivity and, thus, its application in the detection of nucleic acids. In this study, we developed a high-sensitivity biosensor targeting norovirus nucleic acids through rationally introducing a dimeric G-quadruplex structure into the DNAzyme. In this strategy, two separate molecular beacons each having a G-quadruplex-forming sequence embedded in the stem structure are brought together through hybridization with a target DNA strand, and thus forms a three-way junction architecture and allows a dimeric G-quadruplex to form, which, upon binding with hemin, has a synergistic enhancement of catalytic activities. This provides a high-sensitivity colorimetric readout by the catalyzing H₂O₂-mediated oxidation of 2,2′-azino-bis(3-ethylbenzothiazoline -6-sulfonic acid) diammonium salt (ABTS). Up to 10 nM of target DNA can be detected through colorimetric observation with the naked eye using our strategy. Hence, our approach provides a non-amplifying, non-labeling, simple-operating, cost-effective colorimetric biosensing method for target nucleic acids, such as norovirus-conserved sequence detection, and highlights the further implication of higher-order multimerized G-quadruplex structures in the design of high-sensitivity biosensors.     

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.     

Chemiluminescent Determination of MicroRNA-141 Using Target-Dependent Activation of the Peroxidase-Mimicking DNAzyme

A chemiluminescent method was developed for microRNA-141 (miRNA-141) detection based on the target-dependent activation of peroxidase-mimicking DNAzyme. The structure of the probes was optimized which allowed the development of a sensitive method for miRNA-141. Under the optimized conditions, the detection limit and the linear range were 100?pM and 0.1–50?nM, respectively. The sensitivity of the assay was 270,000?nM^?1. The values of coefficient of variation measured within the working range varied less than 2%, which indicates excellent precision for the proposed method.     

Caging-Decaging Strategies to Realize Spatiotemporal Control of DNAzyme Activity for Biosensing and Bioimaging

DNAzymes with RNA-cleaving activity have been widely used as biosensing and bioimaging tools for detection of metal ions. Despite the achievements, DNAzyme-based biosensors sometime suffer from false positive signals and unexpected off-target turn-on in biological environments, which are likely due to the unstable nature of the RNA site. Ways to control DNAzyme activity in order to improve the sensing performance remain a significant challenge. To meet the challenge, there is growing interest to develop synthetic strategies that can cage native DNAzyme under undesired conditions and reactivate it in target environment in order to function in a controlled manner. A variety of caging-decaging strategies have been developed to realize spatiotemporal control of the DNAzyme activity, improving its specificity and sensitivity as well as extending its application regimes. In this review, we focus on strategies to regulate the catalytic activity of DNAzyme, highlight the nucleic acid modification chemistries, and summarize three strategies to cage DNAzyme functions. Examples of using caged DNAzyme for bio-applications have also been reviewed in detail. Finally, we provide our perspectives on the potential challenges and opportunities of this emerging research topic that could advance the DNAzyme field.