Label-Free Fluorescence Molecular Beacon Probes Based on G-Triplex DNA and Thioflavin T for Protein Detection

Protein detection plays an important role in biological and biomedical sciences. The immunoassay based on fluorescence labeling has good specificity but a high labeling cost. Herein, on the basis of G-triplex molecular beacon (G3MB) and thioflavin T (ThT), we developed a simple and label-free biosensor for protein detection. The biotin and streptavidin were used as model enzymes. In the presence of target streptavidin (SA), the streptavidin hybridized with G3MB-b (biotin-linked-G-triplex molecular beacon) perfectly and formed larger steric hindrance, which hindered the hydrolysis of probes by exonuclease III (Exo III). In the absence of target streptavidin, the exonuclease III successively cleaved the stem of G3MB-b and released the G-rich sequences which self-assembled into a G-triplex and subsequently activated the fluorescence signal of thioflavin T. Compared with the traditional G-quadruplex molecular beacon (G4MB), the G3MB only needed a lower dosage of exonuclease III and a shorter reaction time to reach the optimal detection performance, because the concise sequence of G-triplex was good for the molecular beacon design. Moreover, fluorescence experiment results exhibited that the G3MB-b had good sensitivity and specificity for streptavidin detection. The developed label-free biosensor provides a valuable and general platform for protein detection.     

A label-free fluorescent probe based on DNA-templated silver nanoclusters and exonuclease III-assisted recycling amplification detection of nucleic acid

A number of specific nucleic acids are closely related with many serious diseases, in the current research, a platform taking advantage of exonuclease III (Exo III) to realize double recycling amplification and label-free fluorescent DNA-templated silver nanoclusters (DNA-AgNCs) for detecting of nucleic acid had been developed. In this method, a molecular beacon (MB) with 3′-protruding termini and a single-stranded cytosine-rich (C-rich) probe were designed that coexist stably with Exo III. Once the target DNA appeared, portion of the MB could hybridize with target DNA and was digested by Exo III, which allowed the release of target DNA and a residual sequence. Subsequently, the residual sequence could trigger the Exo III to digest C-rich probe, and the DNA-AgNCs was not able to be synthesized because of the C-rich probe was destroyed; finally the fluorescent of solution was quenched. This assay enables to monitor human hemochromatosis gene (as a model) with high sensitivity, the detection limit is as low as 120 pM compared with other fluorescence DNA-AgNCs methods, this assay also exhibits superior specificity even against single base mismatch. The strategy is applied to detect human hemochromatosis gene in real human serum samples successfully.     

Aptamer based fluorescent cocaine assay based on the use of graphene oxide and exonuclease III-assisted signal amplification

The article reports an aptamer based assay for cocaine by employing graphene oxide and exonuclease III-assisted signal amplification. It is based on the following scheme and experimental steps: (1) Exo III can digest dsDNA with blunt or recessed 3-terminus, but it has limited activity to ssDNA or dsDNA with protruding 3-terminus; (2) GO can absorb the FAM-labeled ssDNA probe and quench the fluorescence of probe, while the affinity between FAM-labeled mononucleotide and GO is negligible; (3) Cocaine aptamer can be split into two flexible ssDNA pieces (Probe 1 and Probe 2) without significant perturbation of cocaine-binding abilities; (4) The triple complex consisting of Probe 1, Probe 2 and cocaine can be digested by Exo III with the similar efficiency as normal dsDNA. Cocaine aptamer is split into two flexible ssDNA pieces (Probe 2 and 3′-FAM-labeled Probe 1). Cocaine can mediate the cocaine aptamer fragments forming a triplex. The triple complex has unique characteristic with 3′-FAM-labeled blunt end at the Probe 1 and 3′-overhang end at Probe 2. If exonuclease III is added, it will catalyze the stepwise removal of fluorescein (FAM) labeled mononucleotides from the 3-hydroxy termini of the special triplex complex, resulting in liberation of cocaine. The cocaine released in this step can produce a new cleavage cycle, thereby leading to target recycling. Through such a cyclic bound-hydrolysis process, small amounts of cocaine can induce the cleavage of a large number of FAM-labeled probe 1. The cleaved FAM-labeled mononucleotides are not adsorbed on the surface of graphene oxide (GO), so a strong fluorescence signal enhancement is observed as the cocaine triggers enzymatic digestion. Under optimized conditions, the assay allows cocaine to be detected in the 1 to 500 nM concentration range with a detection limit of 0.1 nM. The method was applied to the determination of cocaine in spiked human plasma, with recoveries ranging from 92.0 to 111.8 % and RSD of <12.8 %.

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Graphical abstract Aptamer based fluorescent cocaine assay based on graphene oxide and exonuclease III-assisted signal amplification

     

A universal platform for amplified multiplexed DNA detection based on exonuclease III-coded magnetic microparticle probes

An amplified multiplexed DNA detection biosensor has been developed, which combines the unique cleavage function of exonuclease III (Exo III) with the separating ability of magnetic microparticles (MMPs). By using different fluorophores, the multiplexed detection of DNA is demonstrated.     

A novel fluorescent aptasensor based on silica nanoparticles,PicoGreen and exonuclease III as a signal amplification method for ultrasensitive detection of myoglobin

Measurement of myoglobin (Mb) in human blood serum is of great interest for quick diagnosis of acute myocardial infarction (AMI). In this study, a novel fluorescent aptasensor was designed for ultrasensitive and selective detection of Mb, based on target-induced high fluorescence intensity, complementary strand of aptamer (CS), PicoGreen (PG) dye, exonuclease III (Exo III) and silica nanoparticles coated with streptavidin (SNPs-Streptavidin). The developed aptasensor obtains characteristics of SNPs as enhancers of fluorescence intensity, Exo III as an enzyme which selectively digests the 3'-end of double-stranded DNA (dsDNA), PG as a fluorescent dye which could selectively bind to dsDNA and high selectivity and sensitivity of aptamer (Apt) toward its target. In the absence of Mb, no free CS remains in the environment of SNPs-Streptavidin, resulting in a weak fluorescence emission. In the present of Mb, dsDNA-modified SNPs-Streptavidin complex forms, leading to a very strong fluorescence emission. The developed fluorescent aptasensor exhibited high specificity toward Mb with a limit of detection (LOD) as low as 52 pM. In addition, the designed fluorescent aptasensor was efficiently used to detect Mb in human serum.     

Sensitive fluorescence biosensor for folate receptor based on terminal protection of small-molecule-linked DNA

Based on the specific folic acid-folate receptor (FA-FR) interaction, macromolecular FR can bind with FA-linked DNA-small molecule chimeras, which can prevent enzymolysis by exonuclease III (Exo III), enabling a novel fluorescence biosensor for FR to be developed using quinaldine red as a G-quadruplex-binding probe.     

基于核酸外切酶Ⅲ诱导的双重信号放大与MoS2纳米片荧光碎灭性质的核酸检测方法

将核酸外切酶Ⅲ诱导的双重信号放大技术与MoS2纳米片的荧光猝灭性质结合,构建了一种高灵敏高选择性的DNA检测方法.首先设计两条末端修饰荧光基团的探针核酸(HP1和HP2).由于两条探针核酸具有3'粘性末端,使其不会被核酸外切酶Ⅲ降解,因而被吸附于MoS2纳米片而猝灭其荧光.当目标DNA存在时,会促使核酸外切酶Ⅲ启动双重信号放大反应,并将探针核酸降解成大量的不能吸附于MoS2纳米片表面的荧光碎片.在优化条件下,目标DNA浓度在0.5~6.0 pmol/L范围内与荧光信号变化呈良好的线性关系,检出限为0.28 pmol/L.与单重信号放大技术相比,本方法极大改善了分析灵敏度和检出限,且具有良好的单碱基错配区分能力.     

Electrochemical Determination of Aflatoxin B1 (AFB1) Using a Copper-Based Metal-Organic Framework (Cu-MOF) and Gold Nanoparticles (AuNPs) with Exonuclease III (Exo III) Assisted Recycling by Differential Pulse Voltammetry (DPV)

Abstract

A sensitive electrochemical biosensor was designed for determination of aflatoxin B1 (AFB1) using a copper-based metal-organic framework (Cu-MOF), which has strong electrochemical activity and exonuclease III (Exo III)-assisted recycling for dual signal amplification. Hairpin DNA (S1) was immobilized on the electrode. The AFB1 was recognized by aptamer DNA (S2) and complementary DNA (S3) was released. The S3 hybridized with the hairpin S1 to form the Exo III hydrolyzed double-stranded DNA, leaving a partial sequence of hairpin DNA (S1′) on the electrode and releasing S3 for the next cycle of the opening and digestion of hairpin S1. The amplified S1′ then was able to combine with more signal probes. Cu-MOF bond gold nanoparticles (AuNPs) by -NH₂ were immobilized to capture DNA (S4) to obtain Cu-MOF/AuNPs/S4. This signal probe Cu-MOF/AuNPs/S4 was able to hybridize with the electrode and generate an amplified electrochemical signal. Under the optimized conditions, this electrochemical biosensor for AFB1 exhibited a low detection limit of 6.7?×?10^?7?ng/mL at a signal-to-noise equal to 3 and a wide linear range from 10^?6 to 1?ng/mL. The biosensor was also used to analyze AFB1-spiked beer sample with recovery values between 96% and 103%. This method has the potential to become a valuable technology for detecting various toxins by the selection of the appropriate aptamer DNA.     

Fluorescence study of DNA binding and bending by EcoRI DNA methyltransferase

We have applied fluorescence anisotropy and fluorescence resonance energy transfer (FRET) techniques to study the interaction between EcoRI DNA methyltransferase (M.EcoRI) and its target DNA in solution. Upon binding with M.EcoRI, the dsDNA containing GAATTC bends to flip out the second adenine for methylation. The binding affinity of M.EcoRI to two dsDNA fragments (20 and 38 bp) was studied with fluorescence anisotropy. Their binding constants at different temperatures from 20 to 40 degrees C were obtained, and the thermodynamic parameters of binding were derived. The results showed that M.EcoRI had a higher binding affinity to the short dsDNA strand than to the long one, and its binding to DNA was primarily entropy-driven. By labeling the 5' ends of the 20-bp dsDNA with two fluorescent dyes, fluorescein (FAM) and tetramethylrhodamine (TMR), we were able to monitor the enhanced TMR fluorescence in the presence of M.EcoRI. The end-to-end distance of the dsDNA determined from the FRET efficiency was changed from 72.4 to 63.4 A, and the DNA bending angle was estimated as 57.8 degrees .     

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.     

聚集诱导发光分子/适配体/外切酶Ⅰ体系对可卡因的检测

目前非法药物的滥用已经成为全球性的公共安全卫生问题之一[1~3].其中可卡因作为一种全球禁用的非法药物,长期滥用会对人体造成许多不良的影响,如精神疾病、失眠、抑郁和暴力倾向等,甚至威胁生命,同时,吸食可卡因还会导致出现各种社会问题[4,5].因此实现对可卡因的快速检测成为打击毒品犯罪、维护社会稳定的关键.目前对于可卡因的检测主要采用气相色谱/质谱(GC/MS)和液相色谱/质谱(LC/MS)等大型仪器.虽然能够实现对可卡因检测,但大多需要专业人员操作且耗时较长,因此开发一种简便、高效且可靠的可卡因检测方法成为研究的热点[6~8].其中,基于荧光探针的检测手段由于具有高效、灵敏及便捷等优势而备受关注,但传统的荧光探针面临聚集导致发光猝灭(ACQ)的难题[9,10],即这类分子在溶液中发光非常强,一旦聚集或在固体中发光显著减弱,非常不利于实际应用.     

Sensitive electrochemical assaying of DNA methyltransferase activity based on mimic-hybridization chain reaction amplified strategy

A mimic-hybridization chain reaction (mimic-HCR) amplified strategy was proposed for sensitive electrochemically detection of DNA methylation and methyltransferase (MTase) activity In the presence of methylated DNA, DNA-gold nanoparticles (DNA-AuNPs) were captured on the electrode by sandwich-type assembly. It then triggered mimic-HCR of two hairpin probes to produce many long double-helix chains for numerous hexaammineruthenium (III) chloride ([Ru(NH₃)₆]³⁺, RuHex) inserting. As a result, the signal for electrochemically detection of DNA MTase activity could be amplified. If DNA was non-methylated, however, the sandwich-type assembly would not form because the short double-stranded DNAs (dsDNA) on the Au electrode could be cleaved and digested by restriction endonuclease HpaII (HapII) and exonuclease III (Exo III), resulting in the signal decrement. Based on this, an electrochemical approach for detection of M.SssI MTase activity with high sensitivity was developed. The linear range for M.SssI MTase activity was from 0.05 U mL⁻¹ to 10 U mL⁻¹, with a detection limit down to 0.03 U mL⁻¹. Moreover, this detecting strategy held great promise as an easy-to-use and highly sensitive method for other MTase activity and inhibition detection by exchanging the corresponding DNA sequence.     

A DNA nanomachine based on rolling circle amplification-bridged two-stage exonuclease III-assisted recycling strategy for label-free multi-amplified biosensing of nucleic acid

An autonomous DNA nanomachine based on rolling circle amplification (RCA)-bridged two-stage exonuclease III (Exo III)-induced recycling amplification (Exo III-RCA-Exo III) was developed for label-free and highly sensitive homogeneous multi-amplified detection of DNA combined with sensitive fluorescence detection technique. According to the configuration, the analysis of DNA is accomplished by recognizing the target to a unlabeled molecular beacon (UMB) that integrates target-binding and signal transducer within one multifunctional design, followed by the target-binding of UMB in duplex DNA removed stepwise by Exo III accompanied by the releasing of target DNA for the successive hybridization and cleavage process and autonomous generation of the primer that initiate RCA process with a rational designed padlock DNA. The RCA products containing thousands of repeated catalytic sequences catalytically hybridize with a hairpin reporter probe that includes a “caged” inactive G-quadruplex sequence (HGP) and were then detected by Exo III-assisted recycling amplification, liberating the active G-quadruplex and generating remarkable ZnPPIX/G-quadruplex fluorescence signals with the help of zinc(II)-protoporphyrin IX (ZnPPIX). The proposed strategy showed a wide dynamic range over 7 orders of magnitude with a low limit of detection of 0.51 aM. In addition, this designed protocol can discriminate mismatched DNA from perfectly matched target DNA, and holds a great potential for early diagnosis in gene-related diseases.     

Turn‐On Fluorescence Sensor Based on Single‐Walled‐Carbon‐Nanohorn–Peptide Complex for the Detection of Thrombin

Proteases play a central role in several widespread diseases. Thus, there is a great need for the fast and sensitive detection of various proteolytic enzymes. Herein, we have developed a carbon nanotube (CNT)‐based protease biosensing platform that uses peptides as a fluorescence probe for the first time. Single‐walled carbon nanohorns (SWCNHs) and thrombin were used to demonstrate this detection strategy. SWCNHs can adsorb a fluorescein‐based dye (FAM)‐labeled peptide (FAM‐pep) and quench the fluorescence of FAM. In contrast, thrombin can cleave FAM‐pep on SWCNHs and recover the fluorescence of FAM, which allows the sensitive detection of thrombin. This biosensor has a high sensitivity and selectivity toward thrombin, with a detection limit of 100 pM .     

基于银纳米粒子构建荧光传感平台用于核酸检测

报道了基于银纳米粒子构建的荧光传感平台,并用于核酸检测.此荧光传感平台对核酸检测基于以下策略:首先,荧光团标记的单链DNA探针被吸附到银纳米粒子的表面,荧光团与银纳米粒子近距离接触,发生荧光猝灭;加入与探针DNA序列互补的目标DNA,两者杂交形成双链DNA,并从银纳米粒子的表面脱离,荧光得到恢复.这种银纳米粒子构建的荧...     

Tungsten disulfide nanosheet and exonuclease III co-assisted amplification strategy for highly sensitive fluorescence polarization detection of DNA glycosylase activity

Herein, we introduced a tungsten disulfide (WS₂) nanosheet and exonuclease III (Exo III) co-assisted signal amplification strategy for highly sensitive fluorescent polarization (FP) assay of DNA glycosylase activity. Two DNA glycosylases, uracil-DNA glycosylase (UDG) and human 8-oxoG DNA glycosylase 1 (hOGG1), were tested. A hairpin-structured probe (HP) which contained damaged bases in the stem was used as the substrate. The removal of damaged bases from substrate by DNA glycosylase would lower the melting temperature of HP. The HP was then opened and hybridized with a FAM dye-labeled single strand DNA (DP), generating a duplex with a recessed 3′-terminal of DP. This design facilitated the Exo III-assisted amplification by repeating the hybridization and digestion of DP, liberating numerous FAM fluorophores which could not be adsorbed on WS₂ nanosheet. Thus, the final system exhibited a small FP signal. However, in the absence of DNA glycosylases, no hybridization between DP and HP was occurred, hampering the hydrolysis of DP by Exo III. The intact DP was then adsorbed on the surface of WS₂ nanosheet that greatly amplified the mass of the labeled-FAM fluorophore, resulting in a large FP value. With the co-assisted amplification strategy, the sensitivity was substantially improved. In addition, this method was applied to detect UDG activity in cell extracts. The study of the inhibition of UDG was also performed. Furthermore, this method is simple in design, easy in implementation, and selective, which holds potential applications in the DNA glycosylase related mechanism research and molecular diagnostics.     

Homogeneous Electrochemical Assay for Real‐time Monitoring of Exonuclease III Activity Based on a Graphene Monolayer

A homogeneous electrochemical assay based on a graphene monolayer electrode was developed for simple, sensitive, rapid and quantitative analysis of the exonuclease III (Exo III) activity. The method utilized a methylene blue (MB) tagged DNA substrate with hairpin structure, and a graphene monolayer attached on the working electrode. Before digestion, the hairpin structure prevents the adsorption of the DNA substrate to the graphene surface. Degradation of the substrate by the 3′–5′ Exo III, however, yields single‐stranded DNA (ssDNA), resulting in its subsequent binding to the graphene surface through π‐π stacking, which produces the voltammetric current from electrochemical reduction of the MB tag anchoring at the end of ssDNA. A direct quantification of the Exo III activity can be achieved by measuring the reductive peak current of the MB tag under easily attainable potential (∼ −0.1 V vs Ag/AgCl) range comparably sensitive to the conventional methods such as a gel‐based or fluorescence‐based assays. Our approach can be applied to measure various exonucleases activity by adjusting the structure of DNA substrate suggesting a new assay method in drug screening and basic research related to the enzymes.     

Glyphosate–Exonuclease Interactions: Reduced Enzymatic Activity as a Route to Glyphosate Biosensing

N-phosphonomethyle-glycine (glyphosate) is the most widely used pesticide worldwide due to its effectiveness in killing weeds at a moderate cost, bringing significant economic benefits. However, owing to its massive use, glyphosate and its residues contaminate surface waters. On site, fast monitoring of contamination is therefore urgently needed to alert local authorities and raise population awareness. Here the hindrance of the activity of two enzymes, the exonuclease I (Exo I) and the T5 exonuclease (T5 Exo) by glyphosate, is reported. These two enzymes digest oligonucleotides into shorter sequences, down to single nucleotides. The presence of glyphosate in the reaction medium hampers the activity of both enzymes, slowing down enzymatic digestion. It is shown by fluorescence spectroscopy that the inhibition of ExoI enzymatic activity is specific to glyphosate, paving the way for the development of a biosensor to detect this pollutant in drinking water at suitable detection limits, i.e., 0.6 nm .     

Ultrasensitive Fluorescence Polarization Aptasensors Based on Exonuclease Signal Amplification and Polystyrene Nanoparticle Amplification

Here, we combine T7 exonuclease (T7 Exo) signal amplification and polystyrene nanoparticle (PS NP) amplification to develop novel fluorescence polarization (FP) aptasensors. The binding of a target/open aptamer hairpin complex or a target/single‐stranded aptamer complex to dye‐labeled DNA bound to PS NPs, or the self‐assembly of two aptamer subunits (one of them labeled with a dye) into a target/aptamer complex on PS NPs leads to the cyclic T7 Exo‐catalyzed digestion of the dye‐labeled DNA or the dye‐labeled aptamer subunit. This results in a substantial decrease in the FP value for the amplified sensing process. Our newly developed aptasensors exhibit a sensitivity five orders of magnitude higher than that of traditional homogeneous aptasensors and a high specificity for the target molecules. These distinct advantages of our proposed assay protocol make it a generic platform for the design of amplified aptasensors for ultrasensitive detection of various target molecules.     

An Exonuclease III‐Powered,On‐Particle Stochastic DNA Walker

DNA‐based machines have attracted rapidly growing interest owing to their potential in drug delivery, biocomputing, and diagnostic applications. Herein, we report a type of exonuclease III (Exo III)‐powered stochastic DNA walker that can autonomously move on a spherical nucleic acid (SNA)‐based 3D track. The motion is propelled by unidirectional Exo III digestion of hybridized DNA tracks in a burnt‐bridge mechanism. The operation of this Exo III‐propelled DNA walker was monitored in real time and at the single‐particle resolution using total internal reflection fluorescence microscopy (TIRF). We further interrogated the morphological effect of the 3D track on the nuclease activity, which suggested that the performance of the DNA walker was critically dependent upon the DNA density and the track conformation. Finally, we demonstrated potential bioanalytical applications of this SNA‐based stochastic DNA walker by exploiting movement‐triggered cascade signal amplification.