Ultrasensitive endonuclease activity and inhibition detection using gold nanoparticle-enhanced fluorescence polarization

We have developed a highly sensitive and selective fluorescence polarization assay method based on the specificity of the DNA cleavage reaction with the enhancement of gold nanoparticles (AuNPs) for assaying endonuclease activity and inhibition. This assay can detect EcoRI endonuclease down to 5.0×10(-4) U mL(-1) with a detection range from 5.0×10(-4) to 10 U mL(-1).     

Cytosine-5 methylation-directed construction of a Au nanoparticle-based nanosensor for simultaneous detection of multiple DNA methyltransferases at the single-molecule level

DNA methylation at cytosine/guanine dinucleotide islands (CpGIs) is the most prominent epigenetic modification in prokaryotic and eukaryotic genomes. DNA methyltransferases (MTases) are responsible for genomic methylation, and their aberrant activities are closely associated with various diseases including cancers. However, the specific and sensitive detection of multiple DNA MTases has remained a great challenge due to the specificity of the methylase substrate and the rareness of methylation-sensitive restriction endonuclease species. Here, we demonstrate for the first time the cytosine-5 methylation-directed construction of a Au nanoparticle (AuNP)-based nanosensor for simultaneous detection of multiple DNA MTases at the single-molecule level. We used the methyl-directed endonuclease GlaI to cleave the site-specific 5-methylcytosine (5-mC). In the presence of CpG and GpC MTases (i.e., M.SssI and M.CviPI), their hairpin substrates are methylated at cytosine-5 to form the catalytic substrates for GlaI, respectively, followed by simultaneous cleavage by GlaI to yield two capture probes. These two capture probes can hybridize with the Cy5/Cy3–signal probes which are assembled on the AuNPs, respectively, to form the double-stranded DNAs (dsDNAs). Each dsDNA with a guanine ribonucleotide can act as the catalytic substrate for ribonuclease (RNase HII), inducing recycling cleavage of signal probes to liberate large numbers of Cy5 and Cy3 molecules from the AuNPs. The released Cy5 and Cy3 molecules can be simply quantified by total internal reflection fluorescence (TIRF)-based single-molecule imaging for simultaneous measurement of M.SssI and M.CviPI MTase activities. This method exhibits good specificity and high sensitivity with a detection limit of 2.01 × 10⁻³ U mL⁻¹ for M.SssI MTase and 3.39 × 10⁻³ U mL⁻¹ for M.CviPI MTase, and it can be further applied for discriminating different kinds of DNA MTases, screening potential inhibitors, and measuring DNA MTase activities in human serum and cell lysate samples, holding great potential in biomedical research, clinical diagnosis, drug discovery and cancer therapeutics.

Cytosine-5 methylation-directed construction of Au nanoparticle-based nanosensors enables specific and sensitive detection of multiple DNA methyltransferases.     

Fluorescence quenching of graphene oxide combined with the site-specific cleavage of restriction endonuclease for deoxyribonucleic acid demethylase activity assay

We report on the development of a sensitive and selective deoxyribonucleic acid (DNA) demethylase (using MBD2 as an example) activity assay by coupling the fluorescence quenching of graphene oxide (GO) with the site-specific cleavage of HpaII endonuclease to improve the selectivity. This approach was developed by designing a single-stranded probe (P1) that carries a binding region to facilitate the interaction with GO, which induces fluorescence quenching of the labeled fluorophore (FAM, 6-carboxyfluorescein), and a sensing region, which contains a hemi-methylated site of 5′-CmCGG-3′, to specifically recognize the target (T1, a 32-mer DNA from the promoter region of p53 gene) and hybridize with it to form a P1/T1 duplex. After demethylation with MBD2, the duplex can be specifically cleaved using HpaII, which releases the labeled FAM from the GO surface and results in the recovery of fluorescence. However, this cleavage is blocked by the hemi-methylation of this site. Thus, the magnitude of the recovered fluorescence signal is related to the MBD2 activity, which establishes the basis of the DNA demethylase activity assay. This assay can determine as low as ∼(0.05 ± 0.01) ng mL⁻¹ (at a signal/noise of 3) of MBD2 with a linear range of 0.2–300 ng mL⁻¹ and recognize MBD2 from other possibly coexisting proteins and cancer cell extracts. The advantage of this assay is its ability to avoid false signals and no requirement of bisulfite conversion, PCR amplification, radioisotope labeling, or separation.     

Label-free monitoring of site-specific DNA cleavage by EcoRI endonuclease using cyclic voltammetry and electrochemical impedance

Cyclic voltammetry (CV) combined with electrochemical impedance spectroscopy (EIS) were proposed to monitor the site-specific DNA cleavage by EcoRI endonuclease without using external label. The alteration of CV and EIS signal demonstrated that double-strands (dsDNA) contain recognition sequence was cleaved by EcoRI endonuclease. Real-time monitoring indicated that the dsDNA was cleaved by EcoRI more than 90% after 2 h of enzyme digestion time. Control experiment showed that the DNA cleavage by EcoRI endonuclease is site-specific for DNA sequence. Experimental results demonstrated that the efficiency of EcoRI cleavage was highly dependent on the concentration of EcoRI concentration in the range from 0.04 to 0.4 U μL⁻¹ with one almost linear relationship.     

Dual Signal Amplification Electrochemical Biosensor for Lead Cation

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

Proximity-based electrochemical biosensor for highly sensitive determination of methyltransferase activity using gold nanoparticle-based cooperative signal amplification

We describe a turn-on electrochemical biosensor for the detection of methyltransferases (MTases) causing DNA adenine methylation. This biosensor is based on insertion, methylation-resistant cleavage, signal enrichment caused by gold nanoparticles (AuNPs), and a signal probe-dragging strategy. A double-stranded DNA (dsDNA) containing identical MTase and methylation-resistant endonuclease (Mbo I) sites was immobilized on the surface of a gold electrode via Au-S covalent binding. The surface was subsequently treated with MTase and Mbo I and then washed. Results revealed that the surface of the electrode contains methylated dsDNA and 12-base nucleotides residual. Depending on biotin-streptavidin interactions that enabled signal probes and nucleotide residue hybridization and AuNP enrichment, a large number of signal probes labeled with ferrocene (Fc) are captured by the electrode. Under optimal conditions, the differential pulse voltammetry signals of Fc tags (at a working voltage of 0.24 V vs. Ag/AgCl) are linearly related to the log of the MTase activity in the 0.1 to 40 U·mL⁻¹ range. The dynamic range extends from 0.05 to 50 U·mL⁻¹, and the limit of detection is 0.024 U·mL⁻¹ (at an S/N ratio of 3). The assay is well reproducible and highly selective. In our perception, this strategy provides a promising approach for simple, sensitive and selective detection of Dam MTase and may be extended to the determination of other MTase by exchanging the corresponding DNA.

Proximity-based electrochemical biosensor for highly sensitive detection of DNA adenine methylation methyltransferase (Dam MTase) activity using methylation-resistant cleavage coupled with gold nanoparticle based cooperative signal amplification.

     

Multianalyte Electrochemical Biosensor Based on Aptamer‐ and Nanoparticle‐Integrated Bio‐Barcode Amplification

In the present work, a signal‐on electrochemical sensing strategy for the simultaneous detection of adenosine and thrombin is developed based on switching structures of aptamers. An Au electrode as the sensing surface is modified with two kinds of thiolated capture probes complementary to the linker DNA that contains either an adenosine aptamer or thrombin aptamer. The capture probes hybridize with their corresponding linker DNA, which has prehybridized with the reporter DNA loaded onto the gold nanoparticles (AuNPs). The AuNP contained two kinds of bio‐barcode DNA: one is complementary to the linker DNA (reporter), whereas the other is not (signal) and is tagged with different metal sulfide nanoparticles. Thus a “sandwich‐type” sensing interface is fabricated for adenosine and thrombin. With the introduction of adenosine and thrombin, the aptamer parts bind with their targets and fold to form the complex structures. As a result, the bio‐barcoded AuNPs are released into solution. The metal sulfide nanoparticles are measured by anodic stripping voltammetry (ASV), and the concentrations of adenosine and thrombin are proportional to the signal of either metal ion. With the dual amplification of the bio‐barcoded AuNP and the preconcentration of metal ions through ASV technology, detection limits as low as 6.6×10^?12 M for adenosine and 1.0×10^?12 M for thrombin are achieved. The sensor exhibits excellent selectivity and detectability in biological samples.     

Highly Sensitive and Selective Fluorescence Probe for 2,4‐Dinitrophenylhydrazine Detection in Wastewater Using Water‐Soluble CdTe QDs

A simple, cheap, sensitive and selective probe for determination of DNPH in wastewater using thioglycolic acid (TGA)‐coated CdTe QDs (TGA‐QDs) as fluorescence probe has been established, and the properties of CdTe QDs were characterized by TEM, FT‐IR, DLS, XRD and zeta potentials. CdTe QDs fluorescence is highly efficiently quenched after adding DNPH on account of electron transfer effect, and the fluorescence quenching behavior of CdTe QDs interaction with DNPH is static quenching process. A good linear relationship is observed between the relative fluorescence intensity (F₀/F) and 0.06–10 ng mL^?1 of DNPH. As compared with some of reported methods, LOD of this method for analysis of DNPH (0.23 ng mL^?1) is the lowest. Masking agents of DDTC and NH₄OH can eliminate the interference of Cu²⁺, Ag⁺ and Hg²⁺. Hence, DNPH can be selectively and accurately detected and the established method was successfully used for detecting DNPH in wastewater with acceptable recovery of 90.6–102%.     

Determination of L‐Cystine by a New Sensitive Cucurbit[7]uril/palmatine Probe

In the presence of cucurbit[7]uril (CB[7]), the CB[7] could react with palmatine, which served as a sensitive fluorescence probe, to form host‐guest stable complexes and the fluorescence intensity of the complexes was greatly enhanced. The fluorescence intensity decreased linearly with an increasing number of L‐cystine in the inclusion system. The experimental results show that there exists a competition between L‐cystine and palmatine for the CB[7] hydrophobic cavity and L‐cystine occupies the space of CB[7] cavity, leading palmatine molecules to be forced to reside in the aqueous environment. Based on the fluorescence quenching of the CB[7]/palmatine complexes resulting from complex formation between CB[7] and L‐cystine, a spectrofluorimetric method for the determination of L‐cystine in aqueous solution in the presence of CB[7] was developed. The linear relationship between the corresponding values of the fluorescence quenching ΔF and L‐cystine concentration was obtained in the range of 6.0 to 1.5×10³ ng·mL^?1, with a correlation coefficient (r) of 0.9996. The detection limit was 2.0 ng·mL^?1. The application of the present method to the determination of L‐cystine in tablets gave satisfactory results. This paper also discussed the mechanism of the fluorescence indicator probe.     

Functionalized carbon dots as sensors for gold nanoparticles in spiked samples: Formation of nanohybrids

This paper reports the synthesis, passivation and functionalization of luminescent carbon dots (CDs) possessing surface thiol ending groups. A simple procedure involving amidation of passivated carbon dots (p-CDs) with cysteamine boosts their photoluminescent properties and enables their use as easily controlled fluorescent nanosensors for determining citrate–gold nanoparticles (AuNPs). The mechanism behind the quenching phenomenon was established from fluorescence measurements at high temperatures and lifetime tests, and found to involve static quenching leading to the formation of CD–AuNP nanohybrids. A method for determining AuNPs in complex matrices was developed and validated by application to spiked drinking water and mussel tissues. The limits of detection and quantitation for AuNPs thus obtained were 0.20 and 0.66 nmol L^–1, respectively.     

A Novel Fluorescence Quenching Method for the Determination of Aloe Polysaccharide

Alizarin red (AR) can bind with aloe polysaccharide (APS) in doubly de‐ionized water to form a red complex resulting in fluorescence quenching of it. The maximum fluorescence quenching wavelength is 572 nm. The chromogenic reaction is rapid and the fluorescence intensity remains stable for at least 2 h at room temperature. The quenched fluorescence intensity (ΔF) is directly proportional to APS concentration. Based on this interaction, a sensitive and selective fluorophotometric method is proposed for the determination of APS. The optimal experiment conditions were established. The corresponding linear equation is (F=0.8807C+1.8132, R²=0.9999. The quantification and detection limits are 0.4752 and 0.1425 µg·mL^?1, respectively. The linear range is 0.444–16.65 µg·mL^?1 for APS and the mean recovery (100.2±2)%, RSD?3%. The effect of various substances on the determination of APS was also investigated in detail, and the results show that most of the studied coexistent substances can be tolerated in considerable amounts. The proposed method is sensitive, simple, fast and suitable for routine assay.     

Fast and sensitive detection of ochratoxin A in red wine by nanoparticle-enhanced SPR

Herein, we present a fast and sensitive biosensor for detection of Ochratoxin A (OTA) in a red wine that utilizes gold nanoparticle-enhanced surface plasmon resonance (SPR). By combining an indirect competitive inhibition immunoassay and signal enhancement by secondary antibodies conjugated with gold nanoparticles (AuNPs), highly sensitive detection of low molecular weight compounds (such as OTA) was achieved. The reported biosensor allowed for OTA detection at concentrations as low as 0.75 ng mL⁻¹ and its limit of detection was improved by more than one order of magnitude to 0.068 ng mL⁻¹ by applying AuNPs as a signal enhancer. The study investigates the interplay of size of AuNPs and affinity of recognition elements affecting the efficiency of the signal amplification strategy based on AuNP. Furthermore, we observed that the presence of polyphenolic compounds in wine samples strongly interferes with the affinity binding on the surface. To overcome this limitation, a simple pre-treatment of the wine sample with the binding agent poly(vinylpyrrolidone) (PVP) was successfully applied.     

The Electrochemical Behavior of Gold Nanoparticle‐Tantalum(V) Phthalocyanine Composites: Applications Towards the Electroanalysis of Bisphenol A

The formation of gold nanoparticle (AuNP) composites with tantalum phthalocyanines (TaPc) complexes { 1a and 1b (Figure 1 )} is reported. The TaPc‐AuNPs conjugates were characterised by atomic force microscopy (AFM) and transmission electron microscopy. The AFM analyses show that conjugates of TaPc with AuNPs are more aggregated when compared to AuNPs alone. The conjugates and TaPc complexes were immobilized on a gold electrode by drop and dry method and these were characterized by electrochemical impedance spectroscopy. The charge transfer behaviour of AuNPs was enhanced in the presence of TaPc complexes. All the modified electrodes showed electrocatalytic oxidation of bisphenol A. The limits of detection for complexes 1a and 1 b were 4.78×10^?10 and 2.76×10^?10 mol L^?1, respectively.     

Impedimetric aptasensor for Staphylococcus aureus based on nanocomposite prepared from reduced graphene oxide and gold nanoparticles

We describe here an aptasensor for the ultrasensitive detection of Staphylococcus aureus by electrochemical impedance spectroscopy (EIS). Single-stranded DNA was linked to a nanocomposite prepared from reduced graphene oxide (rGO) and gold nanoparticles (AuNP). Thiolated ssDNA was covalently linked to the AuNPs linked to rGO, and probe DNA was immobilized on the surface of an AuNP-modified glassy carbon electrode to capture and concentrate Staph. aureus. The probe DNA of the aptasensor selectively captures the target bacteria in its three-dimensional space, and these results in a dramatic increase in impedance. Scanning electron microscopy, cyclic voltammetry and EIS were used to monitor the single steps of the electrode assembly process. The effect was utilized to quantify the bacteria in the concentration range from 10 to 10⁶ cfu mL^?1 and with a detection limit of 10 cfu mL^?1 (S/N?=?3). The relative standard deviation of Staphylococcus aureus detection was equal to 4.3 % (10⁵ cfu mL^?1, n?=?7). In addition to its sensitivity, the biosensor exhibits high selectivity over other pathogens.

Spectroscopy studies of sandwich-type complex of silver(I) co-ordinated to nuclear fast red and adenine and its analytical applications

A novel fluorometric method for the determination of adenine was proposed, based on the fluorescence quenching of a nuclear fast red-silver complex as a small molecule optical probe in the presence of adenine. The characteristic spectra of absorption, resonance Rayleigh scattering (RRS) and the fluorescence of the system were analysed. Adenine, Ag⁺ and nuclear fast red formed a sandwich-type complex. The composition of the compound and the mechanisms of fluorescence quenching were discussed. The optimal conditions for the reaction and the effects of co-existing substances were also investigated. The quenched fluorescence intensity was proportional to the concentration of adenine in the range of 0.03–0.90 µg mL^?1, with the limit of detection of 0.023 µg mL^?1. The method was applied satisfactorily to the determination of adenine in synthetic samples, herring sperm DNA, human sera and vitamin B₄ tablets with recoveries from 95.3 % to 105 %.     

Novel luminescent nanoparticles for DNA detection

Highly luminescent LaF₃:Ce³⁺/Tb³⁺ nanocrystals were successfully prepared and surface functionalized via Layer-by-Layer technology. These as-prepared nanocrystals are highly resistant to photobleaching and pretty dispersible in aqueous solution. Due to the efficient luminescence quenching of the nanocrystals by nucleic acids, a facile fluorescence quenching method was developed for the detection of trace amount of nucleic acids. Under optimal conditions, the fluorescence intensity was proportional to the DNA concentration over the range of 0.60–25.0 μg mL^?1 for calf thymus DNA (ct-DNA) and 0.60–30.0 μg mL^?1 for herring sperm DNA (hs-DNA), respectively. The corresponding detection limit is 0.21 μg mL^?1 for ct-DNA and 0.31 μg mL^?1 for hs-DNA, respectively. The results indicated that the reported method is simple and rapid with wide linear range. Also, the recovery and relative standard deviation of this method are reasonable and satisfactory.     

Biofunctionalized silver and gold nanoparticles as potential curative agents

In this study, the bark of an important medicinal plant, Indigofera aspalathoides is utilized as a bioreductant for the synthesis of silver nanoparticles (AgNPs) and gold nanoparticles (AuNPs). The formation of nanoparticles was monitored, and the reaction parameters were optimized by UV–Vis spectroscopy. The attachment of biocomponents as stabilizer was proved employing Fourier‐transform infrared (FT‐IR) studies. Through transmission electron microscopy (TEM), the morphology was found to be predominantly spherical and a mixture of triangle and hexagon in the case of AgNPs and AuNPs, respectively. The crystallite size of AgNPs and AuNPs was affirmed through X‐ray diffraction (XRD) studies using Sherrer formula as 22.03 and 47.70 nm, respectively. DPPH method was adopted to analyse the free‐radical quenching ability, and the AgNPs, AuNPs and extract showed inhibition of 76%, 89% and 59% at a concentration of 200 μg ml^?1, and the corresponding IC₅₀ values were 86.49, 55.20 and 149.19 μg ml^?1. The binding of nanoparticles to calf‐thymus DNA (CT‐DNA) was through groove and the high binding constants (8.49 × 10⁶ M^?1 and 2.34 × 10⁷ M^?1 for AgNPs and AuNPs) point out the potential of these nanoparticles as curative drugs. The MTT assay showed that AgNPs were 100% toxic, and the low IC₅₀ value suggests that this can be used in the medicinal field as a safe drug.     

健那绿B的荧光猝灭研究及作为核酸测定探针的应用

用紫外可见光谱、稳态荧光发射及荧光寿命测定研究了核酸猝灭十二烷基磺酸钠胶束中的健那绿荧光。水溶液中弱的健那绿荧光在十二烷基磺酸钠胶束中被大大加强，其最大发射从425纳米移至410纳米，核酸的加入将猝灭健那绿的荧光，当健那绿浓度为2.5×10^–5 mol•L^-1时，荧光猝灭(F₀/F)分别与小牛胸腺DNA及鱼精DNA在2.4×10^–8 到 1.08×10^–7及 1.9×10^–8 到 3.8×10^–8 mol•L^-1范围内成正比, 检测限分别为1.3×10^–8 mol•L^-1 (小牛胸腺DNA)及6.3×10^–9 mol•L^-1 (鱼精DNA)。当DNA浓度较高时, 将系统偏离Stern-Volmer方程。这是因为动态猝灭和静态猝灭同时存在。方法已应用于鸡血提取液中DNA的测定, 测定结果与紫外法一致。     

Click‐Conjugation of Nanogold‐Functionalized PAMAM Dendrimer: Toward a Novel Electrochemical Detection Platform

This work reports a new electrochemical monitoring platform for sensitive detection of Cu²⁺ coupling click chemistry with nanogold‐functionalized PAMAM dendrimer (AuNP‐PAMAM). The system involved an alkyne‐modified carbon electrode and an azide‐functionalized AuNP‐PAMAM. Initially, the added Cu²⁺ was reduced to Cu⁺ by the ascorbate, and then the azide‐modified AuNP‐PAMAM was covalently conjugated to the electrode via Cu⁺‐catalyzed azide‐alkyne click reaction. The carried AuNPs accompanying PAMAM dendrimer could be directly monitored by stripping voltammetry after acidic pretreatment. By introduction of high‐loading PAMAM dendrimer with gold nanoparticles, as low as 2.8 pM Cu²⁺ (ppt) could be detected, which was 125‐fold lower than that of gold nanoparticle‐based labeling strategy. The method exhibited high specificity toward target Cu²⁺ against other potentially interfering ions, and was applicable for monitoring Cu²⁺ in drinking water with satisfactory results.     

Target-mediated consecutive endonuclease reactions for specific and sensitive homogeneous fluorescence assay of O-methylguanine-DNA methyltransferase

O⁶-Methylguanine-DNA methyltransferase (MGMT) is one of the most important DNA-repair enzymes. Herein, a simple, sensitive and selective homogeneous fluorescence assay strategy is developed for the detection of MGMT on the basis of target-mediated two consecutive endonuclease reactions. The activity assay of MGMT is firstly accomplished using a hairpin-structured DNA substrate to offer a specific recognition site on the substrate DNA for restriction endonuclease PvuII, and thus to initiate the first endonuclease reaction. The product which activates the second endonuclease reaction allows an efficient amplification approach to create an abundance of fluorescence signal reporters. The first endonuclease reaction offers the method high specificity and the second one furnishes the assay improved sensitivity. The results reveal that the MGMT assay strategy shows dynamic responses in the concentration range from 1 to 120 ng mL⁻¹ with a detection limit of 0.5 ng mL⁻¹. By simply altering the alkylated bases, this strategy can also be extended for the detection of other alkyltransferases. Therefore, the developed strategy might provide an intrinsically convenient, sensitive and specific platform for alkyltransferase activate assay and related biochemical studies due to its label-free, homogeneous, and fluorescence-based detection format.