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.     

Label-free colorimetric aptasensor for sensitive detection of ochratoxin A utilizing hybridization chain reaction

The combination of high selectivity of aptamer with the peroxidase-mimicking property of DNAzyme has presented considerable opportunities for designing colorimetric aptasensor for detection of ochratoxin A (OTA). The activities of both aptamer (as biorecognition element) and DNAzyme (as signal amplification element) are blocked via base pairing in the hairpin structure. Hybridization chain reaction (HCR) between two hairpin DNAs was employed to further improve the sensitivity of this method. The presence of OTA triggers the opening of the hairpin structure and the beginning of HCR, which results in the release of many DNAzyme, and generates enhanced colorimetric signals, which is correlated to the amounts of OTA with linear range between 0.01 to 0.32 nM, and the limit of detection is 0.01 nM under optimal conditions. OTA in yellow rice wine and wheat flour samples was also detected using this method. We demonstrate that a new colorimetric method for the detection of OTA has been established, which is simple, easy to conduct, label-free, sensitive, high throughput, and cost-saving.     

Label-free and non-enzymatic detection of DNA based on hybridization chain reaction amplification and dsDNA-templated copper nanoparticles

A label-free and non-enzymatic amplification fluorescent method for detection of DNA has been developed by using hybridization chain reaction (HCR) and dsDNA-templated copper nanoparticles (CuNPs). First, the biotinylated capture DNA probes were immobilized on the streptavidin-modified beads through the interaction of biotin and streptavidin. Then, target DNA hybridized with the capture DNA probes, which formed a hybridized DNA with sticky end. The sticky end triggered the HCR process and formation of dsDNA polymers while two hairpin probes coexisted. Subsequently, the dsDNA polymers were employed as template for synthesis of CuNPs with excellent fluorescent properties, which provided a label-free, non-enzymatic signal response. Meanwhile, the fluorescence sensing depended on the target DNA triggered HCR, which render this method a high selectivity against single-base mismatch sequences. The concept and methodology developed in this work show great promise in the quantitative detection of DNA in biological and medical applications.     

N-Methylimidazolium modified magnetic particles-assisted highly sensitive Escherichia coli detection based on polymerase chain reaction and capillary electrophoresis

Effective bacteria detection and quantification are essential prerequisite for the prevention and treatment of infectious diseases. Herein, we report a method for the detection and quantification of Escherichia coli (E. coli).N-Methylimidazolium modified magnetic particles (MIm-MPs) are synthesized successfully and used as an efficient magnetic material for the isolation and concentration of E. coli. The factors including pH of binding buffer, concentration of elution buffer and elution time which may affect the capture and elution efficiencies are optimized. The linear correlation between bacteria concentration and peak area of polymerase chain reaction (PCR) product analyzed by capillary electrophoresis (CE) is determined. Rapid preconcentration of trace amount of E. coli (10¹ cfu mL⁻¹) in large volume of aqueous sample (500 mL) is achieved, and the capture efficiency can reach 99%. The quantification of bacteria in large volume of spiked tap water and mineral water samples is realized. The recoveries for different concentrations of E. coli in tap and mineral water samples are in the range between 83% and 93%. The results demonstrate that this MIm-MPs-PCR-CE method can be applied to detect and quantify bacteria in real samples.     

Direct fluorescence detection of point mutations in human genomic DNA using microbead-based ligase chain reaction

This report has described a convenient genotyping method capable of detecting point mutations directly in human genomic DNA based on the combination of ligase chain reaction (LCR) and microbead-enrichment technique. LCR primers, including a biotin-labeled common primer and two fluorescence-labeled allele-specific primers, are designed for two alleles of a mutated site. When genomic DNA carries the mutated site, the common primer and allele-specific primer are ligated to form exponential amplified biotin-labeled fluorescence ligation products. These ligated products are enriched by streptavidin-coated microbeads, and genotypes are identified conveniently according to the fluorescence color of microbeads using fluorescent microscopy. Due to amplification of LCR process and enrichment of microbeads, the detection limit of the proposed method is as low as 10⁻¹⁵ mol/L templates. The method provides a convenient and simple strategy to detect point mutation directly in human genome. We have confirmed the efficiency of this approach with the identification of β-globin gene point mutation, which results in the reduced production of globin in an inherited hemoglobin disorder thalassemia disease.     

A novel fluorescent and chromogenic probe for cyanide detection in water based on the nucleophilic addition of cyanide to imine group

A fluorescent and colorimetric probe bearing salicylaldehyde hydrazone functionality has been prepared for cyanide sensing. The detection of cyanide was performed via the nucleophilic attack of cyanide anion on the imine group of the probe with a 1:1 binding stoichiometry, which could be confirmed by ¹H NMR and MS studies. The specific reaction results in a prominent fluorescence enhancement and a color change from colorless to yellow.     

DNA-based hybridization chain reaction amplification for assaying the effect of environmental phenolic hormone on DNA methyltransferase activity

In this work, a novel electrochemical protocol with signal amplification for determination of DNA methylation and methyltransferase activity using DNA-based hybridization chain reaction (HCR) was proposed. After the gold electrode was modified with dsDNA, it was treated with M.SssI MTase, HpaII endonuclease, respectively. And then the HCR was initiated by the target DNA and two hairpin helper DNAs, which lead to the formation of extended dsDNA polymers on the electrode surface. The signal was amplified by the labeled biotin on the hairpin probes. As a result, the streptavidin-alkaline phosphatase (S-ALP) conjugated on the electrode surface through the specific interaction between biotin and S-ALP. ALP could convert 1-naphthyl phosphate into 1-naphthol and the latter could be electrochemically oxidized, which was used to monitor the methylation event and MTase activity. The HCR assay presents good electrochemical responses for the determination of M.SssI MTase at a concentration as low as 0.0067 unit mL⁻¹. Moreover, the effects of anti-cancer drug and environmental phenolic hormone on M.SssI MTase activity were also investigated. The results indicated that 5-fluorouracil and daunorubicin hydrochloride could inhibit the activity, and the opposite results were obtained with bisphenol A and nonylphenol. Therefore, this method can not only provide a platform to screen the inhibitors of DNA MTase and develop new anticancer drugs, but also offer a novel technique to investigate the possible carcinogenesis mechanism.     

Electrical detection of deoxyribonucleic acid hybridization based on carbon-nanotubes/nano zirconium dioxide/chitosan-modified electrodes

A novel and sensitive electrochemical DNA biosensor based on nanoparticles ZrO₂ and multi-walled carbon nanotubes (MWNTs) for DNA immobilization and enhanced hybridization detection is described. The MWNTs/nano ZrO₂/chitosan-modified glassy carbon electrode (GCE) was fabricated and oligonucleotides were immobilized to the GCE. The hybridization reaction on the electrode was monitored by differential pulse voltammetry (DPV) analysis using electroactive daunomycin as an indicator. Compared with previous DNA sensors with oligonucleotides directly incorporated on carbon electrodes, this carbon nanotube-based assay with its large surface area and good charge-transport characteristics increased DNA attachment quantity and complementary DNA detection sensitivity. The response signal increases linearly with the increase of the logarithm of the target DNA concentration in the range of 1.49 × 10⁻¹⁰ to 9.32 × 10⁻⁸ mol L⁻¹ with the detection limit of 7.5 × 10⁻¹¹ mol L⁻¹ (S/N = 3). The linear regression equation is I = 32.62 + 3.037 log C_DNA (mol L⁻¹) with a correlation coefficient value of 0.9842. This is the first application of carbon nanotubes combined with nano ZrO₂ to the fabrication of an electrochemical DNA biosensor with a favorable performance for the rapid detection of specific hybridization.     

A rapid method for the detection of foodborne pathogens by extraction of a trace amount of DNA from raw milk based on amino-modified silica-coated magnetic nanoparticles and polymerase chain reaction

A method based on amino-modified silica-coated magnetic nanoparticles (ASMNPs) and polymerase chain reaction (PCR) was developed to rapidly and sensitively detect foodborne pathogens in raw milk. After optimizing parameters such as pH, temperature, and time, a trace amount of genomic DNA of pathogens could be extracted directly from complex matrices such as raw milk using ASMNPs. The magnetically separated complexes of genomic DNA and ASMNPs were directly subjected to single PCR (S-PCR) or multiplex PCR (M-PCR) to detect single or multiple pathogens from raw milk samples. Salmonella Enteritidis (Gram-negative) and Listeria monocytogenes (Gram-positive) were used as model organisms to artificially contaminate raw milk samples. After magnetic separation and S-PCR, the detection sensitivities were 8 CFU mL⁻¹ and 13 CFU mL⁻¹ respectively for these two types of pathogens. Furthermore, this method was successfully used to detect multiple pathogens (S. Enteritidis and L. monocytogenes) from artificially contaminated raw milk using M-PCR at sensitivities of 15 CFU mL⁻¹ and 25 CFU mL⁻¹, respectively. This method has great potential to rapidly and sensitively detect pathogens in raw milk or other complex food matrices.     

Evaluation of on-line high-performance size-exclusion chromatography, differential refractometry, and multi-angle laser light scattering analysis for the monitoring of the oligomeric state of human immunodeficiency virus vaccine protein antigen

Chiron has developed a novel mutant form of the human immunodeficiency virus (HIV) envelop protein, o-gp140, that is currently entering Human Phase 1 clinical trials for testing as a prophylactic HIV vaccine. The o-gp140 protein is oligomeric and the quaternary structure is thought to play an important role in its activity as an antigen. As o-gpl40 proceeds through the clinical trial process and prior to marketing approval, analytical methods that are able to demonstrate manufacturing consistency with respect to degree of oligomerization will need to be developed and validated. On-line high-performance size-exclusion chromatography, differential refractometry, and multi-angle laser light scattering analysis (HPSEC-RI-MALLS), a method commonly used to obtain the molar mass of macromolecules based on the Rayleigh-Gans-Debye approximation, was evaluated for this purpose. The results obtained demonstrated intra- and inter-day precisions to be 0.9 and 3.6% R.S.D., respectively. Accuracy was found to be equal to, or better than, 11% when comparing the known molar masses of test proteins to that of the molar masses determined by the method. Additionally, the method compared favorably to orthogonal native polyacrylamide gel electrophoresis and ultracentrifugation analyses. R-factor analysis was used to demonstrate that HPSEC-RI-MALLS is capable of discriminating compositional differences between o-gpl40 test lots. Based on the data presented, HPSEC-RI-MALLS may be a suitable manufacturing control method.     

Application of a new hybrid organic-inorganic monolithic column for efficient deoxyribonucleic acid purification

A new hybrid organic-inorganic monolithic column for efficient deoxyribonucleic acid (DNA) extraction was prepared in situ by polymerization of N-(β-aminoethyl)-γ-aminopropyltriethoxysilane (AEAPTES) and tetraethoxysilane (TEOS). The main extraction mechanism was based on the Coulombic force between DNA and the amino silica hybrid monolithic column. DNA extraction conditions, such as pH, ion concentration and type, and loading capacity, were optimized online by capillary electrophoresis with laser-induced fluorescence detection. Under optimal condition, a 6.0-cm monolithic column provided a capacity of 48 ng DNA with an extraction efficiency of 74 ± 6.3% (X ± RSD). The DNA extraction process on this monolithic column was carried out in a totally aqueous system for the successful purification of DNA and removal of proteins. The PBE2 plasmid could be extracted from Bacillus subtilis (B. subtilis) crude lysate within 25 min, and the purified DNA was suitable for the amplification of a target fragment by polymerase chain reaction. This study demonstrates a new attractive solid-phase support for DNA extraction to meet the increasingly miniaturized and automated trends of genetic analyses.     

Sensitive and selective electrochemical detection of artemisinin based on its reaction with p-aminophenylboronic acid

The electrochemical detection of artemisinin generally requires high oxidation potential or the use of complex electrode modification. We find that artemisinin can react with p-aminophenylboronic acid to produce easily electrochemically detectable aminophenol for the first time. By making use of the new reaction, we report an alternative method to detect artemisinin through the determination of p-aminophenol. The calibration curve for the determination of artemisinin is linear in the range of 2 μmol L⁻¹ to 200 μmol L⁻¹ with the detection limit of 0.8 μmol L⁻¹, which is more sensitive than other reported electrochemical methods. The relative standard deviation is 4.83% for the determination of 10 μM artemisinin. Because the oxidation potential of p-aminophenol is around 0 V, the present method is high selective. When 40 μM, 90 μM and 140 μM of artemisinin were spiked to compound naphthoquine phosphate tablet samples, the recoveries are 107.6%, 105.4% and 101.7%, respectively. This detection strategy is attractive for the detection of artemisinin and its derivatives. The finding that artemisinin can react with aromatic boronic acid has the potential to be exploited for the development of other sensors, such as fluorescence artemisinin sensors.     

基于杂交链式反应的可视化免疫分析检测癌胚抗原

构建了基于杂交链反应的比色免疫分析方法,实现了对肿瘤标志物癌胚抗原的检测。在抗原-抗体的特异性结合作用下,在磁珠表面构建夹心式免疫复合物,进一步结合杂交链式反应(HCR)作为信号放大策略,将染料曙红Y嵌入至DNA长链中。在可见光的照射下,能使反应底液中的四甲基联苯胺(TMB)氧化,发生明显的颜色变化,由无色变为蓝色,且与癌胚抗原的浓度呈正相关性。在最优实验条件下,癌胚抗原的浓度在1 pg/mL^5 ng/mL范围内呈线性变化,检出限为1 pg/mL。     

Synthesis of fluorinated imines and carbodiimides from azides via aza-Wittig reaction

The Staudinger reaction of fluoroalkylazides were studied. A series of N-fluoroalkylimines were synthesized via aza-Wittig reaction of N-fluoroalkyliminophosphoranes. The N,N′-difluoroalkylated carbodiimide was also synthesized via the reaction of N-fluoroalkyliminophosphoranes with carbon dioxide or carbon disulfide.     

Flow-injection chemiluminescence determination of aminomethylbenzoic acid and aminophylline based on N-bromosuccinimide-luminol reaction

A novel and sensitive chemiluminescence (CL) method for the determination of aminomethylbenzoic acid and aminophylline coupled with flow-injection analysis (FIA) technique is developed in this paper. It is based on the inhibition effect of the studied drugs on the chemiluminescence emission of N-bromosuccinimide-luminol (NBS-luminol) system. Under the optimum conditions, the decreased CL intensity is linear with the concentration of aminomethylbenzoic acid in the range of 2×10⁻⁸ to 1.0×10⁻⁶ g ml⁻¹ and with the concentration of aminophylline in the range of 1×10⁻⁷ to 7.0×10⁻⁶ g ml⁻¹, respectively. The detection limit is 7.0×10⁻⁹ g ml⁻¹ for aminomethylbenzoic acid (3σ) and 3.4×10⁻⁸ g ml⁻¹ for aminophylline (3σ). The relative standard deviations (R.S.D.) for 11 parallel measurements of 2.0×10⁻⁷ g ml⁻¹ aminomethylbenzoic acid and 1.0×10⁻⁶ g ml⁻¹ aminophylline are 2.6 and 3.0%, respectively. The proposed methods have been applied for the determination of the studied drugs in their pharmaceutical formulations with satisfactory results. The possible use of the proposed system for the determination of aminomethylbenzoic acid in plasma sample was also tested. The possible inhibition mechanism of aminomethylbenzoic acid and aminophylline on luminol-NBS system was discussed briefly.     

Selective and sensitive determination of peptides using 3,4-dihydroxyphenylacetic acid as a fluorogenic reagent

A novel fluorescence (FL) reaction for N-terminal Gly-containing peptides has been developed using 3,4-dihydroxyphenylacetic acid (3,4-DHPAA). The reaction of the peptides with 3,4-DHPAA was carried out in borate buffer (pH 8.0) in the presence of sodium periodate at 37 °C for 10 min, and the FL was measured with a spectrofluorimeter at the excitation and emission wavelengths of 370 nm and 465 nm, respectively. The 3,4-DHPAA reagent generated particularly strong FL for peptides containing Gly at their N-termini. When various other bio-substances, such as amino acids, sugars, nucleic bases, nucleotides, and proteins, were reacted with 3,4-DHPAA, no FL was observed. Under optimized reaction conditions, the lower detection limit of 0.25 μmol L⁻¹ was obtained for the N-terminal Gly-containing peptides of Gly-Pro (GP) and Gly-Pro-Pro (GPP), which gave 3 times greater FL intensity than that observed for the reagent blank. The proposed reaction with 3,4-DHPAA as a fluorogenic reagent is selective and sensitive for the detection of N-terminal Gly-containing peptides, and therefore, this method could be a useful tool for the determination of these particular oligopeptides.     

Label-free fluorescent strategy for sensitive detection of tetracycline based on triple-helix molecular switch and G-quadruplex

In this assay, a label-free fluorescent sensing platform based on triple-helix molecular switch (THMS) and G-quadruplex was developed for the detection of tetracycline. We demonstrated this approach by using THMS, which consists of a central section with a shortened 8-mer aptamer sequence with high affinity to tetracycline and flanked by two arm segments. G-rich oligonucleotide can specifically bind to thioflavin T (ThT) as a signal transduction probe (STP). In the absence of tetracycline, THMS remains stable, the fluorescence of background is low. By the addition of target tetracycline, the aptamer-target binding results in the formation of a structured aptamer-target complex, which disassembles the THMS and releases the STP. The free STP self-assembles into G-quadruplex and specifically binds to ThT which generates a obvious fluorescence enhancement. Using the triple-helix molecular switch, the developed aptamer-based fluorescent sensing platform showed a linear relationship with the concentration of tetracycline ranging from 0.2 to 20.0 nmol/L. The detection limit of tetracycline was determined to be 970.0 pmol/L. The assay avoids complicated modifications or chemical labeling, making it simple and cost-effective. So, it is expected that this aptamer-based fluorescent assay could be extensively applied in the field of food safety inspection.     

Truncated diastereoselective Passerini reaction, a rapid construction of polysubstituted oxazole and peptides having an α-hydroxy-β-amino acid component

The reaction of aldehydes and ketones, including aliphatic and aromatic ones, with amides of α-isocyano-β-phenylpropionic acid in toluene in the presence of lithium bromide gives 2,4,5-trisubstituted oxazoles in good to excellent yield. Protected chiral α-amino aldehydes participate in this reaction to give, after hydrolysis of the oxazoles, norstatine-containing peptides in good overall yield. The nucleophilic addition of isonitriles to N,N-dibenzylphenylalanal is investigated for the first time and is found to be stereoselective leading predominantly to the anti-adduct (dr=9/1). On the other hand, the reaction between the N-Boc phenylalanal and isonitrile is non-stereoselective.     

Highly sensitive method for determination of N-nitrosamines using high-performance liquid chromatography with online UV irradiation and luminol chemiluminescence detection

A new method for the measurement of N-nitrosamines in part-per-trillion concentrations from water samples without preconcentration steps has been developed. This method is based on online UV irradiation after high-performance liquid chromatographic separation and subsequent luminol chemiluminescence detection without addition of an oxidant. It was confirmed that N-nitrosamines in basic aqueous solution were transformed to peroxynitrite by UV irradiation. The detection limits for this method were 1.5 ng/L, 2.9 ng/L, 3.0 ng/L, and 2.7 ng/L for N-nitrosodimethylamine, N-nitrosomorpholine, N-nitrosomethylethylamine, and N-nitrosopyrrolidine, respectively, at a signal-to-noise ratio of 3. The calibration graphs were linear in the range of 5–1000 ng/L for these N-nitrosamines. This method was used for the determination of N-nitrosamines in tap water, river water, and industrial plant effluent samples. The recoveries of N-nitrosodimethylamine, N-nitrosomorpholine, N-nitrosomethylethylamine, and N-nitrosopyrrolidine present in tap water sample at a concentration of 10 ng/L (mean ± standard deviation, n = 4) were (94.8 ± 2.7)%, (102.0 ± 6.9)%, (99.3 ± 3.9)%, and (102.8 ± 2.5)%, respectively. These results indicate that our proposed method can be applied satisfactorily to the determination of N-nitrosamines in water samples.