Protein analysis based on molecular beacon probes and biofunctionalized nanoparticles

With the completion of the human genome-sequencing project, there has been a resulting change in the focus of studies from genomics to proteomics. By utilizing the inherent advantages of molecular beacon probes and biofunctionalized nanoparticles, a series of novel principles, methods and techniques have been exploited for bioanalytical and biomedical studies. This review mainly discusses the applications of molecular beacon probes and biofunctionalized nanoparticles-based technologies for realtime, in-situ...     

Inhibited aptazyme-based catalytic molecular beacon for amplified detection of adenosine

Combining the inhibited aptazyme and molecular beacon(MB),we developed a versatile sensing strategy for amplified detection of adenosine.In this strategy,the adenosine aptamer links to the 8-17 DNAzyme to form an aptazyme.A short sequence,denoted as inhibitor,is designed to form a duplex spanning the aptamer–DNAzyme junction,which blocks the catalytic function of the DNAzyme.Only in the presence of target adenosine,the aptamer binds to adenosine,thus the inhibitor dissociates from the aptamer portion of the aptazyme and can no longer form the stable duplex required to inhibit the catalytic activity of the aptazyme.The released DNAzyme domain will hybridize to the MB and catalyze the cleavage in the presence of Zn2+,making the fluorophore separate from the quencher and resulting in fluorescence signal.The results showed that the detection method has a dynamic range from 10 nmol/L to 1 nmol/L,with a detection limit of 10 nmol/L.     

Label-free fluorescent molecular beacon based on a small fluorescent molecule non-covalently bound to the intentional gap site in the stem moiety

A label-free fluorescent molecular beacon (MB) based on a fluorescent molecule, 5,6,7-trimethyl-1,8-naphthyridin-2-ylamine (ATMND) which is non-covalently bound to the intentional gap site in the stem moiety of the label-free MB, was developed. In the absence of a cDNA, ATMND fluorescence is significantly quenched because it binds to the unpaired cytosine at the gap site by hydrogen bonding. As a result, the label-free MB shows almost no fluorescence. Upon hybridization with cDNA, the label-free MB undergoes a conformational change to destroy the gap site. This results in an effective fluorescent enhancement because of the release of the ATMND from the gap site to the solution. Fluorescence titration shows that ATMND strongly binds to the cytosine at the gap site (K₁₁ > 10⁶). Circular-dichroism spectroscopy indicates that the binding of ATMND at the gap site of the stem moiety does not induce a significant conformational change to the hairpin DNA. Under optimal conditions, the fluorescent intensity of the label-free MB increases with an increase in cDNA concentration from 50 nM to 1.5 μM. A detection limit of 20 nM cDNA was achieved. A single mismatched target ss-DNA can be effectively discriminated from cDNA. The advantage of the label-free MB is that both its ends can be left free to introduce other useful functionalities. In addition, the label-free MB synthesis introduced in this paper is relatively simple and inexpensive because no label is required.     

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.     

Quencher-free molecular beacon systems with two pyrene units in the stem region

We appended pyrene units covalently onto adenosine and uridine nucleosides (forming A^P and U^P units, respectively) and then incorporated them into oligonucleotides such that they were positioned in complementary locations in opposite strands in the middle positions of hairpin stems. Systems 1 (A^PU^P) and 3 (A^PA^P) individually exhibit aromatic stacking between the opposing pyrene units in the stems of their hairpins and display in their spectra the photophysical properties of strongly red-shifted bands; in contrast, the U^PU^P system 2 exhibits quenching spectra. Systems 1 (A^PU^P) and 3 (A^PA^P) behave as effective molecular beacons (MBs) that change color from green to blue upon duplex formation, whereas 2 (U^PU^P) is an effective MB that changes the intensity of its fluorescence upon forming its perfectly matched duplex.     

Aptamer Molecular Beacon Sensor for Rapid and Sensitive Detection of Ochratoxin A

Ochratoxin A (OTA) is a carcinogenic fungal secondary metabolite which causes wide contamination in a variety of food stuffs and environments and has a high risk to human health. Developing a rapid and sensitive method for OTA detection is highly demanded in food safety, environment monitoring, and quality control. Here, we report a simple molecular aptamer beacon (MAB) sensor for rapid OTA detection. The anti-OTA aptamer has a fluorescein (FAM) labeled at the 5′ end and a black hole quencher (BHQ1) labeled at the 3′ end. The specific binding of OTA induced a conformational transition of the aptamer from a random coil to a duplex–quadruplex structure, which brought FAM and BHQ1 into spatial proximity causing fluorescence quenching. Under the optimized conditions, this aptamer sensor enabled OTA detection in a wide dynamic concentration range from 3.9 nM to 500 nM, and the detection limit was about 3.9 nM OTA. This method was selective for OTA detection and allowed to detect OTA spiked in diluted liquor and corn flour extraction samples, showing the capability for OTA analysis in practical applications.     

Characterisation of a transparent optical test strip for quantification of water hardness

An optical and reversible test strip that uses an ion-exchange mechanism which responds equally to calcium and magnesium and makes it possible to determine water hardness is described. The transparent test strip, made of a polyester sheet, has a circular polymeric film of plasticised poly(vinyl chloride) (PVC) that contains all of the reagents necessary to produce an equal response to calcium and magnesium, namely, a cation-selective neutral ionophore, such as 4,13-[bis(N-adamantylcarbamoyl)acetyl]-1,7,10,16-tetraoxa-4,13-diazacyclooctadecane, a chromoionophore, such as lipophilised Nile Blue, and potassium tetrakis (4-chlorophenyl)borate as a lipophilic salt, which it is evaluated by absorbance measurement at 655 nm in a standard photometer.All experimental variables that influence test strip response, especially in terms of selectivity and response time, have been studied. The sensor responded linearly to hardness up to 14,800 mg l⁻¹, in activities, expressed as CaCO₃. The detection limit is 1.9 mg l⁻¹ as CaCO_3, the reproducibility intermembrane at a medium level of the range was 7.0%, as R.S.D., of and 2.6% as intramembrane. The procedure was applied to the determination of hardness in different types of waters (tap, well, mineral and spring) validating results against a reference procedure. This proposed method is quick, inexpensive, selective and sensitive and uses only conventional instrumentation.     

Real-time PCR detection of telomerase activity using specific molecular beacon probes

Telomerase is a potentially important biomarker and a prognostic indicator of cancer. Several techniques for assessing telomerase activity, including the telomeric repeat amplification protocol (TRAP) and its modified versions, have been developed. Of these methods, real-time quantitative TRAP (RTQ-TRAP) is considered the most promising. In this work, a novel RTQ-TRAP method is developed in which a telomeric repeats-specific molecular beacon is used. The use of the molecular beacon can improve the specificity of the RTQ-TRAP assay, making the method suitable for studying the overall processivity results and the turnover rate of telomerase. In addition, the real-time, closed-tube protocol used obviates the need for post-amplification procedures, reduces the risk of carryover contamination, and supports high throughput. Its performance in synthetic telomerase products and cell extracts suggests that the developed molecular beacon assay can further enhance the clinical utility of telomerase activity as a biomarker/indicator in cancer diagnosis and prognosis. The method also provides a novel approach to the specific detection of some particular gene sequences to which sequence-specific fluorogenic probes cannot be applied directly. Figure Real-time PCR detection of telomerase activity using specific molecular beacon probes Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Rapid on-line analysis of low molecular weight hydrocarbons using glass capillary gas chromatography

Rapid analysis is important for on-line chromatography. Gaseous or vaporized samples have been injected via heated gas sampling valves of less than 500 μl dead volume. The critical sampling and split problems could be solved by temperature programming. The general analysis described could be successfully used inter alia in scouting reactions.     

Fast determination of milk fat content using Raman spectroscopy

In our work, we have demonstrated the capability of VIS Raman spectroscopy in combination with partial least square regression (PLS) as a rapid technique for direct milk fat determination. Raman spectra of milk samples revealed contributions from proteins, but mainly from their fat content with different spectral characteristics. Three different methods of sample preparations were applied: (i) liquid milk contained in an open dish, (ii) dried milk droplets on glass plates covered with Al foil, and (iii) liquid milk contained in quartz cuvettes. Methods (i) and (ii) showed a good PLS model for milk fat prediction with low root mean square errors and high correlation coefficients. The main advantage of milk sample contained in the dish lies in its simplicity as well as the fact that the open container maximizes the signal of interest avoiding background contributions. Our results show that Raman spectroscopy is suited for in-line monitoring purposes.     

Several concerns about the primer design in the universal molecular beacon real-time PCR assay and its application in HBV DNA detection

A universal hepatitis B virus (HBV) DNA detection kit is appealing for the worldwide diagnosis and monitoring of the treatment of different mutant types of hepatitis B virus. A sensitive and reproducible real-time PCR assay based on the universal molecular beacon (U-MB) technique was developed for the detection of HBV DNA in serum. The U-MB probe used in the assay has no interaction with the HBV DNA sequence. The U-MB technique not only reduced the cost of HBV detection but also had the potential for the development of a universal detection kit for different mutant HBV types and other DNA systems. To demonstrate its clinical utility, 90 serum samples were analyzed using the U-MB real-time PCR method. In the experiments we found that several crucial factors needed to be considered in the primer design, such as the avoidance of formation of severe primer–dimer and primer self-hairpin structure. With the optimized primer sets, satisfactory results were obtained for all the tested samples. We concluded that this assay would be an excellent candidate for a universal HBV DNA detection method. Principle of the U-MB real-time PCR method for HBV DNAdetection     

基于分子信标末端现场标记三聚氰胺-Cu~(2+)电活性分子的高灵敏电化学传感器

本文构建了一种基于分子信标自由末端现场标记电活性信号分子的新型DNA传感器.首先将3′修饰巯基的分子信标通过Au–S键自组装到金电极表面,然后在修饰有羧基的5′自由末端通过共价偶合和配位作用依次组装上三聚氰胺(Mel)和铜离子(Cu2+),得到以Mel-Cu2+配合物为电活性信号源的分子信标.该方法简单实现了电活性分子信标的标记、分离和纯化.以[Fe(CN)6]3-/4-为电化学探针,采用循环伏安和电化学阻抗法对层层自组装过程进行了表征.杂交实验表明,Mel-Cu2+信号源所对应的峰电流强度随着杂交液浓度的增大逐渐降低,且氧化峰电流与互补序列浓度对数在1.0×10-15~1.0×10-9 mol/L范围内呈良好的线性关系.根据3σ计算得到检测限为2.4×10-16 mol/L.另外,由于分子信标特殊的茎环结构特征和Mel-Cu2+信号源稳定的无机配位组成,传感器显示了很高的特异性、再生性和稳定性.     

Separation of zinc from aqueous samples using a molecular imprinting technique

In this article, the separation of zinc from aqueous samples by solid-phase extraction based on a molecular imprinting technique is described. Zn-imprinted polymer was prepared by free radical solution polymerisation in a glass tube containing ZnSO₄, morin, 4-vinylpyridine as a functional monomer, ethyleneglycoldimethacrylate as a cross-linking monomer, and 2,2′-azobisisobutyronitrile as an initiator. The obtained polymer block was ground and sieved (55–75 µm) and the Zn–morin complex was separated from polymer particles by leaching with 2M HCl. The synthesised polymer particles have been characterised by IR and differential scanning calorimetric studies either before or after leaching. The effects of different parameters, such as pH, adsorption and desorption time, type and minimum amount of the eluent for elution of the complex from polymer were evaluated. Extraction efficiency more than 99% was obtained by elution of the polymers with 10 mL of CH₂Cl₂–dimethyl sulfoxide (1 : 1, v/v). The detection limit of the proposed method was 2.9 µg L^?1. A dynamic linear range in the range of 25–200 µg L^?1 was obtained. The relative standard deviation was found to be below 9.2%. In addition, the influence of various cationic and anionic interferences on the complex recovery was studied. The method was applied to the recovery and determination of Zn in a few different real samples.     

A label-free, quadruplex-based functional molecular beacon (LFG4-MB) for fluorescence turn-on detection of DNA and nuclease

We demonstrate a novel concept for the construction of a label-free, quadruplex-based functional molecular beacon (LFG4-MB) by using G-quadruplex motif as a substitute for Watson-Crick base pairing in the MB stem and a specific G-quadruplex binder, N-methyl mesoporphyrin IX (NMM) as a reporter. It shows high sensitivity in assays for UDG activity/inhibition and detection of DNA sequence based on the unique fluorescence increase that occurs as a result of the strong interaction between NMM and the folded quadruplex upon removal of uracil by UDG or displacement of block sequence by target DNA. The LFG4-MB is simple in design, fast in operation and could be easily transposed to other biological relevant target analysis by simply changing the recognition portion. The LFG4-MB does not require any chemical modification for DNA, which offers the advantages of simplicity and cost efficiency and obviates the possible interference with the affinity and specificity of the MB as well as the kinetic behavior of the catalysts caused by the bulky fluorescent groups. More importantly, the LFG4-MB offers great extent of freedom to tune the experimental conditions for the general applicability in bioanalysis.     

Rapid analysis of aromatic contaminants in water samples by means of laser ionization mass spectrometry

Three different approaches to laser ionization mass spectrometric analysis of aromatic compounds in water samples are described and their performances are compared. Whereas the first two methods are based on direct laser desorption and subsequent laser ionization of either frozen or adsorbed samples in a time-of-flight mass analyzer, the third performs laser ionization in a quadrupole ion-trap into which the sample is transferred from a GC injector via a short piece of capillary tubing. For the laser-desorption method a detection limit in the 100 µg L^–1 range was determined for fluorene in frozen samples. The easier to handle analysis of adsorbed samples yielded sensitivities which were lower by about two orders of magnitude. As both direct techniques do not reach the sensitivity required for ultra trace analysis in water a preconcentration step in form of solid-phase microextraction was added before measurement using the laser ionization quadrupole ion-trap mass spectrometer. Sensitivity in the desired ng L^–1 range was easily achieved.     

Rapid determination of magnesium and calcium hardness in water by ion chromatography

Magnesium(II) and calcium(II) in hard water are separated by ion chromatography and detected spectrophotometrically after a post-column reaction with arsenazo-I at pH 10. No sample dilution or pretreatment is needed, and the separation is complete in 3 min. Linear calibration plots are obtained in the 2–400 mg l^?1 range. Many actual water samples from a variety of geographical locations were analysed and the results were compared with those obtained by EDTA titration. The advantages of the chromatographic method over titration are summarized.     

Rapid determination of total trihalomethanes index in drinking water

A method for the rapid determination of total trihalomethanes (THMs) index in drinking water has been developed by using a headspace-mass spectrometry (HS-MS) system and partial least squares (PLS) multivariate regression approach. Due to the presence of residual amounts of chlorine and organic matter in the drinking water, the use of a quenching reagent in order to avoid THM generation during the sample manipulation is necessary. The optimization experiments revealed that ascorbic acid was the best quenching reagent compared with sodium thiosulfate and ammonium sulfate. The use of a classification chemometric technique as soft independent modeling of class analogy before the PLS regression improved the results obtained in the prediction of the total THMs index, lowering the relative standard error of prediction (RSEP) from 11.4% to lower than 6.0%. The results obtained by the proposed HS-MS method were compared with those provided by a conventional chromatographic method after analyzing 20 real drinking water samples. A good agreement in the results was observed and no systematic differences were found, which corroborates the good performance of the proposed method.     

高压离子色谱法快速测定饮用水中7种无机阴离子

建立了使用高压离子色谱快速测定饮用水中7种无机阴离子的方法。环境水样经0.22 μm尼龙滤膜过滤后可直接进样分析。采用Dionex Integrion高压离子色谱仪和AS22-Fast-4 μm阴离子交换柱（150 mm×4 mm）,可在5 min内完成对F^-、Cl^-、Br^-、NO₂^-、NO₃^-、SO₄^2-和PO₄^3-这7种阴离子的分析。以4.5 mmol/L碳酸钠和1.4 mmol/L碳酸氢钠为淋洗液,流速为2mL/min。7种阴离子的检出限为0.007~0.07 mg/L（S/N=3）,在较宽范围内有良好的线性关系（相关系数不小于0.999）和重现性（相对标准偏差不大于0.48%,n=8）。实际样品加标回收率为91.4%~109.7%,相对标准偏差为0.30%~0.45%（n=5）。将该方法应用于饮用水厂进出水的分析,结果表明在进出水中检出6种阴离子,以Cl^-、NO₃^-和SO₄^2-为主。该方法简便快速、灵敏准确,尤其适合高通量样品中阴离子的快速分析。     

Flow injection analysis for the determination of thiabendazole and fuberidazole in water by spectrofluorimetry

Flow-injection analysis (FIA) is proposed for determining thiabendazole (TBZ) and fuberidazole (FBZ) by Spectrofluorimetry. A pH 2 aqueous solution was found to be the optimal solvent for the rapid, precise and sensitive fluorescence analysis of both fungicides. Linear dynamic graphs were established over a concentration range of two orders of magnitude. Limits of detection were 0.7ng/ml for TBZ and 0.1 ng/ml for FBZ. Relative standard deviations were 0.5 and 0.8% for TBZ and FBZ, respectively. The method was applied to the determination of both compounds in spiked river and tap water samples, with satisfactory recoveries.On leave from the Department of Analytical Chemistry and Food Technology, University of Castilla-La Mancha, E-13071-Ciudad Real, Spain     

A novel infrared spectrophotometric method for the rapid determination of petroleum hydrocarbons, and animal and vegetable oils in water

To determine the concentrations of total oils,petroleum hydrocarbons,and animal and vegetable oils in water,the conventional analytical methods involve two scans as well as a step of magnesium silicate adsorption to remove the animal and vegetable oils in water samples.In this study,a novel analytical method was developed to determine the above oils in wastewater samples through just one scan—the concentration of animal and vegetable oils,and that of total oils were determined by measuring the absorbance of the >C=O bond in the peak area between 1750 cm and 1735 cm^-1,and of the C-H bond at 2930 cm^-1,2960 cm,and 3030 cm^-1,respectively.The concentration of petroleum hydrocarbons was then calculated by subtracting the concentration of animal and vegetable oils from that of total oils.Compared with the well-known analytical method GB/T 16488-1996,the novel approach displayed similar accuracy in the quantitative determination of oils in wastewater samples,but significantly reduced material cost and operation time.