Purification of genomic DNA by short monolithic columns

The isolation and purification of nucleic acids is essential for many procedures in molecular biology. After showing that bacterial and eukaryotic genomic DNA can be specifically bound to the CIM DEAE monolithic column, this characteristic was exploited in development of a simple and fast chromatographic procedure for isolation and purification of genomic DNA from cell lysates that does not include the usage of toxic organic solutions. The purity and the quality of the isolate as well as the duration of the procedure was similar to other chromatographic methods used today for isolation of genomic DNA, but the initial sample volume was not restricted.     

Design of two-dimensional photonic crystal biosensor using DNA detection

Abstract

In this paper, the photonic crystal biosensor is investigated theoretically with, concomitantly, high quality factor, transmission and sensitivity. This biosensor is made out of two waveguide couplers and one L2 resonant cavity formed by removing two air holes. For biosensor analysis, the 2D finite difference time domain (FDTD) method and the plane-wave expansion (PWE) approach are applied. Four slots placed into the cavity and the three rows of functionalized holes nearby the resonant cavities are filled with DNA. For the optimized structure, the biosensor quality factor is found to be over 3.7468?×?10⁶ and the sensitivity is of order 460?nm/RIU. The designed structure has high sensitivity, which is an important parameter in biosensing applications.     

Graphene oxide-based biosensor for sensitive fluorescence detection of DNA based on exonuclease III-aided signal amplification

Based on the super fluorescence quenching efficiency of graphene oxide and exonuclease III aided signal amplification, we develop a facile, sensitive, rapid and cost-effective method for DNA detection. In the presence of target DNA, the target-probe hybridization forms a double-stranded structure and exonuclease III catalyzes the stepwise removal of mononucleotides from the blunt 3′ termini of probe, resulting in the recycling of the target DNA and signal amplification. Therefore, our proposed sensor exhibits a high sensitivity towards target DNA with a detection limit of 20 pM, which was even lower than previously reported GO-based DNA sensors without enzymatic amplification, and provides a universal sensing platform for sensitive detection of DNA.     

Lowering the detection limit of the acetylcholinesterase biosensor using a nanoporous carbon matrix

Nanostructured carbon matrix has been used for the immobilization and stabilization of the enzyme E.el. AChE. The use of this activated carbon matrix is shown to provide both, significant enzyme stabilization, as well as the means for lowering the detection limit of the biosensor. The enzyme is immobilized by adsorption into the nanostructured conductive carbon, which also acts as the working electrode. The proposed biosensor showed very good stability under continuous operation conditions (L₅₀ > 60 days), allowing its further use in inhibition mode. Using this biosensor, the monitoring of the organophosphorus pesticide dichlorvos at picomolar levels (1000 times lower than other systems reported so far) was achieved. The linear range of detection in flow injection system was six orders of magnitude (10⁻¹² to 10⁻⁶ M). It is suggested that the ability of activated carbon to selectively concentrate the pesticide, as well as the enzyme hyperactivity within the nanopores is the reason for the decrease in the detection limit of the biosensor.     

“发夹”结构DNA用于生物分析传感器研究进展

由于链内碱基互补配对作用形成的"发夹"结构DNA分子被广泛用于生物分子传感分析。双链或多链"发夹"结构DNA分子参与的杂交链式反应信号记录方式多样,主要有荧光法、比色法、电化学方法等。基于杂交链式反应的检测方法具有快速、方便、成本低、准确度高、灵敏度高、特异性强的优点,在分析传感研究中的应用尤其受到人们的关注,近些年发展迅速。本文综述了"发夹"结构DNA与杂交链式反应应用于生物传感分析的原理、信号记录方式及其在蛋白质、重金属离子、小分子、疾病标志物、DNA等检测中的研究进展。     

Droplet-based microscale colorimetric biosensor for multiplexed DNA analysis via a graphene nanoprobe

The development of simple and inexpensive DNA detection strategy is very significant for droplet-based microfluidic system. Here, a droplet-based biosensor for multiplexed DNA analysis is developed with a common imaging device by using fluorescence-based colorimetric method and a graphene nanoprobe. With the aid of droplet manipulation technique, droplet size adjustment, droplet fusion and droplet trap are realized accurately and precisely. Due to the high quenching efficiency of graphene oxide (GO), in the absence of target DNAs, the droplet containing two single-stranded DNA probes and GO shows dark color, in which the DNA probes are labeled carboxy fluorescein (FAM) and 6-carboxy-X-rhodamine (ROX), respectively. The droplet changes from dark to bright color when the DNA probes form double helix with the specific target DNAs leading to the dyes far away from GO. This colorimetric droplet biosensor exhibits a quantitative capability for simultaneous detection of two different target DNAs with the detection limits of 9.46 and 9.67 × 10⁻⁸ M, respectively. It is also demonstrated that this biosensor platform can become a promising detection tool in high throughput applications with low consumption of reagents. Moreover, the incorporation of graphene nanoprobe and droplet technique can drive the biosensor field one more step to some extent.     

DNA hybridization electrochemical biosensor using a functionalized polythiophene

A simple and label-free electrochemical sensor for recognition of the DNA sensor event was prepared by electrochemical polymerization of 4-hydroxyphenyl thiophene-3-carboxylate. Poly(4-hydroxyphenyl thiophene-3-carboxylate) (PHPT) was synthesized electrochemically onto glassy carbon electrode and characterized by cyclic voltammetry, FTIR and AFM measurements. An ODN-probe was physisorbed onto PHPT film and tested on hybridization with complementary ODN segments. A biological recognition can be monitored by comparison with electrochemical signal (cyclic voltammogram) of single and double strand state oligonucleotide. The oxidation current of double strand state oligonucleotide is lower than that of single strand, that is corresponding to the decrease of electroactivity of PHPT with the increase of stiffness of polymer structure. Physisorbed ODN-probe and its hybridization were observed morphologically onto ITO electrodes using AFM. The sensitivity of the electrochemical sensor is 0.02 μA/nmol, detection limit is 1.49 nmol and it has good selectivity.     

Vascular endothelial growth factor as a biomarker for the early detection of cancer using a whole cell-based biosensor

Vascular endothelial growth factor (VEGF) is a cytokine and endothelial cell (EC) mitogen that has been studied for its role in angiogenesis of malignant tumors. Elevated quantities of VEGF in the serum and plasma of patients have been correlated with the presence of cancer and metastasis. Since VEGF induces hyperpermeability of EC monolayers, this protein can be detected in vitro with a whole cell-based biosensor. This biosensor consists of a confluent monolayer of human umbilical vein endothelial cells (HUVECs) attached to a cellulose triacetate (CTA) membrane of an ion-selective electrode (ISE). Previous studies regarding this biosensor have shown that when the biosensor was exposed to a model toxin, such as histamine, the response of the biosensor served as an indirect measurement of the presence of histamine. Similarly, the biosensor responds to the presence of VEGF, but is much more sensitive because VEGF is known to be 50,000-fold more potent than histamine when inducing EC hyperpermeability. The ISE response increased with increasing VEGF concentration. Since lower concentrations required more exposure time, the detection limit was established as a function of exposure time (2–10 h). The practical applicability of the biosensor was also established with cultured human melanoma cells WM793 (nonmetastatic) and 1205LU (metastatic). The resultant change in the potential values revealed significant production of VEGF from the 1205LU cells. A VEGF ELISA was performed to confirm the VEGF concentration in each sample. The biosensor closely predicted the concentrations determined through the ELISA. These results support the use of a cell-based ISE as a quick screening method for the presence of VEGF.     

Chemiluminescent bead-based hybridization assay for the detection of genomic DNA from <Emphasis Type="Italic">E. coli</Emphasis> in purified plasmid samples

A bead-based hybridization assay was developed for detection of traces of E. coli genomic DNA (gDNA) present in purified plasmid DNA (pDNA) samples. Standards of gDNA and pDNA samples were sheared by sonication and adsorbed onto aminopropyl controlled pore glass (CPG) particles (130 μm). A preliminary study was conducted to optimize the amount of DNA adsorbed on the particles. Results indicated that maximum attachment efficiency was obtained by adsorbing DNA for 2 h in 0.2 × SSC, pH 5.7. The DNA-bound particles were hybridized overnight with a 181-bp digoxigenin-labeled probe, specific for gDNA. Following a chemiluminescent detection protocol, signal intensities of the standards were plotted as a function of initial gDNA concentration. The calculated detection limit (LOD) was 1.4 pM of gDNA. The assay was able to detect gDNA in pure plasmid preparations at the 1% level even in the presence of 1,000-fold excess of noncomplementary target. Hybridization results were compared with a quantitative real-time PCR assay. Both methods afforded similar accurate results at the 95% confidence level.     

Penicillamine determination using a tyrosinase micro-rotating biosensor

Tyrosinase [EC 1.14.18.1], immobilized on a rotating disk, catalyzed the oxidation of catechols to o-benzoquinone, whose back electrochemical reduction was detected on glassy carbon electrode surface at −150 mV versus Ag/AgCl/NaCl 3 M. Thus, when penicillamine (PA) was added to the solution, this thiol-containing compound participate in Michael type addition reactions with o-benzoquinone to form the corresponding thioquinone derivatives, decreasing the reduction current obtained proportionally to the increase of its concentration. This method could be used for sensitive determination of PA in drug and human synthetic serum samples. A linear range of 0.02–80 μM (r = 0.999) was obtained for amperometric determination of PA in buffered pH 7.0 solutions (0.1 M phosphate buffer). The biosensor has a reasonable reproducibility (R.S.D. < 4.0%) and a very stable amperometric response toward this compound (more than 1 month).     

Antioxidant capacity of the algae using a biosensor method

Three different methods, i.e. a biosensor method, a voltammetric method and a spectrophotometric method, have been used to evaluate the total antioxidant capacity of certain types of algae. In the final evaluation of the data also the variation in time of the antioxidant capacity of cultivated algae was considered and some experimental factors, such as the use of different solvent mixtures to extract the antioxidant substances contained in the algae, were discussed.     

Array biosensor for detection of toxins

The array biosensor is capable of detecting multiple targets rapidly and simultaneously on the surface of a single waveguide. Sandwich and competitive fluoroimmunoassays have been developed to detect high and low molecular weight toxins, respectively, in complex samples. Recognition molecules (usually antibodies) were first immobilized in specific locations on the waveguide and the resultant patterned array was used to interrogate up to 12 different samples for the presence of multiple different analytes. Upon binding of a fluorescent analyte or fluorescent immunocomplex, the pattern of fluorescent spots was detected using a CCD camera. Automated image analysis was used to determine a mean fluorescence value for each assay spot and to subtract the local background signal. The location of the spot and its mean fluorescence value were used to determine the toxin identity and concentration. Toxins were measured in clinical fluids, environmental samples and foods, with minimal sample preparation. Results are shown for rapid analyses of staphylococcal enterotoxin B, ricin, cholera toxin, botulinum toxoids, trinitrotoluene, and the mycotoxin fumonisin. Toxins were detected at levels as low as 0.5 ng mL^–1.     

Sensitive detection of beryllium using a fiber optic liquid waveguide cell

The metallochromic chelating agent, Chromazurol S, has been utilized in conjunction with a fiber optic liquid waveguide capillary cell to enable the sensitive detection of beryllium in solution (30 ng l⁻¹ detection limit) and following extraction from a contaminated plexiglas surface (0.5 ng cm⁻² detection limit). The addition of a cationic surfactant, cetylpyridinium chloride, to Chromazurol S at pH 10 in Tris-HCl buffer results in the formation of two bathochromic peaks in the visible spectrum following metal chelation by beryllium. The first absorbance band, at 515 nm, is intermediate in nature, permitting maximal sensitivity for low beryllium concentrations, but diminishing in intensity at concentrations above 100 μg l⁻¹. The second absorbance band, centered at 610 nm, dominates for beryllium concentrations of 100 μg l⁻¹ and above. Experimental conditions including pH, buffer type, additive surfactants, masking agents, and dye concentration were investigated in order to optimize detection sensitivity and selectivity. A fiber optic spectrometer is used with both a liquid waveguide capillary cell and 1 cm cuvette cell, to give a sensitive and broad dynamic range for beryllium detection that capitalizes on both beryllium metal chelate absorbance bands formed under these conditions.     

Electrochemical DNA biosensor for the detection of short DNA species of Chronic Myelogenous Leukemia by using methylene blue

A novel assay for the voltammetric detection of 18-bases DNA sequences relating to Chronic Myelogenous Leukemia (CML, Type b3a2) using methylene blue (MB) as the hybridization indicator was reported. DNA was covalently attached onto a glassy carbon electrode (GCE) through amines of the DNA bases using N-hydroxysulfosuccinimide (NHS) and N-(3-dimethylamion)propyl-N′-ethyl carbodiimidehydrochloride (EDC). The covalently immobilized single-stranded DNA (ssDNA) could selectively hybridize with its complementary DNA (cDNA) in solution to form double-stranded DNA (dsDNA) on the surface. A significant increase of the peak current for methylene blue upon the hybridization of immobilized ssDNA with cDNA in the solution was observed. This peak current change was used to monitor the recognition of CML DNA sequence. This electrochemical approach is sequence specific as indicated by the control experiments in which no peak current change was observed if a non-complementary DNA sequence was used. Factors, such as DNA target concentration and hybridization conditions determining the sensitivity of the electrochemical assay were investigated. Under optimal conditions, this sensor has a good calibration range between 1.25 × 10⁻⁷ and 6.75 × 10⁻⁷ M, with CML DNA sequence detection limit of 5.9 × 10⁻⁸ M.     

Enzyme-based electrochemical biosensor for sensitive detection of DNA demethylation and the activity of DNA demethylase

A novel electrochemical method is developed for detection of DNA demethylation and assay of DNA demethylase activity. This method is constructed by hybridizing the probe with biotin tagged hemi-methylated complementary DNA and further capturing streptavidin tagged alkaline phosphatase (SA-ALP) to catalyze the hydrolysis reaction of p-nitrophenyl phosphate. The hydrolysate of p-nitrophenol (PNP) is then used as electrochemical probe for detecting DNA demethylation and assaying the activity of DNA demethylase. Demethylation of target DNA initiates a degradation reaction of the double-stranded DNA (dsDNA) by restriction endonuclease of BstUI. It makes the failed immobilization of ALP, resulting in a decreased electrochemical oxidation signal of PNP. Through the change of this electrochemical signal, the DNA demethylation is identified and the activity of DNA demethylase is analyzed with low detection limit of 1.3 ng mL⁻¹. This method shows the advantages of simple operation, cheap and miniaturized instrument, high selectivity. Thus, it provides a useful platform for detecting DNA demethylation, analyzing demethylase activity and screening inhibited drug.     

基于生物传感器的内毒素检测研究进展

内毒素是造成内毒素血症、多器官功能衰竭的关键因子,对人体健康存在着严重的危害。发展高选择性、高灵敏度、快捷便携且不受现场限制的检测方法具有重要意义。生物传感器以其高效、灵敏、易于自动化和微型化等优点,在相关检测领域中显示出重要的研究价值和巨大的发展空间。本文简要介绍了近年来内毒素的常用检测方法,重点综述了光学生物传感器和电化学生物传感器在内毒素检测应用中的研究进展。对生物传感器在内毒素检测中面临的挑战及其发展趋势进行了讨论和展望。     

基于G-四链体的生物传感器在食品污染物检测中的研究进展

食品污染物不仅对人类健康造成了严重威胁,还会给食品工业造成巨大的经济损失。G-四链体(G4)是由鸟嘌呤的碱基配对形成的核酸三维二级结构,具有灵活的绑定能力,已成为生物传感器的重要组成部分。将G4与生物传感器结合用于食品中污染物的检测得到了广泛的应用。本文对G4进行了简介,综述了2015～2022年间G4在食品污染物检测中的研究进展,并对其未来的发展趋势进行了展望。     

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.     

Direct detection of DNA using 3D surface enhanced Raman scattering hotspot matrix

Silver nanoparticles (AgNPs) are evaporatively self‐assembled into the 3D surface enhanced Raman scattering (SERS) hotspot matrix with the assistant of glycerol to improve the spectral reproducibility in direct DNA detection. AgNPs and DNA in the glycerol‐stabilized 3D SERS hotspot matrix are found to form flexible sandwich structures through electrostatic interaction where neighboring AgNPs create uniform and homogeneous localized surface plasmon resonance coupling environments for central DNA. Nearly two orders of magnitude extra SERS enhancement, more stable peak frequency and narrower peak full width at half maximum can therefore be obtained in DNA SERS spectra, which ensures highly stable and reproducible SERS signals in direct detection of both single strand DNA and double strand DNA utilizing the 3D SERS hotspot matrix. By normalizing the SERS spectra using phosphate backbone as internal standard, identification of single base variation in oligonucleotides, determination of DNA hybridization events and recognition of chemical modification on bases (hexanethiol‐capped at 5’ end) have been demonstrated experimentally. This proposed 3D SERS hotspot matrix opens a novel perspective in manipulating plasmonic nanoparticles to construct SERS platforms and would make the surface enhanced Raman spectroscopy a more practical and reliable tool in direct DNA detection.     

Enhancement of a conducting polymer-based biosensor using carbon nanotube-doped polyaniline

A biosensor with improved performance was developed through the immobilization of horseradish peroxidase (HRP) onto electropolymerized polyaniline (PANI) films doped with carbon nanotubes (CNTs). The effects of electropolymerization cycle and CNT concentration on the response of the biosensor toward H₂O₂ were investigated. It was found that the application of CNTs in the biosensor system could increase the amount and stability of the immobilized enzyme, and greatly enhanced the biosensor response. Compared with the biosensor without CNTs, the proposed biosensor exhibited enhanced stability and approximately eight-fold sensitivity. A linear range from 0.2 to 19 μM for the detection of H₂O₂ was observed for the proposed biosensor, with a detection limit of 68 nM at a signal-to-noise ratio of 3 and a response time of less than 5 s.