Electrochemical detection of a Vibrio parahaemolyticus sequence-specific gene based on a gold electrode modified with a single stranded probe

An electrochemical DNA biosensor for specific-sequences detection of Vibrio parahaemolyticus (VP) was fabricated. A single-stranded 20-mer oligonucleotide (ssDNA) and 6-mercapto-1-hexanol (MCH) were immobilized via a thiol linker on gold disk electrodes by self-assembling. The ssDNA underwent hybridization in a hybridization solution containing complementary or non-complementary or single base pair mismatched DNA sequences of VP. Examination of changes in response to these three target DNAs showed that the developed biosensor had a high selectivity and sensitivity.     

Immobilization of RNase S-Peptide on a single-stranded DNA-fixed gold surface and effective masking of its surface by an acridinyl poly(ethylene glycol)

Oligonucleotide-peptide conjugate was synthesized by coupling of RNase S-peptide to a 24-mer single-stranded DNA (ssDNA) oligonucleotide to be immobilized on its complementary ssDNA oligonucleotide-fixed gold surface of sensor chip or electrode. Immobilization of on the ssDNA-fixed gold surface through DNA duplex formation was confirmed by quartz crystal microbalance (QCM) and electrochemical measurements. After treating with a synthetic acridinyl poly(ethylene glycol) (APEG), specific interaction of S-protein with the S-peptide immobilized on the gold surface was demonstrated by QCM without nonspecific adsorption of unrelated proteins such as BSA and RNase A at the surfaces. This result suggested that the acridine parts of APEG could bind to the DNA duplex on the gold surface and the poly(ethylene glycol) parts were fastened on the surface to resist the adsorption of proteins. Thus, the combination of oligonucleotide-peptide conjugate, ssDNA-fixed chip and APEG with effective masking property provides a new tool for the analysis of specific peptide-protein interactions without disturbance by other unrelated proteins.     

Tethered thiazole orange intercalating dye for development of fibre-optic nucleic acid biosensors

Single-stranded DNA (ssDNA) oligonucleotide in solution, or that is immobilized onto a surface to create a biosensor, can be used as a selective probe to bind to a complementary single-stranded sequence. Fluorescence enhancement of thiazole orange (TO) occurs when the dye intercalates into double-stranded DNA (dsDNA). TO dye has been covalently attached to probe oligonucleotides (homopolymer and mixed base 10mer and 20mer) through the 5′ terminal phosphate group using polyethylene glycol linker. The tethered TO dye was able to intercalate when dsDNA formed in solution, and also at fused silica surfaces using immobilized ssDNA. The results indicated the potential for development of a self-contained biosensor where the fluorescent label was available as part of the immobilized oligonucleotide probe chemistry. The approach was shown to be able to operate in a reversible manner for multiple cycles of detection of targeted DNA sequences.     

Thermally induced isomeric transformations ofbis-(diamine) complexes of nickel(II) nitrate in the solid phase

Summary Thermal reactions of [Ni(diamine)₂(H₂O)₂](NO₃)₂ and [Ni(diamine)₂(NO₃)₂] (where diamine=1,2-ethanediamine,N-methyl-1,2-ethanediamine,N-ethyl-1,2-ethanediamine, 1,3-propanediamine andN-methyl-1,3-propanediamine) have been investigated in the solid phase. The 1,2-ethanediamine andN-methyl-1,2-ethanediamine complexes undergo thermally induced endothermic irreversible isomeric transformations. In the 1,2-ethanediamine complex the transformation is thermochromic, whereas it is not for theN-methyl-1,2-ethanediamine complex. The transformations are explained in terms of the axial interaction of NO₃ ions with nickel as well as to ligand field weakening resulting from conformational changes of the individual diamine chelate rings.Supplememtary data available: X-ray powder diffraction data (Table3).     

Single probe nucleic acid immobilization on chemically modified single protein by controlling ionic strength and pH

In an effort toward determining the feasibility of single molecule analysis, we describe a case whereby the binding of one biotinylated DNA to one streptavidin molecule via electrostatic interactions was controlled by altering in pH 4.0-9.0 and 0.16 of the ion strength. The quantitative analysis of immobilized probe ssDNA was realized in real-time via a quartz crystal microbalance (QCM) and electrochemical (EC) measurement in the range 100 pM to 50 μM of probe oligonucleotide concentration. The variation amount of biotinylated ssDNA immobilized on the streptavidin-modified surface at pH 7.5 was about 0.16 pmol, giving a ratio of streptavidin to biotinylated ssDNA of about 1:1.1. On the other hand, at pH 4.9, it was immobilized about 0.29 pmol. From the shape of the Langmuir plot and QCM, the immobilization efficiency of biotinylated DNA via streptavidin at pH 4.9 was approximately twofold that at pH 7.5. In view points of the reaction velocity, it was increased with decreasing buffer solution pH, indicating a strong interaction of negatively charged probe DNA with the positively charged streptavidin. And also the EC response value of ΔI/I_streptavidin for the immobilized biotinylated ssDNA in pH 4.9 was about 49%, while the corresponding value for the pH 7.5 was approximately 34%. As DNA molecules possess negative charges, electrostatic repulsion occurred between streptavidin and biotinylated ssDNA at pH 7.5. At pH 4.9, the attraction between the biotinylated ssDNA and streptavidin resulted in increased adsorption which has an isoelectric point of about 5.9. It was deduced that the binding of biotinylated ssDNA to one or two of the four binding sites of streptavidin can be controlled by adjusting the pH-controlled electrostatic interaction.     

Nanostructured zirconium oxide based genosensor for Escherichia coli detection

A deoxyribonucleic acid (DNA) biosensor has been fabricated via immobilization of 17 base terminal single stranded DNA (ssDNA) identified from the 16s rRNA coding region of Escherichia coli onto sol–gel derived nanostructured zirconium oxide (NanoZrO₂) film. An oligonucleotide probe with a terminal 5′-phosphate group has been attached to the surface of the electrode via affinity of NanoZrO₂ for phosphate. The results of hybridization studies carried out with the complementary, non-complementary and genomic DNA reveal that ssDNA/NanoZrO₂/ITO bioelectrode has a high selectivity and sensitivity towards hybridization detection with limits of 10^?6–10⁶ pM of complementary DNA.     

微囊藻属DNA电化学传感器的研制

利用自组装法将巯基修饰的DNA探针与6-巯基-1-己醇(MCH)固定到金电极表面,制备了微囊藻属特定DNA传感器,将该传感器与完全互补的微囊藻DNA序列、完全不互补序列,以及单碱基错配序列进行杂交,以Hoechst 33258为杂交指示剂,应用循环伏安法和线性扫描伏安法研究了该传感器对目标DNA的电化学检测行为.研究表明,当与完全互补DNA杂交后,Hoechst 33258氧化信号有明显的增强.实验对自组装时间、MCH浸泡时间及杂交液离子浓度进行了优化.结果表明,当自组装时间为90 min,MCH浸泡时间为1 h,杂交溶液中NaCl浓度为0.3 mol/L时,电化学信号最好.目标DNA的氧化峰电流值与其浓度在1×10~(-8) ～1×10~(-6) mol/L范围内呈良好的线性关系,检出限为8.1×10~(-9) mol/L.     

Towards the optimization of an optical DNA sensor: control of selectivity coefficients and relative surface affinities

Short single-stranded DNA (ssDNA) oligonucleotides can be grown on the surface of fused silica by automated nucleic acid synthesis. The immobilized ssDNA can be deposited at a desired average density. The density of ssDNA provides a controlled parameter that in combination with temperature, ionic strength and pH, can be used to define the selectivity of hybridization. Furthermore, the density of ssDNA can be used to control the affinity of complementary DNA so that it associates with the nucleic acids on the surface rather than areas that are not coated with ssDNA. The characteristic melt temperature observed for immobilized double-stranded DNA (dsDNA) 20mer shifts by up to 10 °C when a single base pair mismatch is present in the center of a target oligonucleotide. Optimization of quantitative analysis of such single base pair mismatches requires use of select experimental conditions to maximize the formation of the fully matched target duplex while minimizing the formation of the mismatched duplex. Results based on fiber optic biosensors that are used to study binding of fluorescein-labeled complementary DNA demonstrate that it is possible to achieve a selectivity coefficient of fully matched to single base pair mismatch of approximately 85-1, while maintaining >55% of the maximum possible signal that can be obtained from the fully matched target duplex.     

Styrene‐N‐phenylacrylamide co‐polymer modified silica monolith particles with an optimized mixing ratio of monomers as a new stationary phase for the separation of peptides in high performance liquid chromatography

A stationary phase was prepared by chemical derivatization of the support particles with a layer of copolymer composed of styrene and N‐phenyl acrylamide. Silica monolith particles of ca. 2.6 µm (volume‐based average) have been prepared as the support particles by sol‐gel reaction followed by differential sedimentation. The particles were reacted with 3‐chloropropyl trimethoxysilane followed by sodium diethyldithiocarbamate to introduce an initiator moiety. Then, the copolymer layer was immobilized via reversible addition‐fragmentation transfer polymerization. The resultant phase was packed in glass‐lined stainless‐steel micro‐columns (1 x 150 mm) and evaluated for the separation of a mixture composed of five peptides (Trp‐Gly, Thr‐Tyr‐Ser, angiotensin I, isotocin and bradykinin). The effect of monomer mixing ratio (styrene versus N‐phenyl acrylamide) on the chromatographic separation efficiency of the stationary phase was examined. A number of theoretical plates (N) as high as 33 600 plates/column (224 000 plates/m, 4.46 µm plate height) was achieved using the column packed with the optimized stationary phase. The column‐to‐column reproducibility based on three columns packed with three different batches of stationary phase was found satisfactory in separation efficiency, retention factor, and asymmetry factor.     

超顺磁性DNA纳米富集器应用于痕量寡聚核苷酸的富集

随着纳米技术的迅速发展 ,纳米材料逐渐被应用到细胞生物学和分子生物学研究领域 ,为生物医学的研究和发展提供了新的技术和手段 [1～ 4 ] .如超顺磁性纳米颗粒由于具有尺寸小、比表面积大、悬浮稳定性好及在外磁场作用下的磁导向性运输和富集等优良特性 ,使其在细胞和生物活性     

Voltammetric determination of DNA hybridization using methylene blue and self-assembled alkanethiol monolayer on gold electrodes

An electrochemical DNA biosensor based on the recognition of single stranded DNA (ssDNA) by hybridization detection with immobilized complementary DNA oligonucleotides is presented. DNA and oligonucleotides were covalently attached through free amines on the DNA bases using N-hydroxysulfosuccinimide (NHS) and N-(3-dimethylamino)propyl-N′-ethylcarbodiimide hydrochloride (EDC) onto a carboxylate terminated alkanethiol self-assembled monolayers (SAM) preformed on a gold electrode (AuE). Differential pulse voltammetry (DPV) was used to investigate the surface coverage and molecular orientation of the immobilized DNA molecules. The covalently immobilized probe could selectively hybridize with the target DNA to form a hybrid on the surface despite the bases being attached to the SAM. The changes in the peak currents of methylene blue (MB), an electroactive label, were observed upon hybridization of probe with the target. Peak currents were found to increase in the following order: hybrid-modified AuE, mismatched hybrid-modified AuE, and the probe-modified AuE which indicates the MB signal is determined by the extent of exposed bases. Control experiments were performed using a non-complementary DNA sequence. The effect of the DNA target concentration on the hybridization signal was also studied. The interaction of MB with inosine substituted probes was investigated. Performance characteristics of the sensor are described.     

Detection of Aeromonas hydrophila DNA oligonucleotide sequence using a biosensor design based on Ceria nanoparticles decorated reduced graphene oxide and Fast Fourier transform square wave voltammetry

A new strategy was introduced for ssDNA immobilization on a modified glassy carbon electrode. The electrode surface was modified using polyaniline and chemically reduced graphene oxide decorated cerium oxide nanoparticles (CeO₂NPs-RGO). A single-stranded DNA (ssDNA) probe was immobilized on the modified electrode surface. Fast Fourier transform square wave voltammetry (FFT-SWV) was applied as detection technique and [Ru(bpy)₃]^2+/3+ redox signal was used as electrochemical marker. The hybridization of ssDNA with its complementary target caused a dramatic decrease in [Ru(bpy)₃]^2+/3+ FFT-SW signal. The proposed electrochemical biosensor was able to detect Aeromonas hydrophila DNA oligonucleotide sequence encoding aerolysin protein. Under optimal conditions, the biosensor showed excellent selectivity toward complementary sequence in comparison with noncomplementary and two-base mismatch sequences. The dynamic linear range of this electrochemical DNA biosensor for detecting 20-mer oligonucleotide sequence of A. hydrophila was from 1 × 10⁻¹⁵ to 1 × 10⁻⁸ mol L⁻¹. The proposed biosensor was successfully applied for the detection of DNA extracted from A. hydrophila in fish pond water up to 0.01 μg mL⁻¹ with RSD of 5%. Besides, molecular docking was applied to consider the [Ru(bpy)₃]^2+/3+ interaction with ssDNA before and after hybridization.     

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.     

N,N,N,N-Tetramethyl-1,3-propanediamine as the catalyst of choice for the Baylis-Hillman reaction of cycloalkenone: rate acceleration by stabilizing the zwitterionic intermediate via the ion-dipole interaction

N,N,N^′,N^′-Tetramethyl-1,3-propanediamine (TMPDA) can be used as an efficient catalyst for the Baylis-Hillman reaction of cycloalkenones. The increased reaction rate was thought be derived from the stabilizing effect of the zwitterionic intermediate via the ion-dipole interaction.     

Preparation of a new 1,3-alternate-calix[4]arene-bonded HPLC stationary phase for the separation of phenols, aromatic amines and drugs

We have synthesized the 1,3-alternate 25,27-dioctyloxy-26,28-bis-[3-aminopropyloxy]-calix[4]arene and then immobilized onto γ-chloropropylsilica gel (CPS). The high-performance liquid chromatographic behavior of some aromatic hydrocarbons, phenolic compounds, aromatic amines and drug compounds was studied on this 1,3-alternate-calix[4]arene-bonded silica gel stationary phase (CIMS). The effect of organic modifier content and pH of the mobile phase on retention and selectivity of these compounds were investigated. According to chromatographic data, it can be concluded that the selectivity of CIMS for analytes ascribes to various interactions between CIMS and the analytes, such as hydrophobic interaction, hydrogen bonding interaction, π-π interaction and inclusion interaction.     

Controlling DNA orientation on mixed ssDNA/OEG SAMs

We present and characterize a mixed self-assembled monolayer (SAM) consisting of single-stranded oligonucleotide (ssDNA)- and oligo(ethylene glycol) (OEG)-terminated thiols. The ssDNA/OEG SAMs are prepared by simultaneous coadsorption from a common thiol solution over a broad range of compositions. Electron spectroscopy for chemical analysis (ESCA) is used to measure the surface coverage of ssDNA, whereas surface plasmon resonance (SPR) sensor is used to measure the hybridization of complementary ssDNA and protein resistance. Through the complementary use of these techniques, we find that the composition of OEG in the assembly solution controls a key parameter: the surface coverage of ssDNA on the surface. There is evidence that it influences the orientation of the immobilized ssDNA probes. Lower OEG concentrations yield a surface with higher ssDNA coverage and less favorable orientation, whereas higher OEG concentrations produce a surface with lower DNA coverage and more favorable orientation. Competition between these two effects controls the hybridization efficiency of the ssDNA surface. Compared to ssDNA surfaces prepared with other diluent thiols, the use of OEG improves the protein resistance of the surface, making it more broadly applicable.     

Latex-functionalized monolithic columns for the separation of carbohydrates by micro anion-exchange chromatography

A novel stationary phase for micro ion chromatography has been prepared by coating a porous poly(butyl methacrylate-co-ethylene dimethacrylate-co-2-acrylamido-2-methyl-1-propanesulfonic acid) monolith with quaternary amine-functionalized latex particles via simple electrostatic binding. This stationary phase enabled the separation of saccharides in the mobile phase with a high-pH value consisting of aqueous ammonia solution in anion-exchange mode using evaporative light scattering for detection. Effects of both porous properties of the monolithic stationary phase and chromatographic conditions on the separation ability were studied. Under optimized conditions, an efficient separation of seven saccharides was achieved in less than 10 min. The stationary phase also enables the separation of saccharides obtained by the enzymatic hydrolysis of corn starch.     

Development and Evaluation of a New Fluorinated Double-Wall Carbon Nanotube HPLC Stationary Phase

A novel column based on silica-containing immobilized fluorinated double-wall carbon nanotubes (F-DWCNTs) was developed. This F-DWCNT stationary phase was synthesized to combine the analytical performance of carbon nanotubes and the fluorine-based unique selectivity for polar compounds. First, the chromatographic support was coated with DWCNTs in a noncovalent way to preserve the sp² internal nanotube structure. Second, the DWCNT silica particles were functionalized with fluorine atoms via a solution of Br₂ and BrF₃ at room temperature. This F-DWCNT stationary phase was applied for a variety of separations. The solute retention behaviour was particularly studied under isocratic conditions with a high fraction of ACN in the ACN/water (v/v) mobile phase. The retention factors of the solute molecule do not depend linearly on the ACN fraction, but follow a quadratic relationship. This fluorinated stationary phase separated compounds based upon a combination of hydrophobic and polar selective stationary phase interactions. This F-DWCNT appeared to work best when fluorinated or halogenated compounds were encountered. They have longer retention time, better selectivity and work well with high fraction of organic modifiers. This novel stationary phase could thus be a good choice for LC–MS experiments.     

HPLC separation of positional isomers on a dodecylamine-N, N-dimethylenephosphonic acid modified zirconia stationary phase

The chromatographic performance of a new zirconia stationary phase (DPZ) modified with dodecylamine-N,N-dimethylenephosphonic acid (DDPA) is studied by using positional isomers as probes. The DDPA modified zirconia via one phosphonic group has a polar inner-layer and a non-polar outer-layer on its surface. The alkyl chain of outer-layer provides the hydrophobic interaction, while the polar inner-layer that consists of an amine group and a free phosphonic group provided dipolar and ion-exchange/columbic repellent interaction sites. The effects of methanol content, ionic strength and pH of mobile phase on capacity factors of the solutes are studied in detail, and baseline separations of toluidine, nitroaniline, aminophenol, dihydroxybenzene, and nitrophenol isomers were achieved on the new zirconia stationary phase. In addition, retention mechanism of the isomers on the DDPA-modified zirconia stationary phase is also proposed.     

Molecular interactions of sodium laureth sulfate with N-alkyl-1,3-propanediamine in aqueous solutions, based on potentiometric and photometric data

The role of Coulomb and hydrophobic interactions in association and aggregation in binary solutions of anionic surfactant sodium laureth sulfate and cationic surfactant N-alkyl-1,3-propanediamine is established from the concentration dependences of the pH of the solutions. It is shown that the development of the processes is initiated by the Coulomb interaction of oppositely charged sodium laureth sulfate and N-alkyl-1,3-propanediamine molecules and enhanced by the hydrophobic interaction between the hydrocarbon tails of neutral associates of the surfactant molecules.