Anion Complexation and Transport by Isophthalamide and Dipicolinamide Derivatives: DNA Plasmid Transformation in E. coli

Tris-arenes based on either isophthalic acid or 2,6-dipicolinic acid have been known for more than a decade to bind anions. Recent studies have also demonstrated their ability to transport various ions through membranes. In this report, we demonstrate two important properties of these simple diamides. First, they transport plasmid DNA into Escherichia coli about 2-fold over controls, where the ampicillin resistance gene is expressed in the bacteria. These studies were done with plasmid DNA (～2.6 kilobase (kb)) in JM109 E. coli cells. Second, known methods do not typically transport large plasmids (>15 kb). We demonstrate here that transformation of large pVIB plasmids (i.e., >20 kb) were enhanced over water controls by ～10-fold. These results are in striking contrast to the normal decrease in transformation with increasing plasmid size.     

Silaffin Peptides as a Novel Signal Enhancer for Gravimetric Biosensors

Application of biomimetic silica formation to gravimetric biosensors has been conducted for the first time. As a model system, silaffin peptides fused with green fluorescent protein (GFP) were immobilized on a gold quartz crystal resonator for quartz crystal microbalances using a self-assembled monolayer. When a solution of silicic acid was supplied, silica particles were successfully deposited on the Au surface, resulting in a significant change in resonance frequency (i.e., signal enhancement) with the silaffin–GFP. However, frequency was not altered when bare GFP was used as a control. The novel peptide enhancer is advantageous because it can be readily and quantitatively conjugated with sensing proteins using recombinant DNA technology. As a proof of concept, this study shows that the silaffin domains can be employed as a novel and efficient biomolecular signal enhancer for gravimetric biosensors.     

A flow-cell optosensor for lead based on immobilized dithizone

Dithizone immobilized on XAD-4 resin has been studied as a sensor element of an optical sensor for lead using a flow-cell. Using this arrangement, lead in solution has been determined in the concentration range 1 x 10(-5)-3 x 10(-7)M with a detection limit of 1 x 10(-8)M(i.e., 2 mug/l.). The standard deviation of the method for the measurement of lead at a concentration of 1 x 10(-6)M was found to be 7%. The response of the sensor was reproducible and can be regenerated using 0.01M hydrochloric acid followed by citrate-hydroxylamine solution.     

Formation of concentration gradient and its application to DNA capillary electrophoresis

A new method to introduce the concentration gradient into the capillary has been developed and its application to DNA capillary electrophoresis is presented. The concentration gradient produced by mixing 5% w/v polyacrylamide-co-poly(N-dimethylacrylamide) (PAM-co-PDMA) solution and 1 x Tris/N-tris(hydroxymethyl)methyl-3-amino-propanesulfonic acid/EDTA (TT) + 5 M urea buffer was successfully achieved by using two programmable syringe pumps with strict control of dead volume, flow rate, and pressure balance. This method has the advantages of high stability, reproducibility, and versatility. The column with concentration gradient greatly improved the resolution, especially for the large DNA fragments, due to a decrease in band width broadening with time. A column containing 2-4% w/v gradient in four steps had a longer read length, shorter separation time and better resolution (after 380 base) than that of 4% w/v single concentration polymer solution. The number of steps in the gradient had almost no effect on the performance. The change in the average concentration by relocating the position of the same step gradient, i.e., a combination of different low concentration to high concentration polymer solution ratios, resulted in a different migration time, read length and resolution.     

培养基碳源对固定化酵母细胞催化乙酰基三甲基硅烷不对称还原反应的影响

 尽管含芳香基等较大取代基团的底物能被生物转化为高对映体纯手性有机硅醇,但生物催化其他底物还原反应的产物收率及对映体选择性均较低. 作者筛选到一株能高效催化羰基/羟基不对称转化的酵母菌株,探讨了用固定化酵母细胞高效催化乙酰基三甲基硅烷不对称还原制1-三甲基硅乙醇的可能性,系统研究了培养基碳源及其浓度对该反应的影响. 发现在水/正己烷两相体系中,固定化酵母细胞能催化乙酰基三甲基硅烷不对称还原成1-三甲基硅乙醇. 可通过调节培养基碳源的种类及其浓度在一定程度上控制反应的产物收率及对映体选择性. 以最适碳源(3.0%麦芽汁)培养的酵母细胞催化该反应的产物收率和对映体过量值分别为91.3%和72.8%,远高于文献报道值.     

DNA分子结构的多态性研究 (Ⅱ) 吖啶橙凝聚体变化诱导的质粒DNA大分子构象的研究

利用吸收光谱和荧光光谱方法,研究了吖啶橙（ＡＯ）与质粒ＤＮＡ水溶液、以及含胶束介质的吖啶橙与质粒ＤＮＡ溶液体系的相互结合作用及减色效应。结果表明：吖啶橙对质粒ＤＮＡ的吸收光谱有减色效应;含十二烷基硫酸钠（ＳＤＳ）的ＡＯ水溶液体系中,随着ＳＤＳ浓度的增加,其光谱结果表现为由凝聚态向单体的转化。而在含十二烷基硫酸钠（ＳＤＳ）的ＡＯ与质粒ＤＮＡ溶液体系中,吖啶橙凝聚态随ＳＤＳ浓度的增加,对ＡＯ与质粒ＤＮＡ相互结合产生协同的减色效应,使质粒ＤＮＡ空间结构发生缩拢。进一步采用电泳法研究了ＡＯ凝聚态可能对质粒ＤＮＡ构象的影响,结果表明：在ＡＯ与质粒ＤＮＡ溶液体系中,ＡＯ浓度的增加对质粒ＤＮＡ构象未产生影响;而在含有ＳＤＳ的ＡＯ与质粒ＤＮＡ的溶液体系中,由于ＳＤＳ对ＡＯ凝聚态的解聚作用,以及ＳＤＳ对质粒ＤＮＡ减色效应的协同作用,使得质粒ＤＮＡ的构象发生变化,诱导质粒ＤＮＡ形成超螺旋构象     

Electrochemical Nucleic Acid Biosensors for the Detection of Interaction Between Peroxynitrite and DNA

We studied the reactivity of peroxynitrite and different nucleic acid molecules using DNA electrochemical biosensors. SIN‐1 (3‐morpholinosydnonimine) has been used for the simultaneous generation of NO?and superoxide, i.e., as a peroxynitrite (ONOO^?) donor. Double strand DNA (dsDNA), single strand DNA (ssDNA) and 15 guanine bases oligonucleotide (Oligo(dG)₁₅) were immobilized on a carbon paste electrode to generate the biosensor and DPV was selected as the electroanalytical technique. Results showed that electrochemical biosensors were very sensitive for detecting interaction between ONOO^? and DNA. A down/up effect was observed, i.e., at low ONOO^? concentrations the guanine oxidation signal decreased while at high ONOO^? concentrations the guanine oxidation current increased. Oligo(dG)₁₅ exhibited greater interaction at low ONOO^? concentrations than the other DNA molecules. The reactivity between ONOO^? and DNA was also evaluated in solution phase, showing the same down/up effect. Finally, the capacity of DNA to hybridize was prevented after interaction with ONOO^?.     

Effect of Low-Temperature Heating on the Properties of Graphene Oxide Aerogel

The paper describes the effect of low-temperature annealing in air on the composition and structure of graphene oxide aerogel. It has been found that the concentration of carbon in the aerogel sharply increases, i.e., its carbonization occurs, already at a temperature of 175°C. At the same time, both the outer shape of the aerogel granules and the internal porous structure are preserved.     

Biological Hydrogen Production Using Chloroform-treated Methanogenic Granules

In fermentative hydrogen production, the low-hydrogen-producing bacteria retention rate limits the suspended growth reactor productivity because of the long hydraulic retention time (HRT) required to maintain adequate bacteria population. Traditional bacteria immobilization methods such as calcium alginate entrapment have many application limitations in hydrogen fermentation, including limited duration time, bacteria leakage, cost, and so on. The use of chloroform-treated anaerobic granular sludge as immobilized hydrogen-producing bacteria in an immobilized hydrogen culture may be able to overcome the limitations of traditional immobilization methods. This paper reports the findings on the performance of fed-batch cultures and continuous cultures inoculated with chloroform-treated granules. The chloroform-treated granules were able to be reused over four fed-batch cultures, with pH adjustment. The upflow reactor packed with chloroform-treated granules was studied, and the HRT of the upflow reactor was found to be as low as 4 h without any decrease in hydrogen production yield. Initial pH and glucose concentration of the culture medium significantly influenced the performance of the reactor. The optimum initial pH of the culture medium was neutral, and the optimum glucose concentration of the culture medium was below 20 g chemical oxygen demand/L at HRT 4 h. This study also investigated the possibility of integrating immobilized hydrogen fermentation using chloroform-treated granules with immobilized methane production using untreated granular sludge. The results showed that the integrated batch cultures produced 1.01 mol hydrogen and 2 mol methane per mol glucose. Treating the methanogenic granules with chloroform and then using the treated granules as immobilized hydrogen-producing sludge demonstrated advantages over other immobilization methods because the treated granules provide hydrogen-producing bacteria with a protective niche, a long duration of an active culture, and excellent settling velocity. This integrated two-stage design for immobilized hydrogen fermentation and methane production offers a promising approach for modifying current anaerobic wastewater treatment processes to harvest hydrogen from the existing systems.     

Label-Free DNA Biosensor for Electrochemical Detection of Short DNA Sequences Related to Human Papilloma Virus

Abstract

Highly sensitive label-free techniques of DNA determination are particularly interesting in relation to the present development of an electrochemical hybridization biosensor for the detection of short DNA fragments specific to the human papilloma virus (HPV). Unlabeled DNA probes have been immobilized by spontaneous coadsorption of thiolated single-stranded oligonucleotides (HS-ssDNA) onto the sensing surface of a screen-printed gold electrode (SPGE). The covalently immobilized single-stranded DNA probe (HS-ssDNA) could selectively hybridize with its complementary DNA (cDNA) in solution to form double-stranded DNA (dsDNA) on the surface. DNA is treated with acid (e.g., 0.5 M chloridric acid), and the acid-released purine bases are directly determined by square wave voltammetry (SWV).

Variables of the probe-immobilization and hybridization steps are optimized to offer convenient quantitation of HPV DNA target, in connection with a short hybridization time. Peak currents were found to increase in the following order: hybrid-modified SPGE, 11-base mismatched modified SPGE, 18-base mismatched SPGE, and the probe modified SPGE. Control experiments with noncomplementary oligonucleotides were carried out to assess whether the suggested DNA sensor responds selectively to the target. The effect of the target DNA concentration on the hybridization signal was also studied. Under optimal conditions, this sensor has a good calibration range with HPV DNA sequence detection limit of 2 pg · ml^?1 (S/N = 3).     

Investigations of the Enhancer Effect of a High-Salt Concentration Medium on the Luminol Chemiluminescent Reaction

The enhancer effect of a high-salt concentration medium on the luminol chemiluminescence reaction catalyzed by either soluble or immobilized peroxidase has been investigated. Some widely used salts were tested at high concentration (up to 3 mol L): potassium chloride, sodium chloride, ammonium sulfate and calcium chloride. The magnitude of the light intensity enhancement depends on the nature of the salt and on the form of the peroxidase, i.e. free in solution or immobilized. The enhancement is observed whether the catalyst of the chemiluminescence reaction is peroxidase or ferricyanide. Both the enhanced or nonenhanced luminol chemiluminescence spectra have a maximum wavelength emission at around 425 nm. The results reported in this study are in favor of an action of the salts on the nonenzymatic steps of the luminol chemiluminescence reaction rather than a modification of the enzymatic process.     

Liquid chromatographic studies of the effect of phosphate on the binding properties of silica-immobilized bovine serum albumin

High-performance liquid chromatography has been used to examine how phosphate ions affect the binding properties of bovine serum albumin (BSA) immobilized to porous silica. In doing this, the time dependence of the protein to reach conformational equilibrium is measured as a function of the concentration of phosphate in the eluent using the D- and L-isomers of tryptophan and kynurenine as solutes. The overall binding and chiral selectivity (alphaD,L) of the protein toward these solutes appear to be related to two types of effects: one being those that are site-selective and only influence the retention of the L-isomers and the other being those that are nonselective and influence the retention of both enantiomers. An interesting feature of the concentration-dependent data is a maximum in alphaD,L at intermediate phosphate concentrations (i.e., 10 to 50mM phosphate) indicative of both cooperative and antagonistic binding effects. Phosphate eluents within this concentration range provide selectivity advantages, and those at higher concentrations decrease the time required for the protein or column to reach equilibrium. A final set of studies has also been carried out using four alternate buffer systems (i.e., borate, carbonate, acetate, and arsenate eluents). Although the borate eluents affect the BSA's binding properties and alphaD,L similar to the phosphate eluents, the other buffers result in poor separations. Observations from this study are useful in helping to optimize separations carried out on immobilized BSA as well as addressing biological and mechanistic questions related to how anions influence the native binding properties of serum albumins.     

Effects of the bead-bead potential on the restricted rotational diffusion of nonrigid macromolecules

The influence of the bead-bead interaction on the rotational dynamics of macromolecules which are immersed into a solution has been investigated by starting from the microscopic theory of the macromolecular motion, i.e., from a Fokker-Planck equation for the phase-space distribution function. From this equation, we then derived an explicit expression for the configuration-space distribution function of a nonrigid molecule which is immobilized on a surface. This function contains all the information about the interaction among the beads as well as the effects from the surrounding solvent particles and from the surface. For the restricted rotational motion, the dynamics of the macromolecules can now be characterized in terms of a rotational diffusion coefficient as well as a radial distribution functions. Detailed computations for the rotational diffusion coefficient and the distribution functions have been carried out for HOOKEAN, finitely extensible nonlinear elastic, and a DNA type bead-bead interaction.     

Considerations for the quantitative transduction of hybridization of immobilized DNA

Immobilized single-stranded DNA (ssDNA) can be used as a selective ‘reagent’ to bind complementary DNA or RNA for applications such as the detection of pathogenic organisms, gene therapy agents and genetic mutations. The density of ssDNA on a surface will determine the charge density due to ionizable phosphate groups. Such a negatively charged interface will attract positive counter-ions from solution, which may result in a local ionic strength, pH and dielectric constant on the surface that is substantially different from that in bulk electrolyte solution. It is the local conditions which influence the thermodynamics of hybridization, and this can studied by the melt temperature (T_m) of double-stranded DNA (dsDNA). Experimental work and theoretical models have been used to examine whether hybridization reactions on a surface can cause dynamic changes in local charge density, and therefore, changes in selectivity and drift in calibration for quantitative analysis. Organosilane chemistry has been used to covalently immobilize hexaethylene glycol linkers and to control the subsequent density of dT₂₀ that was prepared by automated synthesis. Fiber-optic biosensors based on fused silica that was coated with DNA were used in a total internal reflection fluorescence instrument to determine T_m from the dissociation of duplexes of fluorescein-labeled dA₂₀ : dT₂₀. The experimental results suggest that the thermodynamic stability of duplexes that are immobilized on a surface is dependent on the density of immobilized DNA and on the extent of hybridization of DNA. The experimental results show that the thermodynamic stability of immobilized dsDNA is significantly different than that of dsDNA in bulk solution, and include observations of the variation of enthalpy at different ionic strengths, asymmetry in the melt curves, and the possibility of a reduced dielectric constant within a DNA layer relative to that in bulk solution.     

A DNA assay protocol in a lab-on-valve meso-fluidic system with detection by laser-induced fluorescence

An automatic protocol for in-situ assay of dsDNA is presented by employing a micro-sequential injection lab-on-valve meso-fluidic system, which facilitates precise fluidic handling at the 0.1-10 microl level. Sub-nano-liter to a few micro-liters of DNA sample and ethidium bromide (EB) solutions were introduced into the meso-fluidic system, where EB binding onto DNA takes place and an intercalated DNA-EB adduct was formed, which was afterwards excited in the flow cell of the LOV by a 473 nm laser beam, and the emitted fluorescence was monitored in-situvia optical fibers. The experimental variables, i.e., pH of the buffer solution, the concentration and volume of EB solution, the reaction time and the fluid flow rates, were investigated. By loading 600 nl sample and 1.0 microl EB solution, a linear calibration graph was obtained within 0.03-3.0 microg ml(-1)(dsDNA), and a detection limit (3sigma) of 0.009 microg ml(-1) was achieved, along with a sampling frequency of 60 h(-1) and a precision of 1.9% at the 1.0 microg ml(-1) level. The detection limit was further improved to 0.006 microg ml(-1) by increasing the sample volume to 2.0 microl. Plasmid DNA in E. Coli extraction and lambda-DNA/Hind III in four synthetic samples were assayed by using this procedure. For the plasmid DNA, a good agreement with the documented UV method was obtained, while spiking recoveries for the synthetic samples were 95.6-103.4%.     

一种新型疏水改性的两亲性壳聚糖衍生物的表面活性研究

鉴于甲壳质的生物降解性、生物活性和生物相容性等诸多特性 ,其开发利用正受到人们的广泛重视[1] .具有不同性能和功效的衍生物已在医药、食品、日用化工、纺织、水处理等领域发挥了重要的作用 [2～ 4 ] .然而具有表面活性的两亲性衍生物却少见报道 [5,6] .本文将羧甲基壳聚糖进行疏水改性 ,使其分子上同时具有亲水基和疏水基 ,从而具有两亲性质 ,可以降低溶液的表面张力 ,并在溶液中形成胶束 .可望在日用化工、医药、食品等领域起到降低表面张力、增稠、乳化和增溶等作用 .1　实验部分1 .1　原料及仪器　羧甲基壳聚糖 (CMCHS,青岛生化制…     

Synthesis of functionalized dna fragments suitable for reversible attachment to activated cellulose

A system consisting of donor (1), template (2) and immobilized acceptor molecules (58,59,64-67) which may be used for an enzymatic extension (T4 DNA ligase) of immobilized DNA fragments is described. The synthesis of the donor (1), template (2) and the functionalized acceptor molecules (3-8) was performed via phosphotriester intermediates. The functionalized acceptor molecules used in this study contained: base labile bonds (i.e. compounds 3-6), an acid labile bond (i.e. compound 7) or a RNase labile bond (i.e. compound 8). The functionalized acceptor molecules (3,4) could be immobilized to cellulose activated with 2,4,6-trichloro-s-triazine and the other molecules (5-8) to 2-amino-4, 6-dichloro-s-triazine to give the immobilized DNA complexes 58, 59 and 64-67, respectively, in high yield. The immobilized DNA fragments could be released quantitatively from the solid support by: base treatment (i.e. 58, 59, 64 and 65 gave DNA-fragments 60, 61, 68 and 69 respectively), acid treatment (i.e. 66 gave DNA-fragment 70) or RNase digestion (i.e. 67 gave deoxythymidine).     

Electrophoretic behavior of plasmid DNA in the presence of various intercalating dyes

In the present study, the electrophoretic behavior of linear, supercoiled and nicked circular plasmid DNA in the presence of various intercalating dyes was characterized using pGL3 plasmid DNA as a model. The enzymatic digestion of pGL3 plasmid DNA with HindIIIwas monitored by capillary electrophoresis coupled with laser-induced fluorescence detection (CE-LIF). Nicked circular plasmid DNA was found to be relatively sensitive to enzymes, and was almost digested into the linear conformer after 10-min incubation, indicating that nicked circular plasmid DNA has little chance of targeting and entering the cell nucleus. Partly digested plasmid DNA containing only linear and supercoiled conformers can be used as a standard to confirm the migration order of plasmid DNA. In methylcellulose (MC) solution with YO-PRO-1 or YOYO-1, linear plasmid DNA eluted first, followed by supercoiled and nicked plasmid DNA, and nicked plasmid DNA eluted as a broad peak. With SYBR Green 1, nicked plasmid DNA eluted first as three sharp peaks, followed by linear and supercoiled plasmid DNA. The nuclear plasmid DNA from two transfected cell lines was successfully analyzed using the present procedure. Similar results were obtained with an analysis time of seconds using microchip electrophoresis with laser-induced fluorescence detection (mu-CE-LIF). To our knowledge, these results represent the first reported analysis of nuclear plasmid DNA from transfection cells by CE-LIF or mu-CE-LIF without pre-preparation, suggesting that the present procedure is a promising alternative method for evaluating transfection efficiency of DNA delivery systems.     

DNA sensor based on an Escherichia coli lac Z gene probe immobilization at self-assembled monolayers-modified gold electrodes

A novel approach to construct an electrochemical DNA sensor based on immobilization of a 25 base single-stranded probe, specific to E. coli lac Z gene, onto a gold disk electrode is described. The capture probe is covalently attached using a self-assembled monolayer of 3,3′-dithiodipropionic acid di(N-succinimidyl ester) (DTSP) and mercaptohexanol (MCH) as spacer. Hybridization of the immobilized probe with the target DNA at the electrode surface was monitored by square wave voltammetry (SWV), using methylene blue (MB) as electrochemical indicator. Variables involved in the sensor performance, such as the DTSP concentration in the modification solution, the self-assembled monolayers (SAM) formation time, the DNA probe drying time atop the electrode surface and the amount of probe immobilized, were optimized.

A good stability of the single- and double-stranded oligonucleotides immobilized on the DTSP-modified electrode was demonstrated, and a target DNA detection limit of 45 nM was achieved without signal amplification. Hybridization specificity was checked with non-complementary and mismatch oligonucleotides. A single-base mismatch oligonucleotide gave a hybridization response only 7 ± 3%, higher than the signal obtained for the capture probe before hybridization. The possibility of reusing the electrochemical genosensor was also tested.     

Adsorption of plasmid DNA to a natural organic matter-coated silica surface: kinetics, conformation, and reversibility

A quartz crystal microbalance with dissipation (QCM-D) has been used to determine the adsorption rate of ampicillin-resistant linear and supercoiled plasmid DNA onto a silica surface coated with natural organic matter (NOM). The structure of the resulting adsorbed DNA layer was determined by analyzing the viscoelastic properties of the adsorbed DNA layers as they formed and were then exposed to solutions of different ionic composition. The QCM-D data were complemented by dynamic light scattering measurements of diffusion coefficients of the DNA molecules as a function of solution ionic composition. The obtained results suggest that electrostatic interactions control the adsorption and structural changes of the adsorbed plasmid DNA on the NOM-coated silica surface. The adsorption of DNA molecules to the NOM layer took place at moderately high monovalent (sodium) electrolyte concentrations. A sharp decrease in solution ionic strength did not result in the release of the adsorbed DNA, indicating that DNA adsorption on the NOM-coated silica surface is irreversible under the studied solution conditions. However, the decrease in electrolyte concentration influenced the structure of the adsorbed layer, causing the adsorbed DNA to adopt a less compact conformation. The linear and supercoiled DNA had similar adsorption rates, but the linear DNA formed a thicker and less compact adsorbed layer than the supercoiled DNA.