Denaturing Urea Polyacrylamide Gel Electrophoresis (Urea PAGE)

Urea PAGE or denaturing urea polyacrylamide gel electrophoresis employs 6-8 M urea, which denatures secondary DNA or RNA structures and is used for their separation in a polyacrylamide gel matrix based on the molecular weight. Fragments between 2 to 500 bases, with length differences as small as a single nucleotide, can be separated using this method¹. The migration of the sample is dependent on the chosen acrylamide concentration. A higher percentage of polyacrylamide resolves lower molecular weight fragments. The combination of urea and temperatures of 45-55 °C during the gel run allows for the separation of unstructured DNA or RNA molecules.In general this method is required to analyze or purify single stranded DNA or RNA fragments, such as synthesized or labeled oligonucleotides or products from enzymatic cleavage reactions.In this video article we show how to prepare and run the denaturing urea polyacrylamide gels. Technical tips are included, in addition to the original protocol ^1,2.     

Site-Specific Limitations of Using Urea as a Nitrogen Source in Biodegradation of Petroleum Wastes in Soil

Nutrient addition is important to achieving the carbon/nitrogen balance and successful biodegradation of petroleum contaminants. Urea has been considered as a preferred nitrogen source in enhancing biodegradation, because of its high nitrogen content and commercial availability. This study investigated urea in the biodegradation of petroleum-contaminated soils collected from an arid and sandy area in Egypt. Ammonium nitrate served as the nitrogen amendment control in this study. Biodegradation of petroleum-contaminated soils from Wyoming was monitored as a comparison. Addition of urea failed to improve the enhancement of biodegradation of petroleum-impacted soil from the Egyptian site; in addition, urea demonstrates an adverse effect on the biodegradation rates. Results indicate that urea or its intermediates may inhibit the microorganisms involved in petroleum degradation. Data from this study suggest that the application of urea in the enhancement of biodegradation of petroleum compounds should consider site specificity, and may not be applicable in geological areas or soils structures similar to those in this study.     

Simultaneous Enantioseparation of Aldohexoses and Aldopentoses Derivatized With L‐Tryptophanamide by Reversed Phase HPLC Using Butylboronic Acid as a Complexation Reagent of Monosaccharides

Three aldohexoses, glucose, galactose, and mannose, and three aldopentoses, arabinose, xylose, and ribose, were derivatized with L‐tryptophanamide (L‐TrpNH₂) under alkaline conditions. Using a basic mobile phase (pH 9.2), the three aldohexoses or the three aldopentoses were simultaneously enantioseparated, respectively, but all the six monosaccharides could not be simultaneously enantioseparated. A large amount of nonreacted L‐TrpNH₂ was detected after the derivatized monosaccharides. In order to widen the separation window, a large portion of nonreacted L‐TrpNH₂ could be eliminated by liquid–liquid extraction with ethylacetate, and elution order of the derivatized monosaccharides and nonreacted L‐TrpNH₂ was found to be reversed using a neutral mobile phase. All of the six monosaccharides were simultaneously enantioseparated by reversed phase high‐performance liquid chromatography (HPLC) using InertSustainSwift C18 column (4.6 mm i.d. × 150 mm) and a mobile phase containing 180 mM phosphate buffer (pH 7.6), 1.5 mM butylboronic acid, and 5% acetonitrile at 40 °C. Nomenclature of D and L for monosaccharides is based on the configurations of the asymmetric C4 center for aldopentoses and C5 center for aldohexoses. It was found that the enantiomer elution order of these six monosaccharides and fucose in the proposed method conformed to be the absolute configuration of the C2 center. Chirality 27:417–421, 2015. © 2015 Wiley Periodicals, Inc.     

Enhanced Sequence Coverage in Tryptic Fragment Analysis by Two-Dimensional HPLC/MS Using a Monolithic Silica Capillary Column

The HPLC/MS system, in which a monolithic silica capillary column is directly connected to an electronspray-ionization mass spectrometer, showed superior performance at high mobile phase linear velocity. A two-dimensional (2D) HPLC/MS system was established, using an ion-exchange particle-packed capillary column at the first dimension and a monolithic silica capillary column at the second dimension. In an analysis of tryptic fragments from bovine serum albumin, an 81% sequence coverage, obtained by the 2D-HPLC/MS system, increased by 23% as compared to a 1D-HPLC/MS system. This 2D-HPLC/MS system using a monolithic silica capillary column should be useful for enhancing sequence coverage of tryptic fragments in proteomics.     

肿瘤细胞诱导分化剂NADAH在硅胶载体上的固定化及其与DNA作用的研究

1976年Reuben等[1]发现六亚甲基二乙酰胺（hexamethylenebisacetallllde,HMBA）在5×10-3mol/L浓度可诱导99％以上的Friend红白血病细胞分化．已报道HMBA在体外可引起动物多种实体瘤和白血病细胞系的分化［2］．阐明HMBA诱导肿瘤细胞分化的机制有着重要意义．HMBA去掉一个乙酸基后单乙酸己二胺（N-acetyl-diallllnohexaneNADAH）：CH3CONHCHZCHZCHZCHZCHZCHZNHZ,具有与HMBA几乎同样诱导肿瘤细胞分化的活性［3,'」,由于NADAH有一个活泼基因NHZ,为固相化研究其诱导肿瘤细胞分化机理提供了可能。通过两步合成将…     

Solution Phase Synthesis of Dithymidine Phosphorothioate by a Phosphotriester Method Using New S-Protecting Groups

Abstract

ABSTRACT

A phosphotriester method for the synthesis of dithymidine phosphorothioates with eight S-protecting groups has been investigated. Three of the S-protecting groups possesed catalytic activity, however side reactions occurred under deprotection. The best S-protecting group was 4-chloro-2-nitrobenzyl which could be removed with a minimum of side reactions (0.3 %). The coupling reagent PyFNOP (11) gave protected dithymidine phosphorothioate in 96% yield after 15 min coupling.     

HPLC‐Fluorescence Method for the Enantioselective Analysis of Propranolol in Rat Serum Using Immobilized Polysaccharide‐Based Chiral Stationary Phase

A stereoselective high‐performance liquid chromatographic (HPLC) method was developed and validated to determine S‐(?)‐ and R‐(+)‐propranolol in rat serum. Enantiomeric resolution was achieved on cellulose tris(3,5‐dimethylphenylcarbamate) immobilized onto spherical porous silica chiral stationary phase (CSP) known as Chiralpak IB. A simple analytical method was validated using a mobile phase consisted of n‐hexane‐ethanol‐triethylamine (95:5:0.4%, v/v/v) at a flow rate of 0.6 mL min^‐1 and fluorescence detection set at excitation/emission wavelengths 290/375 nm. The calibration curves were linear over the range of 10–400 ng mL^‐1 (R = 0.999) for each enantiomer with a detection limit of 3 ng mL^‐1. The proposed method was validated in compliance with ICH guidelines in terms of linearity, accuracy, precision, limits of detection and quantitation, and other aspects of analytical validation. Actual quantification could be made for propranolol isomers in serum obtained from rats that had been intraperitoneally (i.p.) administered a single dose of the drug. The proposed method established in this study is simple and sensitive enough to be adopted in the fields of clinical and forensic toxicology. Molecular modeling studies including energy minimization and docking studies were first performed to illustrate the mechanism by which the active enantiomer binds to the β‐adrenergic receptor and second to find a suitable interpretation of how both enantiomers are interacting with cellulose tris(3,5‐dimethylphenylcarbamate) CSP during the process of resolution. The latter interaction was demonstrated by calculating the binding affinities and interaction distances between propranolol enantiomers and chiral selector. Chirality 26:194–199, 2014. © 2014 Wiley Periodicals, Inc.     

Chiral Separation of Cathinone and Amphetamine Derivatives by HPLC/UV Using Sulfated ß‐Cyclodextrin as Chiral Mobile Phase Additive

In the last years the identification of new legal and illegal highs has become a huge challenge for the police and prosecution authorities. In an analytical context, only a few analytical methods are available to identify these new substances. Moreover, many of these recreational drugs are chiral and it is supposed that the enantiomers differ in their pharmacological potency. Since nonenantioselective synthesis is easier and cheaper, they are mainly sold as racemic mixtures. The goal of this research work was to develop an inexpensive method for the chiral separation of cathinones and amphetamines. This should help to discover if the substances are sold as racemic mixtures and give further information about their quality as well as their origin. Chiral separation of a set of 6 amphetamine and 25 cathinone derivatives, mainly purchased from various Internet shops, is presented. A LiChrospher 100 RP‐18e, 250 x 4 mm, 5 µm served as the stationary phase. The chiral mobile phase consisted of methanol, water, and sulfated ß‐cyclodextrin. Measurements were performed under isocratic conditions in reversed phase mode using UV detection. Four model compounds of the two substance classes were used to optimize the mobile phase. Under final conditions (methanol:water 2.5:97.5 + 2% sulfated ß‐cyclodextrin) enantiomers of amphetamine and five derivatives were baseline separated within 23 min. In all, 17 cathinones were completely or partially chirally separated. However, as only 3 of 25 cathinones were baseline resolved, the application of this method is limited for cathinone analogs. Additionally, the results were compared with an RP‐8e column. Chirality 26:411–418, 2014. © 2014 Wiley Periodicals, Inc.     

新疆雪莲的高效液相指纹图谱及液-质联用分析

建立新疆雪莲药材的高效液相指纹图谱。以Luna C18为分析柱,用乙腈-0.1%醋酸梯度洗脱,获得分离度较好的新疆雪莲药材HPLC分析条件。通过10批样品的分析和对照,标示出12个共有峰,相似度分析大于0.92。最后通过HPLC-UV-MS/MS联用分析鉴定出其中7个化学成分。该方法可为新疆雪莲药材指纹图谱和质量分析方法的建立提供参考。     

Oxidatively Modified Plasma Phospholipids Containing Reactive Carbonyl Functions Measured by HPLC: Evidence for Phosphatidylcholine-Bound Aldehydes in Plasma of Burn Patients

A HPLC method has been developed to measure phosphatidylcholine (PC) containing reactive carbonyl functions in the sn-acyl residue in order to study processes in which such reactive carbonyls can be formed due to e.g. oxidative fragmentation. The method has been applied to determine PC-bound carbonyls as 2, 4-dinitrophenylhydrazones (DNPH) in plasma of burn patients. Plasma from healthy volunteers served as controls. Additionally, in vitro oxidation experiments (A: plasma, buffer diluted; B: plasma + iron-EDTA complex and C: plasma + iron-EDTA complex + H₂O₂) have been performed to obtain and to identify 2, 4-dinitrophenylhydrazine derivatizable carbonyl functions in plasma PC. Both, the PC-aldehydes and PC-aldehyde DNPH derivatives were cleavable with phospholipase C. Quantification was based on thin-layer chromatography purified soybean phosphatidylcholine, which was identically oxidized and derivatized as the plasma lipids in vitro.     

麦迪霉素产生菌中具强启动活性DNA片段的结构与功能分析

用启动子探针质粒ｐＩＪ４８６从麦迪霉素产生菌（Ｓ．ｍｙｃａｒｏｆａｃｉｅｎｓ）中克隆到１个具启动功能的ＨｉｎｄＩＩＩ－ＨｉｎｄＩＩＩ２．０ｋｂ片段,含该片段的重组质粒ｐ４Ｈ２转化子在ＭＭ基本培养基上对卡那霉素（Ｋｍ）抗性可达５００μｇ／ｍｌ以上。亚克隆缺失分析结果表明,该片段不同部分的缺失对启动活性有不同程度的影响,说明它具有较复杂的转录调控机制。ＤＮＡ序列分析结果显示,该片段含有１９８４个核苷酸,其Ｇ＋Ｃ％为４７．７％,不存在典型的链霉菌的可读框;进一步的分析发现,其６５０ｂｐ、１１５０ｂｐ和１５００ｂｐ区域分别与麦迪霉素酮基还原酶基因等链霉菌基因的启动子序列具有同源性;在５２０－５７０ｂｐ区域与大肠杆菌ｔＲＮＡ基因上游激活序列（ＵＡＳ）有较好的同源性,提示链霉菌中可能存在可增强基因转录的ＤＮＡ元件。     

Validation of a reversed-phase HPLC method for quantitative amino acid analysis.

A semi-automated method for amino acid derivatization and analysis has been validated for use in analysis of protein biopharmaceuticals. The method includes protein hydrolysis, o-phthalaldehyde derivatization, and reversed-phase high-performance liquid chromatography analysis in a general-purpose UV-visible high-performance liquid chromatography system. Amino-acid derivatization is performed automatically by the high-performance liquid chromatography autosampler right before injection. The required validation parameters, i.e., specificity, linearity, accuracy, precision, limit of detection, and limit of quantification, were studied for bovine serum albumin and for a recombinant human Fab fragment. The method can be employed as an absolute quantification method for determination of extinction coefficients of recombinant proteins.     

Optimisation and evaluation of a generic microplate-based HPLC screen for transketolase activity

A microplate-based HPLC assay for transketolase is described for rapidly determining substrate and product concentration suitable for optimisation of biocatalytic process conditions and screening directed evolution libraries. Transketolase catalyses the enantioselective carbon-carbon bond formation of chiral keto-diol products. The assay was used to determine dissociation constants for the two cofactors required by transketolase with 5–11% error. The preparation of samples by microplate-based fermentation, cell lysis, addition of cofactor, addition of substrates was also evaluated and optimised for increased transketolase activity. The whole process enables 3-fold improved enzyme variants to be identified from a single measurement.     

A Method for Preparing DNA Sequencing Templates Using a DNA-Binding Microplate

A DNA-binding matrix was immobilized on the surface of a 96-well microplate and used for plasmid DNA preparation for DNA sequencing. The same DNA-binding plate was used for bacterial growth, cell lysis, DNA purification, and storage. In a single step using one buffer, bacterial cells were lysed by enzymes, and released DNA was captured on the plate simultaneously. After two wash steps, DNA was eluted and stored in the same plate. Inclusion of phosphates in the culture medium was found to enhance the yield of plasmid significantly. Purified DNA samples were used successfully in DNA sequencing with high consistency and reproducibility. Eleven vectors and nine libraries were tested using this method. In 10 μl sequencing reactions using 3 μl sample and 0.25 μl BigDye Terminator v3.1, the results from a 3730xl sequencer gave a success rate of 90–95% and read-lengths of 700 bases or more. The method is fully automatable and convenient for manual operation as well. It enables reproducible, high-throughput, rapid production of DNA with purity and yields sufficient for high-quality DNA sequencing at a substantially reduced cost.     

Microscale HPLC enables a new paradigm for commercialization of complex chiral stationary phases

The small column size (0.3 mm i.d. x 15 cm) used in microscale HPLC contains only a small fraction (<1%) of the chromatographic packing material of a typical analytical HPLC column. Consequently, chromatographic stationary phases that are prohibitively expensive in conventional HPLC, owing either to synthetic complexity or costly starting materials, may become commercially viable in the microscale format. To illustrate this point, a previously described, synthetically complex, crown ether chiral stationary phase was prepared and evaluated in the microscale format, showing excellent separation of the enantiomers of underivatized amine analytes.     

Evaluation of Capillary HPLC/Mass Spectrometry as an Alternative Analysis Method for Gel Electrophoresis of Oligonucleotides

Abstract

A method has been developed to monitor the enzymatic incorporation of nucleotides in DNA by electrospray HPLC mass spectrometry. The main advantages of mass spectrometry over electrophoresis are the ability to directly characterize the reaction products and the shorter analysis time.     

Analysis of fish bile with HPLC — fluorescence to determine environmental exposure to benzo(a)pyrene

Brown bullhead from the Black River, Ohio, have a high incidence of liver neoplasia which is associated with elevated concentrations of polynuclear aromatic hydrocarbons (PAHs) in the sediment. We evaluated the use of biliary concentrations of benzo(a)pyrene [B(a)P] equivalents as a means for determining PAH exposure. Bile was collected from 16 brown bullheads and 8 common carp taken from each of two Lake Erie tributaries in Ohio, the industrialized Black River and the non-industrialized Old Woman Creek. Hatchery bullhead (n = 8) were used to determine base levels of PAHs. A high performance liquid chromatography (HPLC) — fluorescence technique was used to determine the concentration of B(a)P equivalents in the bile samples. The area of all peaks fluorescing at 380/430 nm was summed to give a single value for B(a)P equivalents in each sample. Concentrations of B(a)P equivalents generally reflected concentrations of PAH in sediment where fish were collected. Bile taken from Black River carp contained the highest concentration of B(a)P equivalents and was significantly different from all other groups. The value obtained for Black River bullhead was also high and was found to be significantly different from hatchery bullhead. B(a)P equivalents varied between carp and bullhead from the same habitat possibly because of differing food habits or metabolic pathways. However, our results indicate that relative levels of B(a)P equivalents in the bile of fish correspond well to B(a)P levels in sediment and may offer a means of determining environmental exposure of fish to the parent compound.     

HPLC法分析乳清蛋白对糖尿病模型小鼠血浆氨基酸组分的影响

为寻求有效的氨基酸分离方法并探讨乳清蛋白对2型糖尿病防治的作用机制,采用HPLC法分析乳清蛋白中氨基酸组分及含量;分别以0％、10％、20％和40％的乳清蛋白(WP)灌胃1型、2型糖尿病模型组、正常组小鼠,4周后观察各组血浆氨基酸的变化.乳清蛋白中亮氨酸、异亮氨酸、缬氨酸分别占氨基酸总量的14.40％、5.93％和5....     

Analysis of the Activities of RAD54, a SWI2/SNF2 Protein,Using a Specific Small-molecule Inhibitor

RAD54, an important homologous recombination protein, is a member of the SWI2/SNF2 family of ATPase-dependent DNA translocases. In vitro, RAD54 stimulates RAD51-mediated DNA strand exchange and promotes branch migration of Holliday junctions. It is thought that an ATPase-dependent DNA translocation is required for both of these RAD54 activities. Here we identified, by high-throughput screening, a specific RAD54 inhibitor, streptonigrin (SN), and used it to investigate the mechanisms of RAD54 activities. We found that SN specifically targets the RAD54 ATPase, but not DNA binding, through direct interaction with RAD54 and generation of reactive oxygen species. Consistent with the dependence of branch migration (BM) on the ATPase-dependent DNA translocation of RAD54, SN inhibited RAD54 BM. Surprisingly, the ability of RAD54 to stimulate RAD51 DNA strand exchange was not significantly affected by SN, indicating a relatively smaller role of RAD54 DNA translocation in this process. Thus, the use of SN enabled us to identify important differences in the effect of the RAD54 ATPase and DNA translocation on two major activities of RAD54, BM of Holliday junctions and stimulation of DNA pairing.