Oligonucleotide trapping method for purification of transcription factors

Initial purification of two serotypic variants of recombinant botulinum neurotoxin toxin heavy chain fragment [rBoNT(Hc)], produced intracellularly in the yeast Pichia pastoris, using hydrophobic charge induction chromatography (HCIC) is reported. HCIC employs a matrix containing a weakly ionizable ligand that binds proteins through hydrophobic interactions at neutral pH and elutes the proteins by charge repulsion at acidic pH. HCIC optimization led to different purification conditions for each of the proteins even though they have 58% sequence similarity. The HCIC resin has a higher affinity for the fragment of serotype A than that of serotype B. The 10% dynamic breakthrough capacity for the serotype A fragment is >12.5 mg per ml of resin and is approximately 3.5 mg or the serotype B fragment per ml of resin. Stable elution conditions are also different for the two serotypes. The serotype A fragment is unstable when citrate is used to elute the product. However the serotype B fragment is stable when eluted with citrate buffer, and it is further purified by a overnight precipitation caused by the citrate buffer. This paper reports the development strategy, dynamic capacity breakthrough curves, resin and separation reproducibility, and preliminary scale-up data. The summation of the data demonstrates that HCIC is a scaleable process step for biopharmaceutical production of rBoNT(Hc) proteins.     

Direct visualization of electrophoretic mobility shift assays using nanoparticle-aptamer conjugates

Here, we demonstrate that aptamers tethered to gold nanoparticles enable direct visualization of protein–oligonucleotide interactions during gel electrophoresis. This technique is used to confirm that an aptamer previously identified as binding to C‐reactive protein (CRP) only binds to the monomeric form of CRP. While native, pentameric CRP (pCRP) is used in clinical assays to predict cardiovascular disease (CVD) risk, it is the monomeric isoform that is more strongly associated with pro‐inflammatory and pro‐atherogenic effects. To visualize this selectivity, the CRP–aptamer was conjugated to streptavidin‐coated gold nanoparticles and the mobility of the free oligonucleotide–nanoparticle conjugate (ON‐NP) and the protein/ON‐NP complex bands were visualized and recorded during electrophoresis using a simple digital camera. At a concentration of 6 μg/mL, monomeric CRP showed a significant decrease in the observed ON‐NP mobility, whereas no change in mobility was observed with pCRP up to 18 μg/mL. Advantages of this nanoparticle‐based electrophoretic mobility shift assay (NP‐EMSA) over the traditional EMSA include real‐time detection of protein–oligonucleotide interactions, the avoidance of harmful radioisotopes, and elimination of the need for expensive gel imagers. The availability of both the NP‐EMSA technique and an mCRP‐specific probe will allow for improved clinical diagnostic to more accurately predict future CVD risk.     

High-resolution gel filtration of the ecdysteroid receptor-DNA complex--an alternative to the electrophoretic mobility shift assay.

The mobility shift assay is a well established method for proving binding of protein to DNA. However, this method depends on the stability of the protein-DNA complex during the electrophoretic process. Ecdysteroid receptor shows a strong tendency to aggregate under low-salt conditions of electrophoresis to a non DNA-binding form. We have developed a high-resolution gel filtration method which allows the interaction of ecdysteroid receptor with specific DNA sequences to be studied. The method seems to be generally applicable. It does not depend on the availability of a purified protein. Crude preparations could be used to characterize the stoichiometry and the molecular parameters of the complexes formed between DNA and DNA-binding proteins.     

The potential of electrophoretic mobility shift assays for clinical mutation detection

As the understanding of the links between genetic mutations and diseases continues to grow, there is an increasing need for techniques that can rapidly, inexpensively, and sensitively detect DNA sequence alterations. Typically, such analyses are performed on PCR-amplified gene regions. Automated DNA sequencing by capillary array electrophoresis can be used, but is expensive to apply to large numbers of patient samples and/or large genes, and may not always reveal low-abundance mutations in heterozygous samples. Many different types of genetic differences need to be detected, including single-base substitutions and larger sequence alterations such as insertions, deletions, and inversions. Electrophoretic mobility shift assays seem well suited to this purpose and could be used for the efficient screening of patient samples for sequence alterations, effectively reducing the number of samples that must be subjected to full and careful sequencing. While there is much promise, many of the mobility shift assays presently under development have yet to be demonstrated to have the high sensitivity and specificity of mutation detection required for routine clinical application. Hence, further studies and optimization are required, in particular the application of these methods not only to particular genes but also to large numbers of patient samples in blinded studies aimed at the rigorous determination of sensitivity and specificity. This review examines the state-of-the-art of the most commonly used mobility shift assays for mutation detection, including denaturing gradient gel electrophoresis, TGGE, SSCP, heteroduplex analysis, and denaturing HPLC.     

A nonradioactive electrophoretic mobility shift assay for measurement of pregnane X receptor binding activity to CYP3A4 response element

The electrophoretic mobility shift assay (EMSA) is a method for the study of specific DNA–protein interactions in vitro. The pregnane X receptor (PRX) is a key xenobiotic sensor that regulates the expression of drug‐metabolizing enzymes and many other genes. Radiolabeled ³²P‐DNA‐probes had been used in studies of PXR‐DNA interactions. There is an increasing need for nonradioactive assays, due to the health, safety and environmental issues. In the current study, we present a protocol for the nonradioactive electrophoretic mobility shift assay, allowing studying interactions between human PXR with promoter DNA sequences.     

Determination of homogentisic acid in urine for diagnosis of alcaptonuria: Capillary electrophoretic method optimization using experimental design

Homogentisic acid (HGA) is a diagnostic metabolite that accumulates in the urine and tissues of patients with alkaptonuria which is a rare autosomal recessive disease. HGA is a specific metabolite in urine and serum, which is used for diagnosis of alkaptonuria. This study presents an inexpensive and easy capillary electrophoretic method for the quantitative determination of HGA in urine samples. The method was optimized using full factorial experimental design. The optimal separation electrolyte and separation voltage were revealed as 45 mmol/L phosphate buffer at pH 7.0 and 22 kV, respectively. Under these conditions the presence of HGA was detected in 6 min. Repeatability of migration times and corrected peak areas of HGA (as RSD) were 0.37 and 1.99, respectively. The detection limit was 0.56 μg/mL, 3 times of the average noise, and the quantification limit was 1.85 μg/mL, 10 times the average noise for HGA. Urine samples were directly injected to the capillary without any pretreatment step.     

Molecular volume calculation using AM1 semi-empirical method toward diffusion coefficients and electrophoretic mobility estimates in aqueous solution

Diffusion coefficients and electrophoretic mobility are two important physicochemical parameters used in mass transport phenomenon studies. The volume of the solute is required to determine or estimate these parameters. Classical methods, such as the LeBas method are commonly used. However, although valid, this method may represent a boring and time-consuming task, depending on the nature and number of compounds to be calculated. In this study, the volumes of a series of neutral and charged substances of the main functional groups present in organic molecules, amino acids, drugs and diverse compounds, such as cytosine and glucose, were calculated according to the LeBas method (V_M) and the AM1 semi-empirical method, V_W(AM1). The latter showed to be statistically coincident with the former. Employed as a pure value or corrected by the LeBas molar volume, the AM1 molecular volume was also demonstrated to estimate the diffusion coefficients in infinite aqueous dilution within an acceptable average error, according to the Othmer–Thakar, Wilke–Chang and Hayduk–Laudie methods, as well as the electrophoretic mobility of charged substances, such as carboxylates and protonated amines. According to these results, the AM1 method was seen to be statistically valid to calculate molecular volume. Many advantages in the construction of most diverse structures were noted, as well as a reduction in time and an increase in the quality of the information, when run on molecular modeling software.     

Calculation of electrophoretic mobility in mixed solvent buffers in capillary zone electrophoresis using a mixture response surface method

The electrophoretic mobilities of three beta-blocker drugs, practolol, timolol and propranolol, have been measured in electrolyte systems with mixed binary and ternary water-methanol-ethanol solvents with acetic acid/sodium acetate as buffer using capillary electrophoresis. The highest mobilities for the analytes studied have been observed in pure aqueous, the lowest values in ethanolic buffers. The measured electrophoretic mobilities have been used to evaluate the accuracy of a mathematical model based on a mixture response surface method that expresses the mobility as a function of the solvent composition. Mean percentage error (MPE) has been computed considering experimental and calculated mobilities as an accuracy criterion. The obtained MPE for practolol, timolol and propranolol in the binary mixtures are between 0.9 and 2.6%, in the ternary water-methanol-ethanol solvent system the MPE was about 2.7%. The MPE values resulting from the proposed equation lie within the experimental relative standard deviation values and can be considered as an acceptable error.     

Numerical study of colloidal suspensions of soft spherical particles using the network method. 1. DC electrophoretic mobility

The electrophoretic mobility of a spherical particle coated with a uniformly charged permeable membrane and suspended in a general electrolyte solution is calculated numerically. The network simulation method used makes it possible to solve the problem without any restrictions on the values of the parameters such as the membrane thickness, fixed charge density in the membrane, viscous drag in the membrane, number and valence of the ionic species, and electrolyte concentration. The theoretical model used is similar to the one presented by Ohshima (H. Ohshima, J. Colloid Interface Sci. 228 (2000) 190), except for the inclusion in the force balance equation of an additional term corresponding to the force exerted by the liquid on the core of the moving particle. This inclusion is theoretically proven in the limiting case of a nonconducting suspending medium, in which the equation system can be analytically solved. The results obtained coincide with existing analytical expressions when the electrolyte concentration is high, the membrane is thick, and its resistance to the fluid flow is high.     

一种基于二喹啉甲酸- Cu+显色反应的毛细管电泳检测蛋白质的新方法

采用毛细管电泳法和蛋白质显色反应-二喹啉甲酸(BCA)法,结合微波辅助反应,在60 mmol/L硼酸盐缓冲液(pH 9.5)中,实现了对蛋白质的快速毛细管电泳分析检测。同时以β-环糊精为包合添加剂,实现了BCA-Cu+复合物和游离BCA的分离,从而在波长200 nm处以测定特征生成的BCA-Cu+复合物来间接检测蛋白质,其峰强度比直接检测蛋白质自身吸收的峰强度提高了2个数量级。对于转铁蛋白、蓖麻毒素,其线性范围分别为2～200 mg/L和2～100 mg/L,检出限分别为0.33和0.37 mg/L。将该方法成功地应用于第一届蓖麻毒素国际实验室间比对测试的部分样品,含量测定结果满意。     

Multiple response optimization applied to the development of a capillary electrophoretic method for pharmaceutical analysis

Multiple response simultaneous optimization by using the desirability function was used for the development of a capillary electrophoresis method for the simultaneous determination of four active ingredients in pharmaceutical preparations: vitamins B₆ and B₁₂, dexamethasone and lidocaine hydrochloride. Five responses were simultaneously optimized: the three resolutions, the analysis time and the capillary current. This latter response was taken into account in order to improve the quality of the separations. The separation was carried out by using capillary zone electrophoresis (CZE) with a silica capillary and UV detection (240 nm). The optimum conditions were: 57.0 mmol l⁻¹ sodium phosphate buffer solution, pH 7.0 and voltage = 17.2 kV. Good results concerning precision (CV lower than 2%), accuracy (recoveries ranged between 98.5 and 102.6%) and selectivity were obtained in the concentration range studied for the four compounds. These results are comparable to those provided by the reference high performance liquid chromatography (HPLC) technique.     

Capillary electrophoretic method for Staphylococcus aureus detection by using a novel antimicrobial peptide

A novel peptide containing antimicrobial sequence and gelatinase cleavage sites was designed for Staphylococcus aureus detection. Since Staphylococcus aureus could secrete gelatinase, the fluorescein labeled peptide GKRWWKWWRRPLGVRGC could be recognized and cleaved. The obtained products were able to be analyzed by capillary electrophoresis with fluorescence detection. To explore the effect of Staphylococcus aureus concentration on enzyme digestion ability of peptide, Staphylococcus aureus with different concentrations were incubated with the peptide. Results indicated that capillary electrophoretic method was efficient for determining Staphylococcus aureus content. Compared with traditional approaches for Staphylococcus aureus detection, capillary electrophoresis possessed higher efficiency, enhanced sensitivity, and low sample consumption. Moreover, the proposed peptide also presented desirable antimicrobial activity. It suggested that the novel antimicrobial peptide used in this research opens a new path of detecting Staphylococcus aureus by capillary electrophoretic method.