QuShape: Rapid,accurate, and best-practices quantification of nucleic acid probing information,resolved by capillary electrophoresis

Chemical probing of RNA and DNA structure is a widely used and highly informative approach for examining nucleic acid structure and for evaluating interactions with protein and small-molecule ligands. Use of capillary electrophoresis to analyze chemical probing experiments yields hundreds of nucleotides of information per experiment and can be performed on automated instruments. Extraction of the information from capillary electrophoresis electropherograms is a computationally intensive multistep analytical process, and no current software provides rapid, automated, and accurate data analysis. To overcome this bottleneck, we developed a platform-independent, user-friendly software package, QuShape, that yields quantitatively accurate nucleotide reactivity information with minimal user supervision. QuShape incorporates newly developed algorithms for signal decay correction, alignment of time-varying signals within and across capillaries and relative to the RNA nucleotide sequence, and signal scaling across channels or experiments. An analysis-by-reference option enables multiple, related experiments to be fully analyzed in minutes. We illustrate the usefulness and robustness of QuShape by analysis of RNA SHAPE (selective 2′-hydroxyl acylation analyzed by primer extension) experiments.     

响应曲面法优化毛细管区带电泳分析rhEPO的方法

为了在采用国内常用的60cm毛细管柱检测的条件下,能够完全分离检测重组人促红细胞生成素(rhEPO)8个组分,运用响应面分析法(RSM)对《欧洲药典》中规定的rhEPO的毛细管区带电泳检测法所用缓冲液组成作细微调整,以达到pH值操作允许范围略加宽松,易于控制,又保证所有组分清晰分离的目的。数学分析得到的缓冲液组分为:12 mmol/L氯化钠,12 mmol/L麦黄酮,12 mmol/L醋酸钠,3.0 mmol/L腐胺;用此缓冲液,pH值可拓宽至5.2~5.8范围内。实例检测验证结果表明,采用60 cm毛细管柱,在此缓冲液条件下检测样品,pH值在5.2~5.8范围内,rhEPO的8个糖基化形式在38 min内实现了基线分离,各相邻峰间的分离度达1.63~3.29,柱效达每米1.63×105~3.23×105理论塔板数,峰形良好。本研究提供了一个可行、可靠、高效的rhEPO分析方法。     

Use of nanomaterials in capillary and microchip electrophoresis

This review gives an overview of different separation strategies with nanomaterials and their use in capillary electrophoresis (CE) and capillary electrochromatography, as well as in microchip electrophoresis, including metal and metal oxide nanoparticles, carbon nanotubes, fullerene and polymer nanoparticles, as well as silica nanoparticles. The paper highlights the new developments and innovative applications of nanoparticles as pseudostationary phases or immobilized on the capillary surface for CE separation. The separation and characterization of target nanoparticles with different sizes by CE are reviewed likewise.     

Characterization of proteins in the human serum proteome.

This paper presents a multidimensional profile of the human serum proteome, produced by a two-dimensional protein fractionation system based on liquid chromatography followed by characterization with capillary electrophoresis (CE). The first-dimension separation was done by chromatofocusing over a pH range from 8.5 to 4.0, where proteins were separated by their isoelectric points (pI). In this dimension, fractions were collected based on pH. The first-dimension pI fractions were then resolved in the second dimension by high-resolution, reversed-phase chromatography with a gradient of trifluoroacetic acid (TFA) in acetonitrile and TFA in water. A selected protein fraction collected from the second dimension by time was characterized by CE for molecular-weight estimation and for presence of isoforms. Molecular-weight estimation was done by sodium dodecyl sulfate capillary gel electrophoresis, where proteins were separated in the range of 10,000-225,000 Da. Detection of isoforms was done by capillary isoelectric focusing over a pH range of 3-10. A selected second-dimension fraction that contained the putative serum iron-binding protein transferrin was analyzed by these two CE techniques for molecular-weight determination and the presence of isoforms. The combination of two-dimensional protein fractionation and CE characterization represents an advanced tool for proteomics.     

Determination of the affinity constants of recombinant human galectin-1 and -3 for simple saccharides by capillary affinophoresis

The affinity constants of recombinant human galectin-1 and galectin-3 for sugars were determined by capillary affinophoresis. The monoliganded affinophore contains p-aminophenyl-beta-lactoside as an affinity ligand in the matrix of succinylglutathione and has three negative charges. An analysis of the mobility change of the lectins caused by the affinophore and its inhibition by neutral sugars allowed, for the first time, a determination of the affinity constants between the binding sites of the lectins and sugars. The relative magnitude of the affinity constants for each of the sugars in terms of dissociation constants found to be consistent with previously reported data on the concentrations of sugars that caused a 50% inhibition (I50) in the binding assay of the lectin to oligosaccharide-immobilized agarose beads but the absolute values of the dissociation constants were considerably smaller than the I50 values. Capillary affinophoresis indicated microheterogeneity of the lectin preparations and enabled the separate analysis of the affinity of each component simultaneously showing the advantage in using a separation method for analysis of bioaffinity.     

Electrochemiluminescence detection with integrated indium tin oxide electrode on electrophoretic microchip for direct bioanalysis of lincomycin in the urine

In this article, an antibiotic, lincomycin was determined in the urine sample by microchip capillary electrophoresis (CE) with integrated indium tin oxide (ITO) working electrode based on electrochemiluminescence (ECL) detection. This microchip CE-ECL system can be used for the rapid analysis of lincomycin within 40s. Under the optimized conditions, the linear range was obtained from 5 to 100 microM with correlation coefficient of 0.998. The limit of detection (LOD) of 3.1 microM was obtained for lincomycin in the standard solution. We also applied this method to analyzing lincomycin in the urine matrix. The limit of detection of 9.0 microM was obtained. This method can determine lincomycin in the urine sample without pretreatment, which demonstrated that it is a promising method of detection of lincomycin in clinical and pharmaceutical area.     

无胶筛分毛细管电泳中核酸的迁移行为及分离的研究

无胶筛分毛细管电泳分析小于1kb的核酸,其迁移率与碱基数的对数成线性关系,长度大于1kb核酸的迁移率不是仅由其分子大小决定。据此可推测小于1kb核酸片段的大小。采用不更换聚合物法分析核酸,迁移时间的变异系数小于1.3％,适于大量样本的快速测定。考虑温度对核酸迁移行为的影响时,观察到22℃时,柱效最高。电进样与压力进样相比,分析大于300bp核酸的柱效提高,但不适于定量分析。     

电化学发光PCR技术检测转基因植物

随着转基因植物种类的增多,转基因植物的检测也成了当今的热门话题.电化学发光法是将电化学与化学发光两种高灵敏度方法相结合,实现了检测的高效、准确、无毒害.电化学发光PCR法首次将电化学发光技术、PCR技术和双探针杂交技术结合起来,用于检测CaMV(cauliflower mosaic virus)35 S启动子,从而判断其是否含有转基因成分.PCR产物与生物素标记的探针杂交,可以起到筛选的作用;与三联吡啶钌标记的探针杂交则可用于电化学发光检测.两种探针同时与转基因样品PCR产物杂交,使结果避免假阳性的影响而更加准确.实验表明：此方法可以准确地检测到35 S启动子的存在.该方法灵敏度高,可靠性强,操作简便,结果准确,有望成为一种高效的转基因检测方法.