The biased reptation model of DNA gel electrophoresis: mobility vs molecular size and gel concentration

The biased reptation model provides a good framework for interpreting the results of continuous field DNA electrophoresis experiments performed in agarose gels. Here we discuss the main features of the mobility-molecular size and mobility-gel concentration diagrams as obtained from new extensive computer simulations of the model. Our aim is to suggest a global and coherent picture of this widely used yet poorly understood experimental technique, and to point out the areas where a systematic experimental study is still needed.     

Acrylamide gel electrophoresis of seed proteins from someSolanum (sectionSolanum) species

Polyacrylamide gel electrophoresis was used to investigate the seed proteins of 36 accessions belonging toSolanum sect.Solanum (Solanaceae). These accessions represented 20 species, of four differing ploidy levels, and included infraspecific morphological variants. The resultant band patterns tended to reflect the morphological differences and genetical isolation displayed by many of the species. The most variable band patterns were encountered in the taxa with the greatest infraspecific variation, while many of the more morpho-genetically distinct taxa seemed to have species-specific band patterns.Good matches were found between the band patterns of artificial hybrids, those of their known parents, and mixtures of the parental protein extracts. This illustrates the potential use of such a technique for pinpointing possible genome donors of natural hybrids, and especially of polyploids. These comparative band patterns confirmed experimental work on the origin of the hexaploidS. nigrum from the diploidS. americanum and the tetraploidS. villosum, and also supported the suggestion thatS. nigrum contains two genomes from the diploidS. sarrachoides, but not four genomes of the diploidS. americanum.     

Determination of Wolbachia genome size by pulsed-field gel electrophoresis

Genome sizes of six different Wolbachia strains from insect and nematode hosts have been determined by pulsed-field gel electrophoresis of purified DNA both before and after digestion with rare-cutting restriction endonucleases. Enzymes SmaI, ApaI, AscI, and FseI cleaved the studied Wolbachia strains at a small number of sites and were used for the determination of the genome sizes of wMelPop, wMel, and wMelCS (each 1.36 Mb), wRi (1.66 Mb), wBma (1.1 Mb), and wDim (0.95 Mb). The Wolbachia genomes studied were all much smaller than the genomes of free-living bacteria such as Escherichia coli (4.7 Mb), as is typical for obligate intracellular bacteria. There was considerable genome size variability among Wolbachia strains, especially between the more parasitic A group Wolbachia infections of insects and the mutualistic C and D group infections of nematodes. The studies described here found no evidence for extrachromosomal plasmid DNA in any of the strains examined. They also indicated that the Wolbachia genome is circular.     

空肠弯曲菌脉冲场凝胶电泳分子检测方法的建立及应用

摘要：【目的】建立空肠弯曲菌脉冲场电泳(pulsed-field gel electrophoresis, PFGE)图谱分型方法。【方法】在PFGE基本程序基础上,通过调整菌液浓度、Seakem Gold○R琼脂糖凝胶浓度、蛋白酶K浓度、洗涤方式和限制性内切酶SmaⅠ浓度,进行程序的比较与优化。应用PFGE技术对不同来源分离株进行分析。【结果】37株空肠弯曲菌脉冲场凝胶电泳图谱显示分离株均产生了6-24条电泳带,条带数量适中,清晰易读;系统进化树显示,可分为4个遗传谱系,分离株主要分布于PFGE遗传谱系     

The use of the 2-aminobenzoic acid tag for oligosaccharide gel electrophoresis

Gel electrophoresis of fluorophore labeled saccharides provides a rapid and reliable method to screen enzymatic and/or chemical treatments of polysaccharides and glycoconjugates, as well as a sensitive and efficient microscale method to separate and purify oligosaccharides for further analysis. A simple and inexpensive method of derivatization and analysis using 2-aminobenzoic acid (anthranilic acid, AA) is described and applied to the extracellular polysaccharide released by the desiccation tolerant cyanobacterium Nostoc commune DRH-1. The results of these analyses suggest a possible protective functionality of two pendent groups, as well as a potential relationship between these groups and the desiccation tolerance of the organism.     

Improved agarose gel electrophoresis method and molecular mass calculation for high molecular mass hyaluronan

The molecular mass of the polysaccharide hyaluronan (HA) is an important determinant of its biological activity and physicochemical properties. One method currently used for the analysis of the molecular mass distribution of an HA sample is gel electrophoresis. In the current work, an improved agarose gel electrophoresis method for analysis of high molecular mass HA is presented and validated. HA mobility in 0.5% agarose minigels was found to be linearly related to the logarithm of molecular mass in the range from approximately 200 to 6000 kDa. A sample load of 2.5 μg for polydisperse HA samples was employed. Densitometric scanning of stained gels allowed analysis of the range of molecular masses present in the sample as well as calculation of weight-average and number-average values. The method was validated for a polydisperse HA sample with a weight-average molecular mass of approximately 2000 kDa. Excellent agreement was found between the weight-average molecular mass determined by electrophoresis and that determined by rheological measurement of the solution viscosity. The revised method was then used to show that heating solutions of HA at 100 °C, followed by various cooling procedures, had no effect on the HA molecular mass distribution.     

Techniques and high resolution DNA size markers for pulsed field gel electrophoresis

High resolution DNA size markers are described for pulsed field gel electrophoresis (PFGE). These markers provide resolution of 10–20 kbp over a size range from 10 kbp to more than 400 kbp and are produced by partial restriction digestion of lambda phage DNA concatemers (λ ladder). High resolution markers extending to over 400 kbp are made by partial restriction digestion of λ ladder embedded in agarose. Detailed methods are described for marker production and for DNA separation by contour-clamped homogeneous electric field (CHEF) electrophoresis. These markers and methods are useful for a variety of high resolution DNA mapping by PFGE.     

The molecular weight-dependent distribution of urinary glycosaminoglycans in Werner's syndrome

The macromolecular AGAG in the urine of patients with Werner's syndrome were analyzed by enzymatic methods after digestion with chondroitinases and Streptomyces hyaluronidase. The molecular weight-dependent distribution of the urinary AGAG has been determined by gel filtration on a Sephadex G-100 column. The distribution of HA and HS was predominant in the macromolecular fractions. Chondroitin sulfate isomers were prominent in the low molecular weight fractions but the ratio of the 4-type to the 6-type increased with decreasing molecular weight. These observations indicated that Werner's syndrome is a metabolic disorder of the molecular weight-dependent AGAG composition.