Immobilized pH gradients (IPG) simulator--an additional step in pH gradient engineering: II. Nonlinear pH gradients

While in the companion paper (Tonani, C. & Righetti, P. G., Electrophoresis 1991, 12, 1011-1021) we gave the general outline of our new computer program, immobilized pH gradients (IPG) simulator, able to simulate and optimize linear pH gradients for isoelectric focusing in immobilized pH gradients, in the present report we extend the application of such a program to: (i) convex exponential gradients, (ii) logarithmic and (iii) polynomial gradients. Such gradients are meant to give equal space to protein spots in complex protein mixtures (e.g., cell lysates, biological fluids) and follow the statistical distribution of protein pI values along the pH axis. They will prove of fundamental importance in two-dimensional maps, both because they optimize the spreading of spots in the two-dimensional plane and because of the excellent reproducibility of immobilized pH gradients. The following concave exponential recipes are given: pH 3-8, pH 3-9, pH 3-10, pH 3-11, pH 4-7, pH 4-8, pH 4-9, pH 4-10, pH 4-11, pH 5-8, pH 5-9, and pH 5-10, as well as the most extended pH 2.5-11 interval. Two interesting logarithmic gradients are described: pH 3-6 and pH 3-7 and one sigmoidal (derived with a polynomial of 5th degree): pH 3-11.     

An image system and surface singularity solutions for potential flow past an elliptical cylinder

The Milne-Thomson circle theorem is extended to give a simplegeneral expression for the image system in an elliptical cylinderintroduced into an otherwise specified unbounded potential flowwhich contains no singularities in the region to be occupiedby the ellipse. This image system is used to obtain an expressionfor the corresponding source-sink surface singularity distributionon the ellipse, thus providing new benchmark test cases forsource-sink solutions as obtained numerically by a panel method.Several typical examples are given to illustrate the generaltheoretical approach.     

Diels-Alder versus heterodiene reaction: The effect of acid catalysis.

The difference between thermal, AlCl₃- and CF₃ COOH-catalyzed reaction of (E)-4-benzal-1-phenyl-5-pyrazolone and 2,3-dimethylbutadiene is discussed in terms of Diels-Alder $\text{versus}$ heterodiene reactivity.     

Capillary zone electrophoresis for monitoring r-DNA protein purification in multi-compartment electrolysers with immobiline membranes

Isoforms of human monoclonal antibodies against the gp-41 of AIDS virus and of human recombinant superoxide dismutase have been purified to homogeneity by isoelectric focusing (IEF) in a multi-compartment electrolyser with isoelectric, immobiline membranes. This system allows the processing of large sample volumes and gram-scale protein loads and can resolve isoforms as close as 0.001 in pI difference. The purification progress was usually monitored by analytical IEF in immobilized pH gradients (IPG). Capillary zone electrophoresis (CZE) was applied to the monitoring of the content of each chamber of the electrolyser. CZE was found to be superior in terms of speed of analysis and quantification (but only by UV reading at 200-210 nm, i.e., in the region of the peptide bond) but, notwithstanding the millions of theoretical plates reported, was no match for the resolving power of IPGs, at least for protein analysis. When compared also with chromatofocusing, the resolving power decreases in the order IPG greater than CZE much greater than chromatofocusing.     

Heterodiene synthesis—XI : A study of the isomerization of tetrahydropyran[2′,3′:2,3] 2,3-dihydropyran[6,5-c] pyrazoles

The stereoisomers (1–4) of the tetrahydropyran[2′,3′:2,3] 2,3-dihydropyran[6,5-c] pyrazole system equilibrate in deuterated trifluoroacetic acid at 35°.The mechanism which causes incorporation of deuterium in the 4a-position is discussed.The isomers distribution is rationalized in terms of steric and electronic interactions, and the energy values for the interaction between the phenyl group in 5 and the substituent in position 6 on the pyrazole ring are given.     

Oxidation of cysteine to cysteic acid in proteins by peroxyacids, as monitored by immobilized pH gradients.

It has often been debated whether the presence of persulfate in a polyacrylamide gel could lead to the oxidation of cysteine (Cys) in proteins to cysteic acid. In fact, direct incubation of bovine serum albumin (BSA) with peroxodisulfate and periodate barely alters the isoelectric point (pI) and does not produce any cysteic acid. In contrast, caroate (peroxomonosulfate) and perphthalate strongly lower the pI of BSA. In the former case it as demonstrated that 4-Cys (of a total of 35) were converted into cysteic acid. Perphthalate was found to be, by far, the strongest oxidant: 15 (of 35) Cys residues were oxidized to cysteic acid and all methionine groups were destroyed.     

Screening for the beta-39 mutation in thalassemia by capillary electrophoresis in free solution in strongly acidic, isoelectric buffers

A novel method is reported for screening for point mutations in genomic DNA: free-zone capillary electrophoresis in very acidic buffers. This method exploits the charge difference among the four different bases (C, T, A, G) in a pH window between 2.5 and 3.5, where the four titration curves fan out. The method is applied to the detection of the beta-39 missense mutation in the beta-globin gene in thalassemias. A 60-mer fragment straddling the mutation site has been amplified. In an isoelectric buffer (iminodiacetic acid) of pH 3.3, partial resolution between the wild type and mutated strands is obtained. In a pH 3.0 phosphate buffer, baseline resolution is achieved between the two strands in a heterozygous individual. Due to the short size of the amplified fragment, this method can only be applied to routine screening for known mutations because resolution was lost in a fragment 100 bases long.     

Steady-state heat transfer and thermal zone spreading in gel isoelectric focusing.

The zone spreading caused by a transverse pH profile due to a temperature gradient through the thickness of a gel slab is estimated. The temperature difference (delta T) between the upper and lower gel surfaces can be calculated as a function of the electric power dissipated in the gel and the gel dimensions. It is found that when delta T is only 1 degree C the zone spreading due to this thermal excursion is as high as 0.5 mm. Thus, an admissible delta T is found to be equal to 0.2 degrees C, since this corresponds to a thermal zone spreading of only 0.1 mm, i.e. the same order of magnitude as the spatial resolution of a laser scanner. A thermal zone spreading of 0.1 mm is compatible with a resolving power of 0.01 pH unit, the current limit of conventional isoelectric focusing in amphoteric buffers. A requirement for the thickness of a gel slab is formulated: e.g., at 40 W applied power (over a gel surface area of 25 x 11 cm), a thermal zone spreading limited to 0.1 mm can only be obtained with a gel thickness of approximately 170 microns.