Finite element simulations of electrostatic dopant potentials in thin semiconductor specimens for electron holography.

Two-dimensional finite element simulations of electrostatic dopant potentials in parallel-sided semiconductor specimens that contain p-n junctions are used to assess the effect of the electrical state of the surface of a thin specimen on projected potentials measured using off-axis electron holography in the transmission electron microscope. For a specimen that is constrained to have an equipotential surface, the simulations show that the step in the projected potential across a p-n junction is always lower than would be predicted from the properties of the bulk device, but is relatively insensitive to the value of the surface state energy, especially for thicker specimens and higher dopant concentrations. The depletion width measured from the projected potential, however, has a complicated dependence on specimen thickness. The results of the simulations are of broader interest for understanding the influence of surfaces and interfaces on electrostatic potentials in nanoscale semiconductor devices.

Factors of activation and stabilization of DNA-methylases from Shigella sonnei 47 and Mycobacterium smegmatis butyricum cells.

A comparative study of factors of activation and stabilization of individual DNA-methylases from two bacterial strains--Shigella sonnei 47 and Mycobacterium smegmatis butyricum--isolated by isoelectrofocusing in a pH gradient has been carried out. Storage of enzymes at +4 degrees C (pH 7.5) is accompanied by periodic changes in the methylating activity. No such changes are observed when the enzymes are stored at pI of the protein. In this case the methylases with alkaline or close to neutral values of pI remain stable over a period of at least two weeks, whereas acidic proteins are irreversibly inactivated by the end of a two-week period. A stabilizing effect of BSA on DNA-methylases of Sso 47 and Mbu strains has been demonstrated. A direct correlation between the stabilizing effect of BSA and the degree of enzyme purity has been established. Ca2+ appear to be a universal activator of methylases of the above strains; these cations produce a potent, although a short-term effect and can be used in the production of enzyme preparations with a high specific activity in DNA recombinant technology. Protease inhibitors do not exert any appreciable effect on the methylase activity upon storage. Storage at -20 degrees C and at neutral pH leads to complete inactivation of all DNA-methylases within 24 hours. In this case glycerol is fairly ineffective as a stabilizing agent.

Sequence specificity of isolated DNA-adenine methylases from Mycobacterium smegmatis (butyricum) and Shigella sonnei 47 cells.

A set of four individual DNA-adenine methylases differing in pI (isoelectric point) values (MMbu4.2, MMbu6.4, MMbu7.3, and MMbu8.7), and a sole methylating enzyme with the same base specificity (MSso9.5) are present in M. smegmatis (butyricum) and Sh. sonnei 47 cells, respectively. The sequence specificity of each of those was studied 'in vitro' by a combined approach that comprised isostich (purine tract) analysis and identification of the immediate neighbourhood of the methylated base within the sequence methylated. The MSso9.5 recognition site has been established as the hexanucleotide 'palindromic' 5'-G-A-A-T-T-C-3' sequence which is structurally similar to the analogous MEco RI recognition site. However, in contrast to MEco RI, MSso9.5 methylates the 5'-end adenine residue in the sequence and thus it appears to be an isometimer of MEco RI. By means of the same approach, the partial nucleotide sequences methylated by each of the four individual M. butyricum enzymes were determined. MMbu7.3 and MMbu8.7 exhibit the identical sequence specificity upon methylation of the degenerative trinucleotide 5'-Py-A-Py-3' sequence and thus these enzymes are assumed to represent the different molecular forms of the methylase. MMbu4.2 methylates the 5'-G-G-A-3' sequence and thus it is of a great value as the tool for negating effects of the RBam HI and RAva II-type restriction. MMbu6.4 is of a particular interest on account of its unique DNA methylation pattern which is distinguished in the pronounced clustering of purine bases in the 5'-Pu-Pu-Pu-Pu-Pu-3' sequence methylated.

Isoelectric focusing of bacterial DNA methylases.

The multiplicity of bacterial DNA methylases has been shown for new microorganisms, Mycobacteria and Shigella, by a double-step procedure including column chromatography followed by isoelectric focusing of the total methylase fraction. The profiles of the DNA methylating activity of Sh. sonnei 47 and M. butyricum strains were studied. Sh. sonnei 47 cells were found to contain five different proteins responsible for DNA methylation and having pI 4.2, 5.3, 6.2, 8.4 and 9.2. Four M. butyricum methylases were represented by proteins with pI 4.2, 6.0, 8.0 and 9.0.