Methylation blockage and other improvements to a comprehensive DNA analysis program.

A comprehensive DNA analysis computer program was described in the second special issue of Nucleic Acids Research on the applications of computers to research on nucleic acids by Stone and Potter (1). Criteria used in designing the program were user friendliness, ability to handle large DNA sequences, low storage requirement, migratability to other computers and comprehensive analysis capability. The program has been used extensively in an industrial-research environment. This paper talks about improvements to that program. These improvements include testing for methylation blockage of restriction enzyme recognition sites, homology analysis, RNA folding analysis, integration of a large DNA database (GenBank), a site specific mutagenesis analysis, a protein database and protein searching programs. The original design of the DNA analysis program using a command executive from which any analytical programs can be called, has proven to be extremely versatile in integrating both developed and outside programs to the file management system employed.     

The characterization of a mutant affecting DNA metabolism in the development of D. melanogaster

Using a "single-fly" nucleic acid hybridization method, we have surveyed a collection of D. melanogaster strains in search of variants which affect DNA complementary to the polypyrimidine sequence corresponding to one strand of the 1.705 satellite. Hybridization of labelled polypyrimidine probe to polypurine sequence in nucleic acid extracts of single flies, followed by thermal chromatography over hydroxyapatite led to the identification of one variant. The strain Cy/M(2)S2(10) produced excess hybrid, much of which had low thermal stability. A developmental analysis of the low-melt hybrid phenotype showed that certain tissues, in particular the ovaries, were affected. In addition to the biochemical phenotype, the break down of nurse cell nuclei in Cy/M(2)S2(10) ovaries during oocyte maturation was abnormal. A genetic analysis demonstrated that both the biochemical and cytological phenotypes were the consequences of a single recessive mutation in the DNase-1 gene on chromosome III. Studies with purified DNA demonstrated that the low-melt hybrid phenotype resulted from the accumulation of low molecular weight DNA complementary to the polypyrimidine probe.     

The pH-dependence of the binding of dihydrofolate and substrate analogues to dihydrofolate reductase from Escherichia coli

The interaction of dihydrofolate reductase (EC 1.5.1.3) from Escherichia coli with dihydrofolate and folate analogues has been studied by means of binding and spectroscopic experiments. The aim of the investigation was to determine the number and identity of the binary complexes that can form, as well as pKa values for groups on the ligand and enzyme that are involved with complex formation. The results obtained by ultraviolet difference spectroscopy indicate that, when bound to the enzyme, methotrexate and 2,4-diamino-6,7-dimethylpteridine exist in their protonated forms and exhibit pKa values for their N-1 nitrogens of above 10.0. These values are about five pH units higher than those for the compounds in free solution. The binding data suggest that both folate analogues interact with the enzyme to yield a protonated complex which may be formed by reaction of ionized enzyme with protonated ligand and/or protonated enzyme with unprotonated ligand. The protonated complex formed with 2,4-diamino-6,7-dimethylpteridine can undergo further protonation to form a protonated enzyme-protonated ligand complex, while that formed with methotrexate can ionize to give an unprotonated complex. A group on the enzyme with a pKa value of about 6.3 is involved with the interactions. However, the ionization state of this group has little effect on the binding of dihydrofolate to the enzyme. For the formation of an enzyme-dihydrofolate complex it is essential that the N-3/C-4 amide of the pteridine ring of the substrate be in its neutral form. It appears that dihydrofolate is not protonated in the binary complex.     

Fast-Transported Glycoproteins and Nonglycosylated Proteins Contain Sulfate

35SO4-labeled fast-transported proteins of bullfrog dorsal root ganglion neurons were separated by two-dimensional gel electrophoresis, and their mobilities were compared to similar species labeled with [3H]mannose or [3H]fucose. Fluorography revealed regions of poorly resolved, high molecular weight material, likely to represent sulfated proteoglycans, as well as many well resolved spots that corresponded in mobility to individual [35S]methionine-labeled fast-transported proteins. The majority of these well resolved spots appeared as "families," previously identified as glycoproteins based on their labeling with sugars. Thus, sulfate can be a contributor to the carbohydrate side-chain charge that underlies microheterogeneity. The most heavily 35SO4-labeled species, however, corresponded to fast-transported proteins that were not labeled by either sugar. The relative acid labilities of 35SO4 associated with individual species cut from the gel confirmed the assignments of these spots as glycoproteins or nonglycoproteins. A group of spots intermediate in their acid lability was also detected, suggesting that some proteins may contain sulfate linked to carbohydrate as well as to amino acid residues.     

Transformation of Murine Cells by Two “Slow Viruses,” Visna Virus and Progressive Pneumonia Virus

Visna and progressive pneumonia virus (PPV), two antigenically related, non-oncogenic "slow viruses" which have ribonucleic acid (RNA)-dependent deoxyribonucleic acid (DNA) polymerase activity, were examined for their ability to transform cells. Murine cells which had been exposed to either visna or PPV developed foci of altered, spindle-shaped cells 3 to 4 weeks after infection. Visna and PPV transformed lines were established from these cultures. There was no evidence that other oncogenic DNA or RNA viruses were involved in the observed transformation. Visna or PPV could be "rescued" from all transformed lines by co-cultivation with normal sheep testis cells. "Rescued" virus was identified as visna or PPV, and they retained the capacity to transform mouse cells. These experiments may have important implications in the understanding of both viral carcinogenesis and "slow" viral infections.     

Cultivation and Survival Studies of Neisseria gonorrhoeae in a Human Diploid Cell Strain

Neisseria gonorrhoeae was cultivated in a human diploid cell strain (WI-38). Eighty percent of the cultures contained viable gonococci for at least 4 m at 36°C, as evidenced by subculture to brain heart infusion broth. Monthly subcultures of bacteria could be made to fresh WI-38 cultures for at least 11 monthly passages with a 69% survival rate. The identity of gonococci was confirmed by morphology, gram staining, oxidase testing and fermentation reactions. Viability in brain heart infusion broth, minimum essential medium (Eagle), and WI-38 spent fluid was of much shorter duration. The organisms grown in WI-38 cultures appeared to orient largely in the vicinity of the WI-38 cells as well as within the cytoplasm of the cells.     

Optical rotatory dispersion of mucopolysaccharides and mucopolysaccharide--dye complexes. II. Ultraviolet cotton effects in the amide transition bands

Ultraviolet optical rotatory dispersion curves of mucopolysaccharides exhibit particular Cotton effects in the spectral region of the n–π and π–π amide transitions. Two general patterns emerge: (1) enhancement of negative rotation and of the first negative Cotton effect (troughs 217–220 mμ) and (2) relative dominance of the positive Cotton effect in the π–π transition region (peak ～198 mμ). Groups (1) and (2) can be correlated with a structural difference in the linkages of the amino sugars: (1) occurs with polymers containing 3-1-linked glycosamino sugars and (2) with glycosamino moieties linked 4–1 by either α- or β-glycosidie bonds. Measurements of the circular dichroic absorption bands support the qualitative conclusions from optical rotation. All mucopolysaccharides exhibit a first, negative band centered at 208–211 mμ, while only those in group (2) show, in addition, a positive band centered at 189–192 mμ. A suggested unifying model considers that difference in kind and/or degree of preferred geometry of the amide groups obtains from two forms of secondary order: (1) having a linear hydrogen bond from the N (acceptor) to the (C₂)O—H of the preceding uronic acid and (2) having a linear hydrogen bond from the N (acceptor) to the (C₂ or ₃) O—H of the following sugar. The hydrogen bonds would have similar strength but opposite directions in two systems towards the nonreducing end (1) or towards the reducing end (2)], closing eight-membered rings