Some properties of nucleic acids extracted with phenol

Initiation of SV40 DNA replication after microinjection into Xenopus eggs

We have examined the capacity of Xenopus laevis eggs to support replication of microinjected SV40 DNA. As previously reported, microinjected DNA undergoes semi-conservative replication. Unlabeled SV40 DNA was microinjected with [3H]dTTP and, after a 3 h incubation period, the DNA was recovered and adsorbed to BND-cellulose. Elution with an NaCl gradient removes molecules that are entirely double-stranded but not those with single-stranded regions. The latter DNA population is eluted with caffeine. The radioactive DNA that eluted with NaCl was comprised mostly of supercoiled and open circular SV40 DNAs. The radioactive DNA eluted with caffeine was comprised mainly of endogenous DNA but also contained replicative forms of SV40 DNA. Analysis of SV40 DNA replication intermediates by electron microscopy revealed mainly Cairn's forms of varying degrees of maturation. Digestion with BamH1, which cleaves SV40 DNA almost opposite the normal viral replication origin, indicated that SV40 DNA microinjected into frog eggs does not initiate DNA synthesis at its normal initiation site nor at any other obvious preferred site. Rather, it appears that when this template is injected into activated Xenopus eggs, replication may initiate at random.

Changes in mitochondrial DNA during aging

Mitochondrial DNA (mtDNA) was isolated from liver mitochondria of rats between 2 and 24 months of age. The mtDNA was purified by cesium chloride--ethidium bromide isopycnic density gradient centrifugation. In the gradients, in addition to the two expected bands of ethidium--DNA complex, there was observed a third, more dense band (d = 1.69 g/cm3). This novel band, rarely observed in preparations from younger animals, was present in most preparations from older animals. The latter was characterized using the diphenylamine assay(s) and ascertained to contain DNA and carbohydrate components. Agarose gel electrophoresis revealed the DNA of the novel band to have a migration identical to form I mtDNA. Digestion of the novel band with the restriction endonuclease Bam HI yielded products identical to those obtained upon treatment of form I mtDNA with Bam HI. The observation of mtDNA at a density of 1.69 g/cm3 indicates the presence, predominantly in older animals, of a subclass of mtDNA molecules with altered ethidium binding properties. The significance of this mtDNA and its position in the gradient is unclear at this time.

Streptococcus mutans dextransucrase: functioning of primer dextran and endogenous dextranase in water-soluble and water-insoluble glucan synthesis

The extracellular enzyme activities of Streptococcus mutans 6715 that synthesize glucans from sucrose were concentrated and partially purified by ammonium sulfate precipitation and gel permeation column chromatography. Polyacrylamide gel analysis demonstrated that all of the major proteins precipitated by ammonium sulfate were quantitatively recovered in the high-molecular-weight, enzyme-containing aggregates found in the void volume of the gel column. Anion-exchange column chromatography was used to fractionate the aggregates into preparations, alpha and beta, which produced water-insoluble and water-soluble glucans, respectively. Polyacrylamide gel analysis showed that alpha and beta contained unique proteins and dextransucrase (EC 2.4.1.5) activities. Studies on the time course of glucan synthesis by alpha demonstrated that this enzyme preparation contained dextranase activity, which partially degraded nascent alcohol-insoluble glucan into alcohol-soluble products that were subsequently reincorporated into insoluble product. The beta enzyme preparation contained no detectable dextranase activity. Mixing experiments in the absence of primer dextran demonstrated that the dextranase activity present in alpha could modify glucan production by beta. CsCl density gradient analysis of product glucans demonstrated that exogenous primer dextrans were used as acceptor molecules by both the alpha and beta enzyme preparations, and that water-soluble glucans synthesized by beta could be converted into water-insoluble glucans by alpha. It is proposed that the structural heterogeneity of the native glucans produced from sucrose by S. mutans is a result of the concerted action of glucan-forming dextransucrases and endohydrolytic dextranase activity.

Changes in transfer ribonucleic acids accompanying encystment in Acanthamoeba castellanii

Transfer ribonucleic acid (tRNA) from exponentially growing cells (trophozoites) and from precysts of Acanthamoeba castellanii were examined by reversed-phase column (RPC-2) chromatography. This system gave excellent resolution of isoaccepting species of tRNA. The tRNAs for 12 amino acids were studied. A comparison of trophozoite and precyst tRNA elution profiles revealed no apparent differences in the number of isoaccepting species of alanyl-, arginyl-, asparaginyl-, glycyl-, leucyl-, lysyl-, methionyl-, phenylalanyl-, tryptophanyl-, or valyl-tRNAs. Seryl-tRNAs from trophozoites were eluted as three components, whereas precyst seryl-tRNAs were eluted as only two components. Precharged trophozoite and precyst isoleucyl-tRNAs were both eluted as single components; however, post-chromatography charging of trophozoite tRNA resulted in three components of activity for tRNA(Ile) and only one component for precyst tRNA(Ile). None of the observed changes could be attributed to differences in synthetases or to the presence of altered tRNA lacking the CCA terminus or partially degraded by nucleases. The possible significance of these observations is discussed.

Characterization of the deoxyribonucleic acid of various strains of halophilic bacteria

Bacteria classified as extreme halophiles, in the genera Halobacterium and Halococcus, contain deoxyribonucleic acid (DNA) which displays two components in a CsCl equilibrium density gradient. The base composition of the major DNA component ranges from 66 to 68% guanine plus cytosine (GC), whereas that of the satellite DNA comprising some 11 to 36% of the total, is between 57 and 60% GC. Purification of the bacterial cells in a CsCl density gradient and other more conventional strain purification procedures both indicated that the presence of the satellite DNA component is not a result of mixed cultures.

Biopolymeric associations in bacterial subcellular fractions

Greater amounts of intracellularly bound glucans were present in Escherichia coli, strain B/r cells, in the late lag and logarithmic growth phases than in cells in the early lag and stationary growth phases. Bound alkali-stable and alkali-labile glucose-containing polymers— as well as unbound glucans—were further characterized by their susceptibility to hydrolysis by alpha-amylase and by their trichloroacetic acid (TCA) – ethanol solubility characteristics. A combination of phenol/water fractionation and TCA–ethanol partitioning of acetone-dried cells revealed the presence of bound glucose-containing polymers in the crude lipopolysaccharide, protein, DNA, and RNA subcellular fractions.Purified lipopolysaccharides from Escherichia coli, strains B, B/r, and Bs, contained both alkali-stable and alkali-labile glucose polymers. Similarly, alkaline hydrolysis and TCA–ethanol partitioning of both phenol- and TCA-extracted endotoxin preparations yielded numerous carbohydrate-containing subfractions. The carbohydrate monomers associated with lipopolysaccharide fractions of Escherichia species were more susceptible to alkaline degradation than the monomeric constituents present in Salmonella and Shigella lipopolysaccharide preparations. Upon exposure to either hydrolytic enzymes or gelatin, the phenol-extracted lipopolysaccharides were further partitioned into numerous lipopolysaccharide- and (or) homopolysaccharide–biopolymeric complexes by TCA-ethanol fractionation.

The origin of the polydispersity in sedimentation patterns of rapidly labelled nuclear ribonucleic acid

1. A study was made of the sedimentation properties of purified preparations of the rapidly labelled RNA in the nucleus and the cytoplasm of the HeLa cell. The sedimentation of the rapidly labelled nuclear RNA was very sensitive to changes in ionic strength and bivalent cation concentration. Under the conditions usually used in sucrose-density-gradient centrifugation the rapidly labelled nuclear RNA showed extreme polydispersity, and much of it sedimented more rapidly than the 28s RNA. At low ionic strength and after removal of Mg(2+), however, the rapidly labelled nuclear RNA sedimented as a single peak at about 16s. The conversion of the polydisperse material into the 16s form did not involve degradation of the RNA, since the effect could be reversed by increasing the ionic strength of the solution. 2. The cytoplasm did not contain any RNA that showed polydisperse sedimentation under the usual conditions of sucrose-density-gradient centrifugation, or that had the same sensitivity as the rapidly labelled nuclear RNA to changes in ionic strength. All the radioactivity in the cytoplasmic RNA sedimented with the 28s, 16s and 4s components over a wide range of physical conditions, but these components did contain a labelled fraction with some of the features of the rapidly labelled nuclear RNA on columns of methylated albumin on kieselguhr. 3. In both nucleus and cytoplasm the RNA detected by ultraviolet absorption could also be converted into a 16s form by removal of bivalent cations at low ionic strength; this effect was again, within certain limits, reversible. The nuclear RNA as a whole was more susceptible to changes in ionic strength than the cytoplasmic RNA. 4. It thus appears that all the RNA in the cell, except the 4s RNA, can be prepared, without degradation, as a single peak sedimenting at about 16s. The relationship of these various 16s components to each other is discussed.

A non-nucleotide polymer found in the DNA of the sand dollar, Echinarachnius parma. II. Preliminary characterization

A preliminary characterization of the non-nucleotidic component present in the DNA of Echinarachnius parma was undertaken. This material has an extremely high sedimentation coefficient (907 S). It contains no deoxyribose and presumably no ribose. After acid hydrolysis it was strongly ninhydrin-positive and also gave positive tests for reducing sugars as well as a slightly positive test for amino sugars. Upon electrophoretic analysis of an acid hydrolysate, three ninhydrinpositive spots were detected. One of these migrated to the negative electrode with a mobility identical with that of galactosamine, the other migrated to the positive electrode, and the third was neutral at pH 6.3. The spot with a mobility identical with that of galactosamine also gave a positive test for amino sugar. The material was not attacked by α-amylase. However, digestion with a crude trypsin preparation resulted in loss of the banding property in gradients of cesium chloride. Exposure to purified trypsin did not completely digest it, but caused an increase in buoyant density.

Programming of poliovirus inhibition of deoxyribonucleic acid synthesis in HeLa cells

Ackermann, W. W. (The University of Michigan, Ann Arbor), and D. Wahl. Programming of poliovirus inhibition of deoxyribonucleic acid synthesis in HeLa cells. J. Bacteriol. 92:1051-1054. 1966.-Deletion of arginine from a culture medium reduced the rate of deoxyribonucleic acid (DNA) synthesis in uninfected HeLa cells. The normal rate was promptly restored by addition of arginine. Deletion of arginine also prevented poliovirus from inhibiting DNA synthesis in HeLa cells. However, the inhibitory potential of the infection and the capacity of the host cell for stimulation with regard to DNA synthesis were both retained in arginine-depleted cells which were infected. Upon addition of arginine late in the infection, DNA synthesis was first stimulated and then inhibited.

Effect of poliovirus on deoxyribonucleic acid synthesis in HeLa cells

Ackermann, W. W. (University of Michigan, Ann Arbor), D. C. Cox, H. Kurtz, C. D. Powers, and S. J. Davies. Effect of poliovirus on deoxyribonucleic acid synthesis in HeLa cells. J. Bacteriol. 91:1943-1952. 1966.-Both poliovirus and arginine stimulated deoxyribonucleic acid (DNA) synthesis in cultures of HeLa cells which were preconditioned by incubation in a medium deficient in arginine. However, the number of cells producing DNA was unaffected. DNA synthesis in such preconditioned cells was 10 to 20% of the maximal value obtained with a full complement of amino acids. Inhibition of DNA synthesis was produced in these cultures either by increasing the multiplicity of exposure above 40 plaque-forming units of virus per cell or by increasing the concentration of the deficient amino acid at the time of virus addition. Inhibition of DNA synthesis resulted from a reduction in the fraction of cells producing DNA. The concentration of arginine required for viral inhibition of DNA synthesis is greater than that for viral multiplication.