DNA nuclear satellites of the genus Brassica: variation between species.

The distribution of nuclear DNAs of nine species of the genus Brassica in CsCl density gradients was investigated. The amount of satellite DNA with buoyant density of 1.704 g - cm-minus3 varies widely between the species. The satellite component is completely absent in B. oleracea; in B. nigra its amount reaches 37%, and in the other species it occupies an intermediate position. The absence of satellite DNA in B. oleracea was demonstrated by equilibrium centrifugation using a Cs2SO4 density gradient, containing Hg2+.     

Bovine galactosyl transferase. Substrate.managanese complexes and the role of manganese ions in the mechanism.

The dG+dC-rich fractions obtained by density gradient centrifugation of bovine DNA in Cs2SO4/BAMD [J. Cortadas, G. Macaya & G. Bernardi (1977) Eur. J. Biochem. 76, 13--19] were centrifuged in Cs2SO4/Ag+ density gradients. These experiments led to the preparation of the DNA components which had been detected (by analytical centrifugation in CsCl) in the Cs2SO4/BAMD fractions, and also of DNA components which had identical behaviors in Cs2SO4/BAMD gradients and identical buoyant densities in CsCl. A total of eight satellite components and 11 minor components, accounting for 23% and 4% of the bovine genome, respectively, were thus isolated and charcterized in their relative amounts and buoyant densities. The implications of these results on the interpretation of renaturation kinetic data on the bovine genome are discussed.     

Long-chain triglyceride lipases of pig liver

The blood-group specific glycoproteins of human ovarian cyst fluids have been isolated by equilibrium density gradient centrifugation in CsCl; they have been characterised in terms of buoyant density, selective salvation and apparent molecular weight, both in CsCl and Cs(2)SO(4).     

An interaction between lysozyme and mucus glycoproteins. Implications for density-gradient separations.

1. Some mucus glycoproteins form soluble complexes with lysozyme at neutral pH values. 2. The extent of complex-formation was determined, by an ultracentrifugal difference method, for a range of glycoproteins covering the common blood-group specificities. 3. Interaction was strongest with those glycoproteins of blood-group Lea specificity; these were also richest in sialic acid. 4. Interaction diminished with increase of ionic strength, and was not detectable at I 0.50; however, an asialoglycoprotein was found to retain some activity. The interaction is accordingly primarily, but probably not exclusively, coulombic in origin. 5. The buoyant density of lysozyme in CsCl, CsBr, CsI and Cs2SO4 was determined; the values in the last three salts are anomalously high. This finding accounts for the previously noted difficulty of separating free protein from glycoproteins by single-stage centrifugation in CsBr. 6. Conditions for effective separation of glycoproteins from secretions containing lysozyme by density-gradient centrifugation are reported.     

THE DNA components of the chicken genome.

The organization of the chicken genome was investigated by centrifuging chicken DNA (Mr = 57 X 10(6) in preparative Cs2SO4/Ag+ and Cs2SO4/BAMD density gradients [BAMD = 3.6-bis(acetato-mercurimethyl)dioxane]. An analysis by CsCl density gradient of the DNA fractions obtained from the preparative experiments revealed that 88% of the genome is made up of four DNA components, characterized by buoyant densities of 1.699, 1.702(5), 1.704(5) and 1.708 g/cm3 and representing 39%, 25%, 15%, and 9%, respectively, of the total DNA. The remaining 12% of the genome is formed by seven minor and/or satellite components. The distribution of the ovalbumin gene in a Cs2CO4/BAMD density gradient, as tested with a cloned cDNA probe, coincides with the distribution of the 1.702(5)-g/cm3 component. This shows that the DNA regions flanking the ovalbumin gene are homogeneous in base composition over along distances and that the gene is located on a DNA segment belonging to the 1.702(5)-g/cm3 component.     

Properties of satellite DNA from Brassica nigra

The DNA components of B. nigra were preparatively separated by equilibrium ultracentrifugation in a CsCl density gradient, the buoyant density of the main component being 1,696 g . cm-3, that of the satellite component--1,704 g . cm-3. The properties of individual DNA fractions were investigated. Four major components could be observed on the differential melting curve of satellite DNA. Using the reassociation kinetics method it was shown that 30% of satellite DNA are presented as a fast reassociating component with a length of a repeated unit of approximately 2,5 . 10(3) nucleotide pairs. The calculated values of Tm and buoyant density suggest that the m5C content in satellite DNA is lower than that in the main component. During equilibrium ultracentrifugation in the density gradients of actinomycin D--CsCl and Hg2+--Cs2SO4 the satellite DNA is split into 4 major components.     

Density-gradient centrifugation in lithium metatungstate and tris-(hydroxymethyl)aminomethane phosphotungstate

New substances--lithium metatungstate (MTL) and tris-(hydroxymethyl)aminomethane phosphotungstate (PTT)--have been presented for density-gradient preparation. The buoyant densities of protein, RNA, DNA and some nucleoproteins were determined in solutions of these salts. Nucleic acids have been smaller buoyant density (1.1 g/cm3) than the proteins in contrast to CsCl-gradients. The protein in PTT solution have buoyant density 1.5 g/cm3 and in MTL solution 2.0-2,3 g/cm3. It was shown that MTL gradients allow to reach better resolution in nucleoprotein analysis than CsCl gradients.     

Satellite DNA sequences in the red kangaroo (Macropus rufus)

There is a complex pattern of satellite DNA sequences in M. rufus which are revealed by addition of Ag+ or dye (Hoechst 33258) to the DNA ink Cs2SO4 or CsCl equilibrium density gradients. Six satellite DNA fractions have been isolated; these have buoyant densities in neutral CsCl of 1.692, 1.704, 1.705, 1.707 (two), 1.710 and 1.712 g/ml compared with 1.696 g/ml for the main band DNA. Each satellite accounts for 1-3% of the DNA of the genome. The satellites are located in the centromeric heterochromatin of the chromosomes, in the nucleolar organizer region and in interstitial bands on some of the autosomes, each satellite having a unique distribution. Nucleic acid hybridization showed that six of the satellite sequences are also present in the genomes of the wallaroo and the red-necked wallaby, with sequence divergences of only 1-2% relative to the sequences in the red kangaroo.     

Replication of Bacteriophage Ribonucleic Acid: Some Properties of Native and Denatured Replicative Intermediate

Purified replicative form (RF) and replicative intermediate (RI) prepared from Escherichia coli cells infected with the ribonucleic acid (RNA) bacteriophage R17 were denatured with dimethyl sulfoxide at 37 C or in aqueous solvents of low ionic strength at 97 C. Denaturation was demonstrated for RF and RI by an increase in specific infectivity and a striking change in the hyperchromicity curves after treatment. RI denaturation was also demonstrated by a shift in the buoyant density in Cs(2)SO(4) from 1.619 to the buoyant density of single-stranded R17 RNA (1.627). Analysis of the denatured RI hyperchromicity curves and the equilibrium distributions of denatured RI in Cs(2)SO(4) gradients revealed, however, a residual double-stranded component. Velocity sedimentation of denatured RI was performed, and the weight distribution of S values was calculated. From the known relation between molecular weight and S values, it was possible to transform the weight distribution into a number distribution of chain lengths. This distribution was compared with that predicted from the steady-state hypothesis for RI. Deviations from the predicted distribution may be due to the residual double-stranded component.     

Isolation of a DNA fraction highly enriched in transfer RNA genes from Xenopus laevis.

A DNA fraction highly enriched in tRNA genes can be isolated from the Xenopus laevis genome by the use of Ag+/Cs2SO4 density gradients. Ag+ shows a low affinity for some tRNA cistrons, allowing their separation from bulk DNA upon equilibrium centrifugation in a Cs2SO4 density gradient. Contaminating DNA in the resulting tDNA fraction is further removed by two additional CsCl density gradient centrifugations. The final DNA fraction is 60-fold enriched in tRNA genes, compared to the starting DNA material.     

Bacteriophage phiNS11: a lipid-containing phage of acidophilic thermophilic bacteria. II. Purification and some properties of the phage

An improved procedure for the purification of a lipid-containing acidophilic thermophilic bacteriophage, phiNS11, is described. The procedure involves Cs2SO4 discontinuous density gradient, Cs2SO4 equilibrium density gradient and sucrose gradient centrifugations. The phage has an icosahedral shape, 75 nm in diameter, with spike-like structures radiating from the vertices. It contained about 12% by weight of lipid, 13--14% of DNA and 74--75% of protein. The phage was stable between pH 2 and 5, but rapidly inactivated above pH 6. It was highly sensitive to organic solvents and detergents. Some other basic properties such as the buoyant density and UV spectrum of the purified phage are also described.     

A physical study of the ovine genome

The ovine genome has been divided into some seventy-five fractions using 3,6-bis(acetatomercurimethyl)dioxane (BAMD) in conjunction with Cs2SO4 density-gradient-equilibrium centrifugation. Distinct macromolecular populations detected have buoyant densities in CsCl of 1.700, 1.707, 1.714, 1.716, 1.717, 1.721, 1.724 and 1.725 g/cm3. The 1.724 g/cm3 material appears in a number of non-contiguous fractions obtained from BAMD-Cs2SO4 centrifugation suggesting its presence at a number of different sites in the genome. Within two regions of buoyant density (1.701 g/cm3 to 1.707 g/cm3 and 1.708 g/cm3 to 1.717 g/cm3) the analyses were unable to resolve discrete populations.     

Analysis of the genome of plants. II. Characterization of repetitive DNA in barley (Hordeum vulgare) and wheat (Triticum aestivum).

Barley and wheat DNAs have been characterized by studying their kinetics of reassociation, melting properties and sedimentation behaviour in neutral CsCl gradients as well as in Cs2SO4 gradients containing Ag+ or Hg2+. In both species, reassociation kinetics have revealed the presence of approx. 76% redundant nucleotide sequences which have been grouped into very rapidly reassociating (Cot 0-0.01), rapidly reassociating (Cot 0.01-1.0) and slowly reassociating (Cot 1-100) fractions. The barley Cot 0-0.01 and Cot 0.01-1.0 fractions as well as the wheat Cot 0.01-1.0 fraction form narrow bands upon centrifugation in CsCl gradients. Under similar experimental conditions both Cot 0.01 and Cot 1.0-100 wheat fractions and the barley Cot 1.0-100 fraction form broad bands each having several shoulders. Thermal denaturation studies of most of the above reassociated fractions have shown a considerable degree of order in their duplexes with an average hyperchromicity of 21.5%. When native, high molecular weight barley DNA is centrifuged in Ag+/CS2SO4 density gradients (RF = 0.2), two satellites appear on the heavier side of the main band, as against one in the case of wheat. The two minor peaks, designated as satellites I and II, have buoyant densities of 1.702 and 1.698 g/cm3, respectively, in neutral CsCl gradients and together represent about 8-9% of total barley DNA. Upon centrifugation in Hg2+/CS2SO4 density gradients, one satellite is observed in both barley and wheat and it accounts for 1-2% of their genomes.     

Properties of satellite DNA of Phaseolus vulgaris]

Nuclear DNA components of Ph. vulgaris were preparatively separated by equilibrium ultracentrifugation in Hg++-Cs2SO4 density gradient (buoyant density of the major component in CsCl density gradient 1.694 g/cm3., satellite component--1.703 g/cm3). The properties of individual DNA fractions were investigated. The melting curve of satellite DNA of Ph. vulgaris has biphasic character. The observed heterogeneity of satellite DNA component is of intermolecular nature. This is illustrated by the splitting of unsheared satellite DNA into two components during renaturation, as well as by its behaviour in Hg++-Cs2SO4 density gradient at high rf value. The width of satellite DNA reassociation curve covers three decades of Cot. The length of the major repeating sequences of the satellite component is close to the length of phage T2 DNA. During chromatography on MAK column satellite DNA elutes earlier than the major component due to its higher GC-content. It is suggested that one of the satellite DNA fractions of Ph. vulgaris contains rRNA genes.     

Characterization of the protein and nucleic acid of Aleutian disease virus.

Aleutian disease virus (ADV) was extracted and purified from infected mink. Nucleic acid extracted from the virus was examined in an electron microscope. Three different sizes of molecule, with approximate lengths of 1.2, 0.55, and 0.25 micron, were observed. The ratios of the large molecules to the small molecules were similar in all the particles prepared under different conditions. Equilibrium CsCl density gradient centrifugation showed that ADV nucleic acid had a buoyant density of 1.733 g/cm3. In Cs2SO4, ADV had a lower buoyant density than that of double-stranded RNA. These properties and its sensitivity to DNase suggested that ADV contains DNA. Thermal denaturation curves revealed that the DNA of ADV had a single-stranded configuration. Polypeptide analysis of ADV by polyacrylamide gel electrophoresis revealed the presence of four polypepties, with molecular weights of 30,000, 27,000, 20,500, and 14,000. These polypeptides were present in a ratio of 10:3:10:1, respectively. The data suggested that ADV is closely related to the members of the parvovirus groups.     

Comparative DNA analysis of three South American marsupials.

Published information on marsupials DNA is limited to a group of species belonging to only one genus. No previous reports have been written on South American species. In this paper we characterize the DNA of three out of the four marsupials found in Uruguay. Analytical and preparative ultracentrifugations in neutral CsCl gradients, including four intercalating agents and in Cs2SO4 gradients in presence of increasing amounts of Hg++ ion did not allow us to separate any satellite fraction. The buoyant density of the unique peak measured in CsCl gradients was in every case 1.697 g/cc with a G-C content of 37.7%. Digestion of total DNA with 11 restriction endonucleases produced a different pattern of bands for the three species, although some possible homologies could be established. Hybridization with 32P-rRNA of Southern blots of the gels containing digested DNAs demonstrated that the repeated sequences evidenced do not correspond to the ribosomal cistrons.     

Effect of mercuric and silver ions on cesium sulfate equilibrium buoyant densities of synthetic polydeoxyribonucleotides.

The effect of Hg2+ and Ag+ on the buoyant density (rho) of four synthetic DNA polymers, poly[d(A-T)]; poly(dA) - poly(dT); oikt[d(G-C)]; and poly(dG) - poly(dC), was investigated. The buoyant density of poly[d(A-T)] in Cs2SO4 increased dramatically after complexing with Hg2+, but little change in the buoyant density of other polymers resulted except at very high molar ratios of Hg2+/DNA-P (rf). Hg2+ raised the thermal transition temperature (Tm) of alternating polymers and lowered the Tm of homopolymers. Measurements in the preparative ultracentrifuge indicated that lowered Tm correlated with Hg2+-induced strand separation of one homopolymer [poly(dA) - poly(dT)], but strand separation was not observed with another homopolymer [poly(dG) - poly(dC)] complexed with Hg2+. When Ag+ was mixed with the polymers, the buoyant density of poly(dG) - poly(dC) increased most markedly. A substantial increase in the buoyant density of poly[d(A-T)] and a small increase in the buoyant density of poly[d(G-C)] were also observed. The Tm changes induced by Ag+ were not related in any obvious way to buoyant density changes. These findings indicate that nucleotide sequence as well as overall base composition is of importance in understanding the buoyant density changes induced by metal ions. Although these data do not allow construction of a detailed molecular model of polymer-metal ion interactions, they may be used to explain much of the behavior of naturally occurring DNA sequences, such as heterochromatic satellite sequences and 5 S and rRNA sequences, in Hg2+/Cs2SO4 and Ag+/Cs2SO4 gradients.     

A critical examination of possible fractionations of human DNA according to base composition.

Human DNA has been fractionated according to base composition by sedimentation equilibrium in an HgCl2/Cs2SO4 density gradient, followed by sedimentation equilibrium in an actinomycin/cesium formate density gradient. The fractions of different base composition resulting from this procedure were subsequently analyzed by sedimentation equilibrium in CsCl, DNA renaturation kinetics, and electron microscopy. All fractions contain similar kinetic classes of repeated DNA sequences as judged by renaturation studies. Short (300 nucleotides) interspersed repeated sequences are found in all fractions with no noticeable enrichment for these sequences in any fraction. Repeated sequences from fractions of different base composition are partially able to cross-hybridize, demonstrating that nearly identical repeated sequences occur in molecules of different base composition. These findings are critically compared to reports of successful density gradient fractionations of different human DNA sequence classes.     

DNA nuclear satellites of the genus Brassica]

Distribution of nuclear DNA of nine species of the genus Brassica in caesium chloride density gradient has been studied. It has been shown that the amount of the satellite DNA component with the density of 1.704 g.cm-3 varies within a wide range. It is completely absent in B. oleracea and its amount reaches 37% in B. nigra. The other species have an intermediate position. The absence of the latent satellite DNA component in B. oleracea has been shown by equilibrium ultracentrifugation in Cs2SO4 density gradient containing Hg++. Denaturation-renaturation properties of the nuclear DNA of B juncea have been studied.