Isopycnic centrifugation of sheared L-cell chromatin in metrizamide gradients

Isopycnic gradient centrifugation of L-929 cell chromatin in a 38% (W/V) metrizamide solution yields two distinct fractions. The fraction banding at a density of 1.24 gm/cm² (H chromatin) contains about 10% of the DNA present in the fraction banding at a density of 1.18 gm/cm² (L chromatin). Both fractions contain the same proportions of satellite to main band DNA''s. Some differences can be seen in the DNA: protein ratios and types of proteins present in the H and L chromatin fractions.     

Polypyrimidine segments in drosophila melanogaster DNA: I. Detection of a cryptic satellite containing polypyrimidine/polypurine DNA

Very long runs of pyrimidine nucleotides (polypyrimidines), previously detected in DNA from Drosophila melanogaster, have now been localized to a “cryptic” satellite. These polypyrimidines have an average length of 750 nucleotides and account for about 3% of the thymine residues in total DNA. The buoyant density of the DNA component which contains the polypyrimidines was detected by centrifuging native DNA to equilibrium in a CsCI gradient, and then assaying each fraction for its content of polypyrimidines. A peak was detected at a density of about 1.707 gm/cm³, distinctly heavier than the main band of DNA (1.702 gm/cm³). The buoyant density of polypyrimidine-containing molecules was little affected by differences in the molecular weight of the starting DNA in the range 10⁵-10⁷ daltons (single-stranded). Thus polypyrimidines (and their complementary polypurines) appear to form all or part of a “cryptic” satellite.Polypyrimidines have been isolated and characterized with respect to composition and buoyant density. Direct nucleoside analysis of unlabeled material indicated 34.5% deoxycytidine, 65.5% thymidine. Their banding position in neutral and alkaline CsCI gradients was consistent with a single-stranded DNA polymer of this composition.     

Distribution of estradiol receptor and vitellogenin gene in chick liver chromatin fractions.

The distribution of estradiol receptor and vitellogenin gene was studied in estradiol stimulated chick liver chromatin fractions prepared by limited DNAse II digestion and MgCl2 precipitation. The receptor was found in all fractions, undigested chromatin (P1), Mg2+ insoluble chromatin (P2) and Mg2+ soluble chromatin (S2). This last fraction was rich in acidic proteins, had a high protein:DNA ratio (7.0 w/w), contained 28% of rapidly labelled RNA, 20% of the receptor, 3-5% of chromatin DNA and showed a 2 fold enrichment of vitellogenin DNA sequences over unfractionated chromatin as well as P1 and P2 DNA. On isopycnic metrizamide gradients, all chromatin fractions showed a receptor peak banding at 1.23 g/cm3, the density of nucleoproteins. Hybridization experiments showed that the DNA banding at this density in fraction S2 was enriched 4 fold in vitellogenin DNA sequences over unfractionated chromatin as well as P1 and P2 DNA. These results suggest an association of hormone receptor complex with nucleoprotein structures of an apparently active chromatin fraction.     

Isolation and preliminary characterization of cryptic satellite DNA in pea

Optimum conditions have been established for isolation of ‘cryptic’ satellite DNA from the genome of pea (Pisum sativum), using gradients of CS₂SO₄ containing silver ions. At an Ag⁺ :DNA-P ratio (R) of 0.1, and at alkaline pH, four fractions are obtained: mainband (buoyant density 1.437 g cm³; 67% of total DNA), satellite I (buoyant density 1.582 g/cm³; 7% of total DNA), satellite II (buoyant density 1.520 g/cm³, 11% of total) and satellite III (buoyant density variable between 1.45 and 1.51 g/cm³; 15% of total). The reiterated DNA content of these four fractions has been investigated by reassociation experiments conducted over a Cot range of 1 × 10^?5 to 2.0. All four fractions contain at least two kinetic components; each fraction, including the mainband, consists at least partly of highly reiterated DNA. Ribosomal RNA hybridizes only to the mainband.     

Binding of progesterone by rat uterus in vitro

Circular dichroism (CD) spectra have been determined for chromatin fractions obtained by ECTHAM-cellulose chromatography. The molecular ellipticity at the positive long wavelength maximum is about 3000 deg cm²/dmol for early-eluted chromatin fractions, thought to be relatively repressed $\text{in vivo}$, and 5000–6000 deg cm²/dmol for late-eluted chromatin fractions, those thought to be preferentially transcribable $\text{in vivo}$. CD bands in the peptide bond spectral region also differ for the two chromatin fractions, early-eluted chromatin having a more helical conformation for proteins. In addition to previously known differences in protein content, the biological activity of a native chromatin fraction can now be correlated with the conformation of its DNA.     

Isolation and characterization of satellite DNA from mustard seedlings

The DNA from mustard (Sinapis alba L.) seedlings was examined by neutral CsCl and Ag⁺/Cs₂SO₄ density gradient centrifugation. Different satellite fractions were revealed by these two methods. The satellite fractions obtained from the Ag⁺/Cs₂SO₄ density gradient could not be generally correlated with satellite DNA fractions observed in CsCl. In CsCl density gradient centrifugation, a main band at density 1,695 g/cm³ and a heavy shoulder at density 1,703 g/cm³ are found. By preparative CsCl gradient centrifugation the heavy shoulder can be enriched but not completely separated from the main band DNA.—Gradient centrifugation by complexing the DNA with Ag⁺ rf. 0.25 to DNA phosphate reveals three distinct fractions which are further characterized: The heavy satelite DNA fraction revealed by Ag⁺/Cs₂SO₄ gradient centrifugation has the same density in a CsCl gradient and the same Tm value as the main band, but differs from main band DNA in the details of its melting profile and in its renaturation kinetics. The light Ag⁺/Cs₂SO₄ satellite DNA fraction had a higher melting temperature corresponding to a GC-rich base composition. Differences between these 3 fractions are observed in thermal denaturation and renaturation profiles, hybridization in situ with ribosomal RNA, and their response to restriction endonuclease digestion. The light satellite fraction from the Ag⁺/Cs₂SO₄ gradient, rich in ribosomal cistrons corresponds to the heavy shoulder DNA of neutral CsCl gradients which also is rich in ribosomal cistrons. The heavy satellite fraction from Ag⁺/Cs₂SO₄ gradient which contains highly repetitive short nucleotide sequences could not be revealed by the classical CsCl gradient centrifugation technique.     

A particulate DNA polymerase activity in adult rat brain

A particulate fraction of adult rat brain (sucrose buoyant density 1.24 gm/ml) catalyzed the incorporation of [³H]dTTP into an acid-insoluble product in an endogenously templated reaction sensitive to ribonuclease pretreatment. Upon fractionation, this activity was identified in the cerebellum, pons, frontal lobes and base. The DNA polymerase present in these brain fractions exhibited a strong preference for the synthetic template dT_12–18·poly rA rather than dT_12–18·poly dA; dT₁₀ was completely inactive. Purification and equilibrium Cs₂SO₄ gradient centrifugation of the [³H]DNA product-endogenous template complex suggested that RNA was serving as primer for endogenous DNA synthesis.     

Isolation of 2-μm minichromosomes fromSaccharomyces cerevisiae using shallow metrizamide gradients

Unfixed 2-μm minichromosomes fromSaccharomyces cerevisiae may be isolated uncontaminated by genomic DNA by banding isopycnically in metrizamide [2-(3-acetamido-5-N-methylacetamido-2,4,6-triiodobenzamido)-2-deoxy-d-glucose[ according to the protein/nucleic acid ratio. Two density components are found in A364A cells; one apparently contains ribosomes and genomic chromatin fragments (ϱ = 1.26 g/cm³) and a lighter component (ϱ = 1.24 g/cm³) contains pure 2-μm DNA. The lighter component is not found in (cir⁰) cells.     

Characterisation of DNA from condensed and dispersed human chromatin

Condensed and dispersed chromatin fractions were isolated from human placental nuclei. The DNA of each fraction was purified and characterised by isopycnic centrifugation, thermal fractionation on hydroxylapatite (HAP) and sequence complexity studies. The DNAs had identical buoyant densities in neutral CsCl (1.698 g/cm³) and similar melting profiles on HAP. Analytical ultracentrifugation in Ag⁺-Cs₂SO₄, however, showed that satellite DNAs were present in the condensed fraction DNA (DNA_C) but were not visible in the dispersed fraction DNA (DNA_D). In addition, DNA_C was found to be enriched in highly reiterated sequences (20% reassociated by C₀t 10^?3) which can be correlated with the presence of satellite DNAs, whereas DNA_D contained only 3% of these fast reassociating sequences. In contrast DNA_D contained 30% intermediate sequences (reassociating between C₀t 10^?3 and C₀t 100) which represent only 10% of DNA_C. The reassociated highly repeated sequences of DNA_C showed the presence of two components in both CsCl density gradients and HAP thermal elution studies. This suggests that either there are sequence relationships resulting in partial mismatching between the different highly repeated DNA sequences in this fraction, or that highly repeated sequences are associated with less repetitious DNA. The results are discussed in terms of possible differences in genetic activity between the chromatin fractions.     

Characterization of repetitive DNA in rye (Secale cereale)

Nuclear DNA of rye (Secale cereale), a plant species with a relatively large genome (i.e., 18 pg diploid), has been characterized by determination of its content in repetitive sequences, buoyant density, and thermal denaturation properties. The reassociation kinetics of rye DNA reveals the presence of 70 to 75% repeated nucleotide sequences which are grouped into highly (Cot 1) and intermediately repetitive (Cot 1–100) fractions. On sedimentation in neutral CsCl gradients, native, high molecular weight DNA forms an almost symmetrical band of density 1.702 g/cm³. The highly repetitive DNA (Cot 1), on the other hand, is separated into two distinct peaks; the minor component has a density of 1.703 g/cm³ corresponding to that of a very rapidly reassociating fraction (Cot 0.01) which comprises 10 to 12% of the rye genome. The latter DNA contains segments which are repeated 6×10⁵ to 6×10⁶ times. The major peak of the Cot 1 fraction shows a density of 1.707 g/cm³ and consists of fragments repeated about 3.7×10⁴ times. The intermediately repetitive DNA is much more heterogeneous than the Cot 1 fraction and has a low degree of repetition of the order of 8.5×10². The melting behavior of the Cot 1 fraction reveals the presence of a high degree of base pairing (i.e., 7% mismatching). When native rye DNA is resolved into fractions differing in GC content by hydroxyapatite thermal column chromatography and these fractions are analyzed for the presence of repetitive sequences, it is observed that the highly redundant DNA (Cot 1) is mostly located in the fraction denaturing between 80° and 90°C. This result suggests that highly repetitive rye DNA occurs in a portion of the genome which is neither very rich in AT nor in GC.     

Location of Satellite and Homogeneous DNA Sequences on Human Chromosomes

HUMAN DNA^1,2 contains at least two satellite fractions—satellite I (0.5% of the genome) which bands at a density of 1.687 g/cm³ in neutral CsCl and satellite II (2% of the genome) which bands at 1.693 g/cm³. The main band DNA has an average buoyant density between 1.670 and 1.720 g/cm³ and a light shoulder (constituting 15% of the genome) with a buoyant density of 1.696 g/cm³, referred to as homogeneous mainband. Satellite DNA has been observed in many higher organisms³, usually with an unknown function, notable exceptions being cistrons coding for ribosomal RNA⁴ and the DNA coding for histone messenger RNA⁵. To investigate possible functions of human repetitive DNA we have studied the annealing of complementary RNA fractions to chromosomes using in situ hybridization^6,7. We describe here preliminary observations using human satellite II and homogeneous mainband fractions.     

Subcellular localization of glucosyltransferases involved in cardiac glycoside glucosylation in leaves of Convallaria majalis

The glucosylation of convallatoxin and convallatoxol was investigated using homogenates and various subcellular fractions from leaves of Convallaria majalis. The enzyme activity reached a maximum about 5 weeks after the onset of flowering and was found distributed among the soluble and the light membrane fraction. Upon separation of the light membranes by sucrose density gradient centrifugation, glucosyltransferase activity was found solely in a fraction banding at a density of 1.07 g/cm³, which is thought to represent vacuole membranes.     

Density Centrifugation of Murine Fibrosarcoma Cells Following In Situ Labelling With Tritiated Thymidine

Murine fibrosarcoma (FSa) cells form at least five unique subpopulations after centrifugation in linear Renografin density gradients. Each of these subpopulations has been characterized with respect to selected kinetic parameters using pulse-labelling techniques and flow microfluorometry (FMF) analysis. Tumour-bearing mice were first injected intraperitoneally with a pulse label of tritiated thymidine ([³H]TdR, 50 μCi). Following 15, 30, 60 min or 24 hr these animals were injected with cold thymidine. Animals were killed, their tumours removed and made into suspension, and separated by density gradient centrifugation. Each gradient was fractionated and the density, cell number, tritium activity, and labelling index (LI) per fraction were determined. These data were then compared to FMF data for selected cell density bands. the results indicated a relatively higher uptake of [³H]TdR in the cells recovered at the lighter (1.06–1.12 g/cm³) as compared to the heavier (>1.12 g/cm³) densities. Following a 30-min pulse, the LI's of light cells (<1.12 g/cm³) ranged from 25 to 30%, while the heavier cells (>1.12 g/cm³) had LI's between 10 and 15%. the unseparated control cells had an LI of 19%. Comparable results were found at the other times tested. In contrast, the FMF profiles describing the DNA contents of the cells banding in the gradient showed no difference in proportion of S-phase cells among the separated subpopulations. This lack of correlation between the FMF determination of S-phase cells and labelling index for the denser cell populations implies that DNA content alone is not an effective measurement of the functional activity of cells in solid tumours. Finally, the relatively reduced uptake of [³H]TdR by these denser cells suggests that they may have resided at relatively large distances from the functional vasculature in the tumour.     

Kinetoplast DNA in Trypanosoma equinum1

Identification and characterization of kDNA is described in the naturally occurring totally dyskinetoplastic species Trypanosoma equinum. Fluorescence microscopy of live cells, using the highly sensitive and specific probe DAPI (4,6,-diamidino-2-phenyl-indole), showed the presence of a diversity of extranuclear fluorescent bodies scattered along the length of the organism. Transmission electron microscopic studies revealed a close similarity between the distribution of these DAPI-fluorescing particles and of dense aggregates of nonfibrillar material resembling the kDNA of dyskinetoplastic strains of other species. Variable sized remnants of kDNA, occurring singly or in clusters, were found scattered throughout the mitochondrion. Analytical cesium chloride ultracentrifugation of total cellular DNA extracts showed a kDNA banding profile at a buoyant density equal to 1.691 gm/cm³, representing approximately 11% of the total cellular DNA content. Molecular spreads of isolated kDNA revealed a population of open circular molecules ranging in contour length from 0.11–9.69 μm.     

Characterization of Chromatin Subfractions Enriched in RNA from Lactating Mammary Gland of the Rat

Mammary gland chromatin from lactating rats was fractionated according to the Mg²⁺-solubility method after mild digestion with DNase II. The chromatin properties were compared between the Mg²⁺-soluble (S₂) and the Mg²⁺-insoluble (P₂) fractions. The weight ratio of RNA to DNA was much greater in the S₂ fraction than in the P₂ fraction (S₂, 0.92; P₂, 0.03). The DNA repeat length of the nucleosome was very similar between the two fractions (S₂, 193 ± 7; P₂, 1% ± 8 nucleotide pairs). A significant difference was seen in electrophoretic pattern of H1 histone between the two fractions in the acid-urea gel system. Nonhistone proteins with molecular weights higher than about 40,000 dalton were found to be enriched in the S₂ fraction.     

Induction of DNA synthesis by 2,4-dichlorophenoxyacetic acid during callus induction in Jerusalem artichoke tuber tissues

During the induction of DNA synthesis in Jerusalem artichoke (Helianthus tuberosus L.) tuber by 2,4-D, the 2-¹⁴C-2, 4-D from the agar medium rapidly incorporated into the ethanol soluble and insoluble fractions. Although the 2,4-D level in the ethanol soluble fraction decreased on transplantation of the tissue from the 2-¹⁴C-2,4-D medium to medium without the auxin, its level in the buffer-soluble and -insoluble macromolecular fractions increased. The purified, buffer-insoluble macromolecules were chromatin. The 2,4-D binding to chromatin particularly increased during DNA synthesis. The histone contents of chromatin decreased as DNA synthesis progressed. The polyacrylamide gel electrophoretic patterns of the histones showed a decrease in the moderately lysine-rich histone fraction as compared to other fractions. Thus, the decrease in the histone level caused by 2,4-D and the presence of the 2,4-D moderately lysine-rich histone complex may be closely related to the induction of DNA synthesis by 2,4-D in cells.     

Isolation of chromatin bearing nascent RNA from nuclei of sea urchin embryos

Sea urchin embryos were labeled with C¹⁴ thymidine and H³ Uridine, the nuclei isolated, and a chromatin preparation partially deproteinized in salt and detergent. After banding this preparation in a Cs₂SO₄ gradient, the nascent RNA is associated with a small fraction of the chromatin at a density lighter than the bulk chromatin.