Transcription of superhelical DNA from cell nuclei

A cell-cycle-dependent DNA polymerase activity that replicates intact DNA in chromatin

An insoluble DNA polymerase activity that replicates the intact chromatin template at 85% of the rate found in vivo has been partially characterized. HeLa cells, encapsulated in agarose microbeads, are lysed using an isotonic salt concentration: the resulting encapsulated nuclei contain polymerase associated with a nucleoskeleton and the unbroken template. This preparation can be manipulated freely without aggregation or breaking the DNA and yet is accessible to enzymes and other probes. The major activity, which is sensitive to aphidicolin, is found only in S-phase nuclei and replicates DNA semi-conservatively, forming intermediates that are ligated efficiently into larger products.

Comparative studies on the structural organization of membrane-depleted nuclei and metaphase chromosomes

Interphase membrane-depleted nuclei and metaphase chromosomes were prepared in parallel with a nonionic detergent lysis procedure at low ionic strength. By flow microfluorometry we showed for the first time that cell lysates contain all stages of the cell cycle in the same proportions as the starting cell population. Morphologically intact membrane-depleted nuclei and metaphase chromosomes were isolated as non-aggregated structures on sucrose gradients. When analysed in the electron microscope, membrane-depleted nuclei that had been treated with 2M NaCl appeared as residual structures containing the pore complex-lamina layer attached to a halo of DNA filaments. In contrast, no distinct high salt-resistant structure was found with metaphase chromosomes. They formed a highly fragile network which disintegrated easily into small complexes connected with DNA filaments. High salt-resistant DNA-protein complexes were purified by Metrizamide density gradient centrifugation. The main difference in the protein composition of interphase and metaphase residual complexes was the presence in interphase of a protein triplet in the 60-75 kilodalton molecular weight range and its absence in metaphase. This protein triplet most likely corresponds to the lamins A, B, and C of the nuclear lamina. The combined results suggest that the main difference in the structural organization of interphase nuclei and metaphase chromosomes is the presence or absence of the pore complex-lamina layer.

Folding of prokaryotic DNA. Isolation and characterization of nucleoids from Bacillus licheniformis

Intact and fast-sedimenting nucleoids of Bacillus licheniformis were isolated under low-salt conditions and without addition of detergents, polyamines or Mg2+. These nucleoids were partially unfolded by treatment with RNase and completely unfolded by treatments that disrupt protein-DNA interactions, like incubation with proteinase K, 0.1% sodium dodecyl sulphate and high ionic strength. Ethidium bromide intercalation studies on RNase-treated, proteinase-K-treated and non-treated nucleoids in combination with sedimentation analysis of DNase-I-treated nucleoids revealed that DNA is organized in independent, negatively supertwisted domains. In contrast to the DNA organization in bacterial nucleoids, isolated under high-salt conditions and in the presence of detergents (Stonington & Pettijohn, 1971; Worcel & Burgi, 1972), the domains of supertwisted DNA in the low-salt-isolated nucleoids studied here are restrained by protein-DNA interactions. A major role for nascent RNA in restraining supertwisted DNA was not observed. The superhelix density of B. licheniformis nucleoids calculated from the change of the sedimentation coefficient upon ethidium bromide intercalation, was of the same order of magnitude as that of other bacterial nucleoids and eukaryotic chromosomes, isolated under high-salt conditions: namely, -0.150 (corrected to standard conditions: 0.2 M-NaCl, 37 degrees C; Bauer, 1978). Electron microscopy of spread nucleoids showed relaxed DNA and regions of condensed DNA. Spreading in the presence of 100 micrograms ethidium bromide per ml revealed only condensed structures, indicating that nucleoids are intact. From spreadings of proteinase-K-treated nucleoids we infer that supertwisted DNA and the protein-DNA interactions, responsible for restraining the superhelical DNA conformation, are localized in the regions of condensed DNA.

Theoretical mechanisms for synthesis of carcinogen-induced embryonic proteins. VI. Radiation

The following is an attempt to devise a theory of specific induction processes required of the neoplastic transformation using the non-specific carcinogenic agent - radiation. A variety of biological considerations including comparative radiosensitivity, radiation effects on chromatin and enzymes, radiomimetic chemical induction of chromosomal anomalies, lethality and the tRNA function are also presented. These topics serve as background for elaborating a scheme of how a specific array of genes could become decontrolled. A concept derived involves the fixation of despiralized genic areas which are induced by hypomethylated DNA caused by anomalous DNA methylation. This process could be a potentially critical part of the irradiation-induced carcinogenic event. The concept of fixation of chromatin in an informational sense leads to a mechanism requiring a classic mutation, modified by a repair process that ultimately leads to an epigenetic event. More specifically it would appear that a critical target to induce the neoplastic response from a cell with irradiation could be the DNA responsible for the template sites (or at least a secondary area that indirectly could cause inactivation of this site) of the genes for DNA methylation. This would not necessarily be the only genic change required but one can derive gene derepressions from this type of molecular lesion. A similar scheme for gene repression has not been devised in this writing beyond the simplistic, although not unwarranted, viewpoint of direct DNA damage.

Decrease in the number of DNA topological turns during Friend erythroleukemia differentiation

Murine erythroleukemia cells were induced to undergo erythroid differentiation by growing in presence of dimethylsulfoxide, butyric acid or actinomycin D. topological linking numbers in closed loops of nuclear DNA were measured by means of centrifugation of nucleoids containing superhelical DNA in sucrose gradients containing varying concentrations of ethidium bromide. All cells were grown to G1 stage of the cell cycle. It was found that the mean density of the DNA topological linking number decreases from 0.076 turns per 10 nucleotide pairs in non-differentiated cells to 0.062 turns in the cells induced to differentiate. This decrease in topological linking number of DNA loops is quite sufficient for the change in the DNA double helix secondary structure which in turn may be responsible for coordinate switch in transcription of genes which control cellular differentiation (Luchnik, 1980a, b).

Conformational transitions in closed circular DNA molecules. II. Biological implications

A model of regulation of gene action based on the theory of conformational transitions in closed circular DNA molecules is proposed and discussed in connection with the mechanisms of cellular differentiation. The model predicts two main types of regulation of gene action (1) the change in the topological linking number of the DNA loops leading to the change in the amount of the DNA segments present in the transcriptionally active A-form and (2) the change of some nucleotide sequences in closed superhelical DNA loops resulting in conformational transitions of some of the other sequences in the same loop. The first type of regulation may explain the mechanism of terminal differentiation of the stem cells and the changes accompanying the malignant transformation. The second one may explain the variegated position effect of the gene and determination of the stem cells during ontogenesis.

Absence of anthracycline-induced degradation of nuclear DNA in Ehrlich ascites tumour cells

The in vivo effects of anthracycline antibiotics on the integrity of Ehrlich ascites tumour cell DNA have been studied by sedimentation analysis of nuclear structures containing superhelical DNA in neutral sucrose gradients. These fast-sedimenting protein-DNA complexes may be released by gently lysing cells in solution containing non-ionic detergents and high NaCl concentrations (1.95 M). The supercoiled structure of DNA in these protein-DNA complexes is suggested by the characteristic sedimentation in the presence of intercalating agents. Apparently, no DNA damage could be detected in Ehrlich cells from 7-day-old tumours within 3 h after various doses of daunomycin (0.5--10 mg/kg of body wt.) were administered i.p. to mice. Sedimentation anomalies could not be observed even 15 or 30 h after administration of rtherapeutic doses of daunomycin or adriamycin. In contrast, at 30 min after administration to mice, therapeutic doses of bleomycin (2--8 mg/kg) caused extensive fragmentation of tumour cell DNA, which could be monitored as slowly sedimenting DNA structures (compared with the the control). Similarly, DNA damage could be induced by procarbazine at therapeutic doses. Exposure to bleomycin or procarbazine abolished the characteristic biphasic response to ethidium bromide. The absence of anthracycline-induced degradation of Ehrlich ascites tumour cell DNA is apparently in contrast with the DNA damage observed in L1210 tumour cells. These observations suggest that DNA damage is not a necessary condition for antitumour activity.

Rapid purification of plasmid DNAs by hydroxyapatite chromatography

A method is described for the rapid preparation of plasmid DNAs of molecular weight up to 14 X 10(6). This method involves the chromatography, at room temperature, of bacterial cleared lysates on hydroxyapatite in the presence of high concentrations of phosphate and urea. All detectable protein and RNA contamination of plasmid DNA is removed by this procedure and the conformation of the plasmid DNA is unaffected. Less than 0.5% chromosomal DNA is present in the purified preparation and even this can be removed if necessary by a simple extention of the procedure to include a heat-denaturation step. The method is extremely rapid and amenable to large-scale plasmid preparation; 5 mg ColE1 DNA have been purified within 40 min. The yield of plasmid DNA is similar to that obtained with the conventional dye-centrifugation technique, however the purity is greater.

Spectrofluorometric measurement of the binding of ethidium to superhelical DNA from cell nuclei

Structures retaining many of the morphological features of nuclei may be released by lysing HeLa cells in solutions containing non-ionic detergents and high concentrations of salt. These nucleoids contain few chromatin proteins. We have shown that the DNA of nucleoids is quasicircular and supercoiled by measure spectrofluorometrically the amount of the intercalating dye, ethidium, bound to unirradiated and gamma-irradiated nucleoids. Ethidium binds to nucleoids in the manner characteristic of the binding to superhelical DNA: at low concentrations more ethidium binds to unirradiated nucleoids than to their gamma-irradiated counterparts with broken DNA, and at higher concentrations less ethidium binds to the unirradiated nucleoids. The quasi-circles in nucleoids are 22 times less sensitive to gamma-irradiation than are circles of pure PM2 DNA: they must contain about 2.2 X 10(5) base pairs. The constraints that maintain the quasi-circularity of nucleoid DNA are very resistant to extremes of temperature and alkali; some remain under conditions in which the duplex is denatured. The constraints are destabilised by ethidium suggesting that they are stabilised by free energy of supercoiling. Proteolytic enzymes, but not ribonucleases, remove the constraints. Possible structures for the constraining mechanism are discussed.