Partially condensed DNA conformations observed by single molecule fluorescence microscopy.

To detect partially condensed conformations of a double-stranded DNA molecule, single molecule fluorescence microscopy is performed here. The single DNA molecules are ethidium stained, 670 kilobase pair bacteriophage G genomes that are observed both during and after expulsion from capsids. Expulsion occurs in an agarose gel. Just after expulsion, the entire G DNA molecule typically has a partially condensed conformation not previously described (called a balloon). A balloon subsequently extrudes a filamentous segment of DNA. The filamentous segment becomes gently elongated via diffusion into the network that forms the agarose gel. The elongated DNA molecule usually has bright spots that undergo both appearance/disappearance and apparent motion. These spots are called dynamic spots. A dynamic spot is assumed to be the image of a zone of partially condensed DNA segments (globule). The positions of globules along an elongated DNA molecule 1) are restricted primarily to time-stable regions with comparatively high thermal motion-induced, micrometer-scale bending of the DNA molecule and 2) move within a given region on a time scale smaller than the time scale of recording. Less mobile globules are observed when either magnesium cation or ethanol is added before gel-embedding DNA molecules. These observations are explained by globules induced at equilibrium by a bending-dependent, inter-DNA segment force. Theory has previously predicted that globules are induced by electrostatic forces along an electrically charged polymer at equilibrium. The hypothesis is proposed that intracellular DNA globules assist action-at-a-distance during DNA metabolism.     

Nitric oxide involvement in pancreatic beta cell apoptosis by glibenclamide.

Glibenclamide as a second-generation compound of sulfonylurea has widely been used in the treatment of type 2 diabetes patients. It has been shown that it induces apoptosis in beta cells, which is partially mediated by Ca(2+) influx. Here, we investigated the role of nitric oxide (NO) and nitric oxide synthase (NOS) isoforms on glibenclamide-induced apoptosis in rat insulinoma cells. Our results showed that glibenclamide induces NO generation (measured as nitrite) that is accompanied with decrease of cell viability in a defined concentration of glibenclamide. The effects of glibenclamide on cell viability were partially inhibited after treatment with N(G)-nitro-L-arginine methyl ester (L-NAME), inhibitor more selective for constitutive nitric oxide synthase, and in the presence of D600--a blocker of voltage-gated L-type Ca(2+) channels inhibited Ca(2+) influx into beta cells, whereas aminoguanidine (AG), a preferential inhibitor of inducible NOS, was significantly less effective. Analysis of DNA fragmentation by electrophoresis and staining with Hoechest 33342 and propidium iodide showed that L-NAME, but not AG, prevented DNA fragmentation and decreased the number of cells with condensed and fragmented nuclei. It revealed that the effects of glibenclamide on apoptosis were partially inhibited by treatment with L-NAME. In conclusion, we have shown that NO production in glibenclamide treated cells may be involved in the induction of apoptotic cell death in pure beta cell line and it may be due to Ca(2+) dependent activation of constitutive NOS isoforms.     

The effect of spermine on acid-base equilibrium in DNA molecule

The influence of spermine (Sp) on the acid-induced predenaturational and denaturational transitions in the DNA molecule structure has been studied by means of circular dichroism, spectrophotometric and viscometric titration at supporting electrolyte concentration 10 mM NaCl. The data available indicate that at [N]/[P] less than or equal to 0.60 (here [N] and [P] are molar concentrations of Sp nitrogen and DNA phosphours, respectively) the cooperative structural B----B(+)----S transitions are accompanied by the DNA double-helice winding. No competition for proton acceptor sites in the DNA molecule between H+ and Sp4+ cations has been observed when binding to neutral macromolecule. At 0.60 less than or equal to [N]/[P] less than or equal to 0.75 the displacement of the B----B(+)----S transitions midpoints to acidic pH region has been established. This is accompanied by DNA condensation and the appearance of differential scattering of circularly polarized light. The calculations carried out in the framework of the two-variable Manning theory have shown that the acid-induced reduction of the effective polyion charge density facilitates the Sp-induced DNA condensation. It has been shown that the acid-base equilibrium in the DNA molecule is determined by local [H+] in the 2-3 A hydrated monolayer of the macromolecule. An adequate estimation of [H+] can be obtained on the basis of the Poisson-Boltzman approach. The data obtained are consistent with recently proposed hypothesis of polyelectrolyte invariance of the acid-base equilibrium in the DNA molecule.     

Immunochemical analysis and protective properties of components of Pseudomonas aeruginosa mucus with different molecular weights

P. aeruginosa slime has been separated into fractions XM-300 (3 X 10(5) daltons and more), XM-100 (1 X 10(5) = 3 X 10(5) daltons), PM-30 (3 X 10(4) = 1 X 10(5) daltons) and PM-10, (1 X 10(4) = 3 X 10(4) daltons) by ultrafiltration. The high-molecular slime components (3 X 10(4) daltons and more) have been found to be serologically more active than the low-molecular components (1 X 10(4) = 3 X 10(4) daltons). As shown in experiments on mice, both high-molecular toxic and low-molecular nontoxic slime components have protective activity, but the high-molecular components are more active than the low-molecular ones. The slime components stimulate the formation of immunity to homologous and partially heterologous P. aeruginosa strains in mice. Antigenic relationship between the slime components (especially the high-molecular ones) and the corresponding lipopolysaccharides has been noted.     

A new method for the preparation of metaphase chromosomes for flow analysis

A new method for the preparation of metaphase chromosomes for flow analysis has been evaluated. It has been shown that this method, which involves detergent lysis of metaphase cells and polyamines to stabilize the DNA, yields lower coefficients of variation and background levels in the DNA histograms than is currently obtained by hexylene glycol based methods. A conventional flow cytometer (FACS-II) has been used to resolve the human karyotype into about 14 peaks after ethidium bromide staining and excitation with a relatively low level of illumination (0.4 W at 488 nm). Flow karyotypes have also been obtained from suspension cell lines, in particular from the mouse cell line, Friend 707/B10. The only disadvantage of this method is that the chromosomes are highly condensed and therefore banding studies on sorted chromosomes may not be possible.     

The E3 ligase Topors induces the accumulation of polysumoylated forms of DNA topoisomerase I in vitro and in vivo

Human Topors has originally been identified as binding partner of p53 and DNA topoisomerase I (TOP1). It can function as both an ubiquitin and SUMO-1 E3 ligase for p53. Here we demonstrate that Topors enhances the formation of high-molecular weight SUMO-1 conjugates of TOP1 in a reconstituted in vitro system and also in human osteosarcoma cells, similar to treatment with CPT. In contrast to the situation observed with p53, overall sumoylation levels were rather unaffected. Experiments with TOP1 point mutants strongly suggest that the high-molecular weight conjugates represent SUMO-1 chains formed on a limited number of SUMO-1 acceptor sites.     

Isolation of high molecular weight eukaryotic DNA with the use of potassium acetate

The simple technique for isolation of high-molecular eucaryotic DNA has been proposed. It includes cell or nuclei lysates by sodium dodecylsulfate in the presence of pronase, proteins precipitation by potassium acetate, DNA precipitation by ethanol. The DNA isolated by this technique is easily cleaved by restriction endonucleases and can be used for analysis of the unique genes by blot-hybridization. The yield of DNA is similar or somewhat higher than that in case of using the standard methods including phenol extraction or phenol-chloroform extraction.     

Serum factors stimulating DNA synthesis in the isolated nuclear system from rat liver

³H-TTP incorporation into DNA by the isolated rat liver nuclei was stimulated by the rat serum in proportion to its concentration. Dialysis and gel-filtration of the serum indicated the presence of two factors: one is low-molecular and another is high-molecular. The high-molecular factor is thermolabile while the low-molecular one is thermostable. The latter is resistant to pronase-treatment and can not be adsorbed on charcoal. The sera from normal and partially hepatectomized rats showed similar stimulatory effect.     

The Role of a Microscopic Colloidally Stabilized Phase in Solubilizing Oligoamine-Condensed DNA Complexes

DNA complexes of spermine and spermidine become resolubilized at very high concentrations of the oligoamine. It has been postulated that high oligoamine concentrations shift the DNA from the globule back to the coil phase. The present study indicates that DNA resolubilization at high concentrations of spermine and spermidine is explained by formation of small particles of condensed DNA that cannot be precipitated by centrifugation. The fact that DNA stays condensed during resolubilization was confirmed using a relatively new condensation assay and three independent microscopic techniques. A considerable portion of DNA was found to be in particles with diameter <100 nm. Formation of such small particles is likely to be caused by colloidal forces. The ability to form small, condensed DNA particles in solutions that contain high concentrations of oligocation should aid in the design of synthetic DNA vectors for gene transfer and gene therapy and in the handling of DNA for diagnostic studies.     

DNA-protein binding in interphase chromosomes

The metachromatic dye, azure B, was analyzed by microspectrophotometry when bound to DNA fibers and DNA in nuclei with condensed and dispersed chromatin. The interaction of DNA and protein was inferred from the amount of metachromasy (increased β/α-peak) of azure B that resulted after specific removal of various protein fractions. Dye bound to DNA-histone fibers and frog liver nuclei fixed by freeze-methanol substitution shows orthochromatic, blue-green staining under specific staining conditions, while metachromasy (blue or purple color) results from staining DNA fibers without histone or tissue nuclei after protein removal. The dispersed chromatin of hepatocytes was compared to the condensed chromatin of erythrocytes to see whether there were differences in DNA-protein binding in "active" and "inactive" nuclei. Extraction of histones with 0.02 N HCl, acidified alcohol, perchloric acid, and trypsin digestion all resulted in increased dye binding. The amount of metachromasy varied, however; removal of "lysine-rich" histone (extractable with 0.02 N HCl) caused a blue color, and a purplish-red color (µ-peak absorption) resulted from prolonged trypsin digestion. In all cases, the condensed and the dispersed chromatin behaved in the same way, indicating the similarity of protein bound to DNA in condensed and dispersed chromatin. The results appear to indicate that "lysine-rich" histone is bound to adjacent anionic sites of a DNA molecule and that nonhistone protein is located between adjacent DNA molecules in both condensed and dispersed chromatin.     

Contents of extracellular DNA in blood of irradiated rats]

Intact rat plasma contains high-molecular DNA which moves as a single fraction in 0.5% agarose electrophoresis. As early as 2-5 hours after gamma-irradiation in a dose of 1-100 Gy there appears low-molecular DNA (about 180 nucleotide pairs), the amount of which directly correlates with the irradiation dose 5 hours after the exposure. Blot-hybridization showed that low-molecular DNA has no common nucleotide sequences with high-molecular DNA, though has sites similar to genome repeat sequences.     

Calculation of DNA condensation, caused by adsorption of ligands

A method for calculating the curves of DNA transition from linear to condensed state upon binding of condensing ligands has been developed. The character of the transition and ligand concentration necessary for condensation have been shown to be governed by the length of DNA molecule, energy and stoichiometry parameters of DNA-ligand complex (equilibrium constant between linear and condensed form in the absence of ligands, constants for ligand binding to linear and condensed forms, the number of base pairs covered by one ligand, etc.). The results of the calculations indicate that only slight difference in the free energies of these states in free DNA (less than 6 cal/mole(bp) for DNA of 500 bp long) is sufficient for the existence of stable linear state in the absence of ligands (in free DNA) and the formation of stable condensed state upon complexation.     

AN ANALYSIS OF HETEROCHROMATIN IN MAIZE ROOT TIPS

The B chromosomes of maize are condensed in appearance during interphase and are relatively inert genetically; therefore they fulfill the definition of heterochromatin. This heterochromatin was studied in root meristem cells by radioautography following administration of tritiated thymidine and cytidine, and was found to behave in a characteristic way, i.e. it showed asynchronous DNA synthesis and very low, if any, RNA synthesis. A cytochemical comparison of normal maize nuclei with nuclei from isogenic maize stock containing approximately 15–20 B-chromosomes in addition to the normal complement has revealed the following: (a) the DNA and histone contents are greater in nuclei with B chromosomes; (b) the proportion of DNA to histone is identical with that of nuclei containing only normal chromosomes; (c) the amount of nonhistone protein in proportion to DNA in interphase is less in nuclei with B chromosomes than in normal nuclei. In condensed B chromosomes the ratio of nonhistone protein to DNA is similar to that in other condensed chromatin, such as metaphase chromosomes and degenerating nuclei. The B chromosomes appear to have no effect on nucleolar RNA and protein. Replication of B chromosomes is precisely controlled and is comparable to that of the ordinary chromosomes not only in synthesis for mitosis but also in formation of polyploid nuclei of root cap and protoxylem cells.     

Calculations of DNA Condensation Caused by Ligand Adsorption

A method for calculating the curves of DNA transition from linear to condensed state upon binding of condensing ligands has been developed. The character of the transition and ligand concentration necessary for condensation have been shown to be governed by the length of DNA molecule, energy and stoichiometry parameters of the DNA–ligand complex (equilibrium constant between linear and condensed form in the absence of ligands, constants for ligand binding to linear and condensed forms, the number of base pairs covered by one ligand, etc.). The results of the calculations indicate that a slight difference in the free energies of these DNA states (less than 6 cal/mol(bp) for a DNA of 500 bp) is sufficient for the existence of a stable linear state in the absence of ligands (in free DNA) and the formation of stable condensed state upon complexation.     

Chromosome condensation and sister chromatid pairing in budding yeast

We have developed a fluorescent in situ hybridization (FISH) method to examine the structure of both natural chromosomes and small artificial chromosomes during the mitotic cycle of budding yeast. Our results suggest that the pairing of sister chromatids: (a) occurs near the centromere and at multiple places along the chromosome arm as has been observed in other eukaryotic cells; (b) is maintained in the absence of catenation between sister DNA molecules; and (c) is independent of large blocks of repetitive DNA commonly associated with heterochromatin. Condensation of a unique region of chromosome XVI and the highly repetitive ribosomal DNA (rDNA) cluster from chromosome XII were also examined in budding yeast. Interphase chromosomes were condensed 80-fold relative to B form DNA, similar to what has been observed in other eukaryotes, suggesting that the structure of interphase chromosomes may be conserved among eukaryotes. While additional condensation of budding yeast chromosomes were observed during mitosis, the level of condensation was less than that observed for human mitotic chromosomes. At most stages of the cell cycle, both unique and repetitive sequences were either condensed or decondensed. However, in cells arrested in late mitosis (M) by a cdc15 mutation, the unique DNA appeared decondensed while the repetitive rDNA region appeared condensed, suggesting that the condensation state of separate regions of the genome may be regulated differently. The ability to monitor the pairing and condensation of sister chromatids in budding yeast should facilitate the molecular analysis of these processes as well as provide two new landmarks for evaluating the function of important cell cycle regulators like p34 kinases and cyclins. Finally our FISH method provides a new tool to analyze centromeres, telomeres, and gene expression in budding yeast.     

Mass separation and in vitro immunological activity of membrane-fractionated polysaccharides from fruiting body and mycelium of Agaricus subrufescens

Membrane technology has been applied to separate polysaccharides from Agaricus subrufescens (ASPs). The membrane-retained fractions and unfractionated preparations have been tested for in vitro immunological activity. Both the microfiltration (MF) and ultrafiltration (UF1) membranes were able to separate high-molecular weight polysaccharides from fruiting body (ASP-FB) and submerge-fermented mycelium (ASP-SmF) extracts. All fractions showed immunostimulatory effects on RAW 264.7 macrophages, measured by TNF-??, iNOs gene expression, and NO production. In contrast, antibody and proliferation levels in B lymphoblastoid SKW 6.4 cells were significantly increased after treatment with ASP-FB, but did not with ASP-SmF preparations. The ASPs- and LPS-induced stimulation could be differentiated by the finding that polymyxin B, a specific inhibitor of LPS, did not significantly affect the immunoactivating response and proliferation activity of ASPs on macrophages and B cells, respectively. Furthermore, the ASP-FB treatment was unable to induce IL-6 production by B cells unlike LPS activation, sustaining distinct signaling pathways for ASP-FB and LPS. The overall results provided additional information about the action of ASPs on the immune system and support the membrane method to separate and concentrate high-molecular weight ASPs for immunopharmacological and biotechnological applications.     

Secondary structure of condensed DNA. wide-angle, small-angle x-ray scattering and circular dichroism

Ethanol precipitated DNA shows a CD spectrum of the +psi-type which is similar to that of DNA in the A-form. DNA condensed with cetyl-trimethylammonium-bromide shows, depending on the condensation velocity, a CD spectrum of the -psi-type, or a CD spectrum only slightly modified from that of DNA in solution. The first spectrum is similar to that of DNA in the C-form, and the second one, to that of DNA in the B-form. Using large-angle X-ray scattering of the three DNA condensates and comparing them with the scattering curves calculated from the atom coordinates for the A-, B-, and C-form of DNA it is shown that the secondary structure of the DNA belongs in all three cases to the B-family. It follows from this result that the secondary structure of DNA alone does not determine the type of CD spectrum. The CD spectrum of condensed DNA is essentially determined by the supramolecular structures of the partially crystalline DNA condensates. These supramolecular structures can be demonstrated by the small-angle X-ray diagrams. The condensation of DNA by ethanol and cetyl-trimethylammonium-bromide proceeds in the form of a partial crystallization of the DNA.     

DNA多分子缩合理论模型

在多分子缩合的实验研究基础上,本文以Tanford的递次结合模型为基础,建立了DNA多分子缩合的理论模型.此模型描述了缩合粒子的多分子结合特性,并预测缩合粒子的聚合数分布.模型的理论分布与作者用电镜获得的统计实验分布符合一致.同时,由于一组参量可同时拟合两种不同DNA长度的复曲面分布曲线,因而从理论上阐明缩合粒子的尺度独立于DNA的分子量.此外,还以高斯分布对复曲面的聚合数分布进行了模拟与比较.     

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.