Isolation of chloroplasts and chloroplast DNA from pea leaves]

A method of isolating DNA from pea chloroplasts (ch-DNA) in CsCl density gradient is described. DNA preparations are free of 5-methylcytosine and have a melting temperature of 86.5 degrees. Denatured DNA molecules completely reassociate for 3 hours at 60 degrees C. It is concluded that the preparations obtained are pure ch-DNA.     

The influence of packing on free radical yields in solid-state DNA: film compared to lyophilized frozen solution.

Radiation-induced free radical damage in solid-state DNA arises from direct-type damage mechanisms. In the present study, free radical yields in film and lyophilized Na DNA model systems are compared. The free radical yields in lyophilized samples are significantly greater than those in films. Since DNA conformation cannot account for the differences in free radical yields between different DNA preparations, it is proposed that the intermolecular spacing of DNA is a critical variable. The differences in the hydration dependence of free radical yields between the film and lyophilized DNA model systems are consistent with this thesis. The relatively large free radical yields observed in lyophilized DNA emphasize the fact that DNA is an extremely effective electron and hole scavenger, more so than previously thought.     

Rapid micropreps and minipreps of Ti plasmids and binary vectors fromAgrobacterium tumefaciens

A simple and versatile procedure has been developed for the isolation of both large helper/Ti plasmids and binary vectors fromAgrobacterium tumefaciens. Using a slightly modified alkaline lysis protocol, intact plasmid can be recovered from cultures grown in standard micro-centrifuge tubes or culture tubes in sufficient yield and purity to allow for restriction analysis on ethidium bromide stained gels of the >200 kb Ti plasmid DNA. Contamination by chromosomal DNA is minimal and there is thus no need for isopycnic gradient purification. This same procedure can be combined with a high temperature treatment (37°C) and antibiotic selection to generate preparations containing binary vector DNA that are virtually free of interfering Ti plasmid DNA. Restriction patterns produced from these binary vector DNA preparations are unambiguous and therefore preliminary screening by Southern hybridization can be eliminated.     

Mechanism of additive genetic transformation in Haemophilus influenzae.

Transforming deoxyribonucleic acid (DNA) preparations from Haemophilus influenzae Rd strains carrying a chromosomally integrated, conjugative, antibiotic resistance transfer (R) plasmid were exposed to ultraviolet radiation and then assayed for antibiotic resistance transfer on sensitive wild-type Rd competent suspensions and on similar suspensions of a uvr-1 mutant unable to excise pyrimidine dimers. No host cell reactivation of resistance transfer (DNA repair) was observed. Parallel experiments with ethanol-precipitated, heated, free R plasmid DNA preparations gave much higher survival when assayed on the wild-type strain compared to the survival on the uvr-1 strain. These observations indicate that additive genetic transformation (in this case, the addition of the integrated R plasmid to the recipient genome) involves single-strand insertion.     

Purification of bacteriophage DNA by gel filtration chromatography

Two fast and effective methods for high-scale purification of linear phage lambda DNA and circular double-stranded M13 replicative form are presented. A substantial reduction of time is attained by avoiding the long-term CsCl gradient centrifugations and dialysis common to standard procedures. Biologically active DNA preparations, free of chromosomal DNA and RNA, are obtained by including a simple gel filtration chromatography as the last step of purification. Yields are comparable to those from previously described methods.     

Replication of Nondefective Parvoviruses: Lack of a Virion-Associated DNA Polymerase

We have examined four of the nondefective parvoviruses for an associated DNA polymerase. Virions were purified from neuraminidase-treated infected-cell lysates by isopycnic centrifugation in CsCl or from infected cell material by CaCl(2) precipitation and centrifugation through sucrose into CsCl. Preparations of bovine parvovirus or Kilham rat virus obtained by the former procedure contained DNA polymerase activity but were not free of contaminating cellular proteins. The latter method produced viral preparations free of contaminating cellular proteins, and no DNA polymerase activity was detected in light infectious particles of H-1, LuIII, bovine parvovirus, or Kilham rat virus. Examination of levels of each cellular DNA polymerase in these preparations from each step of both purification procedures revealed that DNA polymerase beta had a greater tendency to copurify with bovine parvovirus and Kilham rat virus than did DNA polymerases alpha or gamma. Disruption of infectious virions obtained by the second purification method with detergents and sonic treatment did not result in the detection of a DNA polymerase activity. The biological activity and purity of each of the four different viruses obtained by the latter procedure were determined by hemagglutination and infectivity assays, polyacrylamide gel electrophoresis, and electron microscopy. In each case, the virions banding at a density of 1.39 to 1.41 g/cm(2) in CsCl were infectious and contained only the virion structural proteins. DNA polymerase activity was not detected in any of these preparations, and we have concluded that a virion-associated DNA polymerase is not required for productive infection with the nondefective parvoviruses.     

Transfer of condensed viral DNA into eukaryotic cells using proteoliposomes

High-molecular-weight viral DNAs have been packed into proteoliposomes prepared by reverse-phase evaporation followed by phospholipid membrane targeting by influenza virus glycoprotein bound to hydrophobic 'anchors'. DNA has been encapsulated in the form of spermine condensates--toroidal structures sized approx. 0.1 micron, resistant to ultrasound. The efficiency of entrapping into liposomes reached 30% for condensed DNA of Mr up to 3 X 10(7). Specific infectivity of simian virus 40 DNA and simian adenovirus DNA packed into such proteoliposomes was 50- to 100-fold higher than that shown by free DNA preparations under Ca.phosphate-precipitation conditions.     

Restriction nuclease digestions driven to completion by Escherichia coli RNA polymerase and T4 gene 32 protein

Restriction enzyme digestions of large scale DNA preparations often do not go to completion. This is due to product inhibition by the newly generated ends of the digested DNA. The addition of exogenous proteins that bind tightly to the free ends of DNA or to single-stranded DNA will relieve this inhibition. We show that a considerable savings on restriction nucleases can be attained by the addition of RNA polymerase or T4 gene 32 protein in stoichiometric amounts to the newly produced DNA ends.     

Purification of S1 muclease from Takadiastase by affinity chromatography on single-stranded DNA-acrylamide columns.

When S1 nuclease from Takadiastase was partially purified according to previously reported methods, it showed a 10 to 15 fold increase in specificactivity. Although such preparations were highly active on single-stranded DNA, they had traces of activity on native DNA and were contaminated by T1-RNase. The S1 enzyme was further purified by a single step of affinity chromatography on single-stranded DNA-acrylamide column to a final purification of 275-fold. This preparation was free of T1-RNase and had an absolute specificity for single-stranded DNA.     

Double labeling with [3H]thymidine and [125I]iododeoxyuridine as a method for determining the fate of injected DNA and cells in vivo

Mice were injected intravenously and intraperitoneally with preparations of intestinal nucleoprotein, spleen nuclei, mouse thymus cells, or human kidney T cells whose DNA had been labeled with both [3H]thymidine (TdR) and [125I]-iododeoxyuridine (IUdR). Since free TdR is reutilized more efficiently than free IUdR produced by enzymic hydrolysis of the exogenous DNA, the ratio of [3H]TdR/[125I]IUdR in the DNA fraction of the tissues of the recipient mice provides a measure of the amount of intact exogenous DNA in the tissue. In most instances, the doubly labeled exogenous DNA was almost completely hydrolyzed within 1 day injection, but survival of the DNA from whole cells could be demonstrated in some cases.     

Studies on the accessibility of deoxyribonucleic acid in deoxyribonucleoprotein to cationic molecules

The binding of deoxyribonucleoprotein to Toluidine Blue, to cetylpyridinium chloride and to polylysine of various molecular weights was studied to determine the percentage of free DNA phosphate groups in deoxyribonucleoprotein. Binding was measured by addition of these reagents to deoxyribonucleoprotein at a range of concentrations such that complete precipitation of the deoxyribonucleoprotein occurred. With Toluidine Blue the binding corresponded to about 48% of the DNA phosphates in deoxyribonucleoprotein. The dye did not cause appreciable displacement of protein from the DNA. With cetylpyridinium chloride the binding corresponded to about 41% of the DNA phosphates. With polylysine preparations of molecular weight 1250 and 7790 the binding values for deoxyribonucleoprotein were 46 and 38% respectively. The results suggest that the free phosphates lie in stretches sufficiently long to accommodate most of each polylysine molecule. With polylysine of molecular weight 62000 cross-linking of free stretches of DNA on different deoxyribonucleoprotein molecules probably occurs. It is concluded that although most of the free phosphates are probably ;hidden' beneath covering histone, corresponding perhaps to runs of non-basic residues in the latter, they are surprisingly accessible to very large molecules. The relevance of this finding to the problem of gene repression is discussed.     

Rearrangement of nucleosomal components by modification of histone amino groups. Structural role of lysine residues

Modification of nucleosomal particles from chicken erythrocytes with the reagents for protein amino groups acetic and dimethylmaleic anhydrides causes a rearrangement of nucleosomal components. Treatment with both reagents is accompanied by liberation of free DNA and formation of residual particles with anomalous histone composition. The residual particles obtained with acetic anhydride contain an excess of histones corresponding to the free DNA produced. In contrast, dimethylmaleic anhydride causes release of histones H1, H5, H2A and H2B and formation of residual particles deficient in these histones but containing an excess of H3 and H4 corresponding to the liberated DNA. Regeneration of the modified amino groups of nucleosomal preparations treated with dimethylmaleic anhydride is accompanied by reconstitution of nucleosomal particles with the sedimentation coefficient and composition of core histones of the original nucleosomes. This reconstitution does not occur when the released fraction containing histones H2A and H2B and free DNA is separated from the residual particles. The studied disassembly of nucleosomal particles obtained by specifically blocking lysine-DNA interactions with these reagents appears to indicate that lysine residues are essential for the binding of DNA to histones with formation of nucleosomal particles.     

ISOLATION OF NUCLEI FROM THE UNICELLULAR ALGA OLISTHODISCUS LUTEUS (CHLOROMONADOPHYCEAE)1

Methods are described for the isolation of nuclei from the marine chloromonad Olisthodiscus luteus. For each of the three alternative methods, the ratios to DNA of RNA, acid-soluble and acid-insoluble protein are 0. 17, 1.1 and 2.0, respectively. The nuclear preparations are free of whole cell and organelle contamination, although some membranes are present. The yield is 65–80% based on the recovery of DNA in the nuclear pellet. The nuclei are in DNA-dependent RNA synthesis.     

Spectral analysis of chromatin and its components in the vacuum ultraviolet region of the spectrum

Electronic absorption spectra of thin films of chromatin and chromatin components in ultraviolet (140-280 nm) were investigated. The absorption coefficients mu (lambda) of chromatin, nucleosomes with and without histone H1, total histones (TH), DNA were compared. The spectra of nucleosomes and chromatin differ from summary spectra of DNA + TH. The lack of additivity of absorption coefficients at different wavelengths may be explained by different conformational changes of free DNA, TH and DNA, TH in nucleosomes and chromatin during the process of drying aqueous solutions for the preparations of thin films. The obtained mu (lambda) values are necessary for the estimation of the DNA and TH parts of absorption in chromatin and nucleosomes in the investigations of UV and VUV irradiation damages.     

Growth hormone acts at a pretranslational level in hepatocyte cultures

We have examined the effects of ovine growth hormone and recombinant DNA synthesized human growth hormone on hepatocytes maintained in serum free cultures. Both growth hormone preparations augmented or attenuated 3 specific mRNA sequences as revealed by two-dimensional gel electrophoresis of [35S] methionine labeled products synthesized in vitro in an mRNA dependent rabbit reticulocyte lysate system. The results clearly indicate that growth hormone, free of potential pituitary contaminants, acts directly on hepatocytes at a pretranslational level.     

On the fidelity of DNA replication: use of synthetic oligonucleotide-initiated reactions

The phi X174 fidelity system provides a biological assay for quantitating the accuracy of DNA polymerases. Expansion of this system to cell extracts and DNA replication complexes from eucaryotes has been limited by the presence of nucleases in these preparations. We have overcome these limitations by priming the phi X template with a synthetic oligodeoxynucleotide, with its free 3'-hydroxyl terminus only a short distance from the amber locus that is the site for determining the frequency of misincorporation. In this paper, this modified phi X system is characterized and compared to that using defined natural DNA restriction fragments as primers. The modified system has been applied to studies on the fidelity of DNA synthesis using different forms of purified DNA polymerase-alpha from calf thymus, as well as crude extracts from human lymphocytes.     

Natural Hidden Autoantibodies React with Negatively Charged Carbohydrates and Xenoantigen Bdi

Immunoglobulin preparations from sera of healthy donors contain polyspecific autoantibodies interacting with DNA and other charged antigens. These antibodies belong to the IgG class and can exist in the free or hidden state. The hidden antibody activity can be revealed after ion-exchange chromatography on QAE-Sephadex A-50. Immunoenzyme assay was used to assess the interactions of both free and hidden antibodies with different carbohydrates. The hidden antibodies were only able to interact with different polyanionic carbohydrates and neutral xenoantigen Bdi.     

Specific measurement of DNA in nuclei and nucleic acids using diaminobenzoic acid

The diaminobenzoic acid (DABA) reaction with DNA, first described by Kissane and Robbins (J. M. Kissane and E. Robbins, 1958, J. Biol. Chem.233, 184–188) and variously modified, was reinvestigated and applied to the measurement of submicrogram quantities of DNA in nuclear fractions and nucleic acid preparations. The reaction conditions were optimized using a small volume of DABA. This method measures 0.1 μg of DNA with a fluorescence twice that of background and is linear to 10 μg of DNA. DABA yeilds a 1000-fold higher fluorescence with DNA compared with RNA, protein, and polysaccharides, and 0.1 μg of DNA is detectable in the presence of 200 μg of RNA or protein. The method is useful for detecting contaminating DNA in RNA preparations prior to hybridization. A simple procedure using ethanol precipitation was developed for removal of common interfering reagents such as sucrose, glycerol, salts, and Triton X-100. Nuclei isolated using detergents and assayed by this method are also free of measurable interfering lipids.     

Effect of Free Radicals and Temperature on Sister Chromatid Exchanges in Hordeum vulgare L.

The clastogenic (chromosome-damaging) effect of many chemical and physical agents is believed to be mediated by reactive oxygen-detived radicals. The interaction of these free radicals with DNA and the significance of the radical-induced DNA lesions in mutagenesis and carcinogenesis have been the subjects of increasing interest during recent years. Sister chromatid exchange (SCE) reflects an interchange between DNA molecules at homologous loci within a replicating chromosome. SCE analysis was found to have increased use for monitoring the exposure of cell to mutagenic carcinogens. The authors found that the induction of SCEs in cells of Hordeum vulgare L. by ascorbic acid, mitomycin C, adriamycin and maleic hydrazid was through the action of free radicals. They also studied the influence of growth temperature on average generation time(AGT) and SCEs. and disclosed a close correlation between AGT and SCEs. The Brdu-Giemsa techniques were used for the detection of SCEs and AGT in cytological preparations of metaphase chromosomes.     

Mitochondrial deoxyribonucleic acid from Tetrahymena pyriformis and its kinetic complexity

1. Mitochondrial DNA from Tetrahymena pyriformis strain T has a buoyant density (rho) of 1.685 compared with rho1.688 for whole cell DNA. Mitochondrial preparations from T. pyriformis strain W show an enrichment of a light satellite (rho1.686), although this is not obtained free from nuclear DNA (rho1.692). 2. T. pyriformis mitochondrial DNA renatures rapidly and the kinetics of this process indicate a complexity of approx. 3x10(7) daltons. 3. The base-pairing in the renaturation product is of a precise nature, since the ;melting' temperature (80.5 degrees C) is indistinguishable from that of the native DNA (80.5 degrees C). 4. Centrifugation of mitochondrial DNA in an alkaline caesium chloride density gradient gives two bands, implying the separation of the complementary strands.