Intracellular organization of bacteriophage T7 DNA: analysis of parenteral bacteriophage T7 DNA-membrane and DNA-protein complexes.

After infection of Escherichia coli with bacteriophage T7, the parenteral DNA forms a stable association with host cell membranes. The DNA-membrane complex isolated in cesium chloride gradients is free of host DNA and the bulk of T7 RNA. The complex purified through two cesium chloride gradients contains a reproducible set of proteins which are enriched in polypeptides having molecular weights of 54,000, 34,000, and 32,000. All proteins present in the complex are derived from host membranes. Treatment of the complex with Bruij-58 removes 95% of the membrane lipid and selectively releases certain protein components. The Brij-treated complex has an S value of about 1,000 and the sedimentation rate of this material is not altered by treatment with Pronase or RNase.     

Size of infectious DNA from human and murine cytomegaloviruses.

Viral DNA was isolated from human and murine cytomegalovirus by equilibrium centrifugation in cesium chloride gradients. The size of the DNA was measured relative to T4 DNA by velocity sedimentation in neutral glycerol gradients, and fractions were assayed for infectious DNA. Infectious murine cytomegalovirus DNA sedimented as a single peak with an estimated molecular weight of 136 X 10(6). Infectious human cytomegalovirus DNA was detected in two peaks with molecular weights of 130 X 10(6) and 150 X 10(6).     

A bacteriophage lambda DNA purification procedure suitable for the analysis of DNA from either large or multiple small lysates

A method for the efficient preparation of high quality bacteriophage lambda DNA from cleared lysates is described. Advantages of the method include high DNA yields (typically around 0.8 micrograms of DNA/1 ml of cleared lysate), speed of processing (approximately 2 h from lysate to DNA), economy, and the absence of any requirement for phenol or chloroform extractions. The technique involves the concentration of phage particles by standard polyethylene glycol precipitation followed by enzymatic treatment to remove contaminating RNA and DNA. Phage particles are then lysed with sodium dodecyl sulfate (SDS) at elevated pH and temperature. Contaminating protein/SDS complexes are rendered insoluble by the addition of potassium acetate and removed by centrifugation. The quality of the resultant DNA is comparable to that prepared by cesium chloride banding for all standard molecular biological purposes providing that spermidine is included in all restriction endonucleases digestions.     

The release and stability of the large subunit of DNA from T2 and T4 bacteriophage

T₂ and T₄ bacteriophage have been exposed to various treatments which are known to release the encapsulated DNA. The unseparated reaction products have been examined by autoradiography. The results indicate the presence of one large subunit of DNA (molecular weight 45 x 10⁶) for each former phage particle. Some smaller subunits of molecular weight 12 x 10⁶ have been observed. The large subunit is sensitive to very small amounts of DNAase, and is resistant to mixed proteases and cannot be dispersed by banding in cesium chloride density gradients. The sensitivity to fragmentation by P³² decay and the increase in this sensitivity following heat treatment are best explained by assuming that the large subunit is a duplex of polynucleotide strands over most of its length. The presence of hypothetical non-DNA interconnections is considered.     

Characterization of the Kilham Rat Virus

Kilham rat virus (KRV) was found to grow in a rat nephroma cell line and to form plaques on secondary rat embryo monolayers. The virus was purified by enzymatic treatment and isopycnic cesium chloride sedimentation. KRV bands at a density of 1.41 g/cm(3) in cesium chloride. It contains about 26.5% deoxyribonucleic acid (DNA). The sedimentation coefficient S(20,w) in sucrose gradients was 122 corresponding to a molecular weight of 6.6 x 10(6) daltons. The reaction of formaldehyde with the KRV virion suggests that the DNA in situ is single-stranded. DNA extracted from KRV had a buoyant density of 1.715 g/cm(3) in cesium chloride. The S(20,w) was determined in sucrose gradients to be 16, and the molecular weight was calculated to be approximately 1.7 x 10(6) daltons. The base composition of the DNA is 26.7% adenine, 30.8% thymine, 20.0% guanine, and 22.5% cytosine. On the basis of its noncomplementary nucleotide ratio, melting curve, and the reaction with formaldehyde, the DNA of KRV is believed to be single-stranded.     

Molecular weight and base composition of DNA isolated from Melanoplus sanguinipes entomopoxvirus

The DNA genome of the orthopteran entomopoxvirus (EPV) isolated from Melanoplus sanguinipes was released from the virus by treatment with proteinase K and sodium dodecyl sulfate (SDS). The average length of the virus DNA molecule was determined by electron microscopy to be 62.8 μm, corresponding to a molecular weight of 124.3 × 10⁶ daltons (80 kb). The buoyant density of Melanoplus EPV DNA in cesium chloride was calculated to be 1.678 g/cm³, which corresponds to a base ratio of 18.6 mole% guanine + cytosine.     

Simple methods of isolation of mitochondrial DNA in vertebrates

Two rapid and simple methods for isolating DNA from certain species of vertebrates are approbated. The both methods exclude the stage of centrifugation in the gradient of cesium chloride. The isolated DNA is hydrolyzed specifically by restricted endonucleases. Applicability of the mentioned methods is shown.     

Uptake of exogenous DNA by carrot protoplasts

Summary An erroneous measurement of DNase-resistant adsorption of donor DNA by plant cell protoplasts may result from the use of polycations and metal cations. A DNAase-resistant complex is formed independent of protoplasts as well as during adsorption to either intact or broken protoplasts. Analysis of adsorbed DNA by cesium chloride density-gradient centrifugation showed extensive degradation of donor DNA.     

Isolation and Characterization of Total DNA from Several Endangered Species and Their Allies

A low pH extraction medium with high salts, which avoids ionization and subsequent oxidation of phenolic compounds during tissue grinding and precipitation of large amounts of materials, were successfully used to obtain total DNA from Cathaya argyrophylla Chun et Kuang, Paeonia suffruticosa var. spontanea, Cimici fuga nanchuanensis Hsiao, Adenophora potaninii (Congeneric species with A. lobophylla) etc. The DNA yields, quality and purity were characterized. These isolated DNA could be used directly for RFLP and RAPD analysis which are useful as molecular genetic markers without sedimentation in cesium chloride gradient or column chromatography. A fast, inexpensive and reliable procedure has been developed for detecting the genetic diversity of endangered plants.     

几种濒危植物及其近缘类群总DNA的提取与鉴定

用低ｐＨ 介质,高盐沉淀蛋白质方法成功地从银杉（Ｃａｔｈａｙａ ａｒｇｙｒｏｐｈｙｌｌａ Ｃｈｕｎ ｅｔＫｕａｎｇ）、矮牡丹（Ｐａｅｏｎｉａ ｓｕｆｆｒｕｔｉｃｏｓａ ｖａｒ． ｓｐｏｎｔａｎｅａ）、南川升麻（Ｃｉｍ ｉｃｉｆｕｇａ ｎａｎｃｈｕａｎｅｎｓｉｓＨｓｉａｏ）、裂叶沙参（Ａｄｅｎｏｐｈｏｒａ ｌｏｂｏｐｈｙｌｌａ）的同属种泡沙参（Ａ． ｐｏｔａｎｉｎｉｉ）等植物中提取和部分纯化了细胞总ＤＮＡ,并对其产率、质量和纯度作了鉴定。此方法的关键是用了一个低ｐＨ提取介质,它能有效防止组织破碎及沉淀大量材料时的电离化作用及酚化合物的进一步氧化。所得ＤＮＡ 不需经氯化铯梯度离心或柱层析,直接可用于限制性片断长度多态性（ＲＦＬＰ）及随机扩增的ＤＮＡ多态性（ＲＡＰＤ）等分子水平的遗传标记。为检测濒危植物的遗传多样性提供了一套迅速、简便和可靠的技术方案     

Extraction of DNA from Phytophthora infestans Using QIAGEN Columns

High molecular weight DNA of Phytophthora infestans was extracted using a modification of the commercial QIAGEN column procedure. Both a 'maxi' and 'mini' procedure are described. The maxi procedure utilizes a QIAGEN-tip 500 column while the mini procedure utilizes a QIAGEN-tip 20 column. When fungal protoplasts were used as starting material from 9 g (fresh weight) of mycelium, nearly 500 μg of DNA in the size range of 20–200 kb was obtained and the product was successfully used in construction of a lambda genomic library. The modified QIAGBN method can replace the more timeconsuming, and expensive cesium chloride density gradient centrifugation for extraction of ultra-pure DNA from P. infestans .     

High frequency DNA rearrangements associated with mouse centromeric satellite DNA

A DNA transformed mouse cell line, generated by the microinjection of a pBR322 plasmid containing the herpes thymidine kinase (tk) gene, was observed to exhibit a high frequency of DNA rearrangement at the site of exogenous DNA integration. The instability in this cell line does not appear to be mediated by the tk inserts or the immediately adjacent mouse DNA, but instead may be a consequence of the larger host environment at the chromosomal site of tk insertion. Results obtained from restriction analysis, in situ chromosome hybridizations, and cesium chloride density-gradient fractionations indicate that the tk inserts are organized as a single cluster of direct and inverted repeats embedded within pericentromeric satellite DNA. To determine the molecular identity of the flanking host sequences, one of the mouse-tk junction fragments was cloned, and subsequent restriction and sequence analyses revealed that this DNA fragment consists almost entirely of classical mouse satellite DNA. On the basis of these observations, we suggest that the instability in this cell line may reflect the endogenous instability or fluidity of satellite DNA.     

Isolation and characterization of kinetoplast DNA from Leishmania tarentolae

Kinetoplast DNA (? = 1.703 g/ml.) was isolated by preparative cesium chloride ultracentrifugation in a fixed-angle rotor from total cell DNA of Leishmania tarentolae and examined in terms of sedimentation properties, melting characteristics, and appearance in the electron microscope. It consisted of several molecular types, either free or bound together in associations of variable size: minicircles (molecular weight = 0.56 ± 0.03 × 10⁶), catenated minicircles, “figure 8” molecules, and long molecules. The associations seem to be held together by the long molecules threading through the smaller circles and catenanes. The large associations could be broken down by sonication, DNase II-treatment, or shear forces. Minicircles, catenated dimers, trimers, and small linear fragments were separated on preparative sucrose gradients of sonicated DNA, and S_20,w values were assigned to each molecular type by band sedimentation in the analytical ultracentrifuge.     

Polyomavirus major capsid protein VP1 is capable of packaging cellular DNA when expressed in the baculovirus system.

Using the p2Bac dual multiple cloning site transfer vector, the polyomavirus major capsid protein gene VP1 was cloned for expression in the baculovirus-insect cell expression system. The 5-day-infected cellular lysate from this recombinant preparation was purified by cesium chloride density gradient centrifugation. Capsid-like particles were observed in the resulting preparation. The purified particle preparation was analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and was shown to have accurately expressed the polyomavirus VP1 protein as cloned. It was found that the preparation revealed the presence of host histones in the stained gels, which is indicative of DNA packaging. To determine if cellular DNA was being packaged in the particles, Sf9 insect cells were prelabeled with [3H] thymidine. The label was removed, and the cells were subsequently infected with a recombinant Autographa californica multiple nuclear polyhedrosis virus (AcMNPV) carrying the polyomavirus VP1 gene. Upon purification through three cesium chloride gradients and DNase I treatment, capsid-like particles, containing [3H]thymidine-labeled DNA, were isolated which were found to coincide with hemagglutination activity. Studies have indicated that the AcMNPV appears to have the ability to fragment Sf9 cellular DNA. When infected with the recombinant AcMNPV carrying the VP1 gene of polyomavirus, these host DNA fragments are being packaged by the VPI major capsid protein; further, these DNA fragments have been shown to be approximately 5 kb in size, which corresponds to the size of the native polyomavirus genome. These studies demonstrate that the recombinant polyomavirus VP1 protein has the ability to package DNA in the absence of the minor structural proteins VP2 and VP3 and independently of the polyomavirus T antigens.     

Filter-supported preparation of lambda phage DNA

A rapid and simple method is described for the isolation of DNA from phage lambda which requires neither special equipment nor expensive material such as cesium chloride for ultracentrifugation nor extractions with organic solvents or ethanol precipitation. Microgram quantities of lambda DNA are obtained in less than 2 h from 90-mm plate lysates or 5-ml liquid cultures. The method allows the simultaneous isolation of large numbers of probes, e.g., clones from phage libraries. Lambda phages are precipitated by polyethylene glycol/sodium chloride and recovered by low speed centrifugation onto glass fiber filters positioned in disposable syringes. The DNA of phages is released by a 50% formamide/4 M sodium perchlorate solution, washed in filter-bound form, eluted with a small volume of low-salt buffer or water, and finally recovered by centrifugation. Comparison of the DNA isolated by this method with that obtained by two conventional procedures reveals both a similar recovery and a similar suitability for restriction enzyme digestion and subcloning.     

Interaction of Hoechst 33258 with repeating synthetic DNA polymers and natural DNA

Fluorescence, circular dichroism and sedimentation through cesium chloride gradient techniques were performed to study the physical properties of the binding of the bisbenzimidazole dye Hoechst 33258 (H33258) to natural DNAs and synthetic polynucleotides of defined repeating units. These studies show that Hoechst 33258 exhibits at least two modes of interaction with duplex DNA: (1) a strong base pair specific mode which requires at least 4 consecutive AT base pairs and (2) a weaker mode of binding which is significantly reduced in the presence of high salt (0.4 M NaCl) and exhibits no apparent base specificity. The H33258 binding was found to be sensitive to the substitutions in the minor groove elements of a series of synthetic polynucleotides supporting the model of H33258 binding in the minor groove of the DNA with AT rich sequences. Similar mode of binding was predicted in natural DNAs by methylation of dye-DNA complexes. Footprint analysis of the complex of dye to a pBR322 fragment also supports that a minimum of 4 consecutive AT base pairs are required for H33258 binding to DNA.     

DNA synthesis in isolated mitochondria and mitochondrial extracts from wheat embryos

DNA synthesis was studied using purified wheat embryo mitochondria as well as mitochondrial lysates deprived of endogenous DNA. The optimal conditions for DNA synthesis are very similar in both systems: ATP stimulates dramatically mitochondrial DNA synthesis and magnesium is a better co-factor than manganese, contrary to what has been reported in animal mitochondrial systems. Wheat mitochondrial DNA synthesis is resistant to aphidicolin and strongly inhibited by dideoxythymidine triphosphate and ethidium bromide. Thus, the DNA polymerase involved in this system seems to be the same as that previously purified and characterized from wheat embryo mitochondria (Christopheet al., Plant Science Letters 21: 181, 1981). Two different approaches: restriction endonuclease digestion followed by electrophoresis, and autoradiography and cesium chloride equilibrium centrifugation of mitochondrial DNA, where BrdUTP has been incorporated instead of TTP, show that long stretches of the mitochondrial genome have been synthesized.     

Repetitious DNA in some Anemone Species

The DNA from several Anemone species, which contain different amounts of heterochromatin as revealed by Giemsa staining, was analysed by ultra-centrifugation and renaturation. No satellite band was observed in any of the samples centrifuged in cesium chloride gradients. Renaturation studies showed the presence of repetitive sequences. The proportion of repetitive DNA per genome varied from 53% to 67% and did not correlate with either the DNA content per cell or the relative amount of heterochromatin.     

DNA Replication of Induced Prophage in Haemophilus influenzae

DNA synthesis during transition from the lysogenic state to the lytic cycle and throughout the latter has been studied in Haemophilus influenzae BC200 (HP1c1). Following exposure to ultraviolet light, there is a 30-min delay in DNA synthesis after which there is a rapidly increasing rate of phage DNA synthesis. The phage genome is replicated without extensive utilization of segments or of breakdown products of the bacterial chromosome. The mode of phage DNA replication was investigated by zonal sedimentation of labeled DNA in 5 to 20% neutral and alkaline sucrose gradients. Tritiated thymidine, incorporated during a 2-min pulse given at 38 min, chases rapidly into DNA, sedimenting like linear DNA of approximately 2 x 10(8) daltons, and then, at the expense of label in this peak, chases into slower-sedimenting phage DNA (2 x 10(7) daltons). The fast-sedimenting, rapidly labeled DNA satisfies certain criteria for being a concatenated replicative intermediate. Observations in the electron microscope revealed linear concatemers in the faster-sedimenting material and circular phage-sized DNA in the slower-sedimenting DNA. When induced cells are gently lysed with lysozyme and Brij 58 to maintain DNA-membrane associations and sedimented in neutral sucrose over a cesium chloride shelf, the concatemer is found with the cell-membrane-wall complex. Membrane-associated label chases to membrane-free material sedimenting like deproteinized HP1c1 DNA. When membrane-associated DNA from the cesium chloride shelf is deproteinized and resedimented in neutral sucrose, the sedimentation profile reveals that sedimentation rates of labeled DNA from this complex are indicative of sizes ranging from 2 x 10(8) daltons down to phage-sized pieces of 2 to 3 x 10(7) daltons. A model is presented which places HP1c1-DNA replication on the cell membrane where a concatemer of phage DNA is synthesized and subsequently degraded to phage-equivalent DNA. Phage-equivalent DNA is then either released from the membrane for packaging or is packaged while still membrane associated. Thus, the cell membrane is not only the site of DNA replication during which phage DNA is synthesized in multiple phage-equivalent concatemers but it is also the site at which these concatemers are selectively reduced to phage-sized pieces.