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At least 559 records · Page 31Linked to original sources
PubMed1991

Three envelope proteins of hepatitis B virus: large S, middle S, and major S proteins needed for the formation of Dane particles.

The infectious particles of hepatitis B virus are called Dane particles and consist of viral nucleic acid encapsulated within a core particle that is enveloped by virus-coded surface proteins. The major S protein constitutes a significant fraction of these surface proteins. In addition, there are two other related proteins (large S and middle S), but their role in envelope formation has not yet been elucidated. We modified the translation initiation codon ATG of each of the envelope proteins by site-directed mutagenesis and found that mutant genomes that did not produce one or two of these proteins were unable to form Dane particles. The particles released into the culture medium by such mutants did not carry DNA. Synthesis of virus-coded RNA still occurred normally, and core particles carrying DNA accumulated intracellularly. The DNA in such core particles was mostly in the double-stranded open circular form, in contrast to the normal situation in which the particles contain mostly RNA and its complementary single-stranded DNA or else contain linear DNA that is partially single stranded and otherwise duplex. The role of the large S and middle S proteins in the formation of Dane particles is discussed.

Blotting, Northern↗
PubMed1996

Concerted integration of linear retroviral DNA by the avian sarcoma virus integrase in vitro: dependence on both long terminal repeat termini.

We have reconstituted integration reactions in vitro with specially designed donor DNAs, a supercoiled plasmid acceptor, purified bacterium-derived Rous sarcoma virus integrase (IN), and a host cell DNA-bending protein, HMG1. The duplex donor DNAs are approximately 300 deoxynucleotides in length and contain only 15 bp of the RSV U3 and U5 termini at the respective ends. The donor has blunt U3 and U5 termini which end with the sequence 5'CATT. Joining of the donor DNA to the acceptor DNA is detected by using a simple biochemical assay. Integration was found to be dependent on both U3 and U5 termini; mutations in either result in a significant decrease in the level of integration in vitro. Restriction digestion of the products is consistent with most integrants representing a concerted integration in which both long terminal repeat termini come from the same donor molecule. The U5 and U3 sequences in the substrate flank a supF tRNA gene, permitting biological selection of integrants. Many integrants have been sequenced, and have all of the hallmarks of authentic viral integration, including the removal of a terminal TT dinucleotide from each donor DNA end, and duplication of acceptor sequences at the integration site without introducing deletions into the acceptor. Target site selection in the acceptor plasmid was random except that the orientation of integrants selected was apparently influenced by supF transcription. Mutations which substituted the conserved CA dinucleotide with a GA pair led to a decreased rate of integration. In 2 of 14 mutant integrants sequenced, deoxynucleotides were deleted from either the U5 or U3 terminus. In one instance, an internal CA dinucleotide was used, which resulted in a 10-bp U5 donor deletion. In the other, an internal GA dinucleotide was used, which produced a 5-bp U3 donor deletion. Both of these integrants provide further evidence that concerted integration in this reconstituted system requires interactions between IN and the U3 and U5 termini from the same donor molecule.

Avian Sarcoma Viruses↗
PubMed2001

Duck hepatitis B virus replication in primary bile duct epithelial cells.

Primary cultures of intrahepatic bile duct epithelial (IBDE) cells isolated from duckling livers were successfully grown for studies of duck hepatitis B virus (DHBV). The primary IBDE cells were characterized by immunohistochemistry using CAM 5.2, a cytokeratin marker which was shown to react specifically to IBDE cells in duck liver tissue sections and in primary cultures of total duck liver cells. Immunofluorescence assay using anti-duck albumin, a marker for hepatocytes, revealed that these IBDE cultures did not appear to contain hepatocytes. A striking feature of these cultures was the duct-like structures present within each cell colony of multilayered IBDE cells. Normal duck serum in the growth medium was found to be essential for the development of these cells into duct-like structures. When the primary cultures of duck IBDE cells were acutely infected with DHBV, dual-labeled confocal microscopy using a combination of anti-DHBV core proteins and CAM 5.2 or a combination of anti-pre-S1 proteins and CAM 5.2 revealed that the IBDE cell colonies contained DHBV proteins. Immunoblot analysis of these cells showed that the DHBV pre-S1 and core proteins were similar to their counterparts in infected primary duck hepatocyte cultures. Southern blot analysis of infected IBDE preparations using a digoxigenin-labeled positive-sense DHBV riboprobe revealed the presence of hepadnavirus covalently closed circular (CCC) DNA, minus-sense single-stranded (SS) DNA, double-stranded linear DNA, and relaxed circular DNA. The presence of minus-sense SS DNA in the acutely infected IBDE cultures is indicative of DHBV reverse transcriptase activity, while the establishment of a pool of viral CCC DNA reveals the ability of these cells to maintain persistent infection. Taken collectively, the results from this study demonstrated that primary duck IBDE cells supported hepadnavirus replication as shown by the de novo synthesis of DHBV proteins and DNA replicative intermediates.

Animals↗
PubMed2003

Feline foamy virus genome and replication strategy.

Crucial aspects of the foamy virus (FV) replication strategy have so far only been investigated for the prototypic FV (PFV) isolate, which is supposed to be derived from nonhuman primates. To study whether the unusual features of this replication pathway also apply to more-distantly related FVs, we constructed feline FV (FFV) infectious molecular clones and vectors. It is shown by quantitative RNA and DNA PCR analysis that FFV virions contain more RNA than DNA. Full-length linear DNA was found in extracellular FFV by Southern blot analysis. Similar to PFV, azidothymidine inhibition experiments and the transfection of nucleic acids extracted from extracellular FFV indicated that DNA is the functional relevant FFV genome. Unlike PFV, no evidence was found indicating that FFV recycles its DNA into the nucleus.

Animals↗
PubMed2003

A prokaryotic condensin/cohesin-like complex can actively compact chromosomes from a single position on the nucleoid and binds to DNA as a ring-like structure.

We show that Bacillus subtilis SMC (structural maintenance of chromosome protein) localizes to discrete foci in a cell cycle-dependent manner. Early in the cell cycle, SMC moves from the middle of the cell toward opposite cell poles in a rapid and dynamic manner and appears to interact with different regions on the chromosomes during the cell cycle. SMC colocalizes with its interacting partners, ScpA and ScpB, and the specific localization of SMC depends on both Scp proteins, showing that all three components of the SMC complex are required for proper localization. Cytological and biochemical experiments showed that dimeric ScpB stabilized the binding of ScpA to the SMC head domains. Purified SMC showed nonspecific binding to double-stranded DNA, independent of Scp proteins or ATP, and was retained on DNA after binding to closed DNA but not to linear DNA. The SMC head domains and hinge region did not show strong DNA binding activity, suggesting that the coiled-coil regions in SMC mediate an association with DNA and that SMC binds to DNA as a ring-like structure. The overproduction of SMC resulted in global chromosome compaction, while SMC was largely retained in bipolar foci, suggesting that the SMC complex forms condensation centers that actively affect global chromosome compaction from a defined position on the nucleoid.

Adenosine Triphosphate↗
PubMed1991

In vitro studies on mild alkali induced lesions in DNA.

S1 nuclease hydrolysis, benzoylated naphthoylated DEAE cellulose (BND-cellulose) chromatography as well as certain immunological and genetic techniques have been used to evaluate the effect of mild alkali (pH10.0) on the DNA molecule. Native calf thymus DNA after exposure to alkaline pH10.0 when subjected to S1 nuclease hydrolysis released significant amount of acid soluble nucleotides as compared to the untreated control. With pBR322 DNA, the population of linear DNA species increased on S1 digestion with concomitant reduction in the supercoiled form. BND cellulose chromatographic studies also suggested the formation of single strandedness and/or distortions in the alkali treated DNA molecule. Antisera raised against the alkali treated DNA exhibited high cross-reactivity with both single stranded and Z DNA. Moreover, a significant reduction in transformation frequency of the treated DNA molecule compared with the untreated control further ascertained the structural alterations in DNA as a result of exposure to mild alkali.

Animals↗
PubMed1989

DNA ring closure mediated by protein HU.

The histone-like protein HU serves as an accessory factor that can facilitate the interaction of certain proteins with their specific DNA binding sites. Examples occur in different systems for prokaryotic DNA replication, transcription, and gene regulation. The protein-DNA interactions that are stimulated by HU generally involve coiling or looping of the DNA, and the possibility has been considered that HU exerts its effect by contributing flexibility to different DNA binding sites, but there has been no direct demonstration of this. To explore the possibility that HU can mediate tight DNA curvatures, we studied its effect on the formation of DNA circles when DNA ligase cyclizes short linear DNA fragments. It is demonstrated that HU greatly increases the cyclization rates of all fragments that were examined having lengths greater than 98 base pairs. Fragments of 99, 108, 120, or 126 base pairs could not cyclize in the absence of HU, but cyclization went rapidly with HU, showing that HU can mediate very tight DNA curvatures.

Bacterial Proteins↗
PubMed1989

RecA protein promoted homologous pairing in vitro. Pairing between linear duplex DNA bound to HU Protein (nucleosome cores) and nucleoprotein filaments of recA protein-single-stranded DNA.

RecA protein promotes two distinct types of synaptic structures between circular single strands and duplex DNA; paranemic joints, where true intertwining of paired strands is prohibited and the classically intertwined plectonemic form of heteroduplex DNA. Paranemic joints are less stable than plectonemic joints and are believed to be the precursors for the formation of plectonemic joints. We present evidence that under strand exchange conditions the binding of HU protein, from Escherichia coli, to duplex DNA differentially affects homologous pairing in vitro. This conclusion is based on the observation that the formation of paranemic joint molecules was not affected, whereas the formation of plectonemic joint molecules was inhibited from the start of the reaction. Furthermore, introduction of HU protein into an ongoing reaction stalls further increase in the rate of the reaction. By contrast, binding of HU protein to circular single strands has neither stimulatory nor inhibitory effect. Since the formation of paranemic joint molecules is believed to generate positive supercoiling in the duplex DNA, we have examined the ability of positive superhelical DNA to serve as a template in the formation of paranemic joint molecules. The inert positively supercoiled DNA could be converted into an active substrate, in situ, by the action of wheat germ topoisomerase I. Taken collectively, these results indicate that the structural features of the bacterial chromosome which include DNA supercoiling and organization of DNA into nucleosome-like structures by HU protein modulate homologous pairing promoted by the nucleoprotein filaments of recA protein single-stranded DNA.

Bacterial Proteins↗
PubMed1980

Supranucleosomal organization of sea urchin sperm chromatin in regularly arranged 40 to 50 nm large granular subunits.

The organization of the chromatin of sperm nuclei of sea urchin (Parcentrotus lividus and Sphaerechinus granularis) was studied by electron microscopy using thin sections of fixed cells and spread preparations of chromatin obtained after various procedures involving incubation in low salt buffers. In fixed cells and in moderately dispersed preparations chromatin appeared in the form of fibrillar chains formed by closely apposed, distinctly sized granules that were larger than chromatin subunit structures so far described in other kinds of chromatin (mean diameters of particle units determined were 36 nm, in thin sections, and 47 nm, in spread preparations). Upon prolonged incubation in low salt buffer an increasing number of these large granular units was transformed into extended nucleosomal chains (nucleofilaments). Estimations indicated that the large granules contained 20 to 26 nucleosomes, i.e. 4.8 to 6.2 kb DNA, resulting in a linear DNA contraction ratio of 33 to 55, which is in a similar range as values reported for the supranucleosomal chromatin particle of the SV40 minichromosome but greater than contraction ratios of "superbead" structures. The unravelling of the large supranucleosomal granule into the extended nucleofilament chain in low salt buffers seemed to be a gradual process since intermediate stages of variable particles sizes and shapes were observed. This novel type of chromatin particle is considered to represent an example of a naturally occurring globular supranucleosomal packing unit of chromatin which is predominating, if not the only forms of supranucleosomal levels of chromatin organization and in relation to the special DNA content and histone composition of sea urchin sperm nucleosomes.

Animals↗
PubMed1984

[Optical properties of DNA complexes with antitumor compounds of bivalent platinum].

The optical properties of the DNA complexes with the compounds of bivalent platinum were studied. The compounds differed by the nature of the anionic and neutral ligands and their spatial arrangement about the platinum atom. It was shown that the same as cis-[Pt (NH3)2Cl2] the platinum compounds with the biological activity, i.e. [Pt (en) Cl2], cis-[PtNH3 (Bz) Cl2] and cis-[Pt (NH3)2NO2Cl] induced at low values of r (a ratio of the number of the platinum moles added to the number of the DNA nucleotide moles in the solution) an increase in the amplitude of the positive band in the spectrum of the circular dichroism (CD) of the linear DNA and a marked decrease in the amplitude of the negative band in the spectrum of the CD of the liquid crystalline microphase of DNA formed in the presence of polyethyleneglycol. By the character of the action on the CD spectrum of the linear and condensed DNA [Pt (tetrameen)Cl2] which had no selective antimitotic effect might be referred to the above platinum compounds. Trans-[Pt (NH3)2NO2Cl], [PtNH3PyCl2], cis-[Pt (NH3)2(NO2)2] and [Pt (NH3)3Cl]Cl having no biological activity either induced only a decrease in the amplitude of the positive band in the CD spectrum of the linear DNA or had no effect on the CD spectrum. The effect of these compounds on the CD spectrum of the liquid crystalline microphase of DNA was slightly pronounced or not observed.

Animals↗
PubMed1977

An endonuclease activity of venom phosphodiesterase specific for single-stranded and superhelical DNA.

A homogeneous preparation of venom phosphodiesterase from Crotalus adamanteus possesses an intrinsic endonuclease activity, specific for superhelical (form I) and single-stranded DNA. The phosphodiesterase degrades single-stranded T7 DNA by endonucleolytic cleavages. Duplex T7 DNA is hydrolyzed by the liberation of acid-soluble products simultaneously from the 3' and 5' termini but without demonstrable internal scissions in duplex regions. Since venom phosphodiesterase is known to hydrolyze oligonucleotides stepwise from the 3' termini, the cleavage at the 5' end of duplex T7 DNA is ascribed to an endonuclease activity. Form I PM2 DNA is nicked to yield first relaxed circles and then linear DNA which is subsequently hydrolyzed only from the chain termini. The linear duplex DNA intermediates consist of a discrete series of fragments (11 are usually resolved on agarose gels) with initial molecular weights ranging from 6.3 x 10(6) (the intact PM2 DNA size) to approximately 1 x 10(6). The cleavage of the form I molecule must, therefore, occur at a limited number of unique sites. The enzyme also cleaves nonsuperhelical, covalently closed circular PM2 DNA but at a 10(4) times slower rate. Both the endonuclease activity on form I DNA and the known exonuclease activity co-migrate on polyacrtkanude gels, are optimally active at pH 9, are stimulated by small concentrations of Mg2+, and are similarly inactivated by heat, reducing agents, and EDTA.

DNA, Single-Stranded↗
PubMed1991

Circularization of human immunodeficiency virus type 1 DNA in vitro.

Linear viral DNA present in cytoplasmic extracts of cells newly infected with human immunodeficiency virus type 1 can be induced to form 1-LTR and 2-LTR circles by incubation of the extracts in the presence of added nucleoside triphosphates. No circular DNA forms are detected when extracts are incubated in the absence of added nucleoside triphosphates. Restriction enzyme analysis and polymerase chain reaction analysis with selected primers, as well as DNA sequence analysis of the polymerase chain reaction products, show that most of the 2-LTR circles are the result of autointegration reactions, while 1-LTR circles result from recombination between the long terminal repeats on the linear viral DNA. In addition, a small amount of simple 2-LTR circles, formed by end-to-end joining of the linear viral DNA, is formed in vitro. Integration of the linear viral DNA into heterologous DNA competes effectively with the formation of 2-LTR circles by autointegration. However, concentrations of target DNA which completely block autointegration have no effect on the formation of 1-LTR circles or simple 2-LTR circles. Factors present in extracts of uninfected cells can mediate the formation of 1-LTR circles and simple 2-LTR circles from purified deproteinated linear viral DNA, indicating that viral proteins are not necessary for the formation of these two types of circular viral DNA. These experiments demonstrate that all the transformations of linear viral DNA which occur in the nuclei of cells infected with human immunodeficiency virus type 1 can be reproduced in vitro.

Bacteriophage phi X 174↗
PubMed1993

Study of mechanisms of electric field-induced DNA transfection. V. Effects of DNA topology on surface binding, cell uptake, expression, and integration into host chromosomes of DNA in the mammalian cell.

Neumann and coworkers (Neumann, E., M. Schaefer-Ridder, Y. Wang, and P. H. Hofschneider. 1982. EMBO J. 1:841-845) have shown that the efficiency of pulsed electric field (PEF)-induced DNA transfection of mouse L-cells by the thymidine kinase gene is several times higher for the linear DNA than for the closed circular DNA. Transfection of Escherichia coli bacteria by several plasmids indicates that the transfection efficiency was much higher for the closed circular/supercoiled (sc-) and circular/relaxed (cr-) DNA than for the linearized (In-) DNA (Xie, T. D., L. Sun, H. G. Zhao, J. A. Fuchs, and T. Y. Tsong. 1992. Biophys. J. 63:1026-1031). To resolve these conflicting observations, we have systematically examined electrotransfection of NIH3T3 mouse fibroblast by the plasmids, pRSVcat, pRSVneo, and pRSVgpt. Mg(2+)-facilitated surface binding of DNA before, and DNA uptake by 3T3 cells after treatment with PEF, were monitored by 3H-labeled plasmids. Transfection efficiency was evaluated by both the transient expression of chloramphenicol acetyltransferase (cat) activity 2-3 days after, and the permanent expression of neomycin phosphotransferase (neo) and xanthine-guanine phosphoribosyltransferase (gpt) genes in the transformants 2 weeks after the PEF treatment. Our results indicate that cell surface binding and PEF-induced cell uptake of DNA did not depend on the topology of DNA. However, both the transient and the permanent expression of the plasmids were three to five times more efficient for the cr-DNA and the sc-DNA than for the in-DNA. These results indicate that electrotransfection of cells involves several steps: the cation-dependent binding of DNA to the cell surface, the electric field-driven DNA entry into the cells, the transient expression of DNA, and the integration of DNA into the host chromosomes. For understanding mechanisms of electrotransfection, only the DNA binding to the cell surface and the electric field assisted membrane-crossing of DNA are relevant. Both the expression of the loaded DNA and the DNA integration into the host chromosomes depend more on the properties of the cell and its interactions with a foreign gene. Since these properties and interactions will be similar irrespective of the method chosen to facilitate DNA transfer, they are not relevant for the study of mechanisms of electrotransfection. Our results also support the idea that the PEF-induced cellular uptake of DNA is mainly by the electrophoresis of the surface bound DNA across the plasma membrane.

3T3 Cells↗
PubMed1983

Unusual properties of AKR MCF-247 murine leukemia virus unintegrated proviral DNA.

Analyses of Hirt extracts from endogeneous murine leukemia virus (MuLV)-infected cells revealed the presence of 9-kbp linear DNA and two superhelical forms with one or two tandem copies of the long terminal repeat (LTR). In contrast, cells that were infected with AKR MCF247 MuLV yielded two major linear forms of 9.0 and 8.4 kbp and one discrete superhelical DNA. In addition, there was a heterogeneous population of superhelical DNAs that were larger and smaller than the major superhelical DNA species. Restriction endonuclease treatment of purified linear and superhelical DNAs have revealed that MCF247 MuLV unintegrated viral DNA is very heterogeneous. Evidence is presented that there are at least two linear DNAs; one is 9-kbp full-length linear DNA, whereas the other major form contains a 0.6 to 0.7-kbp deletion in the envelope gene adjacent to the right LTR. In addition, there are two size classes of the LTR in at least the full-length linear DNA. The major superhelical DNA species is a 8.4-kbp form which contains one copy of the LTR. Other heterogeneous superhelical DNAs appear to contain env-gene deletions or partially deleted copies of a tandem LTR region.

AKR murine leukemia virus↗
PubMed1991

Unique DNA plasmid pRS64 associated with chromosomal DNAs of the plant pathogenic fungus Rhizoctonia solani.

Unique DNA sequences homologous to the linear DNA plasmid pRS64 were investigated in chromosomal DNAs of isolates belonging to anastomosis group 4 (AG-4) of the plant pathogenic fungus Rhizoctonia solani. Chromosome-sized DNAs of isolates RI-64 and 1271 of AG-4 were separated into six bands by orthogonal-field-alternation gel electrophoresis and hybridized to a cloned segment of pRS64. A small chromosome-sized DNA band of approximately 1.1 Mb carried the sequences homologous to pRS64 DNA. Sequences homologous to pRS64 were also maintained within the chromosomal DNA of isolate 127.1 of AG-4 which does not possess the plasmid. The plasmid showed no homology to the mitochondrial DNA of isolate 1271. The possibility that the linear plasmid pRS64 may act as a transposable genetic element is discussed.

Blotting, Southern↗
PubMed2000

Sequence requirements for protein-primed initiation and elongation of phage O29 DNA replication.

The double-stranded linear DNA of Bacillus subtilis phage O29 is replicated by a mechanism in which a terminal protein (TP) acts as a primer. The second 3'-terminal nucleotide of the template directs the incorporation of the 5'-terminal nucleotide into the TP, giving rise to the initiation complex TP-dAMP. Elongation then proceeds by a sliding-back mechanism in which the dAMP covalently linked to the TP pairs to the 3'-terminal nucleotide of the template strand to recover full-length DNA. We have studied the sequence requirements for efficient initiation of replication using mutated TP-free double-stranded DNA fragments. Efficient initiation only requires the terminal repetition 5'-AA. The 3'-terminal T, although not used as template, increases the affinity of DNA polymerase for the initiator nucleotide; in addition, although to a minor extent, the third 3'-terminal position also directs the formation of the initiation complex and modulates the initiation rate at the second position. Efficient elongation requires a previous sliding-back, demanding again a repetition of two nucleotides at the 3' end; if the sliding-back is prevented, a residual elongation can proceed directly from the second position or after jumping back from the third to the first position.

Bacillus Phages↗