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At least 1,423 records · Page 79Linked to original sources
PubMed1986

DNA conformation of Chinese hamster V79 cells and sensitivity to ionizing radiation.

Chinese hamster V79 cells grown for 20 h in suspension culture form small clusters of cells (spheroids) which are more resistant to killing by ionizing radiation than V79 cells grown as monolayers. This resistance appears to be due to the greater capacity of cells grown in contact to repair radiation damage. Attempts to relate this "contact effect" to differences in DNA susceptibility or DNA repair capacity have provided conflicting results. Two techniques, alkaline sucrose gradient sedimentation and alkaline elution, show no difference in the amounts of radiation-induced DNA single-strand breakage or its repair between suspension or monolayer cells. However, using the alkali-unwinding assay, the rate of DNA unwinding is much slower for suspension cells than for monolayer cells. Interestingly, a decrease in salt concentration or in pH of the unwinding solution eliminates these differences in DNA unwinding kinetics. A fourth assay, sedimentation of nucleoids on neutral sucrose gradients, also shows a significant decrease in radiation damage produced in suspension compared to monolayer cultures. It is believed that this assay measures differences in DNA conformation (supercoiling) as well as differences in DNA strand breakage. We conclude from these four assays that the same number of DNA strand breaks/Gy is produced in monolayer and spheroid cells. However, changes in DNA conformation or packaging occur when cells are grown as spheroids, and these changes are responsible for reducing DNA damage by ionizing radiation.

Animals↗
PubMed1997

Somatic and germ cell mutagenesis in lambda lacZ transgenic mice treated with acrylamide or ethylnitrosourea.

The transgenic Muta Mouse in vivo mutagenesis assay was employed to determine the activity of acrylamide and ethylnitrosourea in liver and germ cells after 3, 10 and 100 days following treatment. Each cell of the Muta Mouse carries 80 copies of the lambda gt10 phage including the bacterial lacZ gene, which act as the target gene for the mutagenesis assay. Groups of Muta Mice were given a single intraperitoneal injection of 80 or 160 mg/kg ethylnitrosourea or 50 or 100 mg/kg acrylamide. The tissues were prepared 3, 10 or 100 days post treatment. The liver genomic DNA was extracted with the manufacturer's standard protocol, while the genomic germ cell DNA was extracted with 4 different methods due to problems encountered in DNA yields and packaging efficiency. The mutation analysis of the lacZ gene was carried out by the positive selective assay method [Gossen et al. (1989) Proc. Natl. Acad. Sci. USA, 86, 7971-7975; Dean and Myhr (1994) Mutagenesis, 9, 183-185]. There was a slight increase due to treatment of the observed mutation frequencies in the acrylamide liver group for all three assay times. From the day 3 group to the day 100 group a time dependent decrease in all the absolute mutant frequencies was detectable. The ethylnitrosourea liver group showed a time- and dose-dependent increase in the mutant frequencies from day 3 to day 100. No meaningful results were obtained for the germ cell tissue assays due to the low amount of genomic DNA extracted which was not packageable in the lambda lacZ assay. At present for the mutagenesis assay of isolated spermatozoa in our laboratory we would be forced to pool tissues from animals to obtain enough DNA for an assay. Since 'jackpot'-animals may exist [Heddle et al. (1992) Mutation Res., 272, 195-203] the individual animals of such a pooled analysis group must be tested before pooling.

Acrylamide↗
PubMed1980

Rescue of abortive T7 gene 2 mutant phage infection by rifampin.

Infection of Escherichia coli with T7 gene 2 mutant phage was abortive; concatemeric phage DNA was synthesized but was not packaged into the phage head, resulting in an accumulation of DNA species shorter in size than the phage genome, concomitant with an accumulation of phage head-related structures. Appearance of concatemeric T7 DNA in gene 2 mutant phage infection during onset of T7 DNA replication indicates that the product of gene 2 was required for proper processing or packaging of concatemer DNA rather than for the synthesis of T7 progeny DNA or concatemer formation. This abortive infection by gene 2 mutant phage could be rescued by rifampin. If rifampin was added at the onset of T7 DNA replication, concatemeric DNA molecules were properly packaged into phage heads, as evidenced by the production of infectious progeny phage. Since the gene 2 product acts as a specific inhibitor of E. coli RNA polymerase by preventing the enzyme from binding T7 DNA, uninhibited E. coli RNA polymerase in gene 2 mutant phage-infected cells interacts with concatemeric T7 DNA and perturbs proper DNA processing unless another inhibitor of the enzyme (rifampin) was added. Therefore, the involvement of gene 2 protein in T7 DNA processing may be due to its single function as the specific inhibitor of the host E. coli RNA polymerase.

DNA Replication↗
PubMed2004

Triplex-forming oligonucleotides - sequence-specific DNA ligands as tools for gene inhibition and for modulation of DNA-associated functions.

The down regulation of gene expression is a promising strategy for molecular medicine and experimental biology. Molecules that bind to the DNA double helix may interfere with gene expression and, in addition to potential therapeutic applications, can be helpful for the investigation of DNA processing, chromatin package, or associated biological processes. Triplex-forming oligonucleotides (TFOs) bind to specific sequences in the DNA double helix via hydrogen bonding interactions. TFOs have been shown to down-regulate gene expression, to induce targeted genomic DNA modifications, to stimulate DNA recombination, and to modulate chromatin organization. Additionally, they may be used as carriers to position DNA-modifying agents to selected sequences. TFO-mediated effects have been mostly described in cell culture, but one study reported TFO activity in a mouse model. Critical issues regarding TFO-based technologies are the development of new oligonucleotide analogues with improved binding affinity, better target selectivity, and sufficient stability in the intracellular environment. A prerequisite for the development of such DNA-binding molecules is the availability of appropriate methods to assess their binding properties quantitatively at the desired target sequence in the genome. This review focuses on recent results regarding gene-inhibitory effects of TFOs in cell culture and methods to evaluate TFO-binding to the desired target sequence in the context of the human genome.

Animals↗
PubMed1989

Ultrastructural localization of viral DNA in thin sections of herpes simplex virus type 1 infected cells by in situ hybridization.

We have used in situ hybridization at the ultrastructural level to localize non-encapsidated and encapsidated herpes simplex virus type 1 (HSV-1) genomes in nuclei of infected rabbit fibroblasts. A biotinylated cloned subgenomic HSV DNA fragment was used as hybridization probe. The probe hybridized to the viral DNA accessible at the surface of Lowicryl sections was revealed by immunogold labeling. Non-encapsidated viral DNA was detected exclusively within the virus-induced central region of 4 h to 17 h infected nuclei. Localization of the probe either near the nuclear envelope or within marginated host chromatin was found only on HSV DNA which was packaged into viral nucleoids. The use in parallel of in situ hybridization with specific staining for DNA and autoradiography after tritiated thymidine incorporation, followed by either conventional fixation of the cells or the nucleoprotein loosening procedure, indicated that non-encapsidated viral DNA and marginated host chromatin formed two juxtaposed compartments without interpenetration even after experimentally produced mild dispersion of the nuclear components.

Animals↗
PubMed2006

Construction of a large phage display antibody library by in vitro package and in vivo recombination.

Capacity and diversity are extremely important to the quality of various phage display libraries. In this work, lambda phage-based in vitro package was applied to construct a filamentous phage display antibody library so as to enlarge its capacity and introduce more sequence diversity in the final library. In vivo recombination via Cre recombinase/lox sites was also exploited to create V(H)/V(L) combination diversity based on multivalent package of lambda phage packaging extracts on phagemid DNA concatemers. The library constructed with 10 microg concatenated phagemid DNA and ten vials of lambda phage packaging extracts was calculated to contain 1.40 x 10(10) independent clones. Higher capacity can be easily achieved when more materials are consumed. This strategy is somewhat more efficient than prior methods.

Antibodies↗
PubMed1999

Conformational studies of the C-terminal domain of bacteriophage Pf1 gene 5 protein.

The gene 5 protein (g5p) of the bacteriophage Pf1 is a 144 residue single-stranded (ss) DNA binding protein involved in replication and packaging of the viral DNA. Compared to the gene 5 proteins of other filamentous bacteriophages, such as fd, the Pf1 g5p has an additional C-terminal sequence ( approximately 40 residues) with an unusual amino acid composition, being particularly rich in proline, glutamine and alanine. This C-terminal sequence is susceptible to limited proteolysis, in contrast to the globular N-terminal domain of the protein. The C-terminal sequence has been shown to play a role in the stabilisation of the protein-ssDNA complex. In the present study, the DNA sequence corresponding to the 38 amino acid residue C-terminal peptide has been cloned and expressed. A variety of biophysical techniques suggest that this peptide has a largely irregular conformation in solution, in contrast to the N-terminal globular domain that is principally beta-sheet. However, circular dichroism (CD) spectroscopy indicates that the peptide can be induced to form a structure that resembles a left-handed polyproline-like (P(II)) helix, suggesting that the C-terminal tail of the protein may adopt a more structured conformation in the appropriate physiological environment.

Amino Acid Sequence↗
PubMed2003

Implication of the product of the bovine herpesvirus type 1 UL25 gene in capsid assembly.

The UL25 ORF of bovine herpesvirus type 1 (BHV-1) was demonstrated recently to represent a gene encoding a 63 kDa viral protein. To investigate the role of this gene in virus replication, a BHV-1 UL25 deletion mutant was constructed. Although the UL25 mutant synthesizes late viral proteins and viral DNA, it fails to produce virus progeny in cells that do not express the UL25 gene, demonstrating that the UL25 protein is essential for the replicative cycle of BHV-1. Moreover, Southern blotting analyses of HindIII-digested DNA from infected non-complementing cells probed with the leftward terminal fragment of the BHV-1 linear genome revealed that the cleavage of the viral DNA produced is not impaired. However, the packaging of this cleaved DNA is compromised severely, since only few full C capsids were observed in infected non-complementing cells by transmission electron microscopy.

Animals↗
PubMed2004

DNA repair in a chromatin environment.

DNA mutations and aberrations are a problem for all forms of life. Eukaryotes specifically have developed ways of identifying and repairing various DNA mutations in a complex and refractory chromatin environment. The chromatin structure is much more than a packaging unit for DNA; it is dynamic. Cells utilize and manipulate chromatin for gene regulation, genome organization and maintenance of genome integrity. Once a DNA aberration has occurred, the various DNA repair machineries interact with chromatin proteins, such as the histone variant H2A.X, and chromatin remodeling machines of the SWI/SNF family to gain access and repair the lesion in a timely manner. Recent studies have thus begun to address the roles of chromatin proteins in DNA repair as well as to dissect the functions of DNA repair machinery in vitro on more physiological, nucleosomal templates.

Animals↗
PubMed1989

Upstream half of adenovirus type 2 enhancer adopts a curved DNA conformation.

The putative enhancer domain of human adenovirus type 2 (Ad2) was revealed to contain a bent DNA structure in the upstream half. By using "deletion analysis", this unusual structure was identified experimentally to span from nucleotide 194 to 269 (figures; nucleotide numbers from the left terminal nucleotide of the viral DNA). This region has almost the same nucleotide sequence as the upstream half of the enhancer and packaging region of Ad5 and, therefore, is thought to contain multiple enhancer elements for transcription and the elements required for packaging of Ad2 DNA. The bent DNA structure of this region was further characterized by analyzing temperature-dependent changes in electrophoretic mobility of the DNA fragments used for bending analysis. Ad2 enhancer provides a good system to investigate the relationship between higher order structure of DNA and transcriptional activation.

Adenoviruses, Human↗
PubMed1996

Properties of the novel herpes simplex virus type 1 origin binding protein, OBPC.

We have recently identified a novel 53-kDa herpes simplex virus type 1 (HSV-1) protein encoded by, and in frame with, the 3' half of the UL9 open reading frame, designated OBPC (K. Baradaran, C. Dabrowski and P. A. Schaffer, J. Virol. 68:4251-4261, 1994). Here we show that OBPC is a nuclear protein synthesized at both early and late times postinfection. In gel-shift assays in vitro-synthesized OBPC bound to oriS site I DNA to form a complex identical in mobility to complex A, generated with infected cell extracts and site I DNA. OBPC inhibited both plaque formation and viral DNA replication in transient assays, consistent with its ability to bind to site I DNA and its limited ability to interact with other essential DNA replication proteins. These properties suggest that OBPC may play a role in the initiation, elongation, or packaging of viral DNA.

DNA-Binding Proteins↗
PubMed1998

Genetic analysis of the UL 15 gene locus for the putative terminase of herpes simplex virus type 1.

The herpes simplex virus (HSV-1) UL15 gene encodes one of the six viral gene products required for viral DNA cleavage and packaging. UL15 is a spliced gene and encodes two separately translated proteins, UL15 and UL15.5. Sequence analysis reveals that UL15 shares homology with gp 17, the large catalytic subunit of the bacteriophage T4 terminase, a protein which cleaves the polymeric T4 DNA into monomers. Both proteins contain a putative ATP binding motif known as the Walker A and B boxes. In this report, immunofluorescence was used to show that UL15 localizes to the nucleus in the absence of any other viral proteins; this indicates that UL15 contains its own nuclear localization signal. In addition, we found that UL15 colocalizes with replication compartments at early times (6 h postinfection). Since, at this time, preformed capsids as well as other cleavage and packaging proteins are also recruited to replication compartments, it seems likely that cleavage and packaging occurs in the same compartments in which DNA synthesis occurs. Also in this report, we have investigated UL15.5, the N-terminally truncated gene product of the UL15 open reading frame (ORF). The start codon has been mapped to Met443 within the UL15 ORF. Furthermore, we have shown that plasmids containing a UL15.5 knockout mutation still complement the growth of UL15 insertion mutant viruses, indicating that UL15.5 is not required for viral growth in cell culture. Last, we constructed a UL15 mutant, UL15C(G263A), in which the invariant Gly263 in the Walker box A of the ATP binding motif (GKT) was substituted with an alanine. We show that the mutant gene fails to support the growth of UL15 insertion mutant viruses, indicating that the putative ATP binding motif of UL15 is indispensable for its function.

Animals↗
PubMed2003

Syndromes of disordered chromatin remodeling.

Syndromes of disordered 'chromatin remodeling' are unique in medicine because they arise from a general deregulation of DNA transcription caused by mutations in genes encoding enzymes which mediate changes in chromatin structure. Chromatin is the packaged form of DNA in the eukaryotic cell. It consists almost entirely of repeating units, called nucleosomes, in which short segments of DNA are wrapped tightly around a disk-like structure comprising two subunits of each of the histone proteins H2A, H2B, H3 and H4. Histone proteins are covalently modified by a number of different adducts (i.e. acetylation and phosphorylation) that regulate the tightness of the DNA-histone interactions. Mutations in genes encoding enzymes that mediate chromatin structure can result in a loss of proper regulation of chromatin structure, which in turn can result in deregulation of gene transcription and inappropriate protein expression. In this review we present examples of representative genetic diseases that arise as a consequence of disordered chromatin remodeling. These include: alpha-thalassemia/mental retardation syndrome, X-linked (ATR-X); Rett syndrome (RS); immunodeficiency-centromeric instability-facial anomalies syndrome (ICF); Rubinstein-Taybi syndrome (RSTS); and Coffin-Lowry syndrome (CLS).

Chromatin Assembly and Disassembly↗
PubMed1999

Allele replacement: an application that permits rapid manipulation of herpes simplex virus type 1 genomes.

Herpes simplex virus (HSV) is a new platform for gene therapy. We cloned the human herpesvirus HSV-1 strain F genome into a bacterial artificial chromosome (BAC) and adapted chromosomal gene replacement technology to manipulate the viral genome. This technology exploits the power of bacterial genetics and permits generation of recombinant viruses in as few as 7 days. We utilized this technology to delete the viral packaging/cleavage (pac) sites from HSV-BAC. HSV-BAC DNA is stable in bacteria and the pac-deleted HSV-BAC (p45-25) is able to package amplicon plasmid DNA as efficiently as a comparable pac-deleted HSV cosmid set when transfected into mammalian cells. Moreover, the utility of bacterial gene replacement is not limited to HSV, since most herpesviruses can be cloned as BACs. Thus, this technology will greatly facilitate genetic manipulation of all herpesviruses for their use as research tools or as vectors in gene therapy.

Animals↗
PubMed1988

[Restriction map of permuted DNA of Erwinia carotovora temperate bacteriophage 59].

The cyclic permutation and terminal redundancy were found in the genomes of Erwinia carotovora temperate bacteriophage 59 by electron microscopic studies. The headful mechanism for bacteriophage DNA cleavage and packaging during the phage morphogenesis was confirmed by the restriction analysis technique. Restriction map of the bacteriophage 59 DNA was constructed for restriction endonucleases BamHI, Bg1II, Eco31, Sa1I, SmaI, EcoRI.

Bacteriophages↗
PubMed1988

Effect of phi X C protein on leading strand DNA synthesis in the phi X174 replication pathway.

The influence of the bacteriophage phi X174 (phi X) C protein on the replication of bacteriophage phi X174 DNA has been examined. This small viral protein, which is required for the packaging of phi X DNA into proheads, inhibits leading strand DNA synthesis. The inhibitory effect of the phi X C protein requires a DNA template bearing an intact 30-base pair (bp) phi X origin of DNA replication that is the target site recognized by the phi X A protein. Removal of nucleotides from the 3' end of this 30-bp conserved origin sequence prevents the inhibitory effects of the phi X C protein. Leading strand replication of supercoiled DNA substrates containing the wild-type phi X replication origin results in the production of single-stranded circular DNA as well as the formation of small amounts of multimeric and sigma structures. These aberrant products are formed when the termination and reinitiation steps of the replication pathway reactions are skipped as the replication fork moves through the origin sequence. Replication carried out in the presence of the phi X C protein leads to a marked decrease in these aberrant structures. While the exact mechanism of action of the phi X C protein is not clear, the results presented here suggest that the phi X C protein slows the movement of the replication fork through the 30-bp origin sequence, thereby increasing the fidelity of the termination and reinitiation reactions. In keeping with the requirement for the phi X C protein for efficient packaging of progeny phi X DNA into proheads, the phi X C protein-mediated inhibition of leading strand synthesis is reversed by the addition of proteins essential for phi X bacteriophage formation. Incubation of plasmid DNA substrates bearing mutant 30 base pair phi X origin sequences in the complete packaging system results in the in vitro packaging and production of infectious particles in a manner consistent with the replication activity of the origin under study.

Bacteriophage phi X 174↗
PubMed2006

L1 retrotransposons in human cancers.

Retrotransposons like L1 are silenced in somatic cells by a variety of mechanisms acting at different levels. Protective mechanisms include DNA methylation and packaging into inactive chromatin to suppress transcription and prevent recombination, potentially supported by cytidine deaminase editing of RNA. Furthermore, DNA strand breaks arising during attempted retrotranspositions ought to activate cellular checkpoints, and L1 activation outside immunoprivileged sites may elicit immune responses. A number of observations indicate that L1 sequences nevertheless become reactivated in human cancer. Prominently, methylation of L1 sequences is diminished in many cancer types and full-length L1 RNAs become detectable, although strong expression is restricted to germ cell cancers. L1 elements have been found to be enriched at sites of illegitimate recombination in many cancers. In theory, lack of L1 repression in cancer might cause transcriptional deregulation, insertional mutations, DNA breaks, and an increased frequency of recombinations, contributing to genome disorganization, expression changes, and chromosomal instability. There is however little evidence that such effects occur at a gross scale in human cancers. Rather, as a rule, L1 repression is only partly alleviated. Unfortunately, many techniques commonly used to investigate genetic and epigenetic alterations in cancer cells are not well suited to detect subtle effects elicited by partial reactivation of retroelements like L1 which are present as abundant, but heterogeneous copies. Therefore, effects of L1 sequences exerted on the local chromatin structure, on the transcriptional regulation of individual genes, and on chromosome fragility need to be more closely investigated in normal and cancer cells.

Journal Article↗