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At least 1,117 records · Page 62Linked to original sources
PubMed1981

Characterization of coliphage lambda hybrids carrying DNA fragments from Herpes simplex virus type 1 defective interfering particles.

We describe the characterization of 34 hybrid lambda bacteriophages carrying EcoRI fragments obtained from DNA of defective interfering particles of the Patton strain of Herpes simplex virus type 1 (HSV-1). All cloned fragments contained S region terminal repeat sequences (TRs) fused to unique HSV-1 DNA. Several fragments contained deletions and rearrangements not described previously for DNA of HSV-1 defective interfering particles. A model describing the generation of defective interfering DNA based on recombination events involving the terminal "a" sequence as presented.

Bacteriophage lambda↗
PubMed1992

Identification of a genomic DNA fragment containing the Drosophila melanogaster ovarian tumor gene (otu) and localization of regions governing its expression.

We have identified a genomic DNA fragment which restores fertility to mutants of the ovarian tumor locus (otu) of Drosophila melanogaster. Germ-line transformants bearing this fragment express otu mRNA with the same tissue specificity as, and at levels comparable to, the wild-type otu gene. Transcription from the otu promoter, P(otu), which lacks a TATA element, appears to be initiated at multiple transcription start points (tsp) within an 80-bp region. Deletion of sequences upstream of the tsp indicates that a region between nucleotides -190 and -310 is required for proper expression from the otu gene. A DNA fragment containing 452 bp upstream and 126 bp downstream from the tsp is able to direct expression of the Escherichia coli lacZ gene in the germ cells of the ovary and testis, indicating that cis-acting regulatory elements governing these expression patterns are located in a 578-bp region surrounding the multiple tsp.

Animals↗
PubMed1996

Excitotoxic lesion of rat brain with quinolinic acid induces expression of p53 messenger RNA and protein and p53-inducible genes Bax and Gadd-45 in brain areas showing DNA fragmentation.

Several recent studies have demonstrated that expression of the tumour-suppressor gene p53 increases within the nervous system after injury. In various cell lines wild-type-p53, induced by DNA damage, has been shown to function to halt cell-cycle progression and under certain circumstances to induce programmed-cell death or apoptosis. Since wild type-p53 can act as a transcription factor to regulate the expression of p53-responsive genes it is possible that either, or both, functions of p53 are mediated by down-stream effector genes. However wild-type-p53 only weakly activates transcription and it remains to be determined whether p53-responsive genes are expressed in lesioned brain. Here we report that excitotoxic lesion of rat brain with the N-methyl-D-aspartate receptor agonist, quinolinic acid, induces expression of p53 messenger RNA and protein in brain regions showing delayed DNA fragmentation and that expression of p53 messenger RNA precedes DNA damage detected by terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick end-labelling. In addition, using in situ hybridization and immunocytochemistry we demonstrate increased expression of the p53-responsive gene Gadd-45 (preceding p53 expression) and re-expression of the p53-responsive gene Bax (following p53 expression), in these same areas. Bax has been shown to promote neuronal death by interacting with Bcl-2 family members while Gadd-45 expression has been associated with suppression of the cell-cycle and DNA repair. These results suggest that p53 protein may function as an active transcription factor in lesioned brain perhaps initiating the re-expression of Bax in injured brain regions. However, since Gadd-45 precedes p53 expression it appears unlikely that p53 is involved in regulating the early expression of Gadd-45. Taken together however, these results suggest that p53, Bax and Gadd-45 may play important roles in the response (damage/recovery) of the brain following excitotoxic injury.

Animals↗
PubMed2006

Heat shock protein 70 inhibits the nuclear import of apoptosis-inducing factor to avoid DNA fragmentation in TF-1 cells during erythropoiesis.

Loss of mitochondrial membrane potential (DeltaPsi(m)) and release of AIF (apoptosis-inducing factor) from mitochondria are key steps in apoptosis. In TF-1 model, DeltaPsi(m) was depolarized with AIF release during erythroid development. Yet, no DNA fragmentation was observed. When DeltaPsi(m) depolarization had been blocked, erythropoiesis was suppressed. Interestingly, heat shock protein 70 (Hsp70) was found transiently upregulated during depolarization and it retained AIF in the cytosol to avoid DNA damages. When Hsp inhibitor was added, DNA fragmentation occurred. We show this mechanism for the first time in erythropoiesis how cells with DeltaPsi(m) depolarization and AIF release escape apoptosis.

Apoptosis Inducing Factor↗
PubMed1992

Genetic analysis of an aphid endosymbiont DNA fragment homologous to the rnpA-rpmH-dnaA-dnaN-gyrB region of eubacteria.

Buchnera aphidicola is a Gram- eubacterium with a DNA G+C content of 28-30 mol%. This organism is an obligate intracellular symbiont of aphids. To determine its similarity to or difference from other eubacteria, a 4.9-kb DNA fragment from B. aphidicola containing the gene homologous to Escherichia coli dnaA (a gene involved in the initiation of chromosome replication) was cloned into E. coli and sequenced. The order of genes on this fragment, 60K-10K-rnpA-rpmH-dnaA-dnaN-gyrB, was similar to that found in other eubacteria. The sole difference was the absence of recF between dnaN and gyrB. The deduced amino acid sequence of these proteins resembled those of E. coli by a 41 to 83% identity. Except for E. coli, in all the eubacteria so far examined, dnaA is preceded by multiple 9-nucleotide repeats known as a DnaA boxes. No DnaA boxes were detected in the endosymbiont DNA. The possibility that this observation is a consequence of the low G+C content of this DNA fragment (14 mol% G+C) is unlikely since in Mycoplasma capricolum this fragment (19 mol% G+C) has eight DnaA boxes (Fujita et al., 1992). The presence of the sequence, GATC, recognized by the Dam methyl-transferase system, only within six regions coding for proteins suggests that methylation is not a factor in the regulation of the initiation of endosymbiont chromosome replication.

Amino Acid Sequence↗
PubMed1986

Recombination of homologous DNA fragments transfected into mammalian cells occurs predominantly by terminal pairing.

The mechanism by which double-strand cleavages stimulate the joining of plasmid DNA fragments introduced into cultured mammalian cells was investigated by cotransfecting pairs of plasmids encoding deletion mutations in a dominant selectable gene into LMtk- cells. Plasmid recombination substrates were produced by creating deletions of different sizes within the neo coding region of the pSV2neo plasmid. Complementing pairs of deleted plasmid DNAs were linearized at specific unique sites before cotransfection into mouse LMtk- cells by the calcium phosphate precipitation method. Cleaving one donor plasmid produced a 4- to 10-fold stimulation in the production of colonies able to survive in medium containing G-418. The linearization of the second plasmid further increased the efficiency by another factor of 6 to 15 when the cut was made on the opposite side of the homology, approximately equidistant from the center of the overlap. Fifty-seven individual G-418-resistant colonies representing the products of individual crosses were isolated, and the genomic DNAs containing the presumably integrated, functional recombinant neo genes were analyzed on Southern blots. A band consistent with the exchange of markers flanking the neo gene was present in 90% of the DNAs examined. In only one case was the pattern indicative of either a double crossover or a gene conversion event. These results support the idea that homologous extrachromosomal DNA fragments are joined through annealing of overlapping single-stranded ends. This DNA-joining phenomenon may represent the activity of cellular DNA repair enzymes; its relationship to genetic recombination occurring at the chromosomal level remains to be determined.

Adenine Phosphoribosyltransferase↗
PubMed1989

A model relating cell survival to DNA fragment loss and unrepaired double-strand breaks.

The model of radiation action that is presented relates the surviving fraction of irradiated cells to unrepaired DNA double-strand breaks (DSBs). The following assumptions are made in the model: (i) A DNA fragment created by the induced DSBs may move out of its chromosome (become lost), and the probability of that process depends on the fragment size. (ii) An irradiated cell will lose its proliferative capacity if it has an unrepaired DSB (including DNA fragments) at certain points in the cell cycle. Mathematical expressions of the model yield the dose and time dependencies of the surviving fraction, the number of unrepaired DSBs, and the number of prematurely condensed chromosome fragments. Radiobiological phenomena described include effects of low dose rate, delayed plating, hypertonic solution, araA, and high-LET radiation. The calculated dose dependence of the residual number of unrepaired DSBs for ataxia telangiectasia and normal fibroblast cells is very close to the experimentally obtained [M. N. Cornforth and J. S. Bedford, Radiat. Res. 111, 385-405 (1987)] total number of chromosomal aberrations. This leads to the conclusion that each unrepaired DSB becomes a chromosomal aberration. Analysis in terms of the model shows that the radiosensitivity of various cell lines is predominantly due to the different amounts of time available for DSB repair in these cells.

Cell Survival↗
PubMedDate not supplied

[Cloning, structure and features of a Saccharomyces cerevisiae DNA fragment causing the expression of reporter genes].

A DNA fragment "PX" of 240 b.p. was isolated at random from the genomic sequences of S. cerevisiae by using a plasmid that contained a promoterless reporter gene lacZ of E. coli. "PX" was capable of activating synthesis of three reporter genes (pho5 from yeast and bacterial lacZ and neo) in yeast cells bidirectionally. Results of Southern-blot hybridization with yeast genomic DNA suggest that the cloned sequence is represented in at least ten copies per cell. Nucleotide sequence of "PX" shows that DNA contains putative TATA elements and four tandems of inverted repeats: [sequence: see text].

Autoradiography↗
PubMedDate not supplied

Penclomedine-induced DNA fragmentation and p53 accumulation correlate with reproductive cell death in colorectal carcinoma cells with altered p53 status.

Penclomedine, a synthetic pyridine derivative, has documented antitumor activity and is being investigated in clinical trials. Its mechanism of action is unknown although it may be metabolized to a free radical, DNA-reactive species. We previously reported that telomerase positive colorectal carcinoma (RKO) cells with abrogated p53 function were more sensitive to penclomedine than were telomerase positive cells with wild-type p53. The present study demonstrates that significant differences in DNA fragmentation in response to penclomedine were observed in RKO cells lacking functional p53 compared with RKO cells with normal p53 function. No differences in DNA fragmentation in response to ionizing radiation were seen in RKO cells with normal or abrogated p53 function. RKO cells with functional p53 respond to penclomedine treatment with a dose-dependent increase in p53 protein levels. However, RKO cells with abrogated p53 function did not show any such change in p53 protein levels. Further, p53-independent increase of p21 was observed, although the significance of this response remains uncertain. These studies suggest that penclomedine may have a therapeutic advantage in killing cells that have abrogated p53 function.

Antineoplastic Agents↗
PubMed1992

The 5'-terminal phosphates slow migration of single-stranded DNA fragments during electrophoresis in nondenaturing acrylamide gels.

Removal of the 5'-terminal phosphate results in an observable acceleration of the migration of single-stranded DNA fragments in the course of electrophoresis in nondenaturing acrylamide gels. This effect was observed with fragments 30-450 nucleotides in length. The relative difference in the migration of dephosphorylated and phosphorylated fragments depends on their length and primary structure and on the conditions of electrophoresis. The distinct mobility can advantageously be used to determine the level of terminal phosphorylation of DNA fragments during the work with phosphatases and polynucleotide kinases.

Base Sequence↗
PubMed1986

A molecular dynamics computer simulation of an eight-base-pair DNA fragment in aqueous solution: comparison with experimental two-dimensional NMR data.

The structure and dynamics of an 8-base-pair DNA fragment (dCGCAACGC/dGCGTTGCG) in aqueous solution (14 Na+ ions, 1231 water molecules) have been simulated by using the molecular-dynamics method. Interproton distances have been calculated for various structures and are compared with a set of 174 distances which have been derived from 2D NOE experiments. The averaged MD structures are compared with ideal A-DNA and B-DNA structures in terms of helix parameters, dihedral angles, and so forth. The hydration of various atoms of the DNA fragment and of the Na+ ions is analyzed by calculating coordination numbers and first-neighbor shell residence times.

Base Composition↗
PubMed1994

Analysis of different DNA fragments of Corynebacterium glutamicum complementing dapE of Escherichia coli.

In Corynebacterium glutamicum L-lysine is synthesized simultaneously via the succinylase and dehydrogenase variant of the diaminopimelate pathway. Starting from a strain with a disrupted dehydrogenase gene, three different-sized DNA fragments were isolated which complemented defective Escherichia coli mutants in the succinylase pathway. Enzyme studies revealed that in one case the dehydrogenase gene had apparently been reconstituted in the heterologous host. The two other fragments resulted in desuccinylase activity; one of them additionally in succinylase activity. However, the physical analysis showed that structural changes had taken place in all fragments. Using a probe derived from one of the fragments we isolated a 3.4 kb BamHI DNA fragment without selective pressure (by colony hybridization). This was structurally intact and proved functionally to result in tenfold desuccinylase overexpression. The nucleotide sequence of a 1966 bp fragment revealed the presence of one truncated open reading frame of unknown function and that of dapE encoding N-succinyl diaminopimelate desuccinylase (EC 3.5.1.18). The deduced amino acid sequence of the dapE gene product shares 23% identical residues with that from E. coli. The C. glutamicum gene now available is the first gene from the succinylase branch of lysine synthesis of this biotechnologically important organism.

Amidohydrolases↗
PubMed2003

High-frequency genetic recombination and reactivation of orthopoxviruses from DNA fragments transfected into leporipoxvirus-infected cells.

Poxvirus DNA is not infectious because establishing an infection requires the activities of enzymes packaged in the virion. This barrier can be overcome by transfecting virus DNA into cells previously infected with another poxvirus, since the resident virus can provide the trans-acting systems needed to reactivate transfected DNA. In this study we show that cells infected with a leporipoxvirus, Shope fibroma virus (SFV), can reactivate vaccinia virus DNA. Similar heterologous packaging systems which used fowlpox-infected cells to reactivate vaccinia virus have been described, but SFV-infected cells promoted a far more efficient reaction that can produce virus titers exceeding 10(6) PFU/ micro g of transfected DNA. SFV-promoted reactions also exploit the hyperrecombinogenic systems previously characterized in SFV-infected cells, and these coupled recombination and reactivation reactions could be used to delete nonessential regions of the vaccinia virus genome and to reconstruct vaccinia virus from overlapping DNA fragments. SFV-catalyzed recombination reactions need only two 18- to 20-bp homologies to target PCR amplicons to restriction enzyme-cut vaccinia virus vectors, and this reaction feature was used to rapidly clone and express a gene encoding fluorescent green protein without the need for plaque purification or selectable markers. The ability of SFV-infected cells to reactivate fragments of vaccinia virus was ultimately limited by the number of recombinational exchanges required and one cannot reconstruct vaccinia virus from multiple PCR fragments spanning essential portions of the genome. These observations suggest that recombination is an integral part of poxvirus reactivation reactions and provide a useful new technique for altering the structure of poxvirus genomes.

Animals↗
PubMedDate not supplied

A fast and sensitive technique to study the kinetics and the concentration dependencies of DNA fragmentation during drug-induced apoptosis.

Apoptotic cell death with its characteristic coordinated cellular breakdown can be triggered by cytotoxic drugs. One prominent feature that differentiates apoptotic from necrotic cell death is the caspase-mediated activation of an endonuclease that internucleosomally cleaves DNA resulting in the so-called apoptotic DNA ladder. Here we report a new rapid, sensitive and inexpensive column separation technique to study drug-induced DNA fragmentation from 10(6) or less cells. This technique, which is based on a modified plasmid spin column kit, avoids the use of hazardous chemicals. With this procedure and subsequent densitometric analysis it was possible to study the concentration dependencies and the kinetics of drug-induced DNA fragmentation. The applicability of this technique is shown for okadaic acid- and cantharidic-acid-treated pituitary GH(3) cells as well as highly okadaic-acid-resistant sublines. These studies allowed us to compare as well as to differentiate the effects and potencies of these structurally different but functionally quite similar inhibitors of ser/thr phosphatases 1 and 2A.

Animals↗
PubMed1984

Expression of Epstein-Barr virus (EBV) DNA and cloned DNA fragments in human lymphocytes following Sendai virus envelope-mediated gene transfer.

Purified EBV DNA and cloned DNA fragments were trapped in Sendai virus (SV) envelopes during envelope reconstitution. The DNA-loaded reconstituted envelopes (RSVE/DNA) served as gene-transfer vehicles using the capability of RSVE to fuse with normal and tumor cells. The efficiency of RSVE-mediated EBV DNA transfer into lymphoid tumor cells and fresh human lymphocytes was 5-10% of the enveloped 3H-labeled EcoRI fragment B of EBV DNA. Purified intracellular EBV (B95-8 strain) DNA induced EBV nuclear antigen (EBNA) in 0.2-1% of human lymphocytes, transiently stimulated cellular DNA synthesis, but did not fully transform cells. Cloned Sal I F1 fragment [approximately equal to 9 kilobase pairs (kbp)] and a smaller BamHI K (5.2 kbp) fragment from the same region of B95-8 EBV DNA induced EBNA in 2-4% of human lymphocytes but did not stimulate DNA synthesis nor transform cells. Cloned BamHI D1 fragment (approximately equal to 9 kbp) from AG-876 virus DNA, or a combination of cloned BamHI X and H fragments (approximately equal to 2 and 7 kbp, respectively) from the similar region of B95-8 virus DNA, significantly stimulated lymphocyte DNA synthesis, but EBNA could not be detected and transformation was not achieved. Early antigen and viral capsid antigen were not observed with any of the fragments tested. Our results suggest that the induction of EBNA and stimulation of lymphocyte proliferation are not controlled by the same region of EBV DNA.

Base Sequence↗
PubMed1991

Comparison of the effect of hydroxyurea and methotrexate on DNA fragmentation at various reaction conditions.

Using the changes in DNA breakage as a marker of DNA damage, the direct action of hydroxyurea (HU) and methotrexate (MTX) on DNA was examined. The experimental design was to expose isolated DNA to HU and MTX alone or HU and MTX with accelerators of free radical reaction (H2O2, Fe..) and to determine DNA fragmentation assessed by electrophoresis. The results indicated that HU can damage DNA, but to demonstrate this ability it needs H2O2, Fe.. or prolonged incubation in solution. Unlike HU, MTX with H2O2 was ineffective; MTX with Fe.. at certain degree protected DNA against lesions induced by Fe.. alone. It is concluded that despite several common features of HU- and MTX-induced toxic side-effects in the cells suggesting interference of these drugs with free radical reactions, their direct effect on DNA under oxidizing conditions is quite different at least at the concentrations used by us.

DNA↗
PubMed2004

Inhibition of oocyte fertilization by assisted reproductive techniques and increased sperm DNA fragmentation in the presence of Candida albicans: a case report.

The effects of Candida albicans on sperm parameters and the outcome of infertility treatment are unclear. This report describes a lack of fertilization after assisted reproductive techniques and increased sperm DNA fragmentation in an infertile patient with male accessory gland infection due to Candida albicans. He had normal sperm parameters and, therefore, underwent conventional IVF for a female factor of infertility. No spermatozoa or only one spermatozoon per oocyte were found attached to the zona pellucida of the six mature oocytes retrieved. A new semen sample was then requested from the patient to perform intracytoplasmic sperm injection (ICSI) on the same oocytes, but again no fertilization resulted. Candida albicans was detected in the medium where spermatozoa were co-incubated with oocytes and subsequently in the urethral swabs. It did not have any detrimental effect on sperm parameters soon after ejaculation or following separation of motile spermatozoa by swim-up technique. Fertilization failure after assisted reproduction treatment was associated with an increased percentage of motile spermatozoa having chromatin packaging abnormalities, externalization of phosphatidylserine and DNA fragmentation. In conclusion, Candida albicans did not affect sperm parameters, but increased sperm chromatin packaging damage and apoptosis that might have caused fertilization failure after assisted reproduction treatment in this couple.

Adult↗
PubMed1996

Chromatin isolated from viable human PBLs contains DNA fragmented to >/=50 kb.

Massive chromatin fragmentation (around 50 kb, to several hundred kb) is observed in nuclear lysates of human peripheral blood lymphocytes (PBLs) upon their treatment with nuclease-free protein-denaturants. There is a consistent variation in the fragment size distributions that parallels the proliferative activity of the cells. Predominantly approximately 50 kb fragmentation is exhibited in samples from cells immunsuppressed via CD4 crosslinking, as opposed to the heterogeneous, higher molecular weight DNA of anti-TcR/CD3-, phytohemagglutininor concanavalin A-stimulated cells. Tritiated thymidine incorporated into DNA in the latter cultures can be detected in the approximately 50 kb band. Direct lysis of agarose-embedded, live cells in alkali+detergent also yields fragmented DNA, with a single-strand size of >/=50 kb. These data suggest that (i) the cells yielding fragmented DNA were alive at the time of DNA extraction, (ii) either regularly arranged, preformed nicks or hypersensitive sites may be present at every roughly 50-100 kb in the chromatin of PBLs, (iii) these sites or the fragmentation mechanism acting upon them, appear to be regulated in concert with the transit of cells between the resting and proliferative compartments.

Journal Article↗