SEARCH · Search PubMed

Results for “DNA Fragmentation”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 883 records · Page 49Linked to original sources

PubMed1998

Case report: DNA fragmentation in glial cells in a cerebral biopsy from a multiple sclerosis patient.

Multiple sclerosis is characterized by myelin destruction and oligodendrocyte loss. The neuropathological hallmark of the disease is the presence of demyelinated plaques in the central nervous system. We have recently found a gliotoxic factor in MS cerebrospinal fluid which induces programmed cell death in vitro, in glial cells. Here we show DNA fragmentation and glial cell death in biopsy samples, obtained from a patient who underwent surgery with suspicion of tumor, and whose disease record, including brain autopsy, demonstrated an active multiple sclerosis. We used the in situ TUNEL technique, a method which sensitively detects the DNA fragmentation accompanying programmed cell death in tissue sections, and compatible with classical fixation techniques. We found intense DNA fragmentation in nuclei of glial cells at-or very near-to the site of demyelination. A double labeling technique showed that glial fibrillary associated protein positive astrocytes may undergo programmed cell death in multiple sclerosis.

Astrocytes↗

PubMed1998

Calpain inhibitors, but not caspase inhibitors, prevent actin proteolysis and DNA fragmentation during apoptosis.

Apoptosis, or programmed cell death, involves a cascade of regulatory events leading to the activation of specific proteases. However, the key substrates for these proteases remain to be identified. We previously demonstrated that levels of five unidentified polypeptides were specifically increased in neurons from embryonic chicken ciliary ganglia undergoing apoptosis by trophic deprivation. Here we show by microsequencing of two of these polypeptides that they are fragments of actin. One of them represents cleavage of actin at the site of interaction with DNase I. The same actin fragments are also found at early stages of apoptosis in chicken and rat dorsal root ganglion neurons, chicken spinal motoneurons and rat thymocytes. Actin fragmentation may play a role in the apoptotic process, since calpain inhibitors I and II both inhibit neuronal death and suppress actin fragmentation. In contrast, caspase (ICE family) inhibitors, though effective in delaying neuronal death, do not prevent actin cleavage or DNA fragmentation. These results indicate a key role for calpain-like proteases in neuronal programmed cell death and suggest that actin fragmentation in the cell is correlated with subsequent DNA fragmentation.

Actins↗

PubMed1991

Using sodium chloride step gradients to fractionate DNA fragments.

A method is described for the separation of DNA fragments by ultracentrifugation through a sodium chloride step gradient. The gradients are quickly and easily prepared and require a five- to six-hour centrifugation. Fractionated samples of DNA may be directly examined by agarose gel electrophoresis, then further analyzed by Southern transfer and hybridization. A simple ethanol precipitation followed by several ethanol washes yields fragments that ligate efficiently to vector DNA. The method has been applied to separate chromosomal DNA restriction fragments as well as bacteriophage lambda arms from insert DNA.

Bacillus subtilis↗

PubMed1995

Induction of apoptotic DNA fragmentation by the infection of vesicular stomatitis virus.

Vesicular stomatitis virus (VSV) induced apoptosis of infected HeLa cells. Fragmentation of chromosomal DNA into nucleosomal oligomers as well as a characteristic nuclear fragmentation were observed in the infected cells. The kinetics of the apoptotic response was determined in relation to viral multiplication and cytopathic effect. Comparison of these kinetics revealed that the production of progeny virus occurs at almost similar kinetics to that of the DNA fragmentation, so that viral multiplication is not interrupted by the apoptotic cell damage.

Animals↗

PubMed1993

Ca2+ antagonists inhibit DNA fragmentation and toxic cell death induced by acetaminophen.

Ca2+ accumulates in the nucleus and DNA undergoes enzymatic cleavage into internucleosome-length fragments before acetaminophen and dimethylnitrosamine produce hepatic necrosis in vivo and toxic cell death in vitro. However, Ca(2+)-endonuclease fragmentation of DNA is characteristic of apoptosis, a type of cell death considered biochemically and functionally distinct from toxic cell death. The present studies investigate DNA fragmentation as a critical event in toxic cell death by testing whether the Ca(2+)-calmodulin antagonist chlorpromazine and the Ca2+ channel blocker verapamil prevent acetaminophen-induced hepatic necrosis by inhibiting Ca2+ deregulation and DNA damage. Acetaminophen overdose in mice produced accumulation of Ca2+ in the nucleus (358% of control) and fragmentation of DNA (250% of control) by 6 h, with peak release of ALT occurring at 12-24 h (38,000 U/l). Pretreatment with chlorpromazine prevented increases in nuclear Ca2+ and DNA fragmentation and nearly abolished biochemical evidence of toxic cell death. Verapamil pretreatment also decreased Ca2+ accumulation and DNA damage while attenuating liver injury. The Ca2+ antagonists did not protect against toxic cell death through hypothermia because neither produced the delay in toxicity that is customarily associated with hypothermia. Nor did chlorpromazine or verapamil protect through inhibiting acetaminophen bioactivation. Chlorpromazine failed to diminish glutathione depletion in whole liver and isolated nuclei. Verapamil (250 microM) also failed to alter glutathione depletion in whole liver and had no effect on acetaminophen-glutathione adduct formation by mouse liver microsomes and by cultured mouse hepatocytes. Collectively, these results support the hypothesis that Ca(2+)-induced DNA fragmentation plays a significant role in cell necrosis produced by acetaminophen and may contribute to toxic cell death caused by other alkylating hepatotoxins.

Acetaminophen↗

PubMed1994

A computer simulation accounting for dissimilar electrophoretic behavior between two similarly curved DNA fragments due to a difference in arc-length.

Arc-shaped bent DNA fragments of the same predicted planar curvature but differing in length by 20% were compared in regard to their mobilities in 3 to 10% polyacrylamide. The longer (155 bp) fragment is retarded far more severely than the shorter (124 bp) fragment. The effect of gel concentration in promoting the retardation is far more pronounced for the 155 bp than for the 124 bp fragment. Moreover, a temperature change from 25 degrees C to 4 degrees C does not substantially affect the gel concentration dependent mobility of the 124 bp fragment while it increases the retardation of the 155 bp fragment greatly. The strong increase in retardation brought about by a mere 20% increase in the length of the arc was accounted for by a simple computer simulation of gel electrophoresis which considered the rate of passage of arc-shaped objects through a two-dimensional array of disc-shaped obstacles. Since the simulation relies exclusively on geometric factors, its success in predicting the behavior of the 124 and 155 bp DNA fragments suggests that geometric factors are largely responsible for their electrophoretic properties. The simulation can account for the strong temperature effect on the retardation of a model of the 155 bp DNA in polyacrylamide gels by showing that a decreased degree of random motion has a profound effect on the modeled 155 bp particle, but not on the modeled 124 bp DNA.

Computer Simulation↗

PubMed1978

Localization of the arginine tRNA gene to the D segment of T5 bacteriophage DNA. A new procedure for producing duplex DNA fragments.

The tRNA genes of bacteriophage T5 are located in four clusters on the continuous heavy DNA strand (Chen, M.-J., Locker, J., and Weiss, S.B. (1976) J. Biol. Chem. 251, 536--547). Three of the four clusters are within the DNA C segment; the fourth cluster, to which only tRNAArg has been localized, maps in a 3.02 kilobase (kb) region of which 1.99 kb are at the right end of the C segment and 1.03 kb at the left end of the D segment. In order to localize the tRNAArg gene further and to define its relationship to the C-D nick, we devised a suitable method for preparing T5 DNA fragments whose ends correspond to the position of the T5 DNA nicks contained in the light DNA strand. In this method, DNA is denatured, partially renatured, and digested with low concentrations of S1 nuclease. Agarose-gel electrophoresis of these digests gives a pattern of bands which correlate in size with the pattern expected from the nicked structure of T5 DNA. Annealing of individual purified T5 [35P]tRNA species to the T5 DNA fragments transferred to nitrocellulose filters shows that tRNAArg hybridizes exclusively to the D fragment and is therefore localized to 1.03 kb at the 5' (left) end of the heavy strand of the D segment. This finding suggests that the promotor for this early gene is to the right of the C-D nick in T5 DNA; hence, the C-D nick does not coincide with this early promotor.

Arginine↗

PubMed1992

A flow-cytometric method to study DNA fragmentation in lymphocytes.

A method to measure DNA fragmentation cell by cell in a cell population was implemented based on acridine orange procedure to determine DNA content of single cells by flow cytometry. Using this method it can be observed that the fragmentation process induced by irradiation in thymic cells occurs in a fraction of the population, thus indicating that this process is not evenly distributed over the total population, and that it corresponds to a fast phenomenon in which the cells suddenly lose DNA material.

Acridine Orange↗

PubMed1996

Calcium-dependent, interleukin 1-converting enzyme inhibitor-insensitive degradation of lamin B1 and DNA fragmentation in isolated thymocyte nuclei.

Recent work suggests that the proteolytic degradation of the nuclear lamins is a common event in apoptosis, although the nature of the proteases involved is still not clear. Our previous work showed that the degradation of lamin B1 in glucocorticoid-treated thymocytes occurs via a Ca2+-sensitive mechanism and that exogenous Ca2+ promotes lamin degradation in isolated thymocyte nuclei from untreated cells. Here we demonstrate that peptide-based inhibitors of the interleukin 1beta-converting enzyme family of cysteine proteases (Tyr-Val-Ala-Asp fluoromethyl ketone) and of the nuclear scaffold multicatalytic proteinase (Ala-Pro-Phe chloromethyl ketone) block the degradation of lamin B1 to a 21-kDa fragment in thymocytes treated with glucocorticoid, the Ca2+-mobilizing agent thapsigargin, or antibodies to the T cell receptor. However, among a panel of inhibitors specific for several different proteases implicated in apoptosis, only tosylphenylalanyl chloromethyl ketone and the nuclear scaffold protease inhibitor block lamin degradation, histone H1 cleavage, and DNA fragmentation in isolated thymocyte nuclei incubated with Ca2+. Overexpression of human BCL-2 in nuclei by stable transfection resulted in an inhibition of Ca2+-stimulated lamin degradation and DNA fragmentation, suggesting that endogenous nuclear BCL-2 regulates activation of the nuclear scaffold protease. The results demonstrate the existence of an alternative pathway of lamin degradation and DNA fragmentation mediated by a resident Ca2+-stimulated nuclear protease that is not directly dependent upon activation of the interleukin 1beta-converting enzyme family of cell death regulators.

Amino Acid Chloromethyl Ketones↗

PubMed2003

The 492-bp RM07 DNA fragment from the halophilic Archaea confers promoter activity in all three domains of life.

A 492-bp DNA fragment, designated RM07, was isolated from the chromosomal DNA of the halophilic Archaea, Halobacterium halobium, and was shown to confer promoter activity in Escherichia coli. Sequence analysis revealed that RM07 contained three consensus sequences of the archaeal distal promoter element as well as the typical -35 and -10 box sequences of bacterial promoters. Promoter probe analysis confirmed that RM07 conferred promoter activity in all three domains of life: Archaea (Haloferax volcanii), Eukarya (Saccharomyces cerevisiae) and Bacteria (Escherichia coli). Deletion analysis and site-directed mutagenesis further identified the functional regions within RM07 required for promoter activity. This is the first report of a DNA fragment from Archaea that confers promoter activity in all three domains of life, suggesting that the promoter structure and activity may be viewed as a bridge narrowing the gaps among the different domains of life.

Artificial Gene Fusion↗

PubMed1995

DNA fragmentation in granular cells of human cerebellum following global ischemia.

Vulnerability of human cerebellum in two autopsy cases following global brain ischemia was examined histologically by using a specific in situ nick-end labeling method for DNA breaks. In both cases, DNA fragmentation was observed in approximately one-third of the granular cells in cerebellar cortex, whereas Purkinje cells were still alive and no DNA fragmentation was recognized in the nuclei. The present study suggests that some granular cells of cerebellar cortex are more vulnerable to transient ischemia than Purkinje cells and death of granular cells is induced by an apoptotic DNA fragmentation following global brain ischemia.

Adult↗

PubMed1980

Reaction of systemic lupus erythematosus antinative DNA antibodies with native DNA fragments from 20 to 1,200 base pairs.

Double-stranded DNA fragments of varying sizes were isolated and tested for binding to systemic lupus erythematosus (SLE) antinative DNA antibodies. Fragments of 20-25, 40-50, 90-110, and 160-180 base pairs (bp), along with intermediate-size pieces were isolated by preparative gel electrophoresis of a limited micrococcal nuclease digest of calf thymus DNA. Larger helical polynucleotides of 160-200, 380, 600-1,000, and 1,200 bp were isolated by preparative gel electrophoresis of DNA from chicken erythrocyte nucleosomes and oligonucleosomes. The fragments behaved as base-paired structures as tested by thermal denaturation, resistance to S1 nuclease, and serological assays with antibodies to native or denatured DNA. At a concentration of 0.27 muM, fragments of 20-25 bp were able to react with two SLE sera in competition with native DNA. With these and two other sera, DNA of 40-50 bp was a much more effective competitor. One serum required DNA greater than 180 bp for competition in the concentration range tested. Denatured fragments were much less effective than native fragments. The results emphasize the heterogeneity of SLE antinative DNA antibodies, confirm that secondary structure of the antigen is important for specific binding to these antibodies, and support the suggestion that bivalent binding to one molecule may be important for high functional affinity.

Antibodies↗

PubMed1996

The effect of ethidium bromide on mobility of DNA fragments in agarose gel electrophoresis.

Ethidium Bromide (EtBr) is sometimes added to running buffer during the separation of DNA fragments by agarose gel electrophoresis. It is used because upon binding of the molecule to the DNA and illumination with a UV light source, the DNA banding pattern can be visualized. The mode of binding of EtBr is intercalation between the base pairs. This binding changes the charge, weight, conformation, and flexibility of the DNA molecule. Since DNA molecules are sized by their relative movement through a gel compared to a molecular weight standard, mobility measurements can be critical to size determinations. After running two identical gels, one without EtBr and one with 0.25, 0.5, 0.75 or 1.0 microgram/mL EtBr in the running buffer, the mobilities of lambda HindIII DNA fragments were compared. The mobility of DNA was always less in the gels with EtBr. Using the reptation theory equation, which describes the mobility of DNA molecules through gel, changes in frictional coefficients were calculated. It was determined that the change in frictional coefficients brought about by the addition of EtBr is directly proportional to the fraction of base pairs of a fragment bound to EtBr. This change in friction is greatest in the largest fragments, which suggests that the stiffening of the molecule by the EtBr binding is the cause for the decreased mobility.

Bacteriophage lambda↗

PubMed1998

Protective effects of grape seed proanthocyanidins and selected antioxidants against TPA-induced hepatic and brain lipid peroxidation and DNA fragmentation, and peritoneal macrophage activation in mice.

1. The comparative protective abilities of a grape seed proanthocyanidin extract (GSPE) (25-100 mg/kg), vitamin C (100 mg/kg), vitamin E succinate (VES) (100 mg/kg) and beta-carotene (50 mg/kg) on 12-O-tetradecanoylphorbol-13-acetate (TPA)-induced lipid peroxidation and DNA fragmentation in the hepatic and brain tissues, as well as production of reactive oxygen species by peritoneal macrophages, were assessed. 2. Treatment of mice with GSPE (100 mg/kg), vitamin C, VES and beta-carotene decreased TPA-induced production of reactive oxygen species, as evidenced by decreases in the chemiluminescence response in peritoneal macrophages by approximately 70%, 18%, 47% and 16%, respectively, and cytochrome c reduction by approximately 65%, 15%, 37% and 19%, respectively, compared with controls. 3. GSPE, vitamin C, VES and beta-carotene decreased TPA-induced DNA fragmentation by approximately 47%, 10%, 30% and 11%, respectively, in the hepatic tissues, and 50%, 14%, 31% and 11%, respectively, in the brain tissues, at the doses that were used. Similar results were observed with respect to lipid peroxidation in hepatic mitochondria and microsomes and in brain homogenates. 4. GSPE exhibited a dose-dependent inhibition of TPA-induced lipid peroxidation and DNA fragmentation in liver and brain, as well as a dose-dependent inhibition of TPA-induced reactive oxygen species production in peritoneal macrophages. 5. GSPE and other antioxidants provided significant protection against TPA-induced oxidative damage, with GSPE providing better protection than did other antioxidants at the doses that were employed.

Animals↗

PubMed2000

Detection of DNA fragmentation of myonuclei in myotonic dystrophy by double staining with anti-emerin antibody and by nick end-labeling.

To clarify the occurrence of apoptosis in skeletal muscle in pathological conditions, we studied 44 muscle biopsy specimens by immunohistochemical staining with monoclonal antibody against emerin, which is localized in muscle nuclear membrane, and by ApopTag Plus to detect DNA fragmentation. Five of six patients with myotonic dystrophy (DM) showed three to 35 myonuclei stained with anti-emerin antibody and ApopTag Plus in 1500 muscle fibers. Four of the 18 patients with polymyositis, one of those with thyroid myopathy and one with neurogenic atrophy showed a few myonuclei stained positively by these methods. Our study revealed that DNA fragmentation in myonuclei occurred in skeletal muscle fibers regardless of the type of disease, although the frequency was rather low in all of these diseases except DM. The DNA fragmentation detected in most of the patients with DM suggested a significant role of apoptosis in the pathomechanism of this disease.

Adolescent↗

PubMed2001

Characterization of a Brucella species 25-kilobase DNA fragment deleted from Brucella abortus reveals a large gene cluster related to the synthesis of a polysaccharide.

In the present study we completed the nucleotide sequence of a Brucella melitensis 16M DNA fragment deleted from B. abortus that accounts for 25,064 bp and show that the other Brucella spp. contain the entire 25-kb DNA fragment. Two short direct repeats of four nucleotides, detected in the B. melitensis 16M DNA flanking both sides of the fragment deleted from B. abortus, might have been involved in the deletion formation by a strand slippage mechanism during replication. In addition to omp31, coding for an immunogenic protein located in the Brucella outer membrane, 22 hypothetical genes were identified. Most of the proteins that would be encoded by these genes show significant homology with proteins involved in the biosynthesis of polysaccharides from other bacteria, suggesting that they might be involved in the synthesis of a Brucella polysaccharide that would be a heteropolymer synthesized by a Wzy-dependent pathway. This polysaccharide would not be synthesized in B. abortus and would be a polysaccharide not identified until present in the genus Brucella, since all of the known polysaccharides are synthesized in all smooth Brucella species. Discovery of a novel polysaccharide not synthesized in B. abortus might be interesting for a better understanding of the pathogenicity and host preference differences observed between the Brucella species. However, the possibility that the genes detected in the DNA fragment deleted in B. abortus no longer lead to the synthesis of a polysaccharide must not be excluded. They might be a remnant of the common ancestor of the alpha-2 subdivision of the class Proteobacteria, with some of its members synthesizing extracellular polysaccharides and, as Brucella spp., living in association with eukaryotic cells.

Base Sequence↗

PubMed1976

Molecular cloning of DNA fragments produced by restriction endonucleases Sa1I and BamI.

The highly specific restriction endonucleases Sa1I and BamI produce DNA fragments with complementary, cohesive termini that can be covalently joined by DNA ligase. The Escherichia coli kanamycin resistance factor pML21 has one SalI site, at which DNA can be inserted without interfering with the expression of drug resistance or replication of the plasmid. A more convenient cloning vehicle can be made with the tetracycline resistance factor pSC101, since insertion of DNA either at its single site for Sa1I or at that for BamI inactivates plasmid-specified drug resistance but not replication. To take advantage of this insertional inactivation, pSC101 was joined to a Co1E1-ampicillin resistance plasmid having no Sa1I site, and to a Co1E1-kanamycin resistance plasmid having no BamI site. Chimeras formed with the resulting hybrid vehicles can be identified simply by replica plating. These three vehicles, which all replicate under relaxed control, have been used to clone and amplify Drosophila melanogaster DNA fragments.

Bacillus↗

PubMed1995

Cloning of HindIII digested bovine herpesvirus-1 DNA fragments from an Indian respiratory isolate.

The DNA from an Indian isolate of Bovine Herpesvirus-1 was isolated and analysed with restriction endonucleases. On shot gun cloning seven HindIII digested BHV-1 DNA fragments could be cloned in pBR322 vector. Recombinant clones with viral DNA insert was identified by insertional inactivation of the selection marker and restriction analysis of recombinant plasmids with HindIII. Further, recombinant plasmids were analysed with HindIII, EcoRI and BamHI restriction endonucleases to identify the different viral DNA inserts. The restriction site map of recombinant plasmids were correlated with the map reported earlier. The southern blot of restriction digested recombinant plasmids was hybridized with radio-labelled BHV-1 DNA as probe.

Animals↗