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PubMed1991

DNA fragmentation by 2-nitropropane in rat tissues, and effects of the modulation of biotransformation processes.

The occurrence and persistence of DNA fragmentation, as detected by the alkaline elution technique, have been studied in rats treated with single oral doses of the hepatocarcinogen 2-nitropropane (2-NP). A progressive increase of liver DNA fragmentation was observed at doses ranging from 0.5 to 8 mmol/kg; single strand breaks reached the maximum frequency 6 h after administration, and were partially reduced after 36 h. In contrast, DNA fragmentation was absent in lung, kidney, bone marrow and brain of rats given 8 mmol/kg. The role of cytochrome P-450 in the activation of 2-NP is indicated by the increase of liver DNA damage in rats pretreated with phenobarbital or beta-naphtoflavone, and by its reduction produced by methoxsalen. Both administration of GSH and GSH depletion did not result in clearcut modifications of the genotoxic effect of 2-NP for the liver.

Animals↗
PubMed1989

Calcium-activated DNA fragmentation kills immature thymocytes.

Glucocorticoid hormones kill immature thymocytes by activating a self-destructive process that involves extensive DNA fragmentation. It has been demonstrated that thymocyte suicide is dependent on an early, sustained increase in cytosolic Ca2+ concentration, and new protein synthesis, but the biochemical lesion that leads to cell death has not been established. To determine whether endonuclease activation or activation of another Ca2+-dependent process could mediate cell killing, we treated thymocytes with the glucocorticoid methylprednisolone in the presence of inhibitors of various Ca2+-dependent degradative enzymes. The role of poly(ADP-ribose) polymerase, an enzyme known to be activated by DNA damage, was also assessed. Glucocorticoid-induced chromatin cleavage and cell killing were blocked by the endonuclease inhibitor aurintricarboxylic acid, whereas inhibitors of other Ca2+-dependent degradative processes or of poly(ADP-ribose) polymerase did not abrogate cell death. In addition, stimulation of thymocyte DNA fragmentation by the Ca2+ ionophore A23187 resulted in cell killing that could be blocked by the endonuclease inhibitor. Together, our results suggest that thymocyte suicide is caused by extensive Ca2+-stimulated DNA fragmentation.

Animals↗
PubMed1999

[Influence of sample dilution on separation and detection of DNA fragments by capillary electrophoresis].

Capillary electrophoresis has become an important and useful method to separate and determine DNA fragments. In molecular biochemistry, the volume of DNA sample is very small (microL level) and DNA sample is liable to be contaminated and degraded. According to theoretical inference and experiments, we propose that dilution of DNA sample solution can increase separation efficiency and resolution without evidently reducing height of peaks. By this method, the usage efficiency of DNA sample can be improved. It is also demonstrated the separation and detection of DNA fragments by capillary electrophoresis with hydroxyethyl cellulose non-gel sieving matrix and with laser-induced fluorescence charge-coupled device as detector. By using lower concentration non-gel matrix (0.4%), all 8 larger size fragments of lambda DNA/Hind III (125 bp-23 130 bp) can be completely separated. Twenty smaller size fragments of pBR322-Hae III DNA (18 bp-587 bp) can be separated by higher concentration (1.6%) non-gel matrix. As ratio of sample dilution is 10, two adjacent fragment (123 bp and 124 bp) of pBR322-Hae III DNA can be separated.

DNA↗
PubMed1975

Promoter-dependent transcription of tRNAITyr genes using DNA fragments produced by restriction enzymes.

Two DNA fragments prepared from the transducing bacteriophage strains ø80psuIII+ and ø80hpsuIII+,- by digestion with restriction enzymes contain one tyrosine tRNA gene (suIII+) and two tyrosine tRNA genes (suIII+, su-) in tandem, respectively, a single promoter in both cases, and some additional DNA regions at the two ends of both. Using these fragments, we have studied characteristics of the promoter-dependent transcription of the tyrosine tRNA genes. The promoter-dependent transcripts were shown to correspond to the expected tRNA precursors. Exposure of the transcript from the single gene fragment to an S100 extract from Escherichia coli gave, via intermediates, 4S material which was active in enzymatically accepting tyrosine and contained some modified bases.

Adenosine Triphosphate↗
PubMed1998

Caspase dependent DNA fragmentation might be associated with excitotoxicity in Alzheimer disease.

Recent studies have shown that deficient functioning of glutamate transporters (GTs) in Alzheimer disease (AD) might lead to neurodegeneration via excitotoxicity; however, the characteristics of cell death and pathways involved are not yet clear. The main objective of the present study was to determine if deficient GT functioning in AD could be associated with cell damage and caspase activation. For this purpose, we analyzed the levels of caspase-1 and 3 immunoreactivity in AD and control brains and correlated this data with the numbers of cells displaying DNA fragmentation, GT activity, and amyloid precursor protein (APP) mRNA expression. Compared to controls, AD cases showed extensive positive labeling of neurons and glial cells with an assay for DNA fragmentation suggestive of cell damage, as well as increased neuronal caspase-3 and Bcl-2 immunoreactivity. Linear regression analysis showed a strong negative correlation between GT activity and apoptosis, and between deficient GT functioning and caspase-3 immunoreactivity. Neurons displaying DNA fragmentation presented more intense caspase-3 immunoreactivity than intact neurons. In addition, the altered ratio between the spliced forms of APP correlated with DNA fragmentation and caspase-3 immunolabeling. Taken together, these results support the possibility that excitotoxic injury associated with deficient GT functioning and an imbalance in ratio of spliced APP forms might lead to cell death via caspase-3 activation.

ATP-Binding Cassette Transporters↗
PubMed2003

Dose- and time-dependent effects of a novel (-)-hydroxycitric acid extract on body weight, hepatic and testicular lipid peroxidation, DNA fragmentation and histopathological data over a period of 90 days.

(-)-Hydroxycitric acid (HCA), a natural extract from the dried fruit rind of Garcinia cambogia (family Guttiferae), is a popular supplement for weight management. The dried fruit rind has been used for centuries as a condiment in Southeastern Asia to make food more filling and satisfying. A significant number of studies highlight the efficacy of Super CitriMax (HCA-SX, a novel 60% calcium-potassium salt of HCA derived from Garcinia cambogia) in weight management. These studies also demonstrate that HCA-SX promotes fat oxidation, inhibits ATP-citrate lyase (a building block for fat synthesis), and lowers the level of leptin in obese subjects. Acute oral, acute dermal, primary dermal irritation and primary eye irritation toxicity studies have demonstrated the safety of HCA-SX. However, no long-term safety of HCA-SX or any other (-)-hydroxycitric acid extract has been previously assessed. In this study, we have evaluated the dose- and time-dependent effects of HCA-SX in Sprague-Dawley rats on body weight, hepatic and testicular lipid peroxidation, DNA fragmentation, liver and testis weight, expressed as such and as a % of body weight and brain weight, and histopathological changes over a period of 90 days. The animals were treated with 0, 0.2, 2.0 and 5.0% HCA-SX as feed intake and the animals were sacrificed on 30, 60 or 90 days of treatment. The feed and water intake were assessed and correlated with the reduction in body weight. HCA-SX supplementation demonstrated a reduction in body weight in both male and female rats over a period of 90 days as compared to the corresponding control animals. An advancing age-induced marginal increase in hepatic lipid peroxidation was observed in both male and female rats as compared to the corresponding control animals. However, no such difference in hepatic DNA fragmentation and testicular lipid peroxidation and DNA fragmentation was observed. Furthermore, liver and testis weight, expressed as such and as a percentage of body weight and brain weight, at 30, 60 and 90 days of treatment, exhibited no significant difference between the four groups. Taken together, these results indicate that treatment of HCA-SX over a period of 90 days results in a reduction in body weight, but did not cause any changes in hepatic and testicular lipid peroxidation, DNA fragmentation, or histopathological changes.

ATP Citrate (pro-S)-Lyase↗
PubMed2002

Intranuclear localization of apoptosis-inducing factor (AIF) and large scale DNA fragmentation after traumatic brain injury in rats and in neuronal cultures exposed to peroxynitrite.

Programmed cell death occurs after ischemic, excitotoxic, and traumatic brain injury (TBI). Recently, a caspase-independent pathway involving intranuclear translocation of mitochondrial apoptosis-inducing factor (AIF) has been reported in vitro; but whether this occurs after acute brain injury was unknown. To address this question adult rats were sacrificed at various times after TBI. Western blot analysis on subcellular protein fractions demonstrated intranuclear localization of AIF in ipsilateral cortex and hippocampus at 2-72 h. Immunocytochemical analysis showed AIF labeling in neuronal nuclei with DNA fragmentation in the ipsilateral cortex and hippocampus. Immunoelectronmicroscopy verified intranuclear localization of AIF in hippocampal neurons after TBI, primarily in regions of euchromatin. Large-scale DNA fragmentation ( approximately 50 kbp), a signature event in AIF-mediated cell death, was detected in ipsilateral cortex and hippocampi by 6 h. Neuron-enriched cultures exposed to peroxynitrite also demonstrated intranuclear AIF and large-scale DNA fragmentation concurrent with impaired mitochondrial respiration and cell death, events that are inhibited by treatment with a peroxynitrite decomposition catalyst. Intranuclear localization of AIF and large-scale DNA fragmentation occurs after TBI and in neurons under conditions of oxidative/nitrosative stress, providing the first evidence of this alternative mechanism by which programmed cell death may proceed in neurons after brain injury.

Active Transport, Cell Nucleus↗
PubMed1994

Formation of high molecular mass DNA fragments is a marker of apoptosis in the human leukaemic cell line, U937.

Inhibitors of macromolecular synthesis and topoisomerases induce apoptosis in the human leukaemic cell line, U937. In this study, U937 cells were treated with the RNA synthesis inhibitor, actinomycin D (1 microM), the protein synthesis inhibitors, emetine (1 microM) and cycloheximide (100 microM), the topoisomerase II inhibitor, teniposide (5 microM), or the topoisomerase I inhibitor, camptothecin (1 microM). Apoptotic cell death was assessed both by flow cytometry and agarose gel electrophoresis, and was correlated to the appearance of large (20 to > or = 580 kilobase pairs) DNA fragments, as assessed by field inversion gel electrophoresis. In all cases, the appearance of DNA fragments of 20-50 kilobase pairs accompanied the appearance of an apoptotic population and of internucleosomal cleavage. However, teniposide additionally induced a marked increase in fragmentation to > or = 580 kilobase pairs. The cotreatment of cells with zinc (1 mM) inhibited the formation of all large DNA fragments, internucleosomal cleavage and the appearance of an apoptotic population. We conclude that the generation of large DNA fragments is characteristic of apoptosis induced by various stimuli in U937, as has been found previously in rat thymocytes. However, unlike what occurs in rat thymocytes, zinc treatment does not dissociate the formation of large fragments from conventional markers of apoptosis.

Apoptosis↗
PubMed2001

Accelerated DNA fragmentation of the denture-bearing mucosal epithelium in an animal model of diabetes.

This study examined the effect of masticatory pressure transmitted directly to the hard palate mucosa on the final stage of terminal differentiation of keratinizing system of rats with and without streptozotocin-induced diabetes mellitus. In the nondiabetic rats with masticatory pressure, the number of terminal-deoxynucleotidyl-transferase-mediated deoxyuridine-triphospate-biotin nick end labelling (TUNEL) positive cells tended to increase about twice as much as in the nondiabetic rats without pressure with and without denture. A similar tendency of increase was observed in the diabetic rats without pressure. The synergy of the mechanical pressure and diabetic condition for 2 weeks greatly accelerated the DNA fragmentation, showing 8-fold increase in TUNEL positive cells over the normal control, and caused exfoliation of the stratum corneum. A 4-week exposure of diabetics to the masticatory pressure induced laminar splitting in the midst of the spinosum. Some cells in the stratum granulosum exhibited a sign of DNA fragmentation when laminar splitting took place in the vital cell layer. Premature DNA fragmentation may disturb the adhesion between spinosum cells and prevent the maturation of stratum corneum. Increase in Bax protein-like immunoreactivity in these epithelial cells as revealed by immunocytochemistry may underlie the premature DNA fragmentation in the oral masticatory epithelium under pressure in diabetic patients.

Animals↗
PubMed2002

Rejoining of double-stranded DNA-fragments studied in different size-intervals.

PURPOSE: To measure rejoining of radiation-induced doublestranded DNA-fragments of different sizes and to evaluate the effects of size-resolution in the analysis of rejoining. MATERIAL AND METHODS: Normal human fibroblasts (GM5758) were irradiated with photons or accelerated nitrogen ions (linear energy transfer, LET = 125 keV microm(-1)) and incubated for repair for 0-22 h. Double-stranded DNA-fragments from the irradiated cells were separated by pulsed-field gel electrophoresis in the range approximately 5 kbp to 5.7 Mbp. RESULTS: For cells irradiated with high LET nitrogen ions, there was an increase in the fast half-time from approximately 5 min for fragments < 400 kbp to 10 min when all fragments < 5.7 Mbp were measured. Further, the fraction of fragments rejoined by the slow-rejoining phase increased significantly for increased threshold sizes. The fraction of unrejoined fragments after 22 h and the half-time for the slow-rejoining phase remained constant for all threshold sizes. For cells irradiated with lower doses of low LET radiation the rejoining was shifted towards a slower kinetics when fragments up to 10 Mbp were excluded in the analysis. CONCLUSION: DNA exclusion-size and resolution may affect the estimates of DNA double-strand break rejoining. Using a low-resolution technique that does not detect small fragments will result in an underestimation, or even disappearance of the fast-rejoining phase. This is due to substantial rejoining of fragments taking place before the fragments are of sufficient size to be monitored.

Cell Line↗
PubMed2002

Overexpression of alpha7 nicotinic acetylcholine receptor prevents G1-arrest and DNA fragmentation in PC12 cells after hypoxia.

We investigated the neuroprotective function of alpha7 nicotinic acetylcholine receptor (alpha7nAChR) after transient hypoxia (12 h) and reoxygenation (0-72 h), comparing rat pheochromocytoma (PC12) cells overexpressing FLAG-tagged alpha7nAChR (alpha7pCMV cells) and control PC12 cells (non-transfected or transfected with vector only) in medium with and without nicotine. Plasma membrane degradation in the early phase after hypoxia was inhibited in PC12 cells with nicotine, and more profoundly in alpha7pCMV cells with nicotine. Inhibition of DNA fragmentation in the late phase after hypoxia was most remarkable in alpha7pCMV cells with nicotine, but, surprisingly, it was more remarkable in alpha7pCMV cells without nicotine than in PC12 cells with nicotine. G1-arrest of the cell cycle, observed in control PC12 cells at 12 h after hypoxia, preceding DNA fragmentation, was not evident in alpha7pCMV cells, with or without nicotine. Furthermore, in alpha7pCMV cells with and without nicotine, the basal expression levels of total Akt were approximately 1.5-fold higher, and the up-regulation of Akt phosphorylated at Ser473 after hypoxia was strikingly enhanced, compared with control PC12 cells. These findings suggest that alpha7nAChR functions constitutively in PC12 cells, that its overexpression raises tolerance against G1-arrest and DNA fragmentation after hypoxia, and that it can be considered a candidate target for treatment against hypoxia-induced acute membrane degradation and delayed DNA fragmentation in neurons.

Animals↗
PubMed1991

Cloning and expression of a Clostridium thermocellum DNA fragment that encodes a protein related to cellulosome component SL.

Antibodies raised against the SL subunit of the Clostridium thermocellum cellulosome were used to screen a library of C. thermocellum chromosomal DNA fragments constructed in the vector lambda gt11. A DNA fragment that encoded a polypeptide that crossreacted with the anti-SL antibodies was isolated and its restriction map elucidated. No similarity with other previously cloned DNA fragments has been found. The anti-SL crossreacting polypeptide was isolated from recombinant Escherichia coli and found to have a mol mass of 37,000 Da and to possess low levels of CMCase and Avicelase activity. Using CMC as the substrate, a temperature optimum of 55 degrees C and a pH optimum of 6.6 were observed. These properties were compared to those of C. thermocellum SL isolated by electroelution from an SDS gel, which was also found to possess low levels of CMCase and Avicelase activities. In addition, the SL proteins produced in C. thermocellum and E. coli were able to interact positively against Avicel with an endoglucanase (Ss) purified from the C. thermocellum crude cellulase preparation, and with a recombinant protein that crossreacted with anti-Ss antibodies.

Cellulase↗
PubMed2003

High molecular weight DNA fragments are processed by caspase sensitive or caspase independent pathways in cultures of cerebellar granule neurons.

Many recent reports on internucleosomal DNA fragments have appeared, however, little is known about the mechanisms of the generation of their upstream high molecular weight (HMW) fragments. Caspases are a family of proteases with important functions in the execution of apoptotic cell death. The caspase-sensitivity of the formation of HMW fragments was therefore investigated using a specific caspase-3 inhibitor (Ac-DEVD-cmk) and a general caspase inhibitor (boc-D-fmk). Apoptosis inducing factor (AIF) can translocate to the nucleus and generate HMW fragments independently of caspase. Cultures of cerebellar granule neurons (CGNs) were therefore exposed to glutamate (100 micro M) or deprived of potassium and serum to induce apoptosis, or treated with a high concentration of calcium ionophore A23187 (1 micro M) to induce necrosis. Fragmentation of DNA into two classes of HMW fragments (>680 and 50-300 kbp) was observed after treatment with glutamate or A23187. Traces of approximately 50-kbp fragments were detectable after the K(+)/serum-deprivation. The amount of >680-kbp HMW fragments increased (i.e. their further degradation was inhibited) and cell death was reduced in the presence of Ac-DEVD-cmk or boc-D-fmk following glutamate treatment. Only boc-D-fmk treatment resulted in a similar accumulation of >680-kbp HMW fragments and reduced cell death after K(+)/serum-deprivation. No such changes were observed with caspase inhibitors after A23187 treatment. AIF redistribution was observed following glutamate treatment and K(+)/serum-deprivation. Thus, even in a simple cell culture of CGNs, HMW fragments are formed by diverse mechanisms: the degradation of DNA may be sensitive to different caspases or be caspase and AIF independent.

Animals↗
PubMed2006

Granzyme M directly cleaves inhibitor of caspase-activated DNase (CAD) to unleash CAD leading to DNA fragmentation.

Granzyme (Gzm)M is constitutively highly expressed in NK cells that may play a critical role in NK cell-mediated cytolysis. However, the function of GzmM has been less defined. Just one report showed GzmM induces a caspase-independent death pathway. In this study, we demonstrate a protein transfection reagent Pro-Ject can efficiently transport GzmM into target cells. GzmM initiates caspase-dependent apoptosis with typical apoptotic nuclear morphology. GzmM induces DNA fragmentation, not DNA nicking. GzmM can directly degrade inhibitor of caspase-activated DNase to release the nuclease activity of caspase-activated DNase for damaging DNA. Furthermore, GzmM cleaves the DNA damage sensor enzyme poly(ADP-ribose) polymerase to prevent cellular DNA repair and force apoptosis.

Apoptosis↗
PubMed1997

Isolation and characterization of matrix associated region DNA fragments in rice (Oryza sativa L.).

To investigate the interactions between chromosomal DNA and nuclear matrices in higher plants, matrix associated regions (MARs) of rice (Oryza sativa L.) DNAs were cloned. First, we prepared nuclear matrices from isolated nuclei by digesting them with EcoRI and then extracting with 2 M NaCl. About 6% of the total DNA remained in the nuclear matrices after this digestion and extraction. The residual DNA fragments in the nuclear matrices were cloned. Some of the cloned DNA fragments showed binding to certain nuclear proteins. One of the MAR fragments contained sequences related to known consensus motifs and a hairpin loop structure. A method is presented for isolation of matrix associated region (MAR) DNAs from plant cells.

Base Sequence↗
PubMed2001

DNA fragments in the blood plasma of cancer patients: quantitations and evidence for their origin from apoptotic and necrotic cells.

Increased levels of DNA fragments have frequently been found in the blood plasma of cancer patients. Published data suggest that only a fraction of the DNA in blood plasma is derived from cancer cells. However, it is not known how much of the circulating DNA is from cancer or from noncancer cells. By quantitative methylation-specific PCR of the promoter region of the CDKN2A tumor suppressor gene, we were able to quantify the fraction of plasma DNA derived from tumor cells. In the plasma samples of 30 unselected cancer patients, we detected quantities of tumor DNA from only 3% to as much as 93% of total circulating DNA. We investigated possible origins of nontumor DNA in the plasma and demonstrate here a contribution of T-cell DNA in a few cases only. To investigate the possibility that plasma DNA originates from apoptotic or necrotic cells, we performed studies with apoptotic (staurosporine) and necrotic (staurosporine plus oligomycin) cells in vitro and with mice after induction of apoptotic (anti-CD95) or necrotic (acetaminophen) liver injury. Increasing amounts of DNA were found to be released in the supernatants of cells and in the blood plasma samples of treated animals. A clear discrimination of apoptotic and necrotic plasma DNA was possible by gel electrophoresis. The same characteristic patterns of DNA fragments could be identified in plasma derived from different cancer patients. The data are consistent with the possibility that apoptotic and necrotic cells are a major source for plasma DNA in cancer patients.

Animals↗
PubMed1999

Electrophoretic separation of small DNA fragments in the presence of electroosmotic flow using poly(ethylene oxide) solutions.

A new and simple method was demonstrated for separating phi X-174/Hae III DNA restriction fragments and DNA markers V and VI, respectively, without filling capillaries with polymer solutions prior to analysis. Using this novel method, poly(ethylene oxide) (PEO) solutions containing ethidium bromide migrated into capillaries by electroosmotic flow (EOF) during the separation. Two DNA fragments (123 and 124 bp) in markers V and VI were well-resolved. RSD values for the separation of phi X-174/Hae III DNA restriction fragments were less than 0.52% for 3 runs using a single 75-micron capillary and less than 3.96% using three different 75-micron capillaries. A highly viscous polymer solution prepared from 3% PEO was also used for separation of DNA markers V and VI. Theoretical plates up to 11.91 million/m and separation times of less than 7 min were achieved in the separation of phi X-174/Hae III DNA restriction fragments using a 10-micron capillary and a 2% PEO solution. Advantages of this method include simplicity, short separation times, the ability to use highly viscous polymer solutions for separating small DNA fragments, and the possibility of introducing several different polymer solutions into capillaries to extend the DNA separation range.

DNA↗
PubMed2005

Loss of splicing factor ASF/SF2 induces G2 cell cycle arrest and apoptosis, but inhibits internucleosomal DNA fragmentation.

ASF/SF2 is an SR protein splicing factor that participates in constitutive and alternative pre-mRNA splicing and is essential for cell viability. Using a genetically modified chicken B-cell line, DT40-ASF, we now show that ASF/SF2 inactivation results in a G2-phase cell cycle arrest and subsequent programmed cell death. However, although several hallmarks of apoptosis are apparent, internucleosomal DNA fragmentation was not detected. Furthermore, inactivation of ASF/SF2 also blocks DNA fragmentation normally induced by a variety of apoptotic stimuli. Notably, mRNA encoding the inhibitor of caspase-activated DNase-L (ICAD-L), which acts as an inhibitor as well as a chaperone of caspase-activated DNase (CAD), decreased in abundance, whereas the level of mRNA encoding ICAD-S, which has only inhibitory activity, increased upon ASF/SF2 depletion. Strikingly, expression of appropriate levels of exogenous human ICAD-L restored apoptotic DNA laddering in ASF/SF2-depleted cells. These results not only indicate that loss of an SR protein splicing factor can induce cell cycle arrest and apoptosis, but also illustrate the important role of ICAD and its regulation by alternative splicing in the process of apoptotic DNA fragmentation.

Alternative Splicing↗