Separation of carcinogen-damaged DNA fragments from undamaged DNA.
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Animals↗
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Assessment of colinearity between large cloned DNA fragments and genomic DNA.
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Chromosomes, Fungal↗
Direct excision of 50 kb pair DNA fragments from megabase-sized fragments produced during apoptotic cleavage of genomic DNA.
The DNA of U937 cells exposed to two different apoptotic stimuli, namely the cocktail H2O2/3-aminobenzamide (3AB) and etoposide, was analyzed using field inversion gel electrophoresis (FIGE) as well as programmable, autonomously controlled electrode electrophoresis (PACE). The results obtained indicate that FIGE is not appropriate for sizing apoptotic DNA fragments. PACE appears to be more accurate and reliable and the results obtained with this technique strongly suggest that the 50 kb DNA fragments are directly excised from Mb-sized DNA fragments without the intermediate cleavage of 200-300 kb products.
Apoptosis↗
The effects of field inversion electrophoresis on small DNA fragment mobility and its relevance to DNA polymorphism research.
The electrophoretic mobility of several DNA size markers of molecular lengths from 1.23 x 10(2) to 2.36 x 10(4) base pairs has been investigated in gels of 1% and 1.3% agarose (w/v) by field inversion gel electrophoresis (FIGE), in vertical slabs. Pulsing times studied were in the range of 0.3/0.1 ms to 300/100 ms. (Pulsing times are given in milliseconds, as X/Y, where X is the forward pulsing time and Y is the reverse time.) FIGE differentially retards DNA migration: this effect is more marked for shorter pulsing times, and varies as a function of molecular length of the DNA fragment, down to fragments as small as about 1.7 kb, with the pulsing times we used. Several FIGE conditions were found which generate improved resolution of DNA fragments in different size ranges. DNA separation improves by more than a factor of two for fragments of 23.1-9.4 kb (with 300/100 ms pulsing) and for fragments of 4.4-2.0 kb (3/1 ms). FIGE does not seem to have a marked resolution enhancing effect on DNA sized from 9.4-4.4 kb. An example of improved detection of closely spaced bands on Southern blots is shown.
Blotting, Southern↗
DNA fragmentation induced by cytotoxic T lymphocytes can result in target cell death.
Cytotoxic T lymphocyte (CTL)-mediated lysis is accompanied by fragmentation of target cell DNA into an oligonucleosome ladder, a hallmark of apoptosis. Is this a fortuitous coincidence, or could CTL be inducing lysis by activation of the suicide signal? In this report we demonstrate that CTL-mediated target cell death can be blocked with the drug aurintricarboxylic acid (ATA). The abrogation of death correlates with the inhibition of DNA fragmentation. While ATA prevented DNA fragmentation, it failed to significantly alter protein, RNA, or DNA synthesis in the cell lines over the dose range used. In addition, there was no inhibition of cell-cell interaction or granule exocytosis during CTL-mediated killing. ATA also significantly inhibited the cytolysis and DNA fragmentation mediated by isolated cytolytic granules, as well as the granular protein fragmentin. We developed an assay in which target cells could be separated from CTL after binding and programming for lysis. Once they had received the "kiss of death," target cells could be rescued from lysis (as indicated by inhibition of DNA fragmentation and increased target cell viability) by treatment with ATA. These results suggest that ATA blocks target cell death by inhibition of DNA fragmentation, and further, that chromatin degradation is a cause rather than a result of cell death in CTL-mediated lysis.
Animals↗
Increases in DNA fragmentation and induction of a senescence-specific nuclease are delayed during corolla senescence in ethylene-insensitive (etr1-1) transgenic petunias.
The programmed senescence of flower petals has been shown to involve the fragmentation of nuclear DNA. Nuclear DNA fragmentation, as determined by the TUNEL assay, was detected in Petunia x hybrida corollas during both pollination-induced and age-related senescence. DNA fragmentation was detected late in the lifespan of the flower when corollas were wilting and producing ethylene. The induction of a 43 kDa nuclease (PhNUC1) correlated with increased DNA fragmentation. PhNUC1 is a glycoprotein with activity against DNA and RNA and a pH optimum of 7.5. EDTA was found to inhibit PhNUC1 activity, but the addition of Co2+ restored activity in the presence of the chelating agent. When total protein extracts from senescing petals were fractionated by differential centrifugation, PhNUC1 activity was detected in the nuclear but not the cytoplasmic fraction. Activity of PhNUC1 was induced in non-senescing corollas by treatment with ethylene. Delayed increases in PhNUC1 activity observed in ethylene-insensitive flowers (35S:etr1-1) suggest that ethylene modulates the timing of PhNUC1 induction, but that it is not an absolute requirement for its activation.
DNA Fragmentation↗
Recovery of DNA fragments specifically bound by monoclonal anti-DNA antibody.
A method to recover and identify DNA fragments that were specifically bound by a monoclonal anti-DNA antibody has been developed. A mixture of DNA fragments digested by restriction enzymes was first incubated with a murine monoclonal anti-DNA antibody and then reacted with anti-murine immunoglobulin-conjugated Sepharose 4B. The resulting complex was washed to remove unbound DNA by low-speed centrifugation. The bound DNA fragment was released from antibody by alkaline dimethyl sulfoxide solution or extracted by phenol treatment. The recovered DNA was analyzed by electrophoresis on a polyacrylamide gel.
Antibodies, Antinuclear↗
Neither caspase-3 nor DNA fragmentation factor is required for high molecular weight DNA degradation in apoptosis.
In this paper, we show that there is a two-step process of DNA fragmentation in apoptosis; DNA is first cleaved to large fragments of 50-300 kb that are subsequently cleaved to smaller oligonucleosomes in some, but not all cells. Significantly, only the first stage is considered essential for cell death since some cells, for example human MCF7 breast carcinoma cells and human NT2 neuronal cells, do not show this behavior but still display normal nuclear morphological apoptotic changes. In cells that usually produce small fragments blocking the second (internucleosomal) stage of DNA fragmentation prevents neither nuclear condensation nor apoptosis. We are beginning to understand why the extent of DNA fragmentation during apoptosis varies enormously and why it appears to be a function of the cell type not the inducer. Presumably, this reflects the content of not only endonuclease activit(ies) but also on the ability of the cells to activate caspases, particularly caspase-3, and other proteases that may be involved in endonuclease activation. Since NT2 cells activate caspase-3, but do not correctly process DFF45, other factors must also impinge on the inevitability of that process.
Adenocarcinoma↗
Transport of fragmented DNA in apical dendrites of gerbil CA1 pyramidal neurons following transient forebrain ischemia.
Transport of fragmented DNA in apical dendrites of the CA1 pyramidal neurons of gerbil hippocampus is observed in the apoptotic process following transient forebrain ischemia. The time-course of specific DNA fragmentation was examined after the ischemic insult by in situ nick-end-labeling method and fluorescence detection technique by DAPI. Although the role of the fragmented DNA movement is unclear, the transport mechanism of fragmented DNA is still active in the late phase of apoptotic process.
Animals↗
Effects of oxygen concentration and antioxidants on the in vitro developmental ability, production of reactive oxygen species (ROS), and DNA fragmentation in porcine embryos.
After in vitro maturation and fertilization of porcine oocytes, the fertilized embryos were cultured under 5 or 20% oxygen (O2) for 7 days. In embryos cultured under 5% O2 versus 20% O2, development to the blastocyst stage was higher (36.3% versus 22.5%, P < 0.05); the hydrogen peroxide (H2O2) content as a reactive oxygen species was lower (92 pixels versus 111 pixels, P < 0.05); and fragmentation of DNA in 8- to 16-cell stage embryos (estimated by the comet assay) resulted in a shorter (P < 0.05) DNA tail (36 microm versus 141 microm). Antioxidants such as beta-mercaptoethanol (beta-ME) and Vitamin-E (Vit-E) suppressed oxidative damage in the embryos and improved their developmental ability. For embryos cultured under 20% O2, there were the following differences (P < 0.05) between embryos exposed to 0 microM versus 50 microM beta-ME: 28% versus 57% developed to the blastocyst stage; 125 pixels versus 98 pixels per embryo in H2O2 content; and a DNA tail of 209 microm versus 105 microm. In addition, for embryos cultured under 20% O2, there were also differences (P < 0.05) between those exposed to 0 microM versus 50 microM of Vit-E: 28% versus 40% rate of development to the blastocyst stage; 28.9 cells versus 35.9 cells in the expanded blastocyst; 122 pixels versus 95 pixels per embryo (H2O2 content); and 215 microm versus 97 microm length of the DNA tail. Therefore, a low O2 concentration during in vitro culture of porcine embryos decreased the H2O2 content and, as a consequence, reduced DNA fragmentation, and, thereby, improved developmental ability.
Animals↗
Effect of nitric oxide synthase inhibition during post-hypoxic reoxygenation on Bax and Bcl-2 protein expression and DNA fragmentation in neuronal nuclei of newborn piglets.
Previous studies have shown that cerebral tissue hypoxia results in increased generation of oxygen-free radicals including nitric oxide (NO), expression of the proapoptotic protein Bax and fragmentation of nuclear DNA. The present study tests the hypothesis that post-hypoxic reoxygenation for 6 h following hypoxia (FiO2=0.06 for 1 h) results in continued hypoxia-induced, NO-mediated expression of the Bax protein and nuclear DNA fragmentation in the cerebral cortex of newborn piglets. Piglets were divided into normoxic (Nx), hypoxic (Hx, FiO2=0.06 for 1 h), hypoxic with 6 h reoxygenation (Hx+reox) and hypoxic with 6 h reoxygenation injected with 7-nitroindazole sodium salt (7-NINA), a selective nNOS inhibitor, immediately after hypoxia (Hx+7-NINA). Cerebral tissue hypoxia was documented by levels of ATP and phosphocreatine (PCr). Bax and Bcl-2 were analyzed by Western blot and DNA fragmentation was determined by agarose gel electrophoresis. ATP and PCr values in Hx, Hx+reox and Hx+7-NINA were significantly different from Nx (P<0.05 vs. Nx). Bax protein (ODxmm2) was 128.9+/-38.7 in Nx; 223.6+/-45.8 in Hx (P<0.05 vs. Nx); 340.5+/-73.2 in Hx+reox (P<0.05 vs. Nx, Hx and Hx+7-NINA); and 202.2+/-34.8 in Hx+7-NINA (P=NS vs. Hx). Bcl-2 protein (ODxmm2) was 14.9+/-2.7 in Nx, 12.4+/-2.1 in Hx, (P<0.05 vs. Nx), 15.7+/-3.8 in Hx+reox, (P<0.05 vs. Hx) and 13.1+/-2.2 in Hx+7-NINA (P=NS among groups). Nuclear DNA fragmentation (ODxmm2) was 147+/-15 in Nx; 797+/-84 in Hx (P<0.05 vs. Nx); 1134+/-127 in Hx+reox (P<0.05 vs. Nx, Hx and Hx+7-NINA); and 778+/-146 in Hx+7-NINA (P=NS vs. Hx, P<0.05 vs. Hx+reox). The results show that post-hypoxic reoxygenation results in increased expression of Bax protein without affecting Bcl-2 protein and increased fragmentation of nuclear DNA, which are prevented by 7-NINA. We conclude that during post-hypoxic reoxygenation the increase in Bax protein expression and fragmentation of nuclear DNA are mediated by NO derived from nNOS. We propose that in addition to NO-mediated nuclear DNA damage, the hypoxia-induced increased ratio of Bax/Bcl-2 protein will lead to caspase-activated cascade of hypoxic neuronal death during post-hypoxic reoxygenation.
Analysis of Variance↗
End-labeling of long DNA fragments with biotin and detection of DNA immobilized on magnetic beads.
To immobilize DNA fragments onto magnetic beads coated with streptavidin for isolation purpose, it is important to label one biotin molecule at one terminus of DNA fragment. After failure to label long DNA with biotin by PCR and filling-in reaction, a 9.2 kb DNA was labeled with biotin by a modified ligation strategy. A simple method is also reported to detect the quantity and integrity of DNA immobilized on the magnetic beads.
Base Sequence↗
Correlation of DNA fragmentation and chromatin condensation in apoptotic nuclei of the Ser 6 mouse retina.
The form of cell death known as apoptosis was first described in thymocytes. The hallmarks of apoptosis include chromatin condensation, membrane blebbing, formation of apoptotic bodies, and DNA fragmentation. DNA fragmentation can be visualized morphologically by the TdT-mediated dUTP-biotin nick end labeling (TUNEL) method that labels the cut DNA ends. However, at the light microscopic (LM) level, TUNEL-positive nuclei cannot readily be correlated with the other hallmarks of apoptosis. In the retina, chromatin condensation and DNA fragmentation are the major features of developmental cell death as well as photoreceptor degeneration. We performed TUNEL at the electron microscopic (EM) level, which permitted correlation of DNA fragmentation with chromatin condensation. We studied the retinas of transgenic mice (Ser 6) expressing the Pro347Ser mutant rhodopsin gene during developmental cell death (age 7 days) and photoreceptor degeneration (age 21 days). We found that 90% of the nuclei showing chromatin condensation were TUNEL positive as well. Our results demonstrated DNA fragmentation and chromatin condensation in the same cells as they underwent apoptosis in vivo, confirming the notion that these processes are concomitant events, and by implication, that activation of an endogenous endonuclease is an important step in the death process of retinal neurons.
Animals↗
A unique role of the DNA fragmentation factor in maintaining genomic stability.
DNA fragmentation is a hallmark of apoptosis (programmed cell death). However, the biological function of apoptotic DNA fragmentation remains unclear. Here, we show that DNA fragmentation factor plays an important role for maintaining genomic stability. Inhibition or loss of the DNA fragmentation factor (DFF)/caspase-activated DNase (CAD), whose nuclease activity is responsible for digesting genomic DNA during apoptosis, led to significant increases in spontaneous or induced gene mutations, gene amplifications, and chromosomal instability in primary mouse cells and transformed human cell lines. The mechanism underlying genetic instability in DFF/CAD-deficient cells, at least in part, involves a small but significant elevation in the survival of cells exposed to ionizing radiation, suggesting that apoptotic DNA fragmentation factor contributes to genomic stability by ensuring the removal of cells that have suffered DNA damage. In support of this hypothesis are the observations of increased cellular transformation of mouse embryonic cells from the DFF/CAD-null mice and significantly enhanced susceptibility to radiation-induced carcinogenesis in these mice. These data, in combination with published reports on the existence of tumor-specific gene mutations/deletions in the DFF/CAD genes in human cancer samples, suggest that apoptotic DNA fragmentation factor is required for the maintenance of genetic stability and may play a role in tumor suppression.
Animals↗
[Application of PCR to Haemophilus influenzae typing. I. PCR standardization for bexA gene fragment detection and for detection of DNA fragment specific for H.influenzae type B].
PCR standardization was performed in order to detect a fragment of bexA gene, which is presented in all capsulate H. influenzae isolates, and a DNA fragment specific for H. influenzae type b. Implementing of such PCR into H. influenzae typing may be very useful in cases of isolates from clinical material for which serotyping alone gives unclear results. Standardization of PCR detecting DNA fragments specific for all capsular types will enable to perform complete typing of H. influenzae isolates.
Bacterial Typing Techniques↗
The histone H1 C-terminal domain binds to the apoptotic nuclease, DNA fragmentation factor (DFF40/CAD) and stimulates DNA cleavage.
The apoptotic nuclease, DNA fragmentation factor (DFF40/CAD), is primarily responsible for internucleosomal DNA cleavage during the terminal stages of programmed cell death. Previously, we demonstrated that histone H1 greatly stimulates naked DNA cleavage by this nuclease. Here, we investigate the mechanism of this stimulation with native and recombinant mouse and human histone H1 species. Using a series of truncation mutants of recombinant histone H1-0, we demonstrate that the H1 C-terminal domain (CTD) is responsible for activation of DFF40/CAD. We show further that the intact histone H1-0 CTD and certain synthetic CTD fragments bind to DFF40/CAD and confer upon it an increased ability to bind to DNA. Interestingly, we find that each of the six somatic cell histone H1 isoforms, whose CTDs differ significantly in primary sequence but not amino acid composition, equally activate DFF40/CAD. We conclude that the interactions identified here between the histone H1 CTD and DFF40/CAD target and activate linker DNA cleavage during the terminal stages of apoptosis.
Animals↗
LDFF, the large molecular weight DNA fragmentation factor, is responsible for the large molecular weight DNA degradation during apoptosis in Xenopus egg extracts.
DNA degradation is a biochemical hallmark in apoptosis. It has been demonstrated in many cell types that there are two stages of DNA fragmentation during the apoptotic execution. In the early stage, chromatin DNA is cut into large molecular weight DNA fragments, although the responsible nuclease(s) has not been recognized. In the late stage, the chromatin DNA is cleaved further into short oligonucleosomal fragments by a well-characterized nuclease in apoptosis, the caspase-activated DNase (CAD/DFF40). In this study, we demonstrate that large molecular weight DNA fragmentation also occurs in Xenopus egg extracts in apoptosis. We show that the large molecular weight DNA fragmentation factor (LDFF) is not the Xenopus CAD homolog XCAD. LDFF is activated by caspase-3. The large molecular weight DNA fragmentation activity of LDFF is Mg2+-dependent and Ca2+-independent, can occur in both acidic and neutral pH conditions and can tolerate 45 degrees C treatment. These results indicate that LDFF in Xenopus egg extracts might be a new DNase (or DNases) responsible for the large DNA fragmentation.
Animals↗
Modified DNA fragments activate NaeI cleavage of refractory DNA sites.
Endonuclease NaeI cleaves DNA using a two-site mechanism. The DNA-binding sites are nonidentical: they recognize different families of flanking sequences. A unique NaeI site that is resistant to cleavage resides in M13 double-stranded DNA. NaeI can be activated to cleave this site by small DNA fragments containing one or more NaeI sites. These activators are not practical for genetic engineering because unphosphorylated activators that are consumed during the cleavage of substrate give ends that may interfere with subsequent ligations. We show that a DNA fragment containing phosphorothioate linkages at the NaeI scissile bonds (S-activator) is not cleaved by NaeI, even though this S-activator binds to the substrate site. The S-activator activates NaeI to cleave M13 DNA under conditions that completely exhaust unsubstituted activator. These results demonstrate that activation is not coupled to cleavage of activator, that NaeI reverts to its inactive state soon after dissociation of the EA complex, and that S-activator makes for a nondepletable activator during prolonged incubations.
Base Sequence↗