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PubMed1990

Responses of mouse lymphocytes to extracellular ATP. II. Extracellular ATP causes cell type-dependent lysis and DNA fragmentation.

Extracellular ATP (ATPo) caused dose-dependent lysis of YAC-1 and P-815 mouse tumor cells. This event, assessed by 51Cr release, was accompanied by sustained depolarization of the plasma membrane potential and Ca2+ influx. Plasma membrane depolarization and Ca2+ influx occurred within a few seconds of ATPo addition to both cell types, whereas 51Cr was released without apparent lag in YAC-1 cells and after 2 h in P-815 cells. Furthermore, a rise in [Ca2+]i was required for ATPo-dependent lysis of YAC-1 but not P-815 cells. In P-815 cells, ATPo caused an early and [Ca2+]i-independent DNA fragmentation that occurred at lower nucleotide concentrations than those required to trigger 51Cr release. Instead in YAC-1 cells very low concentrations of ATPo caused early lysis (ED50 for lysis about 200 microM) accompanied by only barely detectable DNA fragmentation. Previous studies disclosed that lymphokine-activated killer cells are fully resistant to the membrane-perturbing effects of ATPo. We show that lymphokine-activated killer cells also do not undergo DNA fragmentation even in the presence of high ATPo concentrations. This study complements previous observations on the lytic effects of ATPo and shows that this nucleotide can also cause DNA fragmentation, one of the earliest target cell alterations observed during CTL-mediated lysis.

Adenosine Triphosphate↗
PubMed2006

[Effect of preliminary irradiation on DNA-ase activity and DNA fragmentation degree in the nuclei of Guerin's carcinoma cells].

The effect of preliminary irradiation on DNA-ase activity and DNA fragmentation degree in the nuclei of Guerin's carcinoma was evaluated. It was found that effective growth of malignant cells involved higher concentrations of acid DNA-ase matched by decreased levels of alkaline one which in turn lowered the rates of DNA fragmentation. Low-dose preliminary irradiation stimulated relevant processes.

Animals↗
PubMed1999

Simultaneous detection of DNA fragmentation (apoptosis), cell proliferation (MIB-1), and phenotype markers in routinely processed tissue sections.

In situ DNA fragmentation assays have proved to be particularly useful in the detection of apoptosis in routinely processed, paraffin-embedded tissue sections. In the present study, a triple-antigen labelling technique was performed to demonstrate DNA fragmentation (apoptosis), cell proliferation (MIB-1), and phenotypic markers in the same tissue section. The in situ apoptosis assay was conducted with the TUNEL method developed by a avidin-biotin alkaline phosphatase complex (ABcomplex/AP). The proliferation-associated MIB-1 antigen was demonstrated in the second staining sequence by the avidin-biotin peroxidase method (ABC). The phenotypic markers chromogranin A or prostate-specific antigen (PSA) were visualized by the alkaline phosphatase anti-alkaline phosphatase method (APAAP) in the third staining sequence. The feasibility of this triple-labelling technique was tested in formalin-fixed, paraffin-embedded tissue of prostatic adenocarcinomas from 8 patients with recurrent, hormone-refractory disease. Although these tumours revealed marked neuroendocrine differentiation, cell proliferation and apoptosis were detected exclusively in non-endocrine (chromogranin A-negative) tumour cells that expressed PSA variably. The triple-labelling protocol described here allows the phenotypic characterization of proliferating and apoptotic cell populations in the same tissue section. It may be useful in studies of tissue kinetics in physiological and pathological processes.

Antigens, Nuclear↗
PubMed2000

Evidence for DNA fragmentation triggered in the self-incompatibility response in pollen of Papaver rhoeas.

Studies of the molecular and biochemical basis of self-incompatibility (SI) in Papaver rhoeas have revealed much about the signalling pathways triggered in pollen early in this response. The aim of the current investigation was to begin to study downstream events in order to elucidate some of the later cellular responses involved in the SI response and identification of the mechanisms controlling the irreversible inhibition of pollen tube growth. We have used the FragEL assay to investigate if there is any evidence for DNA fragmentation stimulated in pollen of P. rhoeas in an S-specific manner. Our data clearly demonstrate that S proteins are responsible for triggering this, specifically in incompatible, and not compatible, pollen. DNA fragmentation was first detected in incompatible pollen tubes 4 h after challenge with S proteins, and continued to increase for a further 10 h. This provides the first evidence, to our knowledge, that this phenomenon is associated with the SI response. We also demonstrate that mastoparan, which increases [Ca2+]i, also triggers DNA fragmentation in these pollen tubes, thereby implicating an involvement of Ca2+ signalling in this process. Together, our data represent a significant breakthrough in understanding of the SI response in Papaver pollen.

Calcium Signaling↗
PubMed1995

Preferential cross-linking of matrix-attachment region (MAR) containing DNA fragments to the isolated nuclear matrix by ionizing radiation.

The sequences that anchor DNA, matrix-attachment regions (MARs), can be identified by their specific and preferential binding to the nuclear matrix. This microenvironment may be hypersensitive to the formation of ionizing radiation-induced DNA damage, including DNA-protein cross-links (DPC). To examine the induction of DPC at or near MARs, we developed an in vitro binding assay by using nuclear matrices isolated from murine erythroleukemia cells by high-salt extraction of DNase I-digested nuclei. The cross-linking of nuclear matrix protein to DNA fragments containing kappa-immunoglobulin (kappa-Ig) or an hsp 70 MAR was studied. Fragments of pBR322 of similar size to the MAR-containing fragments served as non-MAR controls. Two types of experiments were conducted: type A in which nuclei were irradiated and nuclear matrices were isolated and assayed for the binding of exogenous 32P-labeled DNA fragments, and type B in which mixtures of isolated nuclear matrices and [32P]DNAs were irradiated and assayed for binding. Poly(dAT) served as a competitor in the binding assays, because it eliminated nonspecific binding of DNA to the nuclear matrix and revealed the radiation-induced increase in tightly bound DNA. When nuclear matrices were isolated from irradiated nuclei (0-200 Gy) and incubated with the kappa-Ig MAR fragment in the absence of poly(dAT) (type A experiments), much nonspecific, non-dose-dependent binding was observed. With poly(dAT) in the incubation mixture, a dose-dependent decrease (p < 0.001) in the binding was revealed, indicating a radiation-induced loss of available binding sites, perhaps due to the cross-linking of endogenous sequences. The pBR322 fragment did not show a similar loss of binding sites. Irradiation of mixtures of isolated nuclear matrices and end-labeled fragments (type B experiments) allowed the study of radiation-induced cross-linking of exogenous fragments to the matrices. If poly(dAT) was present during irradiation, nonspecific binding was eliminated; however, no significant increase (p = 0.5) in the specific binding of the DNA to the nuclear matrix was observed. In contrast, if poly(dAT) was added after irradiation, in addition to the elimination of nonspecific binding, a radiation dose-dependent increase in binding was revealed for both the kappa-Ig MAR and the hsp MAR (p < 0.001), but not for either of the pBR322 fragments. The results indicate that the specific interaction of MARs with proteins of the nuclear matrix provides a radiation-sensitive substrate for the formation of DNA-protein cross-links.

Animals↗
PubMed1991

Induction of internucleosomal DNA fragmentation in human myeloid leukemia cells by 1-beta-D-arabinofuranosylcytosine.

The present results demonstrate that treatment of human U-937 myeloid leukemia cells with 1-beta-D-arabinofuranosylcytosine (ara-C) is associated with DNA fragmentation at multiples of approximately 200 base pairs. The extent of ara-C-induced DNA fragmentation was dependent on drug concentration and time of exposure. This pattern of internucleosomal DNA cleavage has been observed during programmed cell death and was associated in the present studies with loss of clonogenic survival. The results also demonstrate that the c-jun protooncogene is induced by ara-C during periods of DNA cleavage. These findings suggest that ara-C activates a program involving both oligonucleosomal DNA fragmentation and changes in early response gene expression.

Cell Line↗
PubMedDate not supplied

Induction of DNA fragmentation by tannin- and lignin-related substances.

A variety of tannin and lignin-related compounds were compared for their ability to induce nucleosome-sized DNA fragmentation (a biochemical hallmark of apoptosis), using agarose gel electrophoresis and a fluorescence activated cell sorter. Monomeric, dimeric, trimeric and tetrameric hydrolysable tannins induced nucleosome-sized DNA fragmentation in HL-60 cells, more potently than condensed tannins. The highest activity was detected in gallic acid, a component unit of tannins. Natural lignified materials, except for caffeic acid and its dehydrogenation polymer, showed much weaker activity. Protein-bound polysaccharide (PSK) was inactive. Gallic acid induced DNA fragmentation in four human myelogenous leukaemic cell lines, but not in human T-cell leukaemia and erythroleukaemia cell lines. Ca2+ depletion from the culture medium slightly, but significantly, reduced the apoptosis-inducing activity of gallic acid, but did not significantly affect that of tannic acid or caffeic acid. After treatment with gallic acid, intracellular Ca2+ concentration was significantly elevated. The apoptosis-inducing activity of polyphenols may further emphasize their medicinal efficacy.

Apoptosis↗
PubMed1994

Magnesium cardioplegia reduces cytosolic and nuclear calcium and DNA fragmentation in the senescent myocardium.

Previous reports have indicated that the senescent myocardium is less tolerant to surgically induced ischemia and that diminished functional recovery is associated with alterations in cytosolic calcium ([Ca2+]i) accumulation. Recently, increased [Ca2+]i has been suggested to alter nuclear calcium ([Ca2+]n) accumulation. To investigate the relation between [Ca2+]i and [Ca2+]n, we subjected mature and aged rabbit hearts to normothermic global ischemia, either without treatment or after treatment with potassium cardioplegia, magnesium cardioplegia, or a combination of potassium and magnesium cardioplegia. The relation between altered [Ca2+]n and DNA fragmentation was also investigated. Our results indicate that [Ca2+]i was increased during 30 minutes of normothermic global ischemia without treatment in both the mature and aged hearts (p < 0.05). Accumulation of [Ca2+]i during global ischemia was reduced with the use of potassium, magnesium, and a combination of potassium and magnesium cardioplegia (p < 0.05 versus untreated ischemia) in both the mature and aged hearts. Levels of [Ca2+]n were unaffected by global ischemia or cardioplegia in the mature myocardium; however, in the aged myocardium, [Ca2+]n was increased during global ischemia and with potassium cardioplegia and was associated with increased nuclear DNA fragmentation (p < 0.05). The use of magnesium and a combination of potassium and magnesium cardioplegia attenuated [Ca2+]n accumulation and nuclear DNA fragmentation (p < 0.05). Control of [Ca2+]i and [Ca2+]n was associated with enhanced functional recovery during reperfusion. These results indicate that during normothermic ischemia, there is increased [Ca2+]i and [Ca2+]n in the aged myocardium, and increased [Ca2+]n is associated with increased nuclear DNA fragmentation.(ABSTRACT TRUNCATED AT 250 WORDS)

Aging↗
PubMedDate not supplied

[The role of duplex ends in the spontaneous interaction of homologous linear DNA fragments].

The spontaneous interaction of homologous linear DNA fragments was studied with a model of purified PCR products by agarose gel electrophoresis. To interact, duplexes required not only homology of internal regions, but also complementary ends. Fragments differing in terminal sequences did not interact. The yield of Holliday junctions (HJ), the simplest product of DNA-DNA interaction, depended on dissociation of fragment ends. Compared with genomic fragments, those with low-melting AT ends interacted with each other more efficiently and those with high-melting GC ends, less efficiently. Incubation temperature affected the equilibrium HJ concentration in solution of homologous fragments. A conclusion was made that HJ formation is initiated by nucleation of dissociated duplex ends.

DNA↗
PubMed2006

Genetic mutation analysis by CE with LIF detection using inverse-flow derivatization of DNA fragments.

Inverse-flow derivatization is a novel approach to obtain fluorescent DNA derivatives in DNA analysis based on CE with LIF detection. In the present work, we want to explore the feasibility of the application of this method into the mutation detection based on constant denaturant capillary electrophoresis (CDCE) and SSCP analysis. The DNA fragments were first amplified by PCR using a pair of common primers without fluorescent label, and then the mutations were determined by CDCE or SSCP analysis based on CE-LIF with inverse-flow derivatization of DNA fragments. The experimental conditions were investigated systematically, and different labeling modes including inverse-flow derivatization, on-column derivatization and fluorescent labeled primer technique were compared. The inverse-flow derivatization was successfully used in the detection of C677T mutation in the methylenetetrahydrofolate reductase gene by CDCE or SSCP analysis. Our preliminary results demonstrate that inverse-flow derivatization is very simple, inexpensive and sensitive and well suitable for the genetic analysis in clinical diagnosis.

DNA↗
PubMed2005

Cyclization of short DNA fragments and bending fluctuations of the double helix.

Cloutier and Widom [Cloutier, T. E. & Widom, J. (2004) Mol. Cell 14, 355-362] recently reported that the cyclization efficiency of short DNA fragments, about 100 bp in length, exceeds theoretical expectations by three orders of magnitude. In an effort to resolve this discrepancy, we tried modifying the theory. We investigated how the distribution of the angles between adjacent base pairs of the double helix affects the cyclization efficiency. We found that only the incorporation of sharp kinks in the angle distribution provides the desired increase of the cyclization efficiency. We did not find a model, however, that fits all cyclization data for DNA fragments of different lengths. Therefore, we carefully reinvestigated the cyclization of 100-bp DNA fragments experimentally and found their cyclization efficiency to be in remarkable agreement with the traditional model of DNA bending. We also found an explanation for the discrepancy between our results and those of Cloutier and Widom.

Base Pairing↗
PubMed2003

DNA fragmentation in human spermatozoa: significance in the diagnosis and treatment of infertility.

The integrity of the paternal genome is of paramount importance in the initiation and maintenance of a pregnancy in vivo and in vitro. The presence in the embryonic genome of chemical modifications at the level of DNA nucleotides and/or DNA strand breaks coming from the paternal genome (that have not been repaired by the oocyte after fertilization), is not compatible with normal embryo and fetal development. DNA fragmentation in human spermatozoa has been recently shown to be an important contributing factor to the etiology of unexplained infertility. In this review, the mechanisms responsible for DNA fragmentation in sperm, including defects in chromatin remodeling during the process of spermiogenesis, apoptosis and ROS-induced damage during sperm migration from the seminiferous tubules to the epididymis, are discussed. Also, the different methodologies used to determine DNA fragmentation in human sperm (with special emphasis on the SCSA test) and the applications of the SCSA test in the diagnosis and treatment of infertility, are presented. Finally, answers to common questions asked about the SCSA test are also included.

DNA Fragmentation↗
PubMed1996

Human T-lymphocyte serine proteases (granzymes) 1, 2, and 3 mediated DNA fragmentation in susceptible target cells.

We reported the characterization of three serine proteases (granzymes 1, 2, and 3) from human cytotoxic T lymphocytes. In this study, human granzymes 1, 2, and 3 were purified from the cytoplasmic granules of lymphokine activated killer (LAK) cells by gel filtration and cation exchange chromatography. Human perforin was purified by phenyl superose and heparin-agarose chromatography. Each purified granzyme was used with purified perforin to study DNA fragmentation in target cells of both human and murine origin. As measured by agarose gel electrophoresis and [125I]dUrd assay, the granzymes induced oligonucleosomal DNA fragmentation and [125I]dUrd release respectively from various target cells. Murine target cells were generally more susceptible to nuclear DNA release than were human targets. Both enzyme activity and nuclear DNA breakdown were significantly inhibited by 3,4-dichloroisocoumarin (DCI) or by heat inactivation of each granzyme. Perforin alone or granzyme alone failed to fragment nuclear DNA in various target cells. We conclude that human granzymes are an important family of effector molecules that with perforin induce DNA fragmentation in susceptible target cells.

DNA Fragmentation↗
PubMed2000

Analysis of DNA fragmentation, plasma membrane translocation of phosphatidylserine and oxidative stress in human spermatozoa.

UNLABELLED: The objectives of this cross-sectional observational study were: (i) to detect DNA damage and plasma membrane translocation of phosphatidylserine in purified sperm populations of high and low motility, and (ii) to analyse their relationship with the endogenous generation of reactive oxygen species. Ejaculates from infertile men were examined following gradient centrifugation. The main outcome measures were: sperm motion parameters (assessed with a computer analyser), generation of reactive oxygen species (measured by chemiluminescence), DNA damage (detected by terminal deoxynucleotidyl transferase-mediated dUDP nick-end labelling and monoclonal antibody labelling of single-stranded DNA) and translocation of membrane phosphatidylserine (examined with annexin V staining). DNA fragmentation and membrane translocation of phosphatidyl-serine were observed in the fractions with low and high sperm motility in all patients. The fractions with low sperm motility had significantly higher proportion of cells with DNA damage and production of reactive oxygen species than the fractions with high sperm motility (P < 0.005). DNA fragmentation was significantly and positively correlated with the generation of reactive oxygen species (r = 0.42; P = 0.02). IN CONCLUSION: (i) spermatozoa from infertile men display translocation of membrane phosphatidylserine as diagnosed by annexin V positive staining; (ii) DNA damage (fragmentation and presence of single-stranded DNA) can be detected in ejaculated spermatozoa from infertile men in fractions with low and high sperm motility, and (iii) there is a relationship between DNA damage and oxidative stress.

Adult↗
PubMedDate not supplied

A protocol for DNA fragment extraction from polyacrylamide gels.

A simple and efficient method of purifying linear plasmid DNA from contaminating DNA fragments is described. Both vector and insert containing plasmids may be used without extensive purification, in particular without cesium chloride centrifugation. Careful deproteinization with phenol-chloroform allows efficient restriction enzyme digestion. Fragment separation can be performed immediately after restriction endonuclease digestion in a single 6% polyacrylamide gel. Extraction of DNA fragments from the gel is easy and gives a good yield. The DNA may be used for ligation and transformation without further purification.

Biotechnology↗
PubMed2002

Earlier onset of DNA fragmentation in leaves of wheat compared to barley and rye.

We have found extensive nucleosomal fragmentation of native DNA extracted from leaves of healthy cereal plants, as indicated by ladder patterns on agarose gels and TUNEL staining. The time of first appearance of fragmentation differed among cereals. Native DNA from the first leaf of 10-day-old plants formed a clear ladder pattern of multiples of 180 bp fragments in wheat and triticale but not in barley and oats. In one cultivar of rye a weak ladder pattern occurred but not in another. Freezing and thawing of samples before DNA extraction resulted in much more extensive DNA fragmentation in wheat but not in rye and barley, indicating that DNA-degrading enzymes are present in the cytoplasm of wheat, but not in barley and rye, at this stage. In barley, nucleosomal fragmentation was first detected in 25-day-old plants. These results indicate that programmed cell death takes place in developing leaves of young cereal plants, but that the time of onset differs among cereal species.

DNA Fragmentation↗
PubMed2004

Colocalization of DNA fragmentation and caspase-3 activation during atresia in pig antral follicles.

Apoptosis is the cellular mechanism of ovarian follicular atresia. The major downstream effector of this phenomenon in many tissues is caspase-3 but little is known about its role in pig ovarian apoptosis. In the present study, we detected the localization of caspase-3 in parallel with nuclear fragmentation (TUNEL) on healthy and early atretic antral follicles. In healthy antral follicles caspase-3 and TUNEL positivity were occasionally recorded within theca layer. The incidence of DNA fragmentation, as indicated also by the biochemical detection, increased mainly in the granulosa layer of early atretic follicles. Quantitative analysis revealed, besides, that atresia was accompanied by a higher incidence of caspase-3 (57.20 +/- 20.05 versus 3.64 +/- 0.61 positive cells in atretic versus healthy follicles, respectively; P < 0.05), of TUNEL positivity (20.13 +/- 9.33 versus 0.42 +/- 0.12; P < 0.05) and simultaneous immunostaining for caspase-3 and TUNEL (15.02 +/- 6.95 versus 0.31 +/- 0.05; P < 0.05) in the granulosa layer. In detached granulosa cells isolated from the follicular fluid of early atretic follicles a further significantly increase was recorded in the percentage of TUNEL positivity and in the incidence of cells that showed colocalization of caspase-3 activity and DNA fragmentation. Granulosa cells of early atretic follicles exhibited a higher positivity for caspase-3 localized in the cytoplasm and occasionally in the nucleus area of granulosa cells. These results indicate that capsase-3 was involved and precociously activated during the process of atresia. Finally, the progressively higher incidence of TUNEL positivity and of double immunostaining in atretic cells collected within the follicular fluid seems to indicate that proteases activity leads only tardily in a detectable DNA fragmentation.

Animals↗
PubMed1991

DNA sequence of a Salmonella-specific DNA fragment and the use of oligonucleotide probes for Salmonella detection.

Hybridization specificity of a 1.8-kb HindIII DNA fragment isolated from Salmonella typhimurium by a molecular cloning technique was confirmed by colony hybridization with 327 Salmonella isolates of various serotypes and 56 non-Salmonella isolates including Enterobacteriaceae closely related to Salmonella, such as Escherichia coli, Klebsiella, Citrobacter and Shigella. It was found that this 1.8-kb DNA fragment was highly specific for all the Salmonella isolates tested. The DNA sequence of this 1.8-kb fragment was then determined by the dideoxynucleotide chain termination method. According to this DNA sequence, six oligonucleotide fragments ranging from 17- to 26-mer were then chemically synthesized and tested for their hybridization specificities. Results show that three of the six oligonucleotide fragments are highly specific for all 327 Salmonella strains tested and can be used as probes for the specific detection of Salmonella in foods or other samples.

Base Sequence↗