Search PubMed⌕ Search

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.

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

At least 235 records · Page 13Linked to original sources
PubMed1995

DNA fragmentation and immediate early gene expression in rat striatum following quinolinic acid administration.

Excitotoxic cell death is hypothesized to contribute to numerous neuropathologic conditions, including hypoxic/ischemic encephalopathy, hypoglycemia, Parkinson's disease, and Huntington's disease. Neuronal death from excitotoxic lesions has been shown to be an active process, with activation of immediate early gene transcription, resulting in secondary changes in gene expression. Another feature of neurotoxic cell death that has been examined is the presence of DNA fragmentation, which presumably indicates impending nuclear disintegration. A technique has been described for labeling fragmented DNA in situ, allowing precise determination of the anatomic and temporal distribution of neurons after an excitotoxic lesion. To investigate this phenomenon, we performed in situ nick translation on brain tissue from rats that have undergone stereotaxically placed intrastriatal quinolinic acid injections. Furthermore, in these same animals we analyzed the expression of c-fos mRNA to compare the time course and regional distribution of DNA fragmentation with immediate early gene activation after an excitotoxic lesion. Our analysis indicates that c-fos expression increases soon after quinolinic acid injection, is widespread in rat brain, but is effectively absent by 24 h postinjection. DNA fragmentation, however, is limited to striatum and is maximal at 24 h after injection. These results demonstrate the sensitivity of in situ nick translation for the detection of regional neuropathology and illustrate the temporal and spatial relationship of c-fos expression to excitotoxic neuronal death.

Animals↗
PubMed1995

Evidence of internucleosomal DNA fragmentation and identification of dying cells in X-ray-induced cell death in the developing brain.

Newborn Sprague-Dawley rats received a single dose of 2 Gy X-rays and were killed 6 hr later. Dying cells were characterized by extreme chromatin condensation and nuclear fragmentation. Dying cells were distributed in the primary and secondary germinal zones and in other brain regions. Among these latter, dying cells occurred in the cortical layers of the olfactory bulb, layers II-III and VIb of the neocortex, piriform and entorhinal cortex, stratum oriens and pyramidale of the hippocampus, striatum, thalamus, amygdala, brainstem, internal granular layer of the cerebellum, and cerebral and cerebellar white matter. Dying cells were immature cells, neurons and glial cells (including radial glia). In-situ labeling of nuclear DNA fragmentation identified individual cells bearing fragmented DNA. Since the number of cells stained with this method was larger than the number of dying cells, as revealed with current histological techniques, it is suggested that nuclear DNA fragmentation precedes chromatin condensation and nuclear fragmentation in X-ray-induced apoptosis. Furthermore, agarose gel electrophoresis of extracted DNA from irradiated brains showed a "ladder" pattern which is typical of internucleosomal DNA fragmentation and endonuclease activation.

Aging↗
PubMed2003

Molecular cloning and characterization of CIDE-3, a novel member of the cell-death-inducing DNA-fragmentation-factor (DFF45)-like effector family.

DNA fragmentation is one of the critical steps in apoptosis, which is induced by DNA fragmentation factor (DFF). DFF is composed of two subunits, a 40 kDa caspase-activated nuclease (DFF40) and a 45 kDa inhibitor (DFF45). Recently a novel family of cell-death-inducing DFF45-like effectors (CIDEs) has been identified. Among CIDEs, two from human (CIDE-A and CIDE-B) and three from mouse (CIDE-A, CIDE-B and FSP27) have been reported. In this study human CIDE-3, a novel member of CIDEs, was identified upon sequence analysis of a previously unidentified cDNA that encoded a protein of 238 amino acids. It was shown to be a human homologue of mouse FSP27, and shared homology with the CIDE-N and CIDE-C domains of CIDEs. Apoptosis-inducing activity was clearly shown by DNA-fragmentation assay of the nuclear DNA of CIDE-3 transfected 293T cells. The expression pattern of CIDE-3 was different from that of CIDE-B. As shown by Northern-blot analysis, CIDE-3 was expressed mainly in human small intestine, heart, colon and stomach, while CIDE-B showed strong expression in liver and small intestine and at a lower level in colon, kidney and spleen. Green-fluorescent-protein-tagged CIDE-3 was revealed in some cytosolic corpuscles. Alternative splicing of the CIDE-3 gene was also identified by reverse transcription PCR, revealing that two transcripts, CIDE-3 and CIDE-3alpha, were present in HepG2 and A375 cells. CIDE-3 comprised a full-length open reading frame with 238 amino acids; in CIDE-3alpha exon 3 was deleted and it encoded a protein of 164 amino acids. Interestingly the CIDE-3alpha isoform still kept the apoptosis-inducing activity and showed the same pattern of subcellular localization as CIDE-3. Consistent with its chromosome localization at 3p25, a region associated with high frequency loss of heterozygosity in many tumours, CIDE-3 may play an important role in prevention of tumorigenesis.

Alternative Splicing↗
PubMed1992

Determination of the coding capacity of the BamHI DNA fragment B of apathogenic Herpes simplex virus type 1 strain HFEM by DNA nucleotide sequence analysis.

Herpes simplex virus type 1 (HSV-1) strain HFEM acquired an apathogenic phenotype due to a deletion within the DNA sequences of the BamHI DNA fragment B of the viral genome. In order to investigate the coding strategy of this particular region of the genome of HSV-1 strain HFEM the DNA nucleotide sequence of the BamHI DNA fragment B was determined. This analysis revealed that the BamHI DNA fragment B of HSV-1 strain HFEM comprises 6593 bp, corresponding to the nucleotide positions (np) 113322 to 117088 and np 120643 to 123465 of the genome of HSV-1 strain 17. According to these data the deletion of the genome of HSV-1 strain HFEM occurred between the np 117089 and 120642. The promoter region of the UL56 gene of HSV-1 strain HFEM is a part of the deleted DNA sequences. Therefore, this gene of HSV-1 strain HFEM is affected and cannot be expressed. The first 35 amino acid (AA) residues of the deduced amino acid sequence of the UL56 open reading frame (ORF) were found to be identical to the amino acid sequence of the UL56 genes of HSV-1 strains 17 and F. However, due to a deletion at np 3494 of the BamHI DNA fragment B of HSV-1 strain HFEM the amino acid composition of the predicted UL56 gene of HSV-1 strain HFEM is different from HSV-1 strain 17 between amino acid positions 36 and 233. In addition the deduced amino acid sequence of the IRL (inverted repeat of the long segment) copy of the IE110 gene of HSV-1 strain HFEM was found to be about 342 amino acids shorter than the amino acid sequence of IE110 gene of HSV-1 strain 17 (775 AA). This was based on a point mutation which was detected within the DNA sequences of Exon 3 of this copy of IE110 gene of HSV-1 strain HFEM.

Amino Acid Sequence↗
PubMed2003

Involvement of DNase gamma in apoptotic DNA fragmentation in histiocytic necrotizing lymphadenitis.

DNA fragmentation induced by endonucleases is a hallmark of apoptotic process. One of the endonucleases responsible for apoptotic DNA fragmentation has been identified as DNase gamma. It has been suggested that massive nuclear debris observed in histiocytic necrotizing lymphadenitis (HNL, Kikuchi disease) results mainly from apoptosis of T-lymphocytes rather than necrosis. To identify the role of DNase gamma in apoptotic foci of HNL paraffin embedded tissue sections of HNL and lymphadenopathy with hyperplastic germinal centers and paracortex in the neck lymph nodes were immunohistochemically stained for DNase gamma and the results compared with the reactivity of TdT-mediated dUTP nick end labeling (TUNEL). Immunoreactivity for DNase gamma was detected in fragmented and condensed nuclei found abundantly in HNL as well as TUNEL reactivity. Moreover, the ratio of DNase gamma immunoreactivity to TUNEL reactivity, which represents probability of apoptosis relevant to DNase gamma, was higher in foci of nuclear debris in HNL than in the hyperplastic paracortex in lymphadenopathy including T-cell apoptosis. Our findings suggest that apoptosis detected in HNL depends more specifically upon DNase gamma than apoptosis in the hyperplastic paracortex of lymphadenopathy, and that the dysregulation of DNase gamma activation is involved in apoptosis in HNL.

Adolescent↗
PubMed2005

Salt is necessary for nucleosomal DNA fragmentation induced by caspase.

For nucleosomal DNA fragmentation, one of the hallmarks of apoptosis, activated caspase, an apoptosis specific cysteine protease, is required to cleave ICAD/DFF45 that releases its complexed DNase, CAD/DFF40. The protein complex is located predominantly in the nuclei. Inconsistently, caspase alone cannot induce DNA fragmentation in the isolated nuclei without the addition of a cell extract or purified CAD/DFF40. In this study, however, it is demonstrated that under selected conditions with 50-75 mM: KCl or NaCl, caspase-3 and-7 can induce DNA fragmentation without the additional factor(s).

Animals↗
PubMed1997

Detection of higher-order 50- and 10-kbp DNA fragments before apoptotic internucleosomal cleavage after transient cerebral ischemia.

DNA fragments of 50 and 10 kbp were found in ischemic brain in adult rats following two-vessel occlusion or in neonates following hypoxia-ischemia. These higher-order fragments were detected before any laddered oligonucleosomal DNA fragmentation characteristic of apoptosis. Both the 50- and 10-kbp fragments were also detected during necrosis produced by decapitation, but these led to smeared smaller fragments, not laddered patterns. End-group analysis showed the presence of both 3'-OH and 5'-OH ends in both the 50- and 10-kbp fragments but the predominance of 3'-OH ends in the laddered fragments. A higher proportion of 5'-OH to 3'-OH ends was found in the 10-kbp fragment compared to the larger 50-kbp fragment, suggesting a selective degradation of the 50-kbp DNA fragment to the laddered oligonucleosomal patterns. Overall, the mode of DNA fragmentation appeared different from that described in classic apoptosis of thymocytes.

Animals↗
PubMed1979

Cloning of herpes simplex type 1 DNA fragments in a bacteriophage lambda vector.

DNA isolated from defective and nondefective virions of herpes simplex type 1 (HSV-1) (strain Patton) was digested with restriction endonucleases, and the resulting DNA fragments were inserted in the EK2 coliphage vector lambdagtWES . lambdaB. The recombinant DNA was encapsidated in vitro under P4 maximum containment conditions. These lambda-HSV1 hybrids were purified and amplified, and the DNA was isolated in the P4 facility. DNA, free of viable phage and bacteria, was removed from P4 conditions and analyzed. Represented among the hybrids studied to date are DNA fragments from about 50 percent of the normal HSV-1 genome. The hybrids derived from defective HSV-1 DNA fragments demonstrate the existence of many similar but not identical classes of defective genomes.

Chromosome Mapping↗
PubMedDate not supplied

Functional and ultrastructural features of DNA-fragmented human sperm.

The functional significance of deoxyribonucleic acid (DNA) fragmentation in ejaculated human sperm is unclear. In this study the extent of DNA strand breakage in swim-up selected spermatozoa was evaluated by terminal deoxynucleotidyl transferase-mediated fluorescein-dUTP nick end labeling (TUNEL)-coupled flow cytometry and correlated with several functional and morphological sperm parameters. The extent of DNA fragmentation (mean = 11.07%+/-8.00%, range = 0.79%-42.64%, n = 140) was positively related to abnormal morphology and associated with defects of the sperm tail. A negative correlation was found between DNA breakage and progressive motility. When a stepwise multiple linear regression model was used to analyze the relationship between DNA fragmentation and the aforementioned parameters, only motility results were included in the model. The presence of spermatozoa showing submicroscopic characteristics resembling those of somatic apoptosis has been reported in human ejaculate. To verify whether sperm DNA fragmentation was associated with the presence of such apoptotic-like cells, we performed electron microscopy and TUNEL-coupled flow cytometry in a limited number of sperm samples (n = 24). Although we did not observe any significant relationship between DNA breakage and the characteristics that are suggestive of apoptosis, an association was found with several ultrastructural features, indicating an impaired motility. Hence, we conclude that in ejaculated sperm, DNA fragmentation does not correspond to the apoptosis-like phenomenon and that it is associated with defects of motility.

Cell Size↗
PubMed1999

Osmotically driven radial diffusion of single-stranded DNA fragments on an agarose bed as a convenient measure of DNA strand scission.

The present study describes the development and characterization of a novel technique, the alkaline-halo assay, for the assessment of DNA single strand breakage in mammalian cells. This technique allows the measurement of DNA lesions at the single cell level and presents the additional advantages of being rapid, sensitive, virtually costless and environmentally friendly, because it does not require the use of isotopes. The alkaline halo assay involves a series of sequential steps in which the cells are first treated, then embedded in melted agarose and spread onto microscope slides that are incubated for 2 min at ice-bath temperature to allow complete geling. The slides are then incubated for 20 min in a high salt alkaline lysis solution, for an additional 15 min in a hypotonic alkaline solution and, finally, for 10 min in ethidium bromide. Under these conditions, single-stranded DNA fragments spread radially from the nuclear cage and generate a fluorescent image that resembles a halo concentric to the nucleus remnants. The area of the halos increased at increasing levels of DNA fragmentation and this process was associated with a progressive reduction of areas of the nuclear remnants. These events were conveniently monitored with a fluorescence microscope and quantified by image processing analysis. The sensitivity of the alkaline-halo assay, which is based on the osmotically driven radial diffusion of single-stranded DNA fragments through agarose pores, is remarkably similar to that of the widely used alkaline elution and comet assays.

Animals↗
PubMed1997

[Polymorphism of B1-associated DNA fragments from normal and transform ed murine hepatocytes].

Our study of B1-associated DNA fragment polymorphism in murine hepatocytes by means of polymerase chain reaction (PCR) allowed to reveal as many as 20 DNA fragments differing in their molecular masses (m. m.) and amount of amplified products varying within the range of 100-1000 bp. Within the same inbred strain of mice (C57B1/6), spectra of B1-associated DNA fragments were similar in different periods of ontogenesis (embryos of 15 and 20 days, adult mice), in different mice of the same or different litters. A comparative analysis of the spectra of B1-associated DNA fragments from hepatocytes of two inbred strains, C57B1/6 and C3HA, has shown in general their similarities in m. m. values. But a significant distinction, that was found, involved the presence of DNA fragments with m.m. approximately 600 bp in the spectra of B1-associated DNA fragments from C3HA strain mice, that is absent in the spectra of respective fragments from hepatocytes of C57B1/6 strain mice. The spectra of B1-associated DNA fragments from transformed hepatocytes of murine hepatoma MH-22a, in general, were the same as those from hepatocytes of C3HA strain mice. At the same time, a DNA fragment with m.m. of 450 bp, not detected in normal hepatocytes, was revealed in transformed ones. Nevertheless a DNA fragment with m.m. of 600 bp, characteristic of normal hepatocytes, was not observed in the transformed hepatocytes. The B1-PCR method can be used for studying genomic polymorphism both in different populations of mice, and during malignant growth.

Animals↗
PubMed1988

Regional localization of chromosome 3-specific DNA fragments by using a hybrid cell deletion mapping panel.

A series of human chromosome 3-specific DNA fragments isolated and characterized from a lamda phage genomic library were regionally localized on human chromosome 3. This was accomplished using filter hybridization blot analysis of a human chromosome 3 hybrid cell deletion mapping panel. Twenty-three new anonymous DNA fragments were assigned to one of four physical regions of chromosome 3. Seventeen DNA fragments were mapped to the long arm of chromosome 3, including one DNA fragment that demonstrated a restriction fragment length polymorphism (RFLP). Five DNA fragments were assigned to 3p14.2----pter, including one highly polymorphic fragment sublocalized at 3p25----pter by in situ hybridization. This DNA fragment is the second reported distal 3p polymorphic probe. One DNA fragment was localized to 3p14----p14.2. In addition, three fragments previously assigned to chromosome 3 were confirmed. Polymorphic DNA probes DNF15S2 (formerly D1S1) and D3S2 were mapped to 3p14.2----pter. The previous 3p25 in situ localization of the c-raf-1 oncogene was supported by deletion panel mapping. The physical localization of these twenty-three new DNA fragments has more than doubled the number of cloned DNA fragments assigned to chromosome 3. These and future regional assignments of DNA fragment probes will facilitate construction of both a physical and genetic linkage map of chromosome 3. They may also be useful in characterizing the chromosomal and molecular aberrations involved in small-cell lung cancer (SCLC), renal cell carcinoma, other malignancies, and the 3p14.2 common fragile site.

Bacteriophage lambda↗
PubMed1991

An improved method for the detection of DNA fragmentation.

An application of the Southern blot technique is described which permits the detection of DNA fragmentation due to cell death by apoptosis. DNA fragments were isolated from cell suspensions and tissues, separated on agarose gel, transferred by Southern blot and hybridized with a radiolabeled total cellular DNA probe. The application of this procedure to thymus cell samples, revealed the distinct ladder pattern of DNA fragments in multiples of about 180-200 base pairs, a characteristic feature of DNA fragmentation. In comparison to conventional DNA visualization with ethidium bromide staining, the radiolabeled probe improved the detection of DNA fragments at least eight-fold. This method detects low levels of DNA fragments, as well as physiological tissue DNA fragmentation, while avoiding cell damage due to DNA radiolabeling.

Animals↗
PubMed1999

Isolation of DNA fragments associated with methylated CpG islands in human adenocarcinomas of the lung using a methylated DNA binding column and denaturing gradient gel electrophoresis.

We have constructed a library of DNA fragments heavily methylated in human adenocarcinomas of the lung to permit the comprehensive isolation of methylated CpG islands in cancer. Heavily methylated genomic DNA fragments from tumors of nine male patients were enriched using a methylated DNA binding column and used for construction of the library. From this library, DNA fragments having properties of CpG islands were isolated on the basis of their reduced rate of strand dissociation during denaturing gradient gel electrophoresis. Approximately 1,000 clones, corresponding to 0.3% of the library were analyzed, and nine DNA fragments were identified as being associated with CpG islands that were methylated in tumor DNA. One CpG island was methylated specifically in tumor DNA, whereas the remaining eight CpG islands were methylated both in normal and tumor DNA derived from the same patients. Our results suggest that the number of CpG islands methylated specifically in tumors is not large. The library, which contains DNA fragments from methylated CpG islands comprehensively, is expected to be valuable when elucidating epigenetic processes involved in carcinogenesis.

Adenocarcinoma↗
PubMed1987

Electro-optical analysis of 'curved' DNA fragments.

The structure of some 'short' DNA fragments with 106-108 base-pairs and of a 'long' kinetoplast DNA fragment with 419 base-pairs has been analyzed by electro-optical procedures. According to their electrophoretic mobilities and circularization probabilities, it was concluded that two of our short fragments with clusters of four and five and six adenosines phased at the period of the double helix are inherently curved with an approximate curvature around 200 degrees. The dichroism decay curves of our short fragments exhibited two processes. A fast one with time constants of approx. 100 ns is attributed to bending; the bending amplitudes observed for the fragments with dA4 and dA5/6 clusters are slightly higher (23 and 29%, respectively) than those observed for control fragments (17-20%). The second process reflects the overall rotational diffusion of the whole fragments and shows some variation with the DNA sequence, but on average the rotation of fragments with dA4 and dA5/6 clusters corresponds to that observed for standard DNA. Since the rotational diffusion coefficients are very strongly dependent on the effective hydrodynamic lengths, we must conclude that the effective lengths of our fragments, including the 'curved' ones, are very similar under the conditions of our experiments. The rotation time constant for the long kinetoplast DNA is also rather close to those observed for the usual DNA fragments of corresponding length. One way to resolve the conflict of our results with conclusions obtained from other investigations would invoke the assumption that the curved fragments are not 'elastic'. According to this hypothesis, electric field pulses would stretch the curved fragments to an almost straight form and the stretched DNA would return to its equilibrium state with a time constant longer than the rotation time constant.

Base Sequence↗
PubMed1994

[Cloning of DNA fragments containing promoter activity from Streptomyces mycarofaciens 1748].

A DNA fragment containing promoter activity has been cloned from midecamycin producing strain (S. mycarofaciens 1748)., using promoter-probe plasmid vector pIJ486. The molecular size of this fragment was 2.3kb as shown by restriction analysis. A HindIII-HindIII 2.08KB DNA fragment obtained from the original fragment has been analysed by subcloning it into polylinker of vector pIJ486/7 which have opposite direction. The result showed that HindIII-HindIII 2.08kb DNA fragment has promoter activity in both direction. Transformants of plasmid containing this fragment in vector pIJ487 in S. lividans TK24 were resistant to Km in the level of 20mg/ml, but in vector pIJ 486 were resistant to the level of 3mg/ml. It indicated that a rather strong promoter activity region was in the HindIII/XbaI-HindIII direction. BamHI fragments (A-0.79kg, B-0.67kb, C-0.62kb) in 2.08kb DNA fragment have been studied in regards of their promoter activity. The result suggested that A-0.79kb region has the same promoter activity as in HindIII-HindIII 2.08kb DNA fragment.

Cloning, Molecular↗
PubMed1982

Higher order chromatin structure determines double-nucleosome periodicity of DNA fragmentation.

Double-nucleosome periodicity of DNA fragmentation with DNAse I in the nuclei of cells differing in size of the linker DNA length and lysine-rich histone composition was analyzed by means of nondenaturing agarose gel electrophoresis. DNAse I revealed this type of periodicity in rat thymus and CHO cell nuclei as well as in erythrocyte nuclei. It has been deduced that the so-called nucleodisome structure is also typical of cells possessing a usual DNA repeat length (200 bp or less) and lysine-rich histone H1. Two probably related events are important for establishing a clear double-nucleosome periodicity of DNA fragmentation: the replacement of H1 histone by a specific arginine-rich histone fraction (H5 histone in the case of erythrocyte) and the increase of the linker DNA length. The results are interpreted in terms of supranucleosomal organization of chromatin which may determine the dinucleosome periodicity of DNA fragmentation due to a specific packing of nucleosomes.

Animals↗
PubMed2000

Resistance to paclitaxel induces time-delayed multinucleation and DNA fragmentation into large fragments in MCF-7 human breast adenocarcinoma cells.

DNA fragmentation was investigated in MCF7 and the MCF7TAX19 paclitaxel-resistant subline exposed to paclitaxel for 24 h. No nucleosome-sized DNA fragmentation was observed by DNA agarose gel electrophoresis in both cell lines. However, DNA fragmentation was detected by flow cytometry sub-G1 peak analysis in both cell lines immediately after paclitaxel exposure. Nuclear abnormalities were observed in both cell lines in the range of 35-40% of the total cell population. This value was reached immediately in MCF7 cells but was time-delayed in MCF7TAX19 cells. Significant morphologic differences were observed between sensitive and resistant cell lines, 24 h after exposure to 50 nmol/l paclitaxel. Although no difference in the sub-G1 cell population was observed between sensitive and resistant cells, a significantly higher rate of multinucleated cell features was observed in resistant cells.

Adenocarcinoma↗