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At least 919 records · Page 51Linked to original sources
PubMed1994

On the "door-corridor" model of gel electrophoresis. I. Equations describing the relationship between mobility and size of DNA fragments and protein-SDS complexes.

In a gel, electrophoretic mobility of a DNA fragment and a protein-SDS complex is an exponential function of the ratio between two forces, the resisting force of the gel polymers and the electrokinetic force of the migrating macromolecule. It is also proportional to the mobility of unit size of the migrating molecule, mu 1. Each gel gives an optimal resolution of macromolecules of a defined size. That size must be such that the electrokinetic force of the migrating molecule equals the gel resistance force, so that the ratio of mobility and mu 1 becomes e-1. The optima for several poly[N-acryloyl-tris(hydroxymethyl)aminomethane], polyacrylamide and agarose gels are given. Only two constants are sufficient for description of the relationship between mobility and size of DNA fragments and protein-SDS complexes of the sizes close to that optimally resolved. One is mu 1 and the other, ks, is the slope of the straight line which can be obtained from the size versus reciprocal of the mobility plot. The experimentally observed sigmoidal curves in the plots including the logarithm of size follow directly from the developed equations. The use of mu 1 instead of mu 0 may provide a better interpretation of the Ferguson plots.

DNA↗
PubMed1975

Mapping of late adenovirus genes by cell-free translation of RNA selected by hybridization to specific DNA fragments.

Cytoplasmic RNA, isolated from cells late after infection by adenovirus type 2 and fractionated by hybridization to specific fragments of adenovirus DNA produced by cleavage with the endonuclease R-EcoRI, was used as template for protein synthesis in cell-free mammalian extracts. Each of the R-EcoRI fragments of DNA selects RNA that encodes specific subsets of the viral polypeptides. From the known order of the R-EcoRI fragments, the following partial map is deduced: (III, IIIa, IVa2, V, P-VII, IX), (II, P-VI), 100K, IV-where the relative order of the components enclosed in parentheses has not yet been determined.

Adenoviridae↗
PubMed1992

Multi-priming sequencing: a DNA sequencing method involving restriction enzyme-digested DNA fragments as primers.

An improved strategy for fluorescence-labeled dideoxy chain termination sequencing involving restriction enzyme-digested DNA fragments as primers, which are prepared from the DNA to be sequenced, is described. By using modified nucleoside triphosphates for strand protection in chain termination reactions, newly synthesized chains were detached from a primer at the regenerated recognition site by means of suitable restriction enzyme digestion. The digests could be analyzed with commercial automated DNA sequencers. Thus, by using restriction DNA fragments (double-stranded) as primers, sequence information was obtained from both "minus" and "plus" single-stranded DNA templates without subcloning. Nor is the synthesis of oligonucleotide primers needed. This method, named "Multi-Priming Sequencing," was proven to be time-saving, economical, and effective compared to conventional methods.

Base Sequence↗
PubMed1992

Apoptosis and DNA fragmentation precede TNF-induced cytolysis in U937 cells.

The hypothesis that activation of apoptosis and DNA fragmentation is involved in TNF-mediated cytolysis of U937 tumor cells was investigated. Morphological, biochemical, and kinetic criteria established that TNF activates apoptosis as opposed to necrosis. Within 2-3 h of exposure to TNF, U937 underwent the morphological alterations characteristic of apoptosis. This was accompanied by cleavage of DNA into multiples of nucleosome size fragments. Both of these events occurred 1-2 h prior to cell death as defined by trypan blue exclusion or 51Cr release. DNA fragmentation was not a non-specific result of cell death since U937 cells lysed under hypotonic conditions did not release DNA fragments. The percentage of cells undergoing apoptosis depended on the concentration of TNF and was augmented by the addition of cycloheximide. A TNF-resistant variant derived from U937 did not undergo apoptosis in response to TNF, even in the presence of cycloheximide. Furthermore, TNF could still activate NFkB in this variant, suggesting that this pathway is not involved in TNF-mediated cytotoxicity. Two agents known to inhibit TNF-mediated cytotoxicity, ZnSO4 and 3-aminobenzamide, were shown to inhibit TNF-induced apoptosis. Taken altogether, these data support the hypothesis that activation of apoptosis is at least one essential step in the TNF lytic pathway in the U937 model system.

Benzamides↗
PubMed1979

Transformation of primary rat kidney cells by DNA fragments of weakly oncogenic adenoviruses.

Primary cultures of baby rat kidney (BRK) cells were transformed by intact DNA and DNA fragments of weakly oncogenic human adenovirus types 3 and 7. The smallest fragment found to contain transforming activity was the left-terminal 4% endo R.HindIII fragment (for both adenovirus type 3 and 7 DNAs). The efficiency of transformation of this fragment was low, and no permanent cell line could be established. Left-terminal fragments ranging from 84 to 4,5% of the viral genome could all transform BRK cells with the same efficiency as intact viral DNA. A number of adenovirus type 7 DNA fragment-transformed lines were established and were found to contain persistent viral DNA sequences and adenovirus subgroup B-specific T antigen. Consequently, the transforming functions of adenovirus types 3 and 7 are located at the extreme left-hand end of the genome, and the minimum size for a DNA fragment with transforming activity is 1.0 X 10(6) daltons. These results do not rule out the possibility that viral genes located outside the transforming region may also influence transformation.

Adenoviruses, Human↗
PubMed1993

A three-dimensional plot for the display of transverse pore gradient gel electrophoresis data: application to a kinetoplast DNA fragment of planar circular conformation.

A 219 bp fragment of kinetoplast DNA from Crithidia fasciculata has previously been shown to exhibit a gel concentration dependent, anomalously low migration rate in 3-10% polyacrylamide transverse pore gradient gels relative to that of straight standards. The anomaly was interpreted in accordance with previous results of Marini et al. [1] as being due to the planar circular conformation of the fragment. The transverse pore gradient gel pattern is displayed here as a three-dimensional plot of migration distance vs. gel concentration and DNA length for the kinetoplast fragment and straight DNA standards. The plot yields a smooth surface for the standards clearly separated from the curve of the kinetoplast DNA fragment. Thus, transverse gradient gel electrophoresis in conjunction with the three-dimensional plot provides a unique method for the recognition of abnormal conformational features of DNA on the basis of electrophoretic mobility in a pore-size gradient.

Animals↗
PubMed1997

DNA-fragmentation and expression of apoptosis-related proteins in muscular dystrophies.

Although numerous sarcolemmal protein defects in muscular dystrophies have been identified, the mechanisms linking these defects and muscle fibre degeneration are not fully characterized. As there is evidence that apoptosis is part of muscle fibre loss in dystrophin-deficient mdx-mice, apoptotic muscle fibre death may also play a role in humans with muscular dystrophies. We investigated in-situ DNA-fragmentation by the TUNEL-method and expression of apoptosis-related proteins immunohistochemically in 14 children suffering from deficiencies of dystrophin, adhalin, and merosin, and found TUNEL-positive chromatin-cleavage of muscle fibre nuclei in about 10% of non-necrotic muscle fibres. DNA-fragmentation also occurred in groups of 'necrotic and regenerating' muscle fibres with labelling of nuclei in myogenic cells and phagocytizing macrophages. These lesions also revealed expression of apoptosis-promoting factors, such as bax and ICE, inducing cleavage of myofilaments, and of the apoptosis-inhibiting proteins bcl-XL and bcl-2 which neutralized high bax levels. Mimicking embryonal myogenesis, chromatin-fragmentation in 'necrotic and regenerating' areas seems to be part of the regulating events in muscle regeneration to eliminate excessive proliferating satellite cells. Nevertheless, macrophages are also affected by apoptosis after successful removal of necrotic fibres. In humans, DNA-fragmentation and expression of apoptosis-related proteins indicate that apoptosis plays a role in muscle degeneration and regeneration in muscular dystrophies.

Apoptosis↗
PubMed2003

Overexpression of rat heat shock protein 70 is associated with reduction of early mitochondrial cytochrome C release and subsequent DNA fragmentation after permanent focal ischemia.

Although protective effects of heat shock protein 70 (HSP70) overproduction after ischemic injury have been shown both in vitro and in vivo in neurons, the mechanisms are not fully understood. The hypothesis of this study is that transgenic mice overexpressing HSP70 (HSP70 Tg) show reduced mitochondrial cytochrome c release into cytosol and diminished apoptotic cell death after permanent focal ischemia in comparison to wild-type (Wt) mice. Permanent middle cerebral artery occlusion (pMCAO) was produced by intraluminal suture cannulation in HSP70 Tg and Wt mice. DNA fragmentation was evaluated with DNA gel electrophoresis and terminal deoxynucleotidyl transferase-mediated biotinylated UTP nick end labeling (TUNEL) 24 h after pMCAO. Mitochondrial cytochrome c release into cytosol was assessed with Western blotting and immunohistochemistry 4 h after pMCAO. Cytochrome c levels in the cytosolic fraction were significantly reduced and immunoreactivity of cytochrome c in both cortex and striatum was significantly less in HSP70 Tg mice compared with Wt mice after 4-h pMCAO. DNA laddering, which was clearly observed in Wt mice, was markedly attenuated in HSP70 Tg mice 24 h after pMCAO. The number of TUNEL-positive cells was significantly reduced in HSP70 Tg mice compared with Wt mice. Results are consistent with an association between overexpression of HSP70 and reduction of cytochrome c release with subsequent DNA fragmentation. This may contribute to the HSP70-mediated neuroprotective effect observed after cerebral ischemia.

Animals↗
PubMed1998

Indomethacin inhibits delayed DNA fragmentation of hippocampal CA1 pyramidal neurons after transient forebrain ischemia in gerbils.

Recent studies have shown a close association between reactive oxygen species and DNA fragmentation and that delayed neuronal death after transient forebrain ischemia manifests as DNA fragmentation-like apoptosis. We examined the effect of indomethacin on ischemic-induced delayed hippocampal neuronal death in gerbils using the TUNEL staining method, since indomethacin is neuroprotective in a variety of degenerative processes, such as Alzheimer's disease. Indomethacin (5 mg/kg, i.p.), administered 5 min before the ischemic insult, significantly decreased the number of TUNEL-positive hippocampal CA1 pyramidal neurons and delayed the appearance of TUNEL-positive neurons. Our results indicate that indomethacin is effective in inhibiting DNA fragmentation after transient forebrain ischemia.

Animals↗
PubMed1999

Inhibition of drug-induced DNA fragmentation, but not cell death, of glioma cells by non-caspase protease inhibitors.

The role of non-caspase protease activation in drug-induced cell death of glioma cells was examined. Neither calpain inhibitors I or II, phenylmethylsulfonyl fluoride (PMSF), Nalpha -p-tosyl-L-lysine chloromethyl ketone (TLCK), N-tosyl-L-phenylalanine chloromethyl ketone (TPCK), E64, leupeptin nor pepstatin inhibit the cytotoxicity of vincristine, cisplatin, doxorubicin, cytarabine, camptothecin, BCNU or VM26 in two malignant glioma cell lines, T98G and LN-229. However, DNA fragmentation induced by VM26 is inhibited by calpain inhibitor I, PMSF, TLCK and TPCK, and that induced by camptothecin by calpain inhibitors I and II and TPCK. Moreover, protease inhibitors fail to abrogate CD95 ligand-induced apoptosis even though DNA fragmentation is attenuated by calpain inhibitor II and TPCK. Thus, non-caspase protease activation is not required for drug-induced apoptosis of glioma cells. Protease inhibitor-mediated inhibition of DNA fragmentation operates downstream of the commitment point for cell death.

Antineoplastic Agents↗
PubMed1976

Characterization of yeast ribosomal DNA fragments generated by EcoR1 restriction endonuclease.

The action of Escherichia coli restriction endonuclease R1 (EcoR1) on DNA isolated from Saccharomyces cerevisiae (strain MAR-33) generates three predominent homogenously sized DNA fragments (species of 1.8, 2.2 and 2.5 kilo nucleotide base pairs (KB). Many DNA species of molecular weight greater than 2 million daltons can be recognized upon incomplete EcoR1 digestion of yeast DNA. Four additional DNA species ranging from 0.3--0.9 KB can be identified as the second major class of EcoR1-yeast DNA products. Hybridization with radioactive ribosomal RNA (rRNA) and competition with nonradioactive rRNA show that of the three predominent EcoR1-yeast DNA species, the 2.5 KB species hybridizes only with the 25S rRNA while the lighter 1.8 KB species hybridizes with the 18S rRNA. The intermediate DNA species of 2.2 KB hybridizes to a small extent with the 25S rRNA and could be a result of the presence of the 2.5 KB DNA species. The mass proportions and hybridization values of these 3 DNA species account for about 60% of the total ribosomal DNA (rDNA). The 5 Eco-R1-yeast DNA species of less than 0.9 KB (4 major and 1 minor species) hybridize to varying degrees with the 2 rRNA and can be grouped in two classes. In one class there are 3 DNA species that hybridize exclusively with the 18S rRNA. In the second class there are 2 DNA species that besides hybridizing predominently with the 25S rRNA also hybridize with the 18S rRNA. The 7 EcoR1-yeast DNA species (excluding the 2.2 KB DNA species) that hybridize with the two rRNA account for nearly a 5 million dalton DNA segment, which is very close to the anticipated gene size of rRNA precursor molecule. If the 2.2 KB DNA species is a part of the rDNA that is not transcribed or 5 sRNA then the cistron encoding the rRNA in S. cerevisiae has at least 8 EcoR1 recognition sites resulting in 8 DNA fragments upon digestion with the EcoR1. Consideration is given to the relationship of the rRNA species generated by EcoR1 digestion and the chromosomes containing ribosomal cistrons.

DNA↗
PubMed2002

Involvement of superoxide in excitotoxicity and DNA fragmentation in striatal vulnerability in mice after treatment with the mitochondrial toxin, 3-nitropropionic acid.

Oxidative stress and excitotoxicity have been implicated in selective striatal vulnerability caused by the mitochondrial toxin, 3-nitropropionic acid (3-NP), which may simulate Huntington's disease in animals and humans. The detailed mechanism of the role of superoxide in striatal vulnerability induced by 3-NP is still unknown. The authors investigated oxidative cellular injury and DNA fragmentation after systemic 3-NP injection in wild-type (Wt) mice and mutant mice with a deficiency in manganese superoxide dismutase (MnSOD; Sod2 -/+). Furthermore, they investigated the effects of decortication after 3-NP treatment in Sod2 -/+ mice, and copper/zinc SOD (CuZnSOD) treatment in recently developed Sod2 -/+ mice that overexpress CuZnSOD (SOD1 +/- / Sod2 -/+ mice). Oxidized hydroethidine, 8-hydroxyguanosine immunoreactivity, and nitrotyrosine immunoreactivity were increased in the Sod2 -/+ mice compared with the Wt mice after 3-NP treatment (P < 0.001). Decortication completely abolished oxidative striatal damage after 3-NP treatment in the Sod2 -/+ mice. Increased CuZnSOD attenuated DNA fragmentation and striatal lesion volume after 3-NP treatment in the Sod2 -/+ mice (P < 0.001). These data suggest that production of superoxide may be a critical step to excitotoxicity and subsequent DNA fragmentation in selective striatal vulnerability after 3-NP treatment.

Animals↗
PubMed1991

Ionophore-induced apoptosis: role of DNA fragmentation and calcium fluxes.

Two ionophores specific for K+, valinomycin and beauvericin, induce a type of cell death very similar to apoptosis due to tumor necrosis factor (TNF alpha). Both ionophores cause cytolysis accompanied by internucleosomal DNA fragmentation of the dying cell into units of 200 base pairs. Morphologically, the cell death appears to consist of a mixture of nuclear apoptotic changes and cytoplasmic necrotic changes. As in the case for TNF alpha-mediated death, metabolic inhibitors have no effect on the course of cell death, but DNA fragmentation and cytolysis are decreased by the endonuclease inhibitor, zinc. Beauvericin and valinomycin trigger an increase in the cytoplasmic calcium concentration, most likely due to release of calcium from intracellular stores, and chelation of cytoplasmic calcium with quin-2 inhibits DNA fragmentation. Thus, these ionophores set off apoptosis through a calcium-activatable endonuclease, suggesting that other nonphysiological toxins might also cause apoptosis through their ability to indirectly elevate the cytoplasmic calcium concentration, without the need to invoke specific surface receptors.

Animals↗
PubMed2006

L-carnitine inhibits apoptotic DNA fragmentation induced by a new spin-labeled derivative of podophyllotoxin via caspase-3 in Raji cells.

L-carnitine (beta-hydroxy-trimethylaminobutyric acid) plays an essential metabolic role that consists of transferring the long chain fatty acids through the mitochondrial barrier, thus allowing their energy-yielding oxidation. GP7 (4-[4''-(2'', 2'', 6'', 6''-tetramethyl-l''-piperidinyloxy) amino] -4'-demethyl-epipodophyllotoxin) is a new spin-labeled derivative of podophyllotoxin semi-synthesized by our university. In this study, we examined the activity of L-carnitine in GP7-induced apoptosis in Burkitt's lymphoma cell line, Raji. GP7 induced time- and dose-dependent apoptotic DNA fragmentation accompanied by caspase-3 activation in Raji cells, and the kinetics of caspase-3 activation induced by GP7 was well correlated with that of apoptotic DNA fragmentation. L-carnitine treatment prevented GP7-induced caspase-3 activation, suppressed caspase-3 cleavage and abrogated GP7-induced apoptotic DNA fragmentation in Raji cells. Our findings suggest that L-carnitine is a potent anti-apoptotic agent to human lymphoma cells and may exert its anti-apoptotic effect via inhibition of caspase-3 activity in GP7-treated Raji cells.

Apoptosis↗
PubMed1994

UV radiation induces DNA fragmentation and cell death in B16 melanoma sensitized by bromodeoxyuridine: impaired c-jun induction and defective tyrosine phosphorylation signalling.

The relevance of tyrosine phosphorylation and c-jun protooncogene expression to radiation sensitization was investigated in B16 melanoma. These cells are sensitized by bromodeoxyuridine (BrdU), a thymidine analog, showing extensive DNA fragmentation reminiscent of apoptosis, after UV radiation. UV-irradiated unsensitized cells did not reveal DNA fragmentation but showed increased expression of c-jun and greater protein tyrosine phosphorylation in response to sodium vanadate, an inhibitor of tyrosine phosphatases. However, these responses were inhibited in UV-irradiated BrdU-treated cells. Our data suggest that the bromodeoxyuridine-induced sensitization to radiation can lead to DNA fragmentation and cell death, partly because of a defective tyrosine kinase signalling and an impaired c-jun expression, both of which appear important for cell survival in response to UV radiation.

Animals↗
PubMed2002

The cytotoxic activity of ribosome-inactivating protein saporin-6 is attributed to its rRNA N-glycosidase and internucleosomal DNA fragmentation activities.

Saporin-6 produced by the plant Saponaria officinalis belongs to the family of single chain ribosome-inactivating proteins. It potently inhibits protein synthesis in eukaryotic cells, by cleaving the N-glycosidic bond of a specific adenine in 28 S rRNA, which results in the cell death. Saporin-6 has also been shown to be active on DNA and induces apoptosis. In the current study, we have investigated the roles of rRNA depurination and the activity of saporin-6 on genomic DNA in its cytotoxic activity. The role of putative active site residues, Tyr(72), Tyr(120), Glu(176), Arg(179), and Trp(208), and two invariant residues, Tyr(16) and Arg(24), proposed to be important for structural stability of saporin-6, has been investigated in its catalytic and cytotoxic activity. These residues were mutated to alanine to generate seven mutants, Y16A, R24A, Y72A, Y120A, E176A, R179A, and W208A. We show that for the RNA N-glycosidase activity of saporin-6, residues Tyr(16), Tyr(72), and Arg(179) are absolutely critical; Tyr(120) and Glu(176) can be partially dispensed with, whereas Trp(208) and Arg(24) do not appear to be involved in this activity. The residues Tyr(72), Tyr(120), Glu(176), Arg(179), and Trp(208) were found to be essential for the genomic DNA fragmentation activity, whereas residues Tyr(16) and Arg(24) do not appear to be required for the DNA fragmentation. The study shows that saporin-6 possesses two catalytic activities, namely RNA N-glycosidase and genomic DNA fragmentation activity, and for its complete cytotoxic activity both activities are required.

DNA Damage↗
PubMed1994

Horizontal polyacrylamide gel electrophoresis for the separation of DNA fragments.

A discontinuous borate/formate buffer system is presented for horizontal polyacrylamide gel electrophoresis of DNA fragments. The resolution potential of the system could be altered by changing the total monomer concentration (5-9%T), the concentration of the crosslinker piperazine diacrylamide (2-5%CPDA), as well as the concentration of formate in the gel (40-120 mM), the leading ion of the buffer system. The separation of DNA fragments would be improved by increasing the migration distance from 22 to 28 cm. This discontinuous polyacrylamide gel electrophoresis system proved highly reproducible.

Buffers↗
PubMed2001

Generation of PCR-based DNA fragments for specific detection of Streptomyces saraceticus N45.

Streptomyces saraceticus strain N45, a saprophytic Gram-positive bacteria, has been shown to harbor high chitinase activity. Due to its potential use in biological control, the cloning of chitinase genes and the development of methods to quickly and precisely detect its presence have become necessary. In this study, PCR-based random amplified polymorphic DNA (RAPD) and PCR strategies were used to amplify random DNA fragments from the genome of S. saraceticus N45. Three amplified DNA fragments, 417, 523 and 655 bp in length, were further isolated, subcloned and sequenced. Nest primers were designed from terminal ends of these three fragments and used for further PCR reactions. A single specific band was produced from the genomic DNA of S. saraceticus N45 for each nest primer pair. These three single bands were S. saraceticus N45 specific and were not amplified from other species of Streptomyces or bacteria, such as Ralstonia solanacearum, Agrobacterium tumefaciens, E. coli, Bacillus subtilis and Xanthomonas campestris pv. campestris. Through detection of the coexistence of these three fragments in PCR reaction using DNA or bacterial cells directly, the presence of S. saraceticus N45 can be confirmed. Further Southern analysis indicated that these three DNA fragments were specifically present in the S. saraceticus N45 genome in a single copy manner, and therefore, that they can potentially be used as markers for identification of S. saraceticus N45.

Bacteriological Techniques↗