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At least 19 recordsLinked to original sources
PubMed1978

Mapping of early SV40-specific functions by microinjection of different early viral DNA fragments.

DNA sequences within the early simian virus 40 (SV40) genome region responsible for virus-specific tumor (T) and U antigenicity, stimulation of cell DNA synthesis, initiation of late SV40 gene expression and helper function for human adenovirus 2 were confined by experiments using microinjection of different early SV40 DNA fragments. All these early functions were detected in cells supplied with complete early viral information. Cells microinjected with DNA fragments containing about 80, 70 or 60% of thea early SV40 genome were still stained positively when challenged with antibody against T antigen, and the same cells were stimulated for cellular DNA synthesis when about 70% or more of the early viral information was available. DNA sequences at map position 0.67 are required for intracellular early viral transcription.

Antigens, Neoplasm↗
PubMed1991

Discontinuous buffer system for polyacrylamide and agarose gel electrophoresis of DNA fragments.

DNA fragments up to 9 kb in size were stacked and separated by polyacrylamide gel electrophoresis, and those up to 50 kb in size by agarose gel electrophoresis, using a discontinuous buffer system. Polyacrylamide gels at pH 8.9, 2 degrees C, 0.01 M ionic strength, yielded sharp bands with DNA loads of 8 micrograms/cm2 of gel of a mixture of 19 DNA fragments in the size range of 72-23130 bp, while agarose gels at pH 8.5, 25 degrees C, provided well-resolved, unperturbed bands at 0.04 M ionic strength with DNA loads of 1 microgram/cm2 of the same mixture. Note that the ionic strength of the agarose gels is comparable to the conventionally used 0.5 x TBE (Tris-borate-EDTA) buffer, while that successfully applied to polyacrylamide is seven-fold less than the ionic strength of conventionally used 1 x TBE buffer, with a substantially shorter duration of electrophoresis as a result. The application of a discontinuous buffer system to the gel electrophoresis of DNA results in (i) Band identification by Rf, the migration distance relative to a sharply defined "buffer front" (moving boundary). This is sufficiently labor saving, compared to determining absolute mobilities, so as to render practical the expression of bands as numbers, with benefits for data storage, statistical manipulations and physico-chemical exploitation of mobility data. The use of Rf's also circumvents loss of precision in mobility measurement resulting from progressive band spreading of dye bands used as a front. (ii) A uniformly and highly concentrated starting zone, beneficial to resolution, is obtained, without the losses by which separate concentration steps are usually burdened.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Composition↗
PubMed1990

Variable stringency hybridization of polymerase chain reaction amplified HIV-1 DNA fragments.

DNA isolated from the peripheral blood mononuclear cells of HIV-1 seropositive individuals was used for polymerase chain reaction (PCR) amplification of gag and envelope regions. Eight aliquots of the amplified DNA fragments have been subjected to Southern/dot blot analysis, hybridizing with 32P-labelled-BH10 (HIV-1 strain IIIB) at low stringency. After the filters had been autoradiographed, they were cut so that each hybridized band/dot could be subject to variable stringency washing using various ionic concentrations at a fixed temperature. The filter was reconstructed so that the effect of the variable stringency wash might be visualized following a second exposure to Kodak film. The level of activity for each band/dot was measured by counting the 32P or by densitometry analysis of the photographic record. The results allow a plot to be made of the decrease in bound radioactivity against ionic strength. By comparison with a standard curve obtained for HIV-1 strain IIIB amplified fragments subject to similar hybridization and analysis, an estimation of the degree of nucleotide mismatch relative to the BH10 DNA probe can be obtained. The technique provides a rapid means of characterizing PCR amplified fragments.

DNA, Viral↗
PubMed1991

Lack of correlation between alkaline DNA fragmentation and DNA covalent binding induced by polychloroethanes after in vivo administration. Problems related to the assessment of a carcinogenic hazard.

The DNA-damaging activity of polychloroethanes was tested in mouse liver by the fluorometric assay of DNA unwinding. With the exception of 1,2-dichloroethane, all components of this chemical class had negative results. The failure of the parameter alkaline "DNA fragmentation" to detect the DNA-damaging activity of polychloroethanes is in sharp contrast with the measurement of DNA covalent binding, another short-term parameter of genotoxicity. Since covalent DNA adducts appear to be quantitatively well correlated with the oncogenic potencies of chloroethanes in liver, the negative results obtained with the present method can perhaps be explained in terms of quality of DNA adducts; these may be incapable of producing DNA breaks or alkali-labile sites detectable as alkaline DNA fragmentation. It is however worth noting that carcinogenicity of chloroethanes appears to depend not only on DNA damaging capability, but also on promoting activity during the carcinogenic process.

Alkalies↗
PubMed1988

Avian myeloblastosis virus reverse transcriptase is easier to use than the Klenow fragment of DNA polymerase I for labeling the 3'-end of a DNA fragment.

The 3'----5' exonuclease activity of the Klenow fragment operates in 3'-end labeling of DNA fragments. In the presence of excess deoxyribonucleoside 5'-triphosphates (dNTPs), the 5'----3' polymerase activity is dominant over the exonuclease activity. However, in the presence of a small amount of dNTPs, the exonuclease activity removed deoxyribonucleoside 5'-monophosphate (dNMP) incorporated in the 3'-end of a DNA strand by the polymerase activity. We found that the radioactivity of incorporated dNMP decreased remarkably in the course of 3'-end labeling by the Klenow fragment. On the other hand avian myeloblastosis virus (AMV) reverse transcriptase also possesses the polymerase activity. The decline of the incorporated radioactivity was not observed, indicating that the enzyme has neither exo- nor endonuclease activities. Furthermore, the level of the incorporated radioactivity was the same as that obtained by the Klenow fragment. We conclude that AMV reverse transcriptase is easier to use than the Klenow fragment for labeling the 3'-end of a DNA fragment.

Affinity Labels↗
PubMed1988

Candida albicans- and Candida stellatoidea-specific DNA fragment.

DNA was isolated from whole cells of Candida albicans and digested with MspI restriction enzyme. In addition to the expected large number of low-molecular-weight DNA pieces resulting from the digestion, multiple high-molecular-weight (greater than 3.0 kilobase pairs) fragments were generated by this enzyme, which cleaves DNA at CCGG sequences. Some of these fragments appeared highly repeated. An MspI fragment which was similar in size to one of the repeat elements (2.9 kilobase pairs) was cloned into the ClaI site of the plasmid vector pBR322 and replicated in a suitable Escherichia coli host strain. The candidal fragment was radiolabeled and used to probe Southern blots of DNA from several Candida species, various other fungi, and mouse and human cells. Only DNA from C. albicans and a strain of Candida stellatoidea was found to contain sequences of significant homology for hybridization. The cloned fragment may possibly be of use as a DNA probe for detection of the presence of C. albicans.

Animals↗
PubMed1992

A quantitative assay for fragmented DNA in apoptotic cells.

Cleavage of cellular chromatin at internucleosomal sites is a characteristic change of DNA integrity in cells undergoing apoptosis. We have developed an assay for quantitation of internucleosomal DNA fragmentation in apoptotic cells. This technique involves purification of cellular DNA, dephosphorylation of the DNA ends, labeling of DNA with 32P at the 5'-end, gel electrophoresis through agarose, and quantitation of the radioactivity in DNA bands. This assay, which is about 1000- to 2000-fold more sensitive than visualization of DNA bands by ethidium staining, allows the detection of DNA fragments at picogram levels. A method for quantitatively determining the number of fragmented DNA strands is also described. Application of this new assay to evaluate the time course of internucleosomal DNA fragmentation was demonstrated in apoptotic cells induced by an anticancer nucleoside analogue.

Antimetabolites, Antineoplastic↗
PubMedDate not supplied

Site-directed insertion of long single-stranded DNA fragments into plasmid DNA.

A new site-directed method for inserting long single-stranded DNA fragments into any region of a duplex vector is described. Its major advantage is independence of the location of the restriction sites. The method involves the assembly of single-stranded DNA fragments by ligation to both ends of the inserted fragments of two cohesive flanks that are complementary to the target region. Short oligonucleotide templates are used to direct the ligation. The resulting fragments, designated further as omega fragments with cohesive flanks, are hybridized with a gapped DNA vector. The heteroduplexes are transformed into Escherichia coli cells without enzymatic filling and sealing of gapped DNA. As a consequence of intracellular repair and heteroduplex resolution, insertion mutants are recovered. To demonstrate the method's efficiency, we inserted a 51-nucleotide synthetic DNA fragment containing a modified glucocorticoid receptor binding site into the region of pBR322, near the transcription starting point of the tet gene. The method we developed makes possible site-directed insertion of synthetic and genome-derived DNA fragments at least 200 nucleotides long.

Base Sequence↗
PubMed1991

Streptozocin- and alloxan-induced H2O2 generation and DNA fragmentation in pancreatic islets. H2O2 as mediator for DNA fragmentation.

Streptozocin (STZ) and alloxan (ALX) exhibit the most potent diabetogenicity and are used for induction of experimental diabetes mellitus. An understanding of the mechanisms of action of the typical diabetogenic agents is important for elucidating the causes of diabetes. Okamoto proposed a model in which DNA fragmentation plays an important role in the development of diabetes. DNA fragmentation supposedly results from the accumulation of superoxide or hydroxyl radicals. However, direct evidence for this accumulation is lacking. With isolated rat pancreatic islets in vitro, we demonstrated that STZ and ALX stimulated H2O2 generation and caused DNA fragmentation. Addition of STZ or ALX resulted in an increase in H2O2 generation. On DNA analysis, when incubated without STZ or ALX, DNA sedimented as a single peak; when incubated with STZ or ALX, DNA sedimented slower as a broad peak and was fragmented. Graded doses of STZ and ALX stimulated H2O2 generation and induced DNA fragmentation; their effects on H2O2 generation and DNA fragmentation were evident at a concentration of 0.1 mM and were maximal at 1 mM. Administration of STX or ALX to rats in vivo stimulated H2O2 generation and caused DNA fragmentation in pancreatic islets. H2O2 itself also induced DNA fragmentation. These findings may support Okamoto's proposal that STZ and ALX induce diabetes through the following biochemical events: STZ and ALX----H2O2 generation----DNA fragmentation----beta-cell destruction. This study may constitute the first demonstration of STZ- and ALX-stimulated H2O2 generation, which probably acts as a mediator of STZ- and ALX-induced DNA fragmentation.

Alloxan↗
PubMed1990

Cytochalasin B induces cellular DNA fragmentation.

Cellular DNA fragmentation can be induced in many biological instances without plasma membrane damage. The fungal metabolite, cytochalasin B, is capable of modifying numerous cellular functions related to DNA synthesis. In this work it is demonstrated that cytochalasin B is capable of inducing DNA fragmentation in a number of cells lines. This DNA fragmentation occurs before plasma membrane lysis and over a period of hours. Cytochalasin E and villin, agents that act on the microfilaments, also induce DNA fragmentation. Phorbol dibutyrate, a diacylglyceral analog, is able to inhibit cytochalasin B-induced DNA fragmentation in a dose-dependent fashion. These findings support the interpretation that cytochalasin B is inducing DNA fragmentation via its effect on the actin filaments.

Actins↗
PubMed1985

The irreversible binding of azacytosine-containing DNA fragments to bacterial DNA(cytosine-5)methyltransferases.

DNA containing 5-azacytosine is an irreversible inhibitor of DNA(cytosine-5)methyltransferase. This paper describes the binding of DNA methyltransferase to 32P-labeled fragments of DNA containing 5-azacytosine. The complexes were identified by gel electrophoresis. The EcoRII methyltransferase specified by the R15 plasmid was purified from Escherichia coli B(R15). This enzyme methylates the second C in the sequence CCAGG and has a molecular mass of 60,000 Da. Specific binding of enzyme to DNA fragments could be detected if either excess unlabeled DNA or 0.8% sodium dodecyl sulfate was added to the reaction mixture prior to electrophoresis. Binding was dependent upon the presence of both the CCAGG sequence and azacytosine in the DNA fragment. S-Adenosylmethionine stimulated the formation of the complex. The complex was stable to 6 M urea but could be digested with pronase. These DNA fragments could be used to detect the presence of several different methyltransferases in crude extracts of E. coli. No DNA protein complexes could be detected in E. coli B extracts, a strain that contains no DNA(cytosine-5)methyltransferases. The chromosomally determined methylase with the same specificity as the purified EcoRII methylase could be detected in crude extracts of E. coli K12 strains. The MspI methylase cloned in E. coli HB101 could also be detected in crude extracts. These enzymes are the only proteins that bind azacytosine-containing DNA in crude extracts of E. coli.

Cytosine↗
PubMed1991

Induction of differentiation by tumour necrosis factor in HL-60 cells is associated with the formation of large DNA fragments.

The DNA fragmentation induced by tumor necrosis factor (TNF) of differentiable human myeloid leukemic HL-60 cells has been further characterized. TNF increased the appearance of very high molecular weight DNA fragments detected by agarose gel electrophoresis. The use of pulsed-field gel electrophoresis (PFGE) revealed these fragments to be as high as 200-400 kilobase pairs. The pattern of HL-60 DNA fragmentation contrasted with that of U937 cells, which exhibited lower molecular weight, nucleosome multiple sized fragments, and greater cytotoxicity in response to TNF. The peak increase of fragments from HL-60 occurred between one and two hours of incubation, with TNF concentrations of 10 U/ml or higher, and was inhibitable by 1 mM Zn2+. Southern blotting of these fragments disclosed enrichment for c-myc related sequences compared with control probes including beta-actin and kappa and lambda light chains. Treatment of DNA with NotI or gamma-irradiation, followed by PFGE, disclosed a class of still higher molecular weight DNA, which decreased following TNF treatment, and which was apparently the precursor of the TNF-induced fragments. TNF thus rapidly increases a class of high molecular weight DNA fragments which are enriched for c-myc related sequences and may arise preferentially from higher molecular weight structures which are detectable following linearization by NotI or gamma-irradiation. Such major but non-random alterations in chromatin structure may contribute to TNF-induced monocytoid differentiation of HL-60.

Blotting, Southern↗
PubMed1991

Homologous recombination of exogenous DNA fragments with genomic DNA in somatic cells of mice.

We compared liposomes and empty viral capsids for their use as vehicles for DNA transfer into cells and animals. DNA binding capacity was high for liposomes, but DNase I protection of DNA bound to liposomes was only moderate in comparison to DNA incorporated into viral capsids. Cellular uptake of radiolabeled and physiologically active DNA was also compared. For animal studies we chose an endogenous retroposon as target gene. To identify recombinational events we replaced a part of this gene with an artificial sequence not present in the mouse genome. The recombination rate for DNA fragments transfected in Polyoma capsids in live mice was higher than for liposome mediated transfection. Homologous recombination could be observed for both DNA transfer methods, mediated by positively charged liposomes (DOTMA) and by empty Polyoma viral capsids.

Animals↗
PubMed1992

Acetaminophen-induced cytotoxicity in cultured mouse hepatocytes: effects of Ca(2+)-endonuclease, DNA repair, and glutathione depletion inhibitors on DNA fragmentation and cell death.

Hepatotoxic alkylation of mouse liver cells by acetaminophen is characterized by an early loss of ion regulation, accumulation of Ca2+ in the nucleus, and fragmentation of DNA in vitro and in vivo. Acetaminophen-induced DNA cleavage is accompanied by the formation of a "ladder" of DNA fragments characteristic of Ca(2+)-mediated endonuclease activation. These events unfold well in advance of cytotoxicity and the development of necrosis. The present study utilized cultured mouse hepatocytes and mechanistic probes to test whether DNA fragmentation and cell death might be related in a "cause-and-effect" manner. Cells were isolated by collagenase perfusion, cultured in Williams' E medium for 22-26 hr, and exposed to acetaminophen. Aurintricarboxylic acid, a general Ca(2+)-endonuclease inhibitor, and EGTA, a chelator of Ca2+ required for endonuclease activation, significantly decreased DNA fragmentation at 6 and 12 hr and virtually abolished cytotoxicity. N-Acetylcysteine also eliminated DNA fragmentation and cytotoxicity. 3-Aminobenzamide, an inhibitor of poly(ADP-ribose) polymerase-stimulated DNA repair, failed to alter the amount of DNA fragmentation at 6 hr but substantially increased acetaminophen cytotoxicity in hepatocytes at 12 hr. With the exception of when DNA repair was inhibited by 3-aminobenzamide, Ca2+ accumulation in the nucleus, DNA fragmentation, and hepatocyte death varied consistently and predictably with one another. Collectively, these findings suggest that unrepaired damage to DNA contributes to acetaminophen-induced cell death in vivo and may play a role in necrosis in vivo.

Acetaminophen↗
PubMed1991

Lipopolysaccharide induces double-stranded DNA fragmentation in mouse thymus: protective effect of zinc pretreatment.

Intraperitoneal injection of female NAW/W1 mice with 5 mg of Salmonella typhimurium lipopolysaccharide/kg results in decreased body and thymus weight. Reduced thymic weight is accompanied by fragmentation of DNA into multimers of about 200 bp size. This effect is consistent with the induction of intranucleosomal cleavage of double-stranded DNA in thymus. Maximal fragmentation of DNA occurs between 18 and 24 h after treatment; by 48 h post lipopolysaccharide treatment, there is little evidence of thymic DNA fragmentation. Pretreatment of mice with Zn protects against lipopolysaccharide-induced DNA fragmentation. This effect is maximal at about 72 h after Zn treatment (24 h after lipopolysaccharide treatment) and persists until about 96 h after Zn treatment. At 72 h after pretreatment, the antagonism of thymic DNA fragmentation by Zn is dose-dependent. To examine the role of the acute phase inflammatory response elicited by lipopolysaccharide treatment in the production of changes in thymic weight and DNA integrity, the effects of treatment with casein, a well-characterized inducer of the acute phase inflammatory response in mice, were examined. In contrast to the effect of lipopolysaccharide, casein treatment did not produce a similar pattern of DNA fragmentation in thymus. Taken together, these data suggest that lipopolysaccharide induces DNA fragmentation in thymus by a mechanism which does not occur during the pathophysiological changes which accompany the casein-induced acute phase response. Further, the antagonism by Zn of lipopolysaccharide-induced fragmentation of thymic DNA is consistent with earlier findings that Zn can prevent dexamethasone-induced DNA fragmentation in vitro.

Acute-Phase Reaction↗
PubMed1991

Caesium fluoride-induced changes in the c.d. spectra of synthetic DNA fragments.

Ten DNA fragments containing self-complementary alternating sequences of adenine and thymine differing in length and the starting nucleotide were studied by c.d. spectroscopy. It was found that d(TATATATA) but not d(ATATATAT), d(TATATA), d(CTATATAG) or (dT-dA)20 isomerized into the unusual X-DNA double helix at molar concentrations of CsF in solution. But in contrast to poly(dA-dT), the octamer (dT-dA)4, isomerized very slowly, at relatively low CsF concentrations and the isomerization was strongly dependent on the octamer concentration. A model is proposed to account for the observed properties of the B-to-X isomerization on the oligomer level.

Adenine Nucleotides↗
PubMed1990

CD4+CD8+ thymocytes are susceptible to DNA fragmentation induced by phorbol ester, calcium ionophore and anti-CD3 antibody.

Stimulation of murine thymocytes with phorbol ester or calcium ionophore for 18-24 h resulted in 70%-80% fragmentation of DNA into 180-200-bp multiples, followed by cell death. Experiments with fractionated subpopulations by panning or flow cytometry revealed that DNA fragmentation was selectively observed in CD4+CD8+ cells and in a portion of CD4-CD8+ cells. To investigate whether DNA cleavage is also inducible via antigen-specific receptors, thymocytes were incubated in wells precoated with anti-CD3 antibody. An approximately 20% increase of DNA fragmentation was constantly observed when unseparated thymocytes were stimulated with anti-CD3 antibody. In this anti-CD3-induced DNA degradation, CD4+CD8+ cells are probably the target cells, since (a) fetal thymocytes at day 18 of gestation were found vulnerable to anti-CD3-induced DNA cleavage and (b) flow cytometry analysis of viable cells recovered after cultivation in the anti-CD3-coated wells revealed that CD4+CD8+ cells were preferentially decreased. Further experiments with purified CD4+CD8+ cells, however, could not define a clear-cut increase of DNA fragmentation when isolated CD4+CD8+ cells were stimulated with anti-CD3 antibody. Addition of interleukin (IL) 1, IL 2, IL 3, IL 4 or interferon-gamma to the CD4+CD8+ cell cultures failed to yield a DNA cleavage similar to that of unseparated thymocytes.

Animals↗