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PubMedDate not supplied

[Fractionation of eukaryotic DNA in a pulsating electrical field. I. Detection and properties of discrete DNA fragments].

The fractionation of eukaryotic DNA by field inversion gel electrophoresis results in the appearance of discrete DNA-fragments. The set of these fragments is similar to that of different eukaryotic representatives and consists of various chromosomal DNAs, unified by size. The physical properties of DNA-fragments suggest that they can form multimeric structures due to the presence of sticky ends flanking discrete fragments. We suppose that the set of discrete DNA-fragments results in a specific cleavage of intact nuclear DNA and can reflect different levels of chromatin structural organization.

Animals↗
PubMed2003

[Sodium chloride step gradients centrifuge to fractionate foreign DNA fragment for microinjection].

DNA microinjection is the most popular and reliable method of producing transgenic animals. The purity of foreign DNA plays an important role for the success of microinjection. In this study, we introduced the use of sodium chloride step gradients in fractionating foreign DNA fragment for microinjection. The data demonstrated that,compared with the conventional agarose gel extraction method, NaCl purification scheme of toreign DNA could improve the treated embryo survival and foreign DNA intergration rate markedly.

English Abstract↗
PubMed2000

Development of a mechanism-based, DNA staining protocol using SYTOX orange nucleic acid stain and DNA fragment sizing flow cytometry.

Accurate measurement of single DNA fragments by DNA fragment sizing flow cytometry (FSFC) depends upon precise, stoichiometric DNA staining by the intercalating dye molecules. In this study, we determined the binding characteristics of a commercially available 532 nm wavelength-excitable dye and used this information to develop a universal DNA staining protocol for DNA FSFC using a compact frequency-doubled Nd:YAG laser excitation source. Among twelve 532 nm wavelength-excitable nucleic acid staining dyes tested, SYTOX Orange stain showed the highest fluorescence intensity along with a large fluorescence enhancement upon binding to double-stranded DNA ( approximately 450-fold). Furthermore, using SYTOX Orange stain, accurate fragment-size-distribution histograms were consistently obtained without regard to the staining dye to base pair (dye/bp) ratio. A model describing two binding modes, intercalation (primary, yielding fluorescence) and external binding (secondary, involving fluorescence quenching), was proposed to interpret the performance of the dyes under different dye/bp ratios. The secondary equilibrium dissociation constant was found to be the most critical parameter in determining the sensitivity of each fluorophore to the staining dye/bp ratio. The measurements of both equilibrium dissociation constants provided us with a theoretical framework for developing a universal protocol which was successfully demonstrated over a wide range of DNA concentrations on a compact flow cytometer equipped with a frequency-doubled, diode-pumped, solid-state Nd:YAG laser for rapid and sensitive DNA fragment sizing.

Bacteriophage lambda↗
PubMed1995

Sizing highly fragmented DNA in individual apoptotic cells using the comet assay and a DNA crosslinking agent.

TK6 human B lymphoblast cells exposed to ionizing radiation undergo apoptosis in a time and dose-dependent manner. The resulting highly fragmented DNA is easily detected using the comet assay, a sensitive microscopic gel electrophoresis method capable of measuring DNA strand breaks in individual cells. The degree of DNA fragmentation may be indicative of different stages in the fragmentation process, responses to different agents, and/or cell type-dependent differences. In an effort to determine the number of breaks present in each apoptotic cell, we first applied a DNA-crosslinking agent, mechlorethamine, to TK6 cells containing a known number of DNA double-strand breaks produced by X rays. As the concentration of mechlorethamine increased, crosslinked DNA was less able to migrate during gel electrophoresis. Exposure of TK6 cells to 5 microM mechlorethamine prior to irradiation with 20 Gy was sufficient to "hide" the presence of these breaks by preventing DNA from migrating during electrophoresis. However, in apoptotic TK6 cells, it was necessary to apply a dose of mechlorethamine several times higher in order to produce a similar degree of inhibition of DNA migration. Calibrations using either the alkaline or neutral comet assays indicate that the average DNA fragment size in apoptotic TK6 cells is about 50 kb. Even in cells containing only 10-20% of the original amount of DNA, the remaining fragments still averaged about 50 kb, indicating that fragmentation to much smaller sizes occurs in some parts of the genome before others. When Chinese hamster V79 cells were exposed to hyperthermia (45 degrees C for 20 min), necrosis was induced over a period of several days. The size of DNA fragments in these cells was considerably larger (200-400 kb) and heterogeneity in appearance of comets was larger than observed for TK6 cells. This crosslinking method may be useful in discriminating cells dying by apoptosis from cells damaged or dying by other mechanisms.

Animals↗
PubMed2002

Mononucleosomes assembled on a DNA fragment containing (GGA/TCC)(n) repeats can form a DNA-DNA complex.

A DNA fragment of 163 bp containing 11 GGA repeats formed two-end positioned mononucleosomes as efficiently as that of CTG repeats. However, the rotational positioning of the GGA fragment was weak because clear DNase I cleavage patterns with 10-base periodicity were not seen near the center of the GGA fragment but were detected in the entire region of the CTG fragment. Incubation of the GGA mononucleosomes with the same fragment provided the DNA-DNA complex, which had been shown by using naked DNA fragments. DNase I digestion of the complex exhibited protection in the GGA repeats and in flanking sequences of about 30 bp at both sides, suggesting that both the repeat and flanking regions were involved in the association. Interestingly, histone H1, which enhanced DNA-DNA association on naked DNA, did not affect the complex formation on mononucleosomes. These results imply that GGA microsatellites in genomes could associate with one another at multiple sites and that the association may play a role in functional organization of higher order chromatin architecture.

Cell Nucleus↗
PubMed2005

A new method to analyze boar sperm DNA fragmentation under bright-field or fluorescence microscopy.

We present a new, rapid and simple method to study DNA Fragmentation Index (DFI) in sperm samples from boar under bright-field and fluorescence microscopy. Discrimination of sperm cells containing fragmented DNA relies on the extreme peripheral diffusion of their chromatin fragments, whereas those sperm nuclei without DNA fragmentation do not disperse or show very restricted spreading of DNA loops close to the flagellum. The basic methodology provided in the commercial kit Sperm-Sus-Halomax allows, in addition to a direct estimation of DFI in a sperm sample under bright field microscopy, a direct visualization of DNA breaks by incorporation of labelled nucleotides using the DNA polymerase I following the in situ nick translation assay (ISNT methodology not provided in the kit). An external control using DBD-FISH (DNA breakage detection-fluorescence in situ hybridization) on human and boar sperm samples was used in this experiment. The results obtained show (i) low levels of background DNA fragmentation (from 0.7 to 10%), (ii) no significant differences for DFI after the application of Sperm-Sus-Halomax and ISNT, with a tendency to be underestimated after using DBD-FISH and (iii) a characteristic chromatin organization in boar sperm nucleus, with a particular response to chromatin loop relaxation and preferential DNA labelling by ISNT at the proximal nuclear area, close to the flagellum. This methodology allows the routine assessment of boar sperm samples for DFI, as well as basic and clinical research on this relevant topic in any laboratory of semen analysis.

Animals↗
PubMedDate not supplied

[The effect of temperature and ionic strength on the electrophoretic motility of synthetic DNA fragments].

The following DNA fragments were studied: T5A5, U5G5, C5G5, RI (CCGAATTCGG), and RV (CCGATATCGG). The ligated decamers were run on 8% polyacrylamide gel. The PAGE anomaly was measured by the R-factor. Under standard conditions R is maximum for A5G5 and U5A5 (R = 1.9-2.0); R has intermediate values for RI and T5A5 (R200 = 1.05-1.10). T5A5 exhibits unusual non-monotonous temperature dependence of the R-factor, which reaches its maximum at 35 degrees C. Based on this fact we make two conclusions: (i) PAGE anomaly is highly sensitive to the DNA winding angle tau, (ii) tau = 36 degrees for T5A5 under these conditions. For A5G5, RI and RV the temperature dependence of the R-factor is conventional: R monotonously decreases. Conceivably tau less than 36 degrees for these sequences. In the presence of 10 mM of MgCl2 the anomaly increase for all fragments, except for T5A5; e.g. for C5G5R150 R200 = 1.2. This testifies to the moderate curvature of C5G5. The results of the measurements were interpreted on the basis of the wedge AA and junction An/B models. To get a better agreement with the experiment these models should be supplemented with the bends in the YR dimers (TA, CG, CA) directed into the major groove and with the bends in AT directed into the minor groove.

Base Sequence↗
PubMed1994

Internucleosomal DNA fragmentation in gerbil hippocampus following forebrain ischemia.

Internucleosomal DNA fragmentation, the characteristics feature of programmed cell death, was demonstrated in gerbil hippocampus following 10 min of forebrain ischemia. Quantitative analysis revealed the presence of DNA fragments as early as 12 h after ischemia, reaching a maximum at 48 h. Measurable DNA fragmentation was still present in 3/3 subjects 96 h after the ischemic insult. In situ staining of hippocampus demonstrated pronounced DNA fragmentation that was localized in the CA1 region. The localization of fragmented DNA to the CA1 is consistent with the vulnerability of this layer to ischemic insult, and indicates that DNA fragmentation may be associated with the delayed loss of CA1 neurons in this model of forebrain ischemia.

Animals↗
PubMed1976

Sheared DNA fragment sizing: comparison of techniques.

DNA fragmented by conventional French press shearing procedures (30,000 lbs/in2) has a number-average fragment size of 230 base pairs. This is considerably smaller than the 450 base pairs typically reported for DNA sheared by this method. Comparison of 5 sizing techniques indicates that sheared DNA fragment size is overestimated by either measurement of velocity sedimentation or Kleinschmidt Electron Microscopic visualization. Both adsorption grid electron microscopic visualization and gel electrophoresis yield the most reliable estimates of the mean size of small DNA fragment populations. In addition, the assessment of fragment size distribution (not possible from sedimentation analysis) potentially allows more critical evaluation of DNA hybridization and reassociation kinetic and measurement parameters.

Animals↗
PubMed1996

Genesis of discrete higher order DNA fragments in apoptotic human prostatic carcinoma cells.

Higher order DNA fragmentation may be an essential signal in apoptosis. We found that etoposide (VP-16) induced apoptosis in human DU-145 prostatic carcinoma cells in a time- and concentration-dependent manner. Chromatin condensation was morphologically evident only when cells detached from the monolayer; untreated or VP-16-treated attached cells retained a normal morphology. We describe a radiolabeled alu-I sequence-based quantitative field inversion gel electrophoresis (QFIGE) method that permitted observation and quantification of discrete high molecular weight DNA fragments in detached (apoptotic) and attached (preapoptotic) DU-145 cells. The DNA fragments generated during the apoptotic death of these cells were > or = 1 (mega-base pairs) mbp, 450-600 (kilo-base pairs) kbp, and 30-50 kbp; we observed that these DNA fragments increased 9 +/- 2-, 8 +/- 2-, and 25 +/- 11-fold versus control, respectively, with a 24-hr exposure to 30 microM VP-16 in attached cell populations. In detached VP-16-treated cells, there was accrual of 30-50-kbp DNA fragments with a concomitant loss of the > or = 1-mbp and 450-600-kbp fragments; internucleosomal DNA cleavage was never observed. This pattern of high molecular weight DNA fragmentation was inhibited by cycloheximide treatment and was common to other apoptotic agents, including melphalan and bleomycin. These findings suggest that the > or = 1-mbp and 450-600-kbp DNA fragments are products of endonuclease activation and are not topoisomerase II/DNA interactions. Finally, the generation of the 30-50-kbp DNA fragments may mediate chromatin condensation, which characterizes apoptosis.

Antineoplastic Agents↗
PubMed1986

Anisotropic overall and internal motions of short DNA fragments.

Anisotropic motions of DNA fragments in the size range 6-118 base pairs are studied by the steady-state fluorescence polarization of different excitation transitions in the intercalated ethidium cation. Calculated effective tumbling and twisting times are found to be shorter than predicted for overall motions of rigid DNA, indicating that internal motions and/or dye wobbling contribute to the depolarization. The data are consistent with a model where the DNA fragments are considered to be rigid against bending but torsionally flexible, and where the dye can wobble within the intercalated site. We also discuss the possibility of correlated out-of-plane motions of the dye and the DNA bases.

DNA↗
PubMedDate not supplied

The use of C0t-1 probe DNA for the detection of low levels of DNA fragmentation.

In many apoptotic systems the final demise of the DNA results in the generation of multinucleosomal-sized DNA fragments, which appear as a DNA ladder after agarose electrophoresis. Extensive DNA fragmentation can be detected by ethidium bromide staining. Visualization of low levels of DNA fragmentation, however, requires both a more sensitive detection system, as well as a method of DNA extraction, that limits the extent of high molecular weight DNA shearing. We have found that the use of C0t-1 repetitive DNA as a probe for Southern analysis of DNA ladders is a sensitive method to detect low levels of DNA fragmentation. We have applied this methodology in the detection of DNA fragmentation in the normal developing C57BL/6 mouse retina at stages in which there is known DNA fragmentation, as well as in human Y-79 retinoblastoma cells grown in culture. We have found that in many instances in which there is no detectable DNA ladder with ethidium bromide staining a very definitive DNA ladder can be visualized via Southern blot analysis with a C0t-1 DNA probe.

Animals↗
PubMed1995

Internucleosomal DNA fragmentation in ovine luteal tissue associated with luteolysis: in vivo and in vitro analyses.

Internucleosomal DNA fragmentation, a characteristic of apoptosis, can be visualized with agarose gel electrophoresis as discrete low-molecular-weight DNA fragments (laddering), in multiples of approximately 185 bp. CL were collected from superovulated ewes (control) or at 12 h after injection of prostaglandin F2 alpha (PGF2 alpha) on various days after hCG injection. The ability of PGF2 alpha on Days 8, 10, 12, and 14 (n > or = 3 per day per treatment) to induce luteal cell DNA fragmentation was evaluated. DNA was isolated and visualized on agarose gels. No DNA fragmentation was observed in CL from control ewes on Days 8, 10, or 12. Internucleosomal fragmentation of DNA (indicative of apoptosis) as well as nonspecific DNA fragmentation (indicative of non-apoptotic cell death) in CL from Day 14 controls was observed in two of four animals. Additionally, this pattern of DNA fragmentation was observed in CL from ewes treated with PGF2 alpha on all days. Evidence of DNA fragmentation was observed in luteal tissue after dissociation, yet no fragmentation was observed in unsliced, non-dissociated CL collected from Day 10 control ewes (incubated 4 h), or in sliced, non-incubated CL. Slicing and incubation alone were sufficient to initiate DNA fragmentation. A variety of approaches were utilized to inhibit DNA fragmentation. Only the addition of zinc acetate (1 mM) in the incubation medium throughout the 4-h incubation period prevented DNA fragmentation that was initiated by slicing (p < 0.05). There appear therefore, to be one or more intraluteal factors that directly initiate DNA fragmentation associated with cell death in luteolysis.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed2004

Fragmented DNA transport in dendrites of retinal neurons during apoptotic cell death.

Movement of fragmented DNA in dendrites of retinal neurons during the apoptotic cell death was investigated. The time-course of the movement of fragmented DNA in dendrites of retinal neurons undergoing apoptotic cell death induced by intravitreal N-methyl-d-aspartate (NMDA) injection were examined by in situ terminal dUTP-biotin nick end labeling of DNA fragments (TUNEL) method and fluorescence DNA detection technique by 4',6-diamidino-2-phenylindole (DAPI). The inhibitory effect of axoplasmic transport inhibitor, vincristine was also tested on the NMDA-induced fragmented DNA transport. The movement of fragmented DNA from apoptotic nuclei toward peripheral ends of the dendrites of the retinal neurons was clearly demonstrated. The transport of fragmented DNA, but not fragmentation per se, was completely inhibited by the co-administration of vincristine.

Animals↗
PubMedDate not supplied

[Long-fragment DNA of blood plasma as one of the criteria of individual sensitivity to emotional stress and to cerebral ischemia].

Intravenous injection ofpolyethylenoxide WSR-301 reducing hydrodynamic blood resistance (Toms effect) improves gas exchange in the lungs and halved lethality of the animals with cerebral ischemia. The aim of the study was to establish whether free plasma DNA influences blood gases and lethality of the animals with brain ischemia. Common carotid arteries were ligated for 15 min in intact stressed and tested in the open field Wistar male rats, then some of the rats received intravenous solution of homologous long-fragment DNA (20x10(-6) g/ml of blood). Cerebral circulation, acid-base equilibrium, paO2, paCO2, asymptotic blood viscosity, plasmic concentration and length of DNA fragments in plasma, lethality and neurological status of the survivors were studied. It was found that long fragments of rat DNA show hydrodynamic Toms effect. In normal passive rats sensitive to cerebral ischemia part of plasm DNA is fragmented, gas composition and blood viscosity of blood is worse (p < 0.05) than in active animals. There is a direct correlation between the level of long-fragment DNA in plasm and paO2 (r = 0.55) and inverse--with paCO2 (r = -0.84). Intravenous injection of long-fragment DNA improved the course and reduced lethality of brain ischemia 2-3-fold. Thus, qualitative and quantitative characteristics of plasma circulating DNA are responsible for differences in blood gases in rats differently tolerable to cerebral ischemia and can serve as one of the criteria of individual sensitivity to it being essential in pathogenesis of ischemic stroke.

Acid-Base Equilibrium↗
PubMed1987

Dissociation of 5-fluorouracil-induced DNA fragmentation from either its incorporation into DNA or its cytotoxicity in murine T-lymphoma (S-49) cells.

We have shown previously (W. B. Parker and P. Klubes, Cancer Res., 45:4249-4256, 1985) that uridine (10 microM) enhanced the cytotoxicity of 5-fluorouracil (FUra) in cultured mouse T-lymphoma (S-49) cells. Here we show, by the use of colony formation assays, that approximately 50% of the cytotoxicity of FUra plus uridine could be prevented by the simultaneous administration of thymidine (2.5 to 10 microM). In order to explain our observation of a thymidine-preventable component of the cytotoxicity of the FUra plus uridine combination, we examined the incorporation of FUra into DNA. The DNA from FUra-treated S-49 cells was purified by cesium chloride gradient centrifugation and degraded to nucleosides by DNase I and Crotalus atrox snake venom. 5-[3H]-Fluoro-2'-deoxyuridine was not detected by high-pressure liquid chromatography in the hydrolysate of DNA from S-49 cells treated with 1.0 microM [3H]FUra, 1.0 microM [3H]FUra plus 10 microM uridine, or 2.4 microM [3H]FUra. In contrast, 5-[3H]fluoro-2'-deoxyuridine was detected in the DNA of L1210 cells treated with cytotoxic concentrations of either [3H]FUra or 5-[3H]fluoro-2'-deoxyuridine. Thus incorporation of FUra into the DNA of S-49 cells treated with cytotoxic concentrations of FUra was shown to be minimal or insignificant. Using alkaline elution techniques, however, fragmentation of the DNA was detected in S-49 cells treated with 1.0 microM FUra, 1.0 microM FUra plus 10 microM uridine, or 2.4 microM FUra (115-, 107-, and 159-rad equivalent single strand breaks, respectively). Most of the DNA fragmentation caused by FUra could be prevented by the inclusion of 2.5 microM thymidine with FUra during the incubation. Similar amounts of DNA fragmentation occurred with 1.0 microM FUra in either the presence or absence of 10 microM uridine. Because 1.0 microM FUra plus 10 microM uridine was more cytotoxic than 1.0 microM FUra alone, these results indicated that the enhancement of FUra cytotoxicity by uridine was not related to increased fragmentation of DNA.

Animals↗
PubMed2000

Automated DNA fragment collection by capillary array gel electrophoresis in search of differentially expressed genes.

An automatic DNA fragment collector using capillary array gel electrophoresis has been developed. A sheath flow technique is used for not only detection but also collection of DNA fragments. In a sheath flow cell, the DNA fragments separated by 16 capillaries flow independently into corresponding sampling capillaries. The fraction collector consists of 16 sampling trays and each sampling tray is set beneath each end of the sampling capillaries to collect the flow-through DNA fragments. Certain DNA fragments are automatically sorted by controlling the movement of the sampling trays according to the signals from the system. The collector experimentally separated two mixtures of polymerase chain reaction (PCR) products: one prepared by using eight different sizes (base lengths from 161 to 562) of DNAs; and the other prepared by a differential display (DD) method with cDNA fragments. Collected DNA fragments are amplified by PCR and measured by electrophoresis. DNA fragments with base length differences of one (base lengths 363 and 364) were successfully separated. A separated DNA fragment from the DD sample was also successfully sequenced. In addition, differentially expressed DNA fragments were automatically sorted by comparative analysis, in which two similar cDNA fragment groups, labeled by two different fluorophores, respectively, were analyzed in the same gel-filled capillary. These results show that the automatic DNA fragment collector is useful for gene hunting in research fields such as drug discovery and DNA diagnostics.

Animals↗
PubMed1987

Target cell DNA fragmentation is mediated by lymphotoxin and tumor necrosis factor.

Supernatant fluids containing lymphotoxin (LT) activity were examined for their ability to mediate the fragmentation of cellular DNA in target L929 cells in the manner observed in cytotoxic T lymphocyte mediated killing. These supernatants were able to mediate L929 target cell DNA fragmentation, requiring a time course of 48 hours. In an effort to determine whether or not LT was directly involved in mediating this activity, recombinant-derived human lymphotoxin was tested for its ability to bring about the same effect. Both recombinant-derived LT and recombinant-derived tumor necrosis factor (TNF), a factor produced by macrophages and having some activities in common with LT, were able to cause DNA fragmentation in L929 over the same time course. Electrophoretic analysis of DNA isolated from LT-treated L929 target cells revealed that it is fragmented into low molecular weight fragments in a pattern similar to that produced in DNA isolated from target cells after attack by cytotoxic T cell lethal hit.

Animals↗