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PubMed2005

Automated DNA fragments recognition and sizing through AFM image processing.

This paper presents an automated algorithm to determine DNA fragment size from atomic force microscope images and to extract the molecular profiles. The sizing of DNA fragments is a widely used procedure for investigating the physical properties of individual or protein-bound DNA molecules. Several atomic force microscope (AFM) real and computer-generated images were tested for different pixel and fragment sizes and for different background noises. The automated approach minimizes processing time with respect to manual and semi-automated DNA sizing. Moreover, the DNA molecule profile recognition can be used to perform further structural analysis. For computer-generated images, the root mean square error incurred by the automated algorithm in the length estimation is 0.6% for a 7.8 nm image pixel size and 0.34% for a 3.9 nm image pixel size. For AFM real images we obtain a distribution of lengths with a standard deviation of 2.3% of mean and a measured average length very close to the real one, with an error around 0.33%.

Algorithms↗
PubMed1996

DNA fragmentation and BCL-2 expression in infantile spinal muscular atrophy.

Chromatin cleavage, a hallmark of apoptosis, was identified by in situ labeling in 55 +/- 7% of the muscle fibers in infantile spinal muscular atrophy (ISMA) and, to a lesser extent, in peripheral neuropathy indicating that DNA fragmentation is not specific to ISMA but a common feature in defect innervation. However, as DNA breaks are also known as a temporary process in differentiating myotubes DNA fragmentation may not always proceed to cell death. Therefore, it is currently not certain whether high rates of DNA fragmentation in ISMA are part of delayed muscle maturation due to neuronal defect or part of fibre breakdown. While atrophic muscle fibres in peripheral neuropathy displayed strong expression of bcl-2, a protein delaying onset of apoptosis, only 30% of the ISMA cases revealed weak bcl-2 expression assuming that immature muscle fibers are not able to produce a sufficient level of bcl-2.

Aged↗
PubMed1991

Two dimensional single-strand conformation polymorphism analysis: a useful tool for the detection of mutations in long DNA fragments.

A new two-dimensional gel system for the analysis of single strand conformational polymorphisms has been developed to identify point mutations, deletions and insertions in long DNA fragments (e.g. 2.7 kb) generated by the polymerase chain reaction. In this procedure, such DNA fragments are first restricted with frequent-cutter enzymes. The resulting small fragments are then separated in the first dimension according to their size by electrophoresis under denaturing conditions; these single stranded DNA fragments are subsequently fractionated in the second dimension by electrophoresis on a non denaturing slab gel based on their fold-back conformation which is completely sequence-dependent. The method was tested on three previously characterized pH 4.5 resistant mutants of HRV14 and was then used to determine changes in three further mutants.

Base Sequence↗
PubMed1991

The binding of the ferric uptake regulation protein to a DNA fragment.

Using proton NMR, we have studied the binding of a DNA fragment in double-stranded form to the ferric uptake regulation protein, Fur. We have also looked at the binding of [Cr(CN)6]3- to Fur with a view to testing whether binding is due to electrostatic interaction between Fur and the negative surface of the DNA. No competition at the DNA binding site was observed. Additionally, we have examined the binding of manganese ions to Fur in the presence of the DNA fragment and go on to discuss the likely way in which the Fur.DNA complex responds to metal-ion binding to Fur.

Bacterial Proteins↗
PubMed2000

Initiation of DNA fragmentation during apoptosis induces phosphorylation of H2AX histone at serine 139.

Histone H2AX is a ubiquitous member of the H2A histone family that differs from the other H2A histones by the presence of an evolutionarily conserved C-terminal motif, -KKATQASQEY. The serine residue in this motif becomes rapidly phosphorylated in cells and animals when DNA double-stranded breaks are introduced into their chromatin by various physical and chemical means. In the present communication we show that this phosphorylated form of H2AX, referred to as gamma-H2AX, appears during apoptosis concurrently with the initial appearance of high molecular weight DNA fragments. gamma-H2AX forms before the appearance of internucleosomal DNA fragments and the externalization of phosphatidylserine to the outer membrane leaflet. gamma-H2AX formation is inhibited by N-benzyloxycarbonyl-Val-Ala-Asp-fluoromethyl ketone and the inhibitor of caspase-activated DNase, and it is induced when DNase I and restriction enzymes are introduced into cells, suggesting that any apoptotic endonuclease is sufficient to induce gamma-H2AX formation. These results indicate that gamma-H2AX formation is an early chromatin modification following initiation of DNA fragmentation during apoptosis.

Apoptosis↗
PubMed2003

Sizing of single fluorescently stained DNA fragments by scanning microscopy.

We describe an approach to determine DNA fragment sizes based on the fluorescence detection of single adsorbed fragments on specifically coated glass cover slips. The brightness of single fragments stained with the DNA bisintercalation dye TOTO-1 is determined by scanning the surface with a confocal microscope. The brightness of adsorbed fragments is found to be proportional to the fragment length. The method needs only minute amount of DNA, beyond inexpensive and easily available surface coatings, like poly-L-lysine, 3-aminoproyltriethoxysilane and polyornithine, are utilizable. We performed DNA-sizing of fragment lengths between 2 and 14 kb. Further, we resolved the size distribution before and after an enzymatic restriction digest. At this a separation of buffers or enzymes was unnecessary. DNA sizes were determined within an uncertainty of 7-14%. The proposed method is straightforward and can be applied to standardized microtiter plates.

Algorithms↗
PubMedDate not supplied

Sperm DNA fragmentation is increased in couples with unexplained recurrent pregnancy loss.

Previous studies have indicated that sperm quality may be related to unexplained recurrent pregnancy loss. This study evaluated the degree of sperm DNA fragmentation using the TUNEL assay on sperm from 24 couples with unexplained recurrent pregnancy loss (RPL) compared to sperm from 2 control groups: donors of known fertility and unscreened men from the general population. The percentage of sperm staining positive for DNA fragmentation was increased (p < .001) in the RPL group (38 +/- 4.2) compared to the donor (11.9 +/- 1.0) or general population (22 +/- 2.0) control groups. In the RPL group, no correlation was observed between semen quality parameters and the TUNEL data. These data indicate that some RPL patients have a significant increase of sperm DNA fragmentation, which may be causative of pregnancy loss in some patients.

Abortion, Habitual↗
PubMed1997

Propyl gallate-induced DNA fragmentation in isolated rat hepatocytes.

Incubation of isolated rat hepatocytes with propyl gallate (PG) at concentrations of > or = 1 mM induced cell killing, whereas PG at < or = 0.5 mM did not cause cell death during a 3-h incubation. PG at > or = 0.5 mM elicited the ladder formation of soluble low-molecular weight DNA fragments with integer multiples of approximately 180 bp and specific nuclear DNA cleavages detected cytopathologically by labeling of a digoxigenin-nucleotide complex to new 3'-OH ends. Both of these PG-induced changes observed in hepatocytes are characteristic features of apoptosis. In contrast, the pretreatment of N-acetylcysteine (4 mM), a precursor of intracellular glutathione (GSH) and antioxidant, prevented PG (0.5 mM)-induced formation of soluble DNA fragments and loss of cellular GSH, ATP, and formation of blebbing. These results suggest that when the concentration of PG is decreased, the effects of PG on hepatocytes change from acute necrotic to apoptotic mode, and that the onset of DNA fragmentation is associated with GSH depletion.

Acetylcysteine↗
PubMed2002

DNA fragmentation and cell proliferation correlated with tumor grade in patients with hepatocellular carcinoma.

BACKGROUND: DNA fragmentation and cell proliferation in patients with hepatocellular carcinoma (HCC) have not been well described on fine-needle aspiration biopsies (FNABs). To investigate the contribution of apoptosis, a major mechanism of cell death, to the growth of HCC, the authors analyzed both apoptosis and cell proliferation in patients with HCC. METHODS: The authors studied 50 tumors from 50 patients with HCC: Ten tumors were well-differentiated HCC, 24 tumors were moderately differentiated HCC, and 16 tumors were poorly differentiated HCC. The detection of DNA fragments in situ using the terminal deoxyribonucleotidyl transferase (TDT)-mediated dUTP-digoxigenin nick-end labeling (TUNEL) assay was applied to investigate active cell death (apoptosis), and the MIB-1 antigen was used to investigate cell proliferation. RESULTS: The TUNEL indices were 0.34 +/- 0.08, 082 +/- 0.30, and 2.0 +/- 0.95 in well-differentiated HCC, moderately differentiated HCC, and poorly differentiated HCC, respectively. The MIB-1 antigen labeling indices were 6.7 +/- 0.10, 13.2 +/- 3.4; and 26.9 +/- 6.5, respectively, in the same order of tumor differentiation. The differences in both TUNEL and MIB-1 labeling indices were significant between well differentiated HCC, moderately differentiated HCC, and poorly differentiated HCC, and a positive correlation was found between the TUNEL indices and the MIB-1 indices. CONCLUSIONS: Apoptosis (cell death) and cell proliferation increase as the grade of differentiation decreases in HCC, suggesting a rapid turnover of tumor cells in tumors with lower grades of differentiation, and apoptosis may play an important role in the growth of tumors in patients with HCC.

Apoptosis↗
PubMed1996

Radiosensitization of HL-60 human leukaemia cells by bryostatin-1 in the absence of increased DNA fragmentation or apoptotic cell death.

Ionizing radiation produced a dose-dependent reduction in the proliferative capacity of HL-60 human promyelocytic leukaemia cells. A small percentage of the cell population demonstrated morphological evidence of apoptosis at 24h following radiation doses of > or = 5 Gy (i.e. 8% at 5 Gy and 16% at 10 Gy respectively) and produced a laddered oligonucleosomal pattern of DNA fragments by static-field gel electrophoresis. The antiproliferative effects of 1 and 2.5 Gy ionizing radiation were significantly enhanced by preincubating cells with bryostatin-1 at a concentration (10 nM) and time frame (24h) associated with down-regulation of total cellular protein kinase C (PKC) activity. Potentiation by bryostatin-1 of the radiation effect on proliferation was not associated with a concomitant increase in internucleosomal DNA fragmentation, in the fraction of cells exhibiting apoptotic morphology, or in the extent of radiation-induced single- or double-strand breaks in bulk DNA. Staurosporine, a potent but nonspecific inhibitor of PKC, was ineffective in altering the radiosensitivity of HL-60 cells or the degree of DNA fragmentation induced by ionizing radiation. These findings indicate that bryostatin 1 increases the sensitivity of human myeloid leukaemic cells to low radiation doses without enhancing DNA fragmentation or apoptosis, and that this capacity may involve factors other than, or in addition to, down-modulation of PKC activity.

Apoptosis↗
PubMed1995

Protease inhibitors block apoptosis at intermediate stages: a compared analysis of DNA fragmentation and apoptotic nuclear morphology.

The possible correlation between DNA digestion and changes in nuclear morphology in apoptosis was studied by blocking the apoptotic process at intermediate stages. The apoptogenic action of three drugs: etoposide, puromycin, tributyltin, was contrasted with protease inhibitors with different specificity on U937 cells. The inhibitors interfered with the development of the apoptotic features without shifting cell death to necrosis: treated cells showed abnormal morphologies, which could be recognized as intermediate stages of apoptosis; accordingly, DNA analysis showed an inhibitor-dependent block of the apoptotic DNA digestion. The comparison between size of DNA fragments and nuclear morphology suggested the following correlations: loss of normal nuclear shape with the appearance of a > or = 2 Mb DNA band; ongoing chromatin condensation with the progressive DNA digestion up to 50 kb; nuclear fragmentation with DNA laddering. Protease inhibitors in etoposide-treated cells did not allow the formation of 700-300 kb fragments, suggesting that they possibly derive from a cell-mediated effect.

Apoptosis↗
PubMed1992

Internucleosomal DNA fragmentation during phorbol ester-induced monocytic differentiation and G0/G1 arrest.

The treatment of human myeloid leukemia cell lines with phorbol esters, such as 12-O-tetradecanoylphorbol-13-acetate (TPA), is associated with loss of proliferative capacity and induction of monocytic differentiation. The present results demonstrate that treatment of asynchronous human U-937 leukemia cells with 10 nM TPA is also associated with oligonucleosomal DNA cleavage. This pattern of DNA fragmentation, which is observed in programmed cell death, was detectable in populations of TPA-treated cells that had entered a nonproliferative G0/G1 phase. Similar findings were obtained after TPA treatment of a synchronous population of G1 cells. These cells progressed through S and G2/M phases before undergoing internucleosomal DNA cleavage during G0/G1 arrest. These G0/G1 cells displayed characteristics of monocytic differentiation, including down-regulation of c-myc expression and induction of c-fms transcripts. DNA fragmentation was also studied in cells treated with 5 nM TPA for 48 h and then monitored in drug-free long-term culture. Endonucleolytic cleavage was similarly observed in the differentiated G0/G1 population. However, longer periods of culture were associated with a decrease in DNA fragmentation to undetectable levels. This effect was followed by retrodifferentiation and reentry of cells into cycle. Taken together, these findings demonstrate that internucleosomal DNA fragmentation occurs during induction of monocytic differentiation, and that both of these events are detectable in G0/G1 cells.

Cell Differentiation↗
PubMed1993

Use of glucomannan for the separation of DNA fragments by capillary electrophoresis.

Glucomannan, a natural polysaccharide extracted from Amorphophallus konjac, was employed as a sieving additive for the separation of restriction DNA fragments in capillary electrophoresis. A stable solution of entangled glucomannan was successfully prepared under mild conditions. The separation capillary filled with 0.25% glucomannan exhibited excellent resolution and reproducibility on separation of DNA fragments over the range of ca. 1400 base pairs. The separation was dependent on the size of the fragments, which allowed the determination of the size of separated DNAs directly from the migration time. In addition to these separation characteristics, glucomannan has practical advantages in its chemical stability, non-toxicity and ease of handling. Because the method is applicable to the separation and characterization of the DNA fragments generated by digestion with restriction enzymes or produced by polymerase chain reactions, it is concluded that glucomannan is a good alternative to the conventional sieving additives for capillary electrophoresis, such as polyacrylamide and hydroxymethylcellulose.

Bacteriophage phi X 174↗
PubMed1999

Activation of Rac1 increases c-Jun NH(2)-terminal kinase activity and DNA fragmentation in a calcium-dependent manner in rat myoblast cell line H9c2.

We examined the role of intracellular Ca(2+) in c-Jun NH(2)-terminal kinase (JNK) activation and DNA fragmentation in the rat myoblast cell line H9c2 using small GTP-binding protein Rac1. A constitutively active mutant of Rac1 (V12-Rac1) increased JNK-responsive gene expression 6-fold, although this increase was attenuated by the intracellular Ca(2+) chelator BAPTA-AM. V12-Rac1 also increased the number of DNA fragmentated cells. However, V12-Rac1-mediated JNK activation was not affected by BAPTA-AM as determined by direct measurement of active forms, and V12-Rac1 did not affect intracellular Ca(2+) concentration. These results suggest that Rac1 can activate JNK and induces cell injury, but [Ca(2+)](i) is necessary for V12-Rac1 to induce DNA fragmentation downstream of JNK activation.

Animals↗
PubMed2002

Caspase-3 is not essential for DNA fragmentation in MCF-7 cells during apoptosis induced by the pyrrolo-1,5-benzoxazepine, PBOX-6.

Effector caspases-3, -6 and -7 are responsible for producing the morphological features associated with apoptosis, such as DNA fragmentation. The present study demonstrates that a member of a novel series of pyrrolo-1,5-benzoxazepines, PBOX-6, induces apoptosis in MCF-7 cells, which lack caspase-3. Apoptosis was accompanied by DNA fragmentation and the activation of caspase-7, but not caspases-3 and -6. Inhibition of caspase-7 activity reduced the extent of apoptosis induced, indicating that activation of caspase-7 is involved in the mechanism by which PBOX-6 induces apoptosis in MCF-7 cells. This study suggests that caspase-3 is not necessarily essential for DNA fragmentation and the morphological changes associated with apoptosis.

Antineoplastic Agents↗
PubMed1994

A program for selecting DNA fragments to detect mutations by denaturing gel electrophoresis methods.

A computer program was developed to automate the selection of DNA fragments for detecting mutations within a long DNA sequence by denaturing gel electrophoresis methods. The program, MELTSCAN, scans through a user specified DNA sequence calculating the melting behavior of overlapping DNA fragments covering the sequence. Melting characteristics of the fragments are analyzed to determine the best fragment for detecting mutations at each base pair position in the sequence. The calculation also determines the optimal fragment for detecting mutations within a user specified mutational hot spot region. The program is built around the statistical mechanical model of the DNA melting transition. The optimal fragment for a given position is selected using the criteria that its melting curve has at least two steps, the base pair position is in the fragment's lowest melting domain, and the melting domain has the smallest number of base pairs among fragments that meet the first two criteria. The program predicted fragments for detecting mutations in the cDNA and genomic DNA of the human p53 gene.

Algorithms↗
PubMedDate not supplied

[Molecular-biological study of vaccinia virus genome. I. Cloning of vaccinia virus DNA fragments in bacterial vectors].

The HindIII DNA fragments of vaccinia virus strain L-IVP were cloned in pBR322 bacterial plasmid. A hybrid plasmids collection of pVHn series contains all fragments of virus genome except terminal HindIII-B and HindIII-G, and also a large HindIII-A. The latter was cloned in cosmid pHC79. The obtained collection of hybrid DNA molecules allows to carry out a wide range of molecular biological experiments on the vaccinia virus genome.

Blotting, Southern↗
PubMed1996

Biochemical pathways of apoptosis: nicotinamide adenine dinucleotide-deficient cells are resistant to tumor necrosis factor or ultraviolet light activation of the 24-kD apoptotic protease and DNA fragmentation.

The function of nicotinamide adenine dinucleotide (NAD) and adenosine diphosphate (ADP) ribosylation reactions in the mechanism of apoptotic cell death is controversial, although one theory postulates an essential role for NAD depletion by poly-ADP-ribose polymerase. The present study examined the role of intracellular NAD in tumor necrosis factor (TNF) and ultraviolet (UV) light-induced activation of the 24-kD apoptotic protease (AP24) leading to internucleosomal DNA fragmentation and death. Our results demonstrate that nutritional depletion of NAD to undetectable levels in two leukemia lines (U937 and HL-60) renders them completely resistant to apoptosis. This was attributed to a block in the activation of AP24 and subsequent DNA cleavage. Normal cells show an elevation of ADP-ribosyl transferase (ADPRT) in both the cytosol and nucleus after exposure to TNF, but before DNA fragmentation. ADPRT activity as well as cell death was suppressed by an inhibitor specific for mono-ADPRT. Nuclei from NAD-depleted cells were still sensitive to DNA fragmentation induced by exogenous AP24, indicating a selective function for NAD upstream of AP24 activation in the apoptotic pathway. We confirmed a requirement for intracellular NAD, activation of ADPRT, and subsequent NAD depletion during apoptosis in KG1a, YAC-1, and BW1547 leukemia cell lines. However, this mechanism is not universal, since BJAB and Jurkat leukemia cells underwent apoptosis normally, even in the absence of detectable intracellular NAD. We conclude that TNF or UV light-induced apoptotic cell death is not due to NAD depletion in some leukemia cell lines. Rather, NAD-dependent reactions which may involve mono-ADPRT, function in signal transduction leading to activation of AP24, with subsequent DNA fragmentation and cell death.

3-Iodobenzylguanidine↗