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PubMed2006

Clinical correlates of the biological variation of sperm DNA fragmentation in infertile men attending an andrology outpatient clinic.

Determination of sperm DNA fragmentation, as assessed by the sperm chromatin structure assay (SCSA), has become an important tool for the evaluation of semen quality. The aim of the present study was to describe the biological variation of sperm DNA fragmentation in men attending an andrology clinic and to identify clinical correlates of the biological variation of sperm DNA fragmentation. For this study, two consecutive semen samples from 100 patients attending our andrology outpatient clinic were subjected to semen analysis, performed in parallel according to WHO guidelines and by SCSA. A good agreement between pairs of samples was found for SCSA-derived variables, as indicated by a significantly lower median coefficient of variation (CV) of the DNA Fragmentation Index (DFI) and the high DNA stainability (HDS) compared with WHO semen parameters. In half of the men attending our andrology clinic, however, the individual biological variation of DFI and HDS, expressed as CV of two samples, exceeded 10%. Dysregulation of spermatogenesis, as seen as testicular insufficiency or varicocele, was not associated with increased variability of DFI or HDS. A backward multiple linear regression analysis, however, indicated that the biological variation of DFI may be more profound in men with characteristics of normal spermatogenesis. In conclusion, we confirm previous reports that sperm DNA fragmentation has a lower biological variability than classical semen parameters. We hypothesize that the sperm chromatin structure may be more influenced in patients with normal spermatogenesis, whereas in men with disturbed spermatogenesis, the chromatin structure may be already so impaired that the effect of unidentified factors leading to variability of sperm DNA fragmentation in time may not be as profound.

Chromatin↗
PubMed1986

Complementary addressed modification and cleavage of a single stranded DNA fragment with alkylating oligonucleotide derivatives.

A single stranded DNA fragment was modified with alkylating derivatives of oligonucleotides complementary to a certain nucleotide sequences in the fragment. The derivatives carried aromatic 2-chloroethylamino groups at their 3'- or 5'-terminal nucleotide residues. Some of the derivatives carried both alkylating group and intercalating phenazine group which stabilized complementary complexes. It was found that these oligonucleotide derivatives modify the DNA fragment in a specific way near the target complementary nucleotide sequences, and the DNA fragment can be cleaved at the alkylated nucleotides positions. Alkylating derivatives carrying phenazine groups were found to be the most efficient in reaction with the DNA fragment.

Alkylation↗
PubMed1997

Induction of a receptor-mediated genomic DNA fragmentation in rat thymus following administration of glucocorticoids with different biopotencies: an approach by a cell-free system.

To further understand a receptor-mediated apoptosis in rat thymus, we undertook experiments to examine the relationship between the induction of genomic DNA fragmentation and the depletion and the replenishment of cytosolic glucocorticoid receptor in rat thymus. Following administration of dexamethasone and prednisolone which had been known as synthetic glucocorticoids with different biological activities, we observed the fragmentation of thymus DNA in a dose-dependent manner. The time course and the extent of DNA fragmentation induced by these glucocorticoids were closely related to the degree of receptor depletion and the length of the depletion period. Relative biopotencies of dexamethasone and prednisolone estimated by their abilities to induce the DNA fragmentation were approximately 50:1. Administration of dexamethasone in combination with 2-deoxy-D-glucose, a potent inhibitor of the glycolytic pathway, significantly decreased the ability of dexamethasone to induce the DNA fragmentation, suggesting that a receptor-mediated DNA fragmentation by glucocorticoids is an ATP-dependent process. As an attempt to elucidate the molecular mechanism of DNA fragmentation in vivo, we reconstituted a cell-free system of thymus nuclei and cytosol fraction. Using the thymus cytosol fraction from dexamethasone-treated rats, we demonstrated for the first time an ATP-dependent fragmentation of nuclear DNA into nucleosomal units in vitro. Toward further understanding of the biochemical process of glucocorticoid-induced apoptosis in the thymocyte, the cell-free system reconstituted in the present study might provide a useful model system.

Animals↗
PubMed1996

Non-radioactive assay of natural killer cell-mediated cytotoxicity against cytomegalovirus-infected fibroblasts by DNA fragmentation ELISA.

Cell-mediated cytotoxicity against cytomegalovirus (CMV)-infected fibroblasts (FS-4 cells) was investigated by a non-radioactive assay, and by DNA fragmentation ELISA and LDH release assay and the assays were compared to the standard chromium release assay. Fragmentation of DNA and LDH activity were detected in the supernatant of CMV-infected FS-4 cells cultured with non-adherent peripheral blood mononuclear cells (PBMC). The DNA fragmentation ELISA was most sensitive to cytotoxicity against CMV-infected FS-4 cells and showed excellent correlation with the standard chromium release assay. DNA fragmentation of CMV-infected FS-4 cells by non-adherent PBMC was reduced markedly by treatment with anti-leu 11b plus complement. Thus, the present DNA fragmentation ELISA is non-radioactive, highly sensitive and a useful method for detecting natural killer cell-mediated cytotoxicity against CMV-infected fibroblasts.

Adult↗
PubMed1988

Determination of the molecular weight of DNA-bound protein(s) responsible for gel electrophoretic mobility shift of linear DNA fragments examplified with purified viral myb protein.

A protein-DNA complex has less gel electrophoretic mobility than the free DNA fragment. One parameter for the degree of retardation of a linear DNA fragment in a protein-DNA complex is the molecular weight of the bound protein(s). The quotient of the migration distances of free DNA (m) and protein-DNA complex (m') is a function of the molecular weight (MW) of the bound protein(s). Based on the evaluation of the lac repressor induced mobility shift of a 203 bp DNA fragment containing the lac operator in a 5% non-denaturating polyacrylamide gel a direct proportionality could be shown between (m/m'-1) and MW with the proportionality factor K = 215 kDa. The factor K depends on the acrylamide concentration in the gel, getting lower values with increasing acrylamide concentrations. A calculation is given to determine the molecular weight of DNA-binding factors responsible for the decreased electrophoretic mobility of a linear DNA fragment. As an example this calculation was used in order to analyse DNA-binding of the isolated viral myb protein. It could be demonstrated that the viral myb protein binds to DNA as a monomer and as a dimer.

Avian Myeloblastosis Virus↗
PubMed1991

[Cloning and sequencing of a highly repeated DNA fragment of rabbit].

We obtained highly repeated DNA fragments from a rabbit by using restriction endonuclease HindIII digestion of chromosomal DNA; the smallest highly repeated DNA fragment was cloned into vector plasmid pUC12. We used the recombinant plasmid to transform E. coli JM101, selected and identified the positive clone by DNA probe in situ hybridization as well as Southern blotting. We obtained a recombinant clone [termed pRAb (Hind III)-1] which contains the highly repeated DNA fragment [termed RAb (Hind III)-1]. The complete nucleotide sequence of the 345bp RAb (Hind III)-1 fragment was determined by the dideoxynucleotide termination sequencing method. We analyzed the characteristics of the structure of the sequence with a microcomputer, and the results suggested that the RAb (Hind III)-1 sequence is quite different from alphoid DNA of primates.

Animals↗
PubMed2001

Caspase-dependent and serine protease-dependent DNA fragmentation of myocytes in the ischemia-reperfused rabbit heart: these inhibitors do not reduce infarct size.

Some infarcted myocytes undergo caspase-dependent DNA fragmentation, but serine protease-dependent DNA fragmentation may also be involved. There is controversy regarding whether caspase inhibitors can reduce infarct size, so the present study investigated whether serine protease inhibitor can reduce the DNA fragmentation of infarcted myocytes and whether serine protease or caspase inhibitors attenuates myocardial infarct size in Japanese white rabbits without collateral circulation. Rabbits were subjected to 30-min coronary occlusion followed by 48-h reperfusion. A vehicle (dimethylsulfoxide, control group, n=8) or Z-Val-Ala-Asp(Ome)-CH2F (ZVAD-fmk, a caspase inhibitor, ZVAD group, 0.8 mg/kg iv at 20 min before coronary occlusion and 0.8 mg/kg at 90 min after reperfusion, n=8) or 3,4-dichloroisocoumarin (DCI, a serine protease inhibitor, 2 mg/kg iv at 20 min before coronary occlusion, DCI group, n=8) was administered. Animals were killed at 48h after reperfusion for the detection of myocardial infarct size and at 4h after reperfusion for the detection of dUTP nick end-labeling (TUNEL)-positive myocytes, the electrophoretic pattern of DNA fragmentation and ultrastructural analysis. The left ventricle (LV) was excised and sliced. The myocardial infarct size as a percentage of the area at risk was assessed by triphenyltetrazolium chloride staining. DNA fragmentation was assessed by in situ TUNEL at the light microscopic level. ZVAD and DCI significantly reduced the mean blood pressure during reperfusion without affecting heart rate. There was no significant difference in the % area at risk (AAR) of LV among the 3 groups (control: 26.3+/-3.0%; ZVAD: 25.6+/-2.6%; DCI: 25.6+/-2.0%). The % infarct size as a percentage of the AAR in the ZVAD group (41.3+/-4.5%) and the DCI group (50.4+/-3.8%) was not significantly different from the control group (43.5+/-4.5%). However, the percent DNA fragmentation in the infarcted area in the ZVAD (3.5+/-0.8%) and DCI groups (4.2+/-0.9%) was significantly reduced compared with the control group (10.7+/-1.9%). The DNA ladder pattern observed in the control group was attenuated in both the ZVAD and DCI groups. There was no difference in electron microscopic changes among the 3 groups. Serine protease-dependent DNA fragmentation is present in infarcted myocytes, in addition to caspase-dependent DNA fragmentation, but an infarct-size reducing effect was not observed with either of these inhibitors.

Amino Acid Chloromethyl Ketones↗
PubMed1998

[Polymorphism of B1-associated DNA fragments on various stages of ontogenesis of mice in tissues of different histogenesis].

Pattern of B1-associated DNA fragments was studied by means of polymerase chain reaction (PCR) in the mouse tissues of different histogenesis of 15 and 20 day old embryos and of adult mice C57B1/6. As many as 20 DNA fragments were revealed on electrophoregrams differing in their molecular masses (m. m.) and amounts of amplified products. DNA fragments varied within a 100-10,000 bp range. The clusters of B1-associated DNA fragments, containing 100-200, 300-400 and 800-1000 bp, were most intensive in all studied electrophoregrams. The B1-associated DNA fragments from muscles of adult mice differed from those of other tissues by the presence of a DNA fragment with 800 bp. A comparative analysis of the spectra of B1-associated DNA fragments from hepatocytes of two inbred strains, C57B1/6 and C3HA, has shown their general similarities in m. m. values. But a significant distinction, that was found, involved the presence of a DNA fragment with m. m. approximately 6000 bp in the spectra of B1-associated DNA fragments from C3HA strain mice, that is absent in the spectra of respective fragments from hepatocytes of C57B1/6 strain mice. The obtained results allow to use the B1-PCR method for studying genome recombination during ontogenesis, intraspecies divergence and also at malignant cell transformation.

Animals↗
PubMed1974

A colinear map relating the simian virus 40 (SV40) DNA segments of six adenovirus-SV40 hybrids to the DNA fragments produced by restriction endonuclease cleavage of SV40 DNA.

The simian virus 40 (SV40) DNA segments present in a series of adenovirus-SV40 hybrids have been mapped with respect to the sites of cleavage of SV40 DNA by restriction endonucleases. Two approaches have been used. First, nucleic acid hybridizations were performed between equimolar quantities of the denatured DNAs of SV40 and each hybrid virus and the radiolabeled transcripts of 11 DNA fragments obtained by cleavage of SV40 DNA by restriction endonuclease from Hemophilus influenzae. Secondly, selected fragments of SV40 DNA produced by the H. influenzae or H. parainfluenzae restriction endonucleases were used to form heteroduplex DNA molecules with adenovirus and adenovirus-SV40 hybrid DNA, which were then analyzed by electron microscopy. The two sets of data were consistent and have permitted alignment of the map of the SV40 segments of the hybrid viruses with the H. influenzae and H. parainfluenzae cleavage maps of SV40. Since cells infected with some of the hybrid viruses contain one or more SV40-specific antigens, the genetic determinants of these antigens could be localized on the cleavage map.

Adenoviridae↗
PubMed2001

[Subcloning and sequencing of DNA fragment related to salt tolerance in Sinorhizobium meliloti 042B].

A 4 kb ClaI DNA fragment related to salt tolerance from S. meliloti 042B was digested by HindIII down 2.4 kb fragment, and a 1.6 kb ClaII-HindIII fragment was retained on plasmid pML122. Then, the 2.4 kb DNA fragment was ligated with plasmid pBBR1-MCS2, and the recombinant plasmid was transformed to E. coli DH5 alpha, and transformant GS2 was obtained. Three-parental mating experiments were carried out with transformant GS2 as donor, salt sensitive strains GZ17 as recipient and pRK2013 as helper plasmid, then the transconjugant GG2 was selected on FY plates containing kanamycin and 0.4 mol/L NaCl. The remaining DNA fragment was self ligated with pML122 and then transformed into E. coli S17-1 and transformat GS0 was obtained. Two-parental mating experiment was carried out with transformant GS0 as donor and salt sensitive strain GZ17 as recipient, but no transconjugant was obtained on the FY plates. Then, the 2.4 kb HindIII DNA fragment was ligated into sequencing vector pGEM-7Zf(+) for sequencing. The result of sequencing and analysis showed that the 2.4 kb DNA fragment contained three ORFs. According to the result of sequencing, further subcloning was conducted and 1.9 kb HindIII-Sac II DNA fragment related to salt tolerance was obtained.

Amino Acid Sequence↗
PubMed1986

Inhibition in maturation of nascent DNA fragments in cultured mouse FM3A cells after treatment with DNA-damaging agents.

The effect of DNA-crosslinking agents (cisplatin and mitomycin C), a DNA-intercalating agent (adriamycin) or monofunctional psoralen (4-Met-4', 5'-dihydropsoralen plus near-ultraviolet radiation) on DNA replication in cultured mouse FM3A cells was studied by sedimentation of the pulse-labeled DNA in an alkaline sucrose gradient. There was no inhibition of the maturation process of the nascent DNA 1 h after treatment of the cells with cisplatin, mitomycin C or adriamycin. However, this process was inhibited progressively during further incubation for 4 to 16 h without the agents, and accumulation of the nascent DNA fragments was observed. In the case of DNA-crosslinking agents, this inhibition may be correlated with an increase in the number of DNA-crosslinks formed during incubation. However, direct inhibition of maturation was not likely since the number was small, up to 4.9 per 10(9) Da. After treatment of cells with monofunctional psoralen, no inhibition of maturation of the nascent DNA fragments was observed. In all cases, there was no degradation of DNA during incubation.

Animals↗
PubMed1993

Delayed internucleosomal DNA fragmentation in programmed cell death.

DNA fragmentation was evaluated in three instances of programmed cell death, interdigital cell death in embryonic mouse limbs, and metamorphic death of both the labial glands and intersegmental muscle in the tobacco hornworm Manduca sexta. In the mouse, we evaluated both developmental cell death and expanded-range cell death induced by retinoic acid. The status of DNA was examined in several ways. Nuclei were examined by electron microscopy and Feulgen staining. Quantitative assessment of total DNA content in Feulgen-stained degenerating nuclei was made for the gland. In the labial gland, DNA content does not drop during the early phases of cell death; nor is an endonucleolytic ladder seen when DNA was examined by ethidium bromide staining or prelabeling with [3H]thymidine. Only by using end labeling of DNA could we detect DNA fragmentation at a very late stage in cell death, day 4 of the collapse of the gland. In contrast, WEHI 7.1 lymphoma cells display an early and extensive ladder after treatment with glucocorticoids. In mouse limb, for which cell death follows a more classic apoptotic morphology, a ladder is likewise not seen. We conclude that activation of an endonuclease is neither a trigger nor a necessary or defining component of the early phases of developmental programmed cell death, and that reported failure by others to find such a ladder may depend on limitations in the system that is under investigation.

Animals↗
PubMed1998

Endonucleolytic DNA fragmentation is not required for apoptosis of cultured rat cerebellar granule neurons.

Depolarizing concentrations of potassium (K+) promote maturation and survival of cerebellar granule neurons in vitro. Withdrawal of potassium from differentiated neurons induces morphological and biochemical features of apoptosis, including membrane blebbing, nuclear condensation, activation of caspases, and internucleosomal DNA fragmentation. Significant DNA fragmentation is detectable at 6 h after K+ withdrawal and slowly increases thereafter. Two observations indicate that endonucleolytic DNA degradation is neither required nor sufficient for K+ withdrawal-induced apoptosis in cerebellar granule neurons: (i) neurons are rescued from apoptosis by readdition of K+ up to 8 h after K+ withdrawal, when DNA fragmentation has already occurred. (ii) The endonuclease inhibitor, aurintricarboxylic acid, inhibits DNA fragmentation as assessed by quantitative DNA fluorometry, TUNEL staining, and DNA gel electrophoresis, but not cell death or chromatin condensation induced by K+ withdrawal.

Animals↗
PubMed1998

Distinct steps in DNA fragmentation pathway during camptothecin-induced apoptosis involved caspase-, benzyloxycarbonyl- and N-tosyl-L-phenylalanylchloromethyl ketone-sensitive activities.

Monocytic-like leukemia U-937 cells rapidly undergo morphological changes and DNA fragmentation that is typical of apoptosis following treatment with DNA topoisomerase I inhibitor [20-S-camptothecin lactone (CPT)]. The tripeptide derivative benzyloxycarbonyl-Val-Ala-Asp(OMe)fluoromethyl ketone blocks Asp-Glu-Val-Asp-ase (DEVDase) activity and prevents the occurrence of high molecular weight and oligonucleosome-sized DNA fragments associated with apoptosis in CPT-treated cells. In contrast, N-tosyl-L-phenylalanylchloromethyl ketone (TPCK) does not prevent DEVDase activity and high molecular weight DNA fragmentation but completely abrogates the appearance of oligonucleosome-sized DNA fragmentation. These results suggest that caspase 3-like activities are involved with high molecular weight DNA fragmentation pathway, whereas TPCK-sensitive activities are involved in oligonucleosome-sized DNA fragmentation pathway in CPT-treated cells. Electron micrographs reveal that caspase inhibition by benzyloxycarbonyl-Val-Ala-Asp(OMe)fluoromethyl ketone also abrogates the typical morphological changes associated with apoptosis, whereas TPCK does not delay these morphological changes that are typical of apoptosis. Caspase inhibition slows passage of the cells through G2 and causes a transient accumulation of these cells at the G0/G1 phase of the cell cycle following CPT treatment. In a cell-free system, when purified nuclei are incubated with apoptotic cytosolic extracts obtained from CPT-treated U-937 cells, TPCK causes a similar effect in abrogating the oligonucleosome-sized DNA fragmentation but does not affect DEVDase activity. Addition of either benzyloxycarbonyl-Val-Ala-Asp-free carboxyl group or acetyl-Asp-Glu-Val-Asp-aldehyde completely inhibits DEVDase activity in these extracts. However, acetyl-Asp-Glu-Val-Asp-aldehyde does not affect the occurrence of oligonucleosome-sized DNA fragmentation in the cell-free system, whereas the benzyloxycarbonyl derivatives benzyloxycarbonyl-Val-Ala-Asp-free carboxyl group, benzyloxycarbonyl-Val-Ala-free hydroxyl group, benzyloxycarbonyl-Val-free hydroxyl group, and benzyloxycarbonyl hydrazide abolish it markedly. Taken together, these observations show the pivotal role of DEVDase activity in triggering the apoptotic process and high molecular weight DNA fragmentation, whereas TPCK- and benzyloxycarbonyl-sensitive activities are involved in the oligonucleosome-sized DNA fragmentation pathway induced by CPT.

Amino Acid Chloromethyl Ketones↗
PubMed2000

[Subcloning and sequencing of DNA fragment related to salt tolerance in Sinorhizobium fredii RT19].

A 23 kb DNA fragment related to salt tolerance was obtained from the gene library of S. fredii strain RT19. In this study, BamH I was selected to digest 23 kb DNA fragment into different length of DNA fragments. The resulting fragments were ligated with plasmid pML122, then the recombinant plasmids were transformed to competent cells of E. coli S17-1 on selective medium and three transformants TR were obtained. Two-parental mating experiments were carried out with these transformants as donor and salt sensitive S. fredii strain RC3-3 as recipient, and the transconjugant BR2 was selected on FY plates containing gentamycin and 0.4 mol/L NaCl. Thus, a 4.4 kb DNA fragment related to salt tolerance was obtained. Based on its physical map, six restriction fragments were subcloned into plasmid pUC18 for DNA sequencing. Subsequently, sequencing and analysis of 4.4 kb DNA fragment showed that fixO, fixN genes and three ORFs were obtained.

Amino Acid Sequence↗
PubMed2005

Factors affecting SFHR gene correction efficiency with single-stranded DNA fragment.

A 606-nt single-stranded (ss) DNA fragment, prepared by restriction enzyme digestion of ss phagemid DNA, improves the gene correction efficiency by 12-fold as compared with a PCR fragment, which is the conventional type of fragment used in the small fragment homologous replacement method [H. Tsuchiya, H. Harashima, H. Kamiya, Increased SFHR gene correction efficiency with sense single-stranded DNA, J. Gene Med. 7 (2005) 486-493]. To reveal the characteristic features of this gene correction with the ss DNA fragment, the effects on the gene correction in CHO-K1 cells of the chain length, 5'-phosphate, adenine methylation, and transcription were studied. Moreover, the possibility that the ss DNA fragment is integrated into the target DNA was examined with a radioactively labeled ss DNA fragment. The presence of methylated adenine, but not the 5'-phosphate, enhanced the gene correction efficiency, and the optimal length of the ss DNA fragment (approximately 600 nt) was determined. Transcription of the target gene did not affect the gene correction efficiency. In addition, the target DNA recovered from the transfected CHO-K1 cells was radioactive. The results obtained in this study indicate that length and adenine methylation were important factors affecting the gene correction efficiency, and that the ss DNA fragment was integrated into the double-stranded target DNA.

Adenine↗
PubMed1986

Visualization of intermediary transcription states in the complex between Escherichia coli DNA-dependent RNA polymerases and a promoter-carrying DNA fragment using the gel retardation method.

DNA-dependent RNA polymerase in complex with a DNA fragment was analyzed by electrophoresis in non-denaturing gels as core enzyme, holoenzyme, during initiation and elongation. The DNA fragment carried the promoter A1 of the phage T7. The stoichiometry between holoenzyme and promoter and between sigma and core enzyme in complex with DNA was determined. Holoenzyme bound as a monomer to the DNA, whereas core enzyme formed aggregates before binding to the DNA. If the molar ratio of holoenzyme to DNA exceeded 0.5:1 a second holoenzyme molecule interacted with the DNA fragment with diminished affinity. A large difference in the frictional coefficient of the holoenzyme-promoter and the core enzyme-DNA complex indicated a drastic conformational difference between the two types of complexes. The stability of the holoenzyme-promoter complex decreased with decreasing temperature, accompanied by at least partial dissociation of holoenzyme into core enzyme and sigma factor. Addition of nucleoside triphosphates did not change the electrophoretic mobility of the complex if abortive transcription only was allowed, but increased it after addition of all four nucleoside triphosphates owing to release of the sigma factor.

DNA, Bacterial↗
PubMedDate not supplied

[DNA fragment DARC146 from a complex form of DNA polymerase alpha contains several nuclear protein binding segments].

Earlier, a number of DNA fragments were identified in the complex form of DNA polymerase alpha. One of them, DARC146, can support autonomous replication in mammalian cells. We have subcloned 146 bp from DARC146 (here called DARC146). This fragment has an ability to replicate autonomously in mammalian cells. This ability permits one to speak about DARC146 as a putative replication origin. From this conclusion, we suggest that all signals for initiation of DNA synthesis are located on the nucleotide sequence under study. Here, we have shown that the nuclear extract contains four polypeptides binding specifically to synthetic oligonucleotides covering the AT-rich region of the DARC146 sequence. The first protein is Oct-1, a nuclear transcription-replication factor. The second protein (named p65) binds to the TCTCTTA site of the DARC146 nucleotide sequence. There are two sites for Oct-1 protein and two sites for p65 in the DARC146 fragment. Octamer motifs and sites for p65 are located tandemly side by side. Moreover, we identified 28kDa polypeptide from nuclear matrix which bound to DARC146. Based upon the data presented, we suggest a hypothetical model of the pre-initiation state of the DARC146 sequence.

Animals↗