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PubMed2006

[Unusual nucleotide sequence of a DNA fragment isolated from nuclear envelopes of mouse hepatocytes].

Fragments of chromosomal DNA isolated from nuclear envelopes of mouse hepatocytes were previously cloned and partially characterized in our laboratory. One of the cloned fragments (EnvM4) had unusual characteristics: abundant representability in the clone library (about 50%) and homology with DNA of archebacteria. An analysis of nucleotide sequence of this fragment conducted in more detail allowed the detection of an evolutionary conserved region present in the genomes of various organisms (from bacteria to human). Other characteristics of fragment EnvM4 suggest a possible functional role of chromosomal DNA regions determining the attachment of chromosomes to the nuclear envelope.

Animals↗
PubMed1999

Isolation of a specific DNA fragment and development of a PCR-based method for the detection of Mycobacterium genavense.

The rise of Mycobacterium genavense infections is making identification ever more important for diagnosis and treatment. Moreover, isolation and identification of M. genavense are made difficult by the lack of growth on solid media and by its low generation rate in BACTEC liquid media. Thus, amplification by PCR or similar techniques represents the only possibility of detecting and identifying M. genavense from tissue samples. In order to set up a simple and species-specific method based on the use of PCR and non-radioactive hybridization technique, we decided to search for and clone a specific DNA fragment of this bacterial species. In the present study, a 1734-bp fragment was isolated. This fragment was found to be highly specific for M. genavense strains. A species-specific pair of primers (MG22 and MG23) and two oligonucleotide probes (MG18 and MG19) were selected. They were successfully used to amplify and detect a 155-bp DNA fragment from the 13 available strains of M. genavense which were isolated from clinical specimens or from birds. Conversely, the primers and probes did not hybridize with DNA from any of the 20 other mycobacterial species tested. It is worth noting that the chosen primers and probes did not hybridize with DNA of M. simiae, although it is closely related to M. genavense. The present PCR technique uses species-specific primers for M. genavense. Followed by a non-radioactive hybridization technique on microplates it is able to distinguish M. genavense from other mycobacteria in one step, without sequencing or restriction analysis. On the basis of the Southern blot hybridization, PCR and sandwich hybridization results, we concluded that the isolated 1.7-kb sequence was specific for the M. genavense chromosome. The method developed here for M. genavense identification uses a simple methodology and commonly available reagents. Furthermore it can be easily automated.

Base Sequence↗
PubMed1983

Establishment and characterization of rat cell lines transformed by the left-end DNA fragments of adenovirus type 31.

A rat cell line, 3Y1, was transfected with the left-end DNA fragments of adenovirus (Ad) 31 DNA and transformed cell lines were established. A cell line 31BY4-1, which was induced by Ad31 BamHI-B (left-most 17.4% of the genome), showed typical transformation phenotypes, while cell lines 31GY1-2, 31GY2-5, and 31GY3-4, which were induced by Ad31 HindIII-G (left-most 6.7% of the genome), showed intermediate phenotypes between transformed and untransformed cells, with the following properties: (1) percent plating efficiencies in Eagle's minimum essential medium with 2% fetal calf serum and in soft-agar culture were extremely low, like those of 3Y1 cells; (2) they form tumors in newborn rats only after long latent periods. Southern blot hybridization revealed that, in all the transformed cell lines, viral DNA sequences were integrated at multiple loci in large-molecular-weight cell DNAs. Northern blot hybridization showed that viral mRNAs of early region 1A (E1A) and early region 1B (E1B) were both transcribed in 31BY4-1 cells as well as in KB cells early after infection with Ad31. On the other hand, E1B viral mRNA was present in a much lesser amount in 31GY cell lines, or was undetectable.

Adenoviridae↗
PubMed1979

Specific chemical labeling of DNA fragments.

We describe a simple method for specific chemical labeling of DNA fragments at their 3'-termini. The procedure includes enzymatic addition of 4-thiouridine, followed by reaction in mild non-denaturing conditions with the highly reactive alpha-haloacetamido derivatives of several chemical labels. The attached reporter molecule can be removed by extended treatment with beta-mercaptoethanol. Among the potential applications of this labeling method is the study of specific protein-DNA interactions in solution.

Chemical Phenomena↗
PubMed1991

Induction of DNA fragmentation in chronic B-lymphocytic leukemia cells.

Chronic lymphocytic leukemia of B cell type (B-CLL) is a neoplastic disorder characterized by the accumulation of small resting lymphocytes in the periphery. The phenotype of these cells suggests that they are "frozen" at an early stage of maturation. Glucocorticoid hormones are commonly used to treat patients with B-CLL, resulting in a reduction in the peripheral lymphocyte count by an undefined mechanism. Here we report that glucocorticoids stimulate DNA fragmentation characteristic of a suicide process known as apoptosis or programmed cell death (PCD) in suspensions of cells from patients with B-CLL. The effects can be mimicked by Ca2+ ionophore and involve a sustained increase in the cytosolic Ca2+ concentration. Specific antibodies binding to membrane-associated IgM on the leukemic cells can also induce PCD by a similar mechanism. Phorbol esters block DNA fragmentation and cell killing in response to all of the agents, suggesting that activation of protein kinase C desensitizes the cells to PCD. Targeting the B-CLL cells with antibodies that induce an unbalanced, sustained Ca2+ increase may therefore represent a rational strategy for the destruction of leukemic cells.

Antibodies, Monoclonal↗
PubMed1991

The effects of lithium, rubidium, cesium and magnesium ions on the close packing of persistence-length DNA fragments.

By application of scaled particle theory to persistence-length DNA fragments in sedimentation-equilibrium at speeds high enough to maintain close packing, the range of interhelical electrostatic repulsion was evaluated with LiCl, RbCl, CsCl, and MgCl2 as supporting electrolytes. Analysis of the data in terms of the Zimm cluster function confirmed that the net interaction between helices is purely repulsive in all cases. At constant ionic strength the electrostatic radius of the rod-like DNA decreases as the counterion changes from Li+ to Rb+ to Cs+. In contrast to univalent counterions, electrostatic radius increases with Mg2+ concentration, except at very low (mM) MgCl2 concentrations. All solutions undergo a reversible transition to a turbid, optically anisotropic phase at a slightly salt-dependent, critical DNA concentration, as observed previously for NaDNA.

Animals↗
PubMed2005

Helicobacter genus DNA fragments are commonly detectable in bile from patients with extrahepatic biliary diseases and associated with their pathogenesis.

Several Helicobacter species are known to colonize the biliary tract in animals and have been identified in the gallbladder bile of a high proportion of Chilean patients with gallbladder cancer. In this study, we tried to examine the presence of Helicobacter species in the bile to know their participation in the development of extrahepatic biliary diseases. DNA was extracted from 57 bile samples from 30 patients with benign biliary diseases (cholecystolithiasis and choledochocystolithiasis), 6 malignant biliary diseases (gallbladder cancer and common bile duct cancer), and 21 nonbiliary diseases. The presence of Helicobacter genus-, H. pylori-, H. hepaticus-, and H. bilis-specific 16S rRNA genes, the H. pylori urease A gene, and the H. pylori 26K protein gene in the bile was determined by PCR and sequencing analysis. Helicobacter genus DNA (shorter amplicons, 400 bp) was statistically frequently detected in biles from 53% (16/30) and 86% (5/6) of benign and malignant biliary diseases, compared with 9% (2/21) of nonbiliary diseases, but longer amplicons (1200 bp) were not detectable in any samples. The H. pylori urease A gene (nested amplicon) was also frequently found in bile, whether benign, malignant, or control, though neither H. pylori 16S rRNA nor the 26K protein gene was detectable in any bile samples. H. bilis-16S rRNA genes were detectable in only two cases. H. hepaticus was not detectable in any samples. DNA fragments of Helicobacter species other than H. pylori, H. hepaticus, and H. bilis are commonly detectable in the bile of patients with extrahepatic biliary diseases, whether benign or malignant, implying that the Helicobacter genus may be directly or indirectly involved in the pathogenesis of these diseases.

Bile↗
PubMed1997

Cyanide induced DNA fragmentation in mammalian cell cultures.

Cyanide is a mitochondrial poison and its toxicity is mediated through histotoxic hypoxia. Although cyanide is regarded as a neurotoxin, its other toxic manifestations are also well documented. Cyanide triggers all those events which can lead to DNA damage, but its genotoxic potential has not been established yet. The present investigation addresses the DNA damage induced by cyanide in rat thymocytes in vitro. Cell viability (eosin Y exclusion and LDH leakage) along with DNA strand breaks were measured in thymocytes exposed to 1.25-10 mM KCN for various time intervals. Cleavage into oligonucleosomal fragments of extracted DNA from cyanide treated thymocytes were visualized on gel electrophoresis. Cyanide produced both time and dose dependent DNA fragmentation accompanied by cytotoxicity. The DNA damage was sensitive to elevated levels of extracellular Ca2+ and was minimal in Ca2+ free medium. The DNA fragmentation was attenuated by Zn2+ (modulator of Ca2+/Mg2+-dependent endonuclease), N-acetylcysteine (free radical scavenger) and diltiazem (Ca2+ channel blocker). Cyanide induced DNA damage was further observed in baby hamster kidney cells (BHK-21), where unlike thymocytes, internucleosomal DNA fragmentation was not observed. Thymocytes were more sensitive to cyanide as compared to BHK-21 cells.

Animals↗
PubMed1998

A DNA fragment from the cyanobacterium Synechocystis sp. PCC 6803 mediates gene expression inducible by osmotic stress in E. coli.

Fragments of Synechocystis-DNA driving salt-induced gene expression in E. coli were isolated with translational fusions to a 'lacZ gene. One fragment (fragment 19) showed a NaCl-dependent activation of betaGal expression with the maximum of a ninefold increase in enzyme activity. A similar induction was triggered by the nonionic osmolyte sucrose, indicating an osmotically dependent activation. On the contrary, transcriptional activity of the DNA fragment 19 was only slightly enhanced under salt stress conditions, suggesting a posttranscriptional mechanism of induction. Primer extension assay was performed to identify the transcription initiation site. Upstream regions share weak homology to the "-10" hexamer consensus of E. coli sigma70 promoters. The most thermodynamically stable secondary structure for the nontranslated part of the mRNA indicated that potential translation initiation sites might be blocked, leading to a low basal translation, whereas osmotic stress-induced changes of mRNA structure could be involved to increase translation. In order to analyze the function of fragment 19 in Synechocystis, promoter-probe plasmids were constructed allowing the stable integration of transcriptional and translational reporter gene fusions into the cyanobacterial chromosome. Quantitative assessment of reporter gene expression revealed a weak constitutive promoter activity of fragment 19 in Synechocystis. Sequence analysis showed that fragment 19 comprises 223 bp of the ORF sll0747 of the Synechocystis genome.

Base Sequence↗
PubMed1998

A highly conserved genomic region in baculoviruses: sequence analysis of an 11.3 kbp DNA fragment (46.5-55.1 m.u.) of the Spodoptera exigua multicapsid nucleopolyhedrovirus.

A DNA fragment of 11.3 kilobase pairs (kbp) in size of the baculovirus Spodoptera exigua multicapsid nucleopolyhedrovirus (SeMNPV) genome (46.5 to 55.1 m.u.) was completely sequenced. Analysis of the sequence revealed eleven potential open reading frames (ORF). Ten of these ORFs showed significant amino acid identity to Autographa californica MNPV (AcMNPV) and Orgyia pseudotsugata MNPV (OpMNPV) genes p6.9, lef5, 38K, p19, p143, p25, p18, vp33, lef4, and vp39. One ORF (XC12) has no homolog in other baculoviruses and may be unique to SeMNPV. All but three of these putative genes are preceded by the consensus baculovirus late promoter element (5'-ATAAG-3'). The genetic organization and the putative map of transcripts of this fragment suggested that this region is highly similar to a region in AcMNPV fragment EcoRI-D. Comparison of the genetic organization of this 11.3 kbp fragment with the genomes of AcMNPV, OpMNPV, Bombyx mori NPV (BmNPV) and SeMNPV revealed that this region is highly conserved among baculovirus genomes. This is in contrast to the genetic organization of the polyhedrin-p10 region, which is much more diverged, but has been taken as point of reference to orient baculovirus physical maps. Through its diversity the latter region, however, would be an excellent candidate to determine baculovirus relatedness and phylogeny. The presence of conserved and diverged regions in baculovirus genomes with respect to gene order is reminiscent to the situation in other large DNA viruses, such as herpes- and poxviruses, where conserved central and diverged terminal parts are common characteristics. The role of this feature in the genomic organization of large DNA viruses is discussed with particular emphasis on virus replication and evolution.

Animals↗
PubMed2006

Human fibroblasts undergo oxidative stress-induced apoptosis without internucleosomal DNA fragmentation.

In order to evaluate the reliability of fibroblasts as a cell model for studying apoptosis, we tested the response of normal human fibroblasts to the oxidative stress inducers H(2)O(2) and 2-deoxy-D-ribose (dRib). Our results showed that fibroblasts treated with dRib and H(2)O(2) are induced to undergo apoptosis as demonstrated by reduction in total cell number, chromatin condensation, phosphatidylserine (PS) exposure, activation of caspase-3 and 7, changes in mitochondrial membrane potential and increase in the number of terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling (TUNEL)-positive nuclei. However we only found a slight increase in the percentage of cells in the sub-G1 region evaluated by flow cytometry, and we did not observe DNA fragmentation by agarose gel electrophoresis. Early in apoptosis, DNA cleavage generates high molecular weight (HMW) fragments which can be detected by TUNEL assay; successively followed by a pronounced DNA brake down into low molecular weight (LMW) fragments, detected as a "DNA ladder" by conventional agarose gel electrophoresis and as an hypodiploid peak by propidium iodide (PI) flow cytometry assay. Our results thus suggest that only HMW fragmentation occurs in fibroblasts exposed to dRib or H(2)O(2) and the lack of internucleosomal DNA fragmentation may depend on the peculiar characteristics of human fibroblasts themselves, irrespective of the apoptotic stimulus used. The existence of distinct events leading to cell death in different cell types makes it necessary to use a combination of strategies and techniques to evaluate the occurrence of apoptosis.

Apoptosis↗
PubMed1982

Toxicity, interstrand cross-links and DNA fragmentation induced by 'activated' cyclophosphamide in yeast: comparative studies on 4-hydroperoxy-cyclophosphamide, its monofunctional analogon, acrolein, phosphoramide mustard, and nor-nitrogen mustard.

Activated cyclophosphamide (CP) is known to achieve its cytotoxic and alkylating capacity upon spontaneous hydrolytic breakdown of the oxazaphosphorine ring structure. Treatment of yeast cells with the chemically activated form of CP (4-hydroperoxy-CP, 4-OOH-CP) and with several potentially toxic cleavage products revealed that cytotoxicity is closely linked to the formation of DNA interstrand cross-links and to DNA fragmentation. While this holds true for 4-OOH-CP and its bifunctional alkylating breakdown products, phosphoramide mustard (PM) and nor-nitrogen mustard (NNM), equimolar concentrations of acrolein and the monofunctional analogon of activated CP were inactive. NNM, the ultimate cleavage product within the successive degradation of the oxazaphosphorine structure was five times more toxic than 4-OOH-CP, whereas the cytotoxic action of PM was only slightly enhanced. The high cytotoxicity of NNM was matched by its ability to induce DNA interstrand cross-links: at concentrations and treatment times producing equal cell killing, 4-OOH-CP and NNM produced the same extent of cross-linking and DNA fragmentation. Biochemical potency of NNM is in contrast to data found with the NBP colorimetric assay which suggest that NNM loses its alkylating activity at neutral pH. 4-OOH-CP and PM are much more stable than predicted from half-life measurements performed via the NBP colorimetric assay: they retain a considerable fraction of their cytotoxic and cross-linking activity in spite of a 12-h preincubation at pH 7 and 36 degrees C.

Acrolein↗
PubMed1993

Nucleotide sequence of a Trichophyton mentagrophytes HindIII mitochondrial DNA fragment containing a tRNA gene cluster.

A 0.85-kb HindIII mitochondrial DNA fragment of the dermatophytic fungus Trichophyton mentagrophytes has been sequenced. The fragment contains eight complete genes which corresponds to a tRNA gene cluster. From 5' to 3', the sequenced genes code for tRNA(thr), tRNA(glu), tRNA(val), tRNA(met1), tRNA(met3), tRNA(leu), tRNA(ala), and tRNA(phe). This tRNA gene cluster is located downstream of the larger ribosomal RNA gene. The particularities of the sequenced genes and their comparison with other fungal tRNA mitochondrial genes are reported.

Base Sequence↗
PubMed1989

Characterization of RNA transcripts from herpes simplex virus-1 DNA fragment BamHI-B.

Herpes simplex virus type 1 (HSV-1) DNA fragment BamHI-B (0.738-0.809 map units) was recently reported to be associated with the phenotype of intraperitoneal pathogenicity and to encode a latency-associated RNA transcript. Part of this fragment resides within the internal repeat sequence of the long (L) region of the viral genome. In this study, RNA transcripts from BamHI-B were characterized. In addition to immediate-early mRNAs IE-1 and IE-2, eight novel RNA species were found. Three transcripts were mapped in the repeat regions of this fragment and five transcripts in the unique L region of BamHI-B. In addition, transcription activity from these regions was compared in several HSV-1 strains. These included the intraperitoneal virulent F and KOS strains, the avirulent strain HFEM, as well as the HFEM/F intratypic virulent recombinant R-MIC1. Several differences were noted and their possible relevance to virulence is discussed.

Animals↗
PubMed1999

Characteristics of different nucleic acid staining dyes for DNA fragment sizing by flow cytometry.

An efficient and reliable double-stranded DNA (dsDNA) staining protocol for DNA fragment sizing by flow cytometry is presented. The protocol employs 0.8 microM of PicoGreen to label a wide range of DNA concentrations (0.5 ng/mL to 10,000 ng/mL) without regard to the solution dye/bp ratios and without initial quantification of the DNA analyte concentration. Using a combination of spectrofluorometry and flow cytometry experiments, we found that PicoGreen exhibited better overall performance than all the tested dsDNA binding dyes, such as TOTO-1. Fluorometric titration revealed that typical DNA staining protocols designed on the basis of the dye/bp ratio were highly dependent upon the DNA concentration for optimal results. PicoGreen was the least sensitive to the solution dye/bp ratio and was highly fluorescent in the presence of dsDNA. Using this new protocol, accurate histograms of HindIII digested lambda DNA were demonstrated for DNA concentrations ranging from 5 to 2000 ng/mL, and for dye/bp ratios from 106:1 to 1:4 at 0.8 microM of PicoGreen. The new one-step protocol is broadly applicable to any sensitive, laser-induced fluorescence method for detection of nucleic acids.

Coloring Agents↗
PubMed1998

Characterization of a human genomic DNA fragment which rescues defective lipid-linked oligosaccharide synthesis in a mutant G258 cell line isolated from the FM3A mouse mammary carcinoma cell line.

The G258 mutant cell line, isolated from the FM3A mouse mammary carcinoma cell line, is temperature-sensitive for both cell growth and asparagine-linked glycosylation due to mutation at a single location. The biochemical defect in the G258 mutant resides in the formation of lipid-linked oligosaccharide, presumably in one of the steps of GDP-mannose-dependent mannosylation (Y. Nishikawa, J. Cell. Physiol. 119, 260-266, 1984; Y. Nishikawa, Biochim. Biophys. Acta 1091, 135-140, 1991). In the present study, we transfected human genomic DNA fragments into the G258 mutant by the radiation hybrid method and isolated transformants (KK-1, -3 and -4) which showed recovery from both temperature-sensitive cell growth and asparagine-linked glycosylation. These transformants contained a common Alu-containing human DNA fragment (1.3 kb) which will be used as a marker for isolating the gene that complements the defect of lipid-liked oligosaccharide synthesis in the G258 mutant.

Alu Elements↗
PubMed2005

Impact of reservoir potentials on the analyte behavior in microchip electrophoresis: computer simulation and experimental validation for DNA fragments.

Fundamental understanding of the impact of reservoir potentials on the analyte behavior on the microfluidic chips is an important issue in microchip electrophoresis (MCE) for suitable injection and separation of analytes, since the applied potentials may significantly affect the shape of sample plug, sample leakage from the injection channel to the separation channel, injected sample amount, and separation efficiency. This study addressed this issue for the case of a conventional cross-geometry microchip with four reservoirs using computer simulations, the results of which were verified by the analysis of DNA fragments. For the microchip with a definite structure and migration distance, the injected sample amount was shown to be the vital parameter for improving the limit of detection and resolution. During injection, the shape of the sample plug could be adjusted by varying the reservoir potentials. It was demonstrated that a "magnified injection" (applying high voltage on the three reservoirs to the sample reservoir) is useful to enhance the detection sensitivity depending on the analyte composition, although such injection was previously avoided because of introducing too large amounts of the analyte in comparison with two established modes, floating and pinched injection. Optimal magnified injection was proved to improve the sensitivity for about 4 times over that of pinched injection for the analysis of DNA step ladders using microchip gel electrophoresis (MCGE). Sample leakage of DNA fragments could be suppressed by applying a high positive voltage on injection channel during separation, but the voltage degraded the injected amount and resolution.

Computer Simulation↗
PubMed2005

Multicapillary electrophoresis of unlabeled DNA fragments with high-sensitive laser-induced fluorescence detection by counter-current migration of intercalation dye.

Analysis of PCR fragments for applications, such as screening of nucleotide polymorphisms, detection of somatic mutations, or quantification of reverse-transcription PCR products, becomes central in clinical research as well as preventive testing, diagnostic screening, and pharmacogenomic genotyping. A variety of CE techniques, utilizing great potential of multicapillary-array sequencers, is now commonly applied in prevention, diagnosis, and treatment of a wide range of genetic diseases (cancer, cardiovascular, and neurodegenerative diseases, etc.). Costs of fluorescently labeled primers is often a major factor in large-scale projects requiring mutation analysis in hundreds or thousands of samples. In the present paper we introduce a simple approach of detecting unlabeled DNA fragments through intercalation without a need for adding intercalator to the separation polymer matrix. The dye is only added to the anode reservoir, and mixing with the separated DNA fragments takes place upon its migration opposite to the direction of the CE separation. Using two common intercalating dyes (ethidium bromide and SYBR Green II) we present this method as a tool for routine PCR detection and quantification.

Coloring Agents↗