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At least 649 records · Page 36Linked to original sources
PubMed2003

Growth control of mouse mammary epithelial cells by keratin antibody-targeted liposome containing oligonucleotides antisense to epidermal growth factor receptor.

NMuMG cells were incubated with 17beta-estradiol (E)+progesterone (P)+epidermal growth factor (EGF), with or without various types of oligomers (21-mers) to the EGF receptor activity domain (amino acid residues 718 to 724). Sense or antisense oligomers were encapsulated in protein A-bearing liposomes. Uncoupled protein A and unencapsulated sense or antisense oligomers were separated from liposomes on a Sepharose 4B column (the encapsulation efficiency of oligomers in liposome-protein A was 0.8%). The addition of various concentrations of EGF to E+P showed an interaction between them during DNA synthesis (P<0.05). Antisense oligomers (1 microM) decreased DNA synthesis induced by E+P+EGF (65.0% inhibition, P<0.05). Sense oligomers also inhibited DNA synthesis induced by E+P+EGF (P<0.05). However, random-sequence oligomers did not inhibit EGF-induced DNA synthesis. We cannot rule out the possibility that sense oligomers match an unknown functional gene mRNA involved in cell growth, which causes their inhibitory effect. Cells were incubated with a keratin monoclonal antibody and then with dilutions of protein A-bound liposomes containing sense or antisense oligomers in the presence of E+P+EGF. Dose dependent inhibition of DNA synthesis was observed. The encapsulated oligomers in protein A-bound liposomes inhibited DNA synthesis at a 100-fold lower concentration than that of unencapsulated oligomers or the oligomer+liposome mixture. The tyrosine kinase activity domain has an important role in EGF regulation of mammary growth. The effect of a cytokeratin-targeted antibody on DNA synthesis in normal mouse mammary epithelial cells was marginal.

Animals↗
PubMed1998

Specific inhibition of influenza virus RNA polymerase and nucleoprotein gene expression by circular dumbbell RNA/DNA chimeric oligonucleotides containing antisense phosphodiester oligonucleotides.

We have designed a new class of oligonucleotides, 'dumbbell RNA/DNA chimeric oligonucleotides', consisting of a sense RNA sequence and its complementary antisense DNA sequence, with two hairpin loop structures. The reaction of the nicked (NDRDON) and circular (CDRDON) dumbbell RNA/ DNA chimeric oligonucleotides with RNase H gave the corresponding antisense phosphodiester oligodeoxynucleotide together with the sense RNA cleavage products. The liberated antisense phosphodiester oligodeoxynucleotide was bound to the target RNA, which gave RNA cleavage products by treatment with RNase H. The circular dumbbell RNA/DNA chimeric oligonucleotide showed more nuclease resistance than the linear antisense phosphodiester oligonucleotide (anti-ODN) and the nicked dumbbell RNA/DNA chimeric oligonucleotide. The CDRDON with four target sites (influenza virus A RNA polymerases (PB1, PB2, PA) and nucleoprotein (NP)) was synthesized and tested for inhibitory effects by a CAT-ELISA assay using the clone 76 cell line. The circular dumbbell DNA/ RNA chimeric oligonucleotide (CDRDON-PB2-as) containing an AUG initiation codon sequence as the target of PB2 showed highly inhibitory effects.

DNA↗
PubMed2005

Evaluation of arrayed primer extension for TP53 mutation detection in breast and ovarian carcinomas.

Mutations in the tumor suppressor gene TP53 are associated with a wide range of different cancers and may have prognostic and therapeutic implications. Methods for rapid and sensitive detection of mutations in this gene are therefore required. In order to make screening more effective, a commercially available TP53 genotyping microarray from Asper Biotech has been constructed by arrayed primer extension (APEX). The present study is the first report that blindly evaluates the efficiency of the second generation APEX TP53 genotype chip outside the Asper laboratory and compares it to temporal temperature gradient electrophoresis (TTGE) and sequencing of TP53 for mutation detection in ovarian and breast cancer samples. All nucleotides in the TP53 gene from exon 2-9 are included on the chip by synthesis and application of sequence-specific oligonucleotides. The chip was validated by screening 48 breast and 11 ovarian cancer cases, all of which had previously been analyzed by TTGE and sequencing. APEX scored 17 of 20 sequence variants, missing one deletion, one insertion, and a missense mutation. Resequencing efficiency using APEX was 92% for both DNA strands and 99.5% for sense and/or antisense strand. We conclude that the APEX TP53 microarray is a robust, rapid, and comprehensive screening tool for sequence alterations in tumors.

Alleles↗
PubMed1994

The rapid dissociation of the T4 DNA polymerase holoenzyme when stopped by a DNA hairpin helix. A model for polymerase release following the termination of each Okazaki fragment.

We have examined the molecular mechanism that enables the T4 bacteriophage DNA polymerase holoenzyme to synthesize DNA processively on the leading strand of the replication fork for many minutes, while allowing an identical holoenzyme on the lagging strand to recycle from one Okazaki fragment to the next in less than 4 s. We use a perfect hairpin helix of 15 base pairs to mimic the encounter of the polymerase with the end of a previously synthesized Okazaki fragment. Polymerase dissociation is monitored during the stall at the hairpin helix by the addition of excess T4 gene 32 protein (SSB protein), which rapidly melts the helix and allows a stalled polymerase molecule to continue DNA synthesis. In the accompanying paper, we show that polymerase holoenzyme dissociation is slow (half-life of 2.5 min) when this enzyme is stalled by nucleotide omission (Hacker, K. J., and Alberts, B. M. (1994) J. Biol. Chem. 269, 24209-24220). In contrast, the holoenzyme dissociates with a half-life of 1 s after hitting the hairpin helix, a rate sufficient to allow efficient polymerase recycling on the lagging strand in vivo. We conclude that, upon completing each Okazaki fragment, the holoenzyme senses an encounter with duplex DNA and then switches to a state that rapidly dissociates.

Base Sequence↗
PubMed2000

Endogenous parathyroid hormone-related peptide enhances proliferation and inhibits differentiation in the osteoblast-like cell line ROS 17/2.8.

To investigate potential effects of endogenous parathyroid hormone-related peptide (PTHrP) on osteoblast function, ROS 17/2.8 cells were transfected with full-length PTHrP cDNA in a sense or antisense orientation to alter PTHrP production. Compared with vector-transfected control cells, PTHrP-overproducing (sense-transfected) cells showed increased DNA synthesis ([(3)H]-thymidine incorporation) and increased growth (cell number). The extent of apoptosis was compared for the different clones using the terminal deoxynucleotide-mediated dUTP nick-end-labeling assay (TUNEL) and Hoechst staining. No differences in percentages of apoptotic cells were found under basal culture conditions or after 3 days of serum deprivation, which, itself, markedly increased numbers of apoptotic cells. The effect of PTHrP on osteoblast differentiation was assessed by examining two protein markers of differentiation, alkaline phosphatase, and bone morphogenetic protein (BMP)-2. Alkaline phosphatase activity was decreased in sense-transfected cells and increased in antisense-transfected cells, compared with cells transfected with empty vector. PTHrP-overproducing cells also showed decreased numbers of BMP-2-positive cells, whereas antisense-transfected cells showed no difference compared with vector control. The results indicate that: (a) endogenously produced PTHrP can increase growth of these osteoblastic cells by stimulating proliferation while not affecting apoptosis; and (b) the increased cell proliferation produced by PTHrP was accompanied by a reduction in activity or amount of two proteins normally expressed by differentiated osteoblasts.

Alkaline Phosphatase↗
PubMed2002

New developments in high-throughput resequencing and variation detection using high density microarrays.

We developed a high-throughput method for resequencing for single nucleotide polymorphism (SNP) discovery using high-density microarrays. Over the two-year course of this study a number of improvements in sample preparation methods, hybridization assay, array handling, and analysis method were developed and implemented. DNA from 40 unrelated individuals of three different ethnic origins was amplified, labeled, and hybridized to arrays designed with probes representing genomic, coding, and regulatory regions. Protocol improvements including the use of long PCR and semi-automation reduced labeling and fragmentation costs by 33%. Automation improvements include the development of a scanner autoloader for arrays, a faster array wash station, and a linked laboratory tracking and data management system. Validation of a smaller feature size, 20 x 24 microns, allowed the simultaneous screening of 30-kb sense and 30-kb antisense DNA on each microarray, increasing throughput to 1.4 Mb per day per two laboratory personnel. More than 15,000 SNPs were identified in 8.3 Mb of the human genome using high-density resequencing and variation detection arrays (microarrays).

Automation↗
PubMed2006

DomainSieve: a protein domain-based screen that led to the identification of dam-associated genes with potential link to DNA maintenance.

MOTIVATION: The Dam methyltransferase (DamMT) activity, broadly distributed in association with restriction endonucleases, as part of the restriction-modification defense systems, has evolved to become intimately associated with essential biological functions in a few organisms. In Escherichia coli, DamMT is involved in multiple aspects of DNA maintenance, replication initiation, daughter chromosome segregation, DNA mismatch repair, gene expression control, etc. The participation of DamMT in such a diverse set of functions required that other genes adapted, or emerged through evolution, in response to the DamMT-induced modification of the genomic environment. One example is SeqA, a protein that senses the methylation status of the origin of replication of the chromosome to control the timing of replication initiation. Interestingly, seqA is only present in a few DamMT-specifying proteobacteria. This observation led us to hypothesize that other genes, specifying related functions, might also be found in these organisms. To test this hypothesis, we implemented a large-scale comparative genomic screen meant to identify genes specifying DNA methylation sensing domains, probably involved in DNA maintenance functions. RESULTS: We carried out a phylogenetic analysis of DamMT, identifying two contrasting behaviors of the protein. Based on this phylogeny, we defined precisely a set of genomes, in which the protein activity is likely to be involved in DNA maintenance functions, the 'resident' dam genomes. We defined a second set of genomes, in which DamMT is not resident. We developped a new tool, 'DomainSieve', in order to screen these two sets for protein domains that are strictly associated with 'resident' dam genomes. This approach was rewarding and generated a list of genes, among which some, at least, specify activities with clear linkage to DamMT-dependent DNA methylation and DNA maintenance. AVAILABILITY: DomainSieve is implemented as a web resource and is accessible at http://stat.genopole.cnrs.fr/ds/.

Algorithms↗
PubMed2003

Transcriptional regulation of the ospAB and ospC promoters from Borrelia burgdorferi.

OspA, OspB and OspC are the major outer surface proteins of Borrelia burgdorferi that are differentially synthesized in response to environmental conditions, including culture temperature. We found that DNA was more negatively supercoiled in B. burgdorferi cultures grown at 23 degrees C compared with cultures grown at 35-37 degrees C. We examined the regulation of ospAB and ospC transcription by temperature and DNA supercoiling. DNA supercoiling was relaxed by adding coumermycin A1, an antibiotic that inhibits DNA gyrase. Syntheses of the major outer surface proteins, expression of the ospA and ospC genes and the activities of the ospAB operon and ospC gene promoters were assayed. ospA product levels decreased, whereas ospC product levels increased after shifting from 23 degrees C to 35 degrees C or after adding coumermycin A1. In addition, OspC synthesis was higher in a gyrB mutant than in wild-type B. burgdorferi. Promoter activity was quantified using cat reporter fusions. Increasing temperature or relaxing supercoiled DNA resulted in a decrease in ospAB promoter activity in B. burgdorferi, but not in Escherichia coli, as well as an increase in ospC promoter activity in both bacteria. ospC promoter activity was increased in an E. coli gyrB mutant with an attenuated DNA supercoiling phenotype. These results suggest that B. burgdorferi senses environmental changes in temperature by altering the level of DNA supercoiling, which then affects the expression of the ospAB operon and the ospC gene. This implies that DNA supercoiling acts as a signal transducer for environmental regulation of outer surface protein synthesis.

Aminocoumarins↗
PubMed2004

Synthesis of DNA-polypyrrole nanocapsule.

A template synthesis technique of encapsulating DNA molecules inside polypyrrole (PPy) nanotubes, termed as DNA-PPy nanocapsule, has been described here. The insertion of DNA molecules inside polypyrrole nanotubes is spontaneous in nature. The structural characterizations and possible applications of DNA-PPy nanocapsule in bio-sensing devices have been discussed.

Biosensing Techniques↗
PubMed1993

Expression of antisense E1A in 293 cells results in altered cell morphologies and cessation of proliferation.

To determine whether continued E1A expression is required to maintain immortalization, 293 cells, a cell line that has been immortalized and transformed by adenovirus E1A and E1B, respectively, were transfected by an antisense E1A expression vector. In the presence of low serum, 293 cells underwent a transient, viable, nonproliferative phase wherein cells with altered morphologies were detected. However, only those clones which did not integrate the antisense sequences and exhibited a morphology similar to the original 293 cells were able to survive. High serum concentrations resulted in fewer clones, which rapidly discarded the antisense DNA. Similar experiments with an antisense CAT vector did not give rise to cells with either altered morphologies or growth rates. Furthermore, CAT antisense DNA was integrated into the 293 cell DNA. Hela cells, which were not immortalized or transformed by E1, were unaffected by the expression of antisense E1A and integrated the antisense DNA into genomic DNA. Consistently, the addition of synthetic antisense, but not sense oligonucleotides resulted in a transient inhibition of 293 cell DNA synthesis. These data demonstrate that even after extended periods of time in culture, cells immortalized by E1A still require E1A expression to activate the cell cycle and prevent them from senescing.

Adenovirus E1A Proteins↗
PubMed2005

Molecular analysis of Arabidopsis endosperm and embryo promoter trap lines: reporter-gene expression can result from T-DNA insertions in antisense orientation, in introns and in intergenic regions, in addition to sense insertion at the 5' end of genes.

Random insertions of promoterless reporter genes in genomes are a common tool for identifying marker lines with tissue-specific expression patterns. Such lines are assumed to reflect the activity of endogenous promoters and should facilitate the cloning of genes expressed in the corresponding tissues. To identify genes active in seed organs, plant DNA flanking T-DNA insertions (T-DNAs) have been cloned in 16 Arabidopsis thaliana GUS-reporter lines. T-DNAs were found in proximal promoter regions, 5' UTR or intron with GUS in the same (sense) orientation as the tagged gene, but contrary to expectations also in inverted orientation in the 5' end of genes or in intergenic regions. RT-PCR, northern analysis, and data on expression patterns of tagged genes, compared with the expression pattern of the reporter lines, suggest that the expression pattern of a reporter gene will reflect the pattern of a tagged gene when inserted in sense orientation in the 5' UTR or intron. When inserted in the promoter region, the reporter-gene expression patterns may be restricted compared with the endogenous gene. Among the trapped genes, the previously described nitrate transporter gene AtNRT1.1, the cyclophilin gene ROC3, and the histone deacetylase gene AtHD2C were found. Reporter-gene expression when positioned in antisense orientation, for example, in the SLEEPY1 gene, is indicative of antisense expression of the tagged gene. For T-DNAs found in intergenic regions, it is suggested that the reporter gene is transcribed from cryptic promoters or promoters of as yet unannotated genes.

Arabidopsis↗
PubMed2003

TCDD-induced apoptosis in EL-4 cells deficient of the aryl hydrocarbon receptor and down-regulation of IGFBP-6 prevented the apoptotic cell death.

Although the potent environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) has been well known for its immunosuppressive activity, the mechanisms of its action have been difficult to elucidate, partly because of its inability of exerting its effects in vitro. We previously reported that insulin-like growth factor-binding protein-6 (IGFBP-6) expression in the thymus was increased by TCDD treatment of mice and that the TCDD-up-regulation of the IGFBP-6 gene was also observed with EL-4 mouse thymoma cells. In the present study, we examined the effects of IGFBP-6 on the TCDD-mediated cytotoxicity in EL-4 cells. By stably expressing IGFBP-6 sense or anti-sense mRNA in the EL-4 line of mouse thymoma cells, it was possible to isolate clones in which IGFBP-6 expression was increased or decreased. Clones expressing IGFBP-6 sense mRNA displayed increased sensitivity to cytotoxicity mediated by TCDD, whereas clones expressing IGFBP-6 anti-sense mRNA displayed reduced sensitivity. TCDD-induced DNA fragmentation was less pronounced in clones expressing IGFBP-6 anti-sense mRNA than clones expressing IGFBP-6 sense mRNA or the empty vector. Caspase 3 was activated by TCDD and anti-sense IGFBP-6 expression reduced its activity. Interestingly, the effects of TCDD were exerted without aromatic hydrocarbon (Ah) receptor (AhR). Taken together, the results have shown that IGFBP-6 mediates the immunotoxic effects of TCDD in EL-4 cells in an AhR-independent pathway.

Animals↗
PubMed2002

Expression of cell cycle-related gene products in Langerhans cell histiocytosis.

BACKGROUND The pathogenesis of Langerhans cell histiocytosis (LCH), a disease characterized by an abnormal accumulation of the dendritic Langerhans cells, is still unknown. Based on the monoclonality of the CD1a+ cell and reports of familial clustering, it is hypothesized that a genetic alteration at a cellular level may be causative. This genetic change may have an effect on the cellular mechanisms controlling proliferation and apoptosis. MATERIALS AND METHODS LCH-lesions were studied for the expression of Ki-67, present in the nucleus of proliferating cells. Furthermore, the expression of cell cycle-related gene products TGF-beta receptor I and II, MDM2, p53, p21, p16, Rb, and Bcl2 were studied. The TGF-betaR genes play a role in tumor suppression, whereas Bcl2 inhibits apoptosis. The remaining genes are part of either the p53-p21 and/or p16-Rb pathways, which induce cell cycle arrest or apoptosis in response to DNA damage. RESULTS In 30 biopsies the diagnosis of LCH could be confirmed on the basis of CD1a positivity (27 bone and 3 skin). All cases showed scattered nuclear-positive staining for the proliferation marker Ki-67. In more than 90% (n >/=27) of these cases, expression of TGFbeta receptor I and II, MDM2, p53, p21, p16, Rb, and Bcl2 was detected in lesional LCH cells. The overexpression was in general heterogeneous, ranging from limited focal staining of scattered cells within the lesion to strong diffuse staining. CONCLUSIONS These findings suggest that the cellular mechanisms that sense and respond to DNA-damage, namely the p53-p21 pathway and the p16-Rb pathway, are activated. The expression of Ki-67 indicates that the cells in LCH are proliferating. The observed overexpression of Bcl2 may play a role in the activation of p53 and p16 and/or the arrest of apoptosis.

Activin Receptors, Type I↗
PubMed1994

Suppression of simian immunodeficiency virus replication in primary peripheral mononuclear cells by antisense RNA.

It has been demonstrated that human immunodeficiency virus (HIV) replication can be effectively blocked by an antisense sequence that was introduced into the lymphoid cell line through retroviral-mediated gene transfer. In this study, it is demonstrated that antisense RNA can also inhibit simian immunodeficiency virus (SIV) replication in the peripheral blood mononuclear cells (MNCs) of healthy donors. MNCs were transduced with amphotropic recombinant virus encoding either sense or antisense constructs of SIV DNA fragments. After challenge with SIV, the viral replication was suppressed in the antisense-recombinant virus-transduced MNCs compared to sense-recombinant virus-transduced and untransduced MNCs. These data indicate that amphotropic retroviral vectors can be used to introduce antiviral factors (antisense sequence) into human primary MNCs and render them resistant to viral replication.

Base Sequence↗
PubMedDate not supplied

[Nature of the optimum DNA code].

It is shown that the four-letter code of the messenger DNA sequences is optimal in the sense that it provides minimal volume of the total information < < stuffing > > of the cell. The optimal code holds true only for the simplest DNA. This fact is indirect evidence that these very DNAs were the object of < < construction > > at earlier stages of biological evolution.

DNA↗
PubMed2000

Transient depletion of xDnmt1 leads to premature gene activation in Xenopus embryos.

In Xenopus laevis zygotic transcription begins at the midblastula transition (MBT). Prior to this the genome is organized into chromatin that facilitates rapid cycles of DNA replication but not transcription. Here we demonstrate that DNA methylation contributes to the overall transcriptional silencing before MBT. Transient depletion of the maternal DNA methyltransferase (xDnmt1) by anti sense RNA during cleavage stages is associated with a decrease in the genomic 5-methyl-cytosine content and leads to the activation of zygotic transcription approximately two cell cycles earlier than normal. Hypomethylation allows the early expression of mesodermal marker genes such as Xbra, Cerberus, and Otx2, which are subsequently down-regulated during gastrulation of the xDnmt1-depleted embryos. The temporal switch in gene expression may account for the appearance of body plan defects that we observe. Loss of xDnmt1 can be rescued by the coinjection of mouse or human Dnmt1 protein. These results demonstrate that DNA methylation has a role in the regulation of immediately early genes in Xenopus at MBT.

5-Methylcytosine↗
PubMed1971

Heterochromatin, satellite DNA, and cell function. Structural DNA of eucaryotes may support and protect genes and aid in speciation.

With the assumption that a portion that comprises some 10 percent of the genomes in higher organisms cannot be without a raison d'être, an extensive review led us to conclude that a certain amount of constitutive heterochromatin is essential in multicellular organisms at two levels of organization, chromosomal and nuclear. At the chromosomal level, constitutive heterochromatin is present around vital areas within the chromosomes. Around the centromeres, for example, heterochromatin is believed to confer protection and strength to the centromeric chromatin. Around secondary constrictions, heterochromatic blocks may ensure against evolutionary change of ribosomal cistrons by decreasing the frequency of crossing-over in these cistrons in meiosis and absorbing the effects of mutagenic agents. During meiosis heterochromatin may aid in the initial alignment of chromosomes prior to synapsis and may facilitate speciation by allowing chromosomal rearrangement and providing, through the species specificity of its DNA, barriers against cross-fertilization. At the nuclear level of organization, constitutive heterochromatin may help maintain the proper spatial relationships necessary for the efficient operation of the cell through the stages of mitosis and meiosis. In the unicellular procaryotes, the presence of a small amount of genetic information in one chromosome obviates the need for constitutive heterochromatin and a nuclear membrane. At higher levels of organization, with an increase in the size of the genome and with evolution of cellular and sexual differentiation, the need for compartmentalization and structural components in the nucleus became imminent. The portion of the genome that was concerned with synthesis of ribosomal RNA was enlarged and localized in specific chromosomes, and the centromere became part of each chromosome when the mitotic spindle was developed in evolution. Concomitant with these changes in the genome, repetitive sequences in the form of constitutive heterochromatin appeared, probably as a result of large-scale duplication. The repetitive DNA's were kept through natural selection because of their importance in preserving these vital regions and in maintaining the structural and functional integrity of the nucleus. The association of satellite (or highly repetitive) DNA with constitutive heterochromatin is understandable, since it stresses the importance of the structural rather than transcriptional roles of these entities. Nuclear satellite DNA's have one property in common despite their species specificity, namely heterochromatization. In this sense the apparent species specificity of satellite DNA may be the result of natural selection for duplicated short polynucleotide segments that are nontranscriptional and can be utilized in specific structural roles.

Animals↗
PubMed2002

Effect of pentoxifylline on tumor suppressor and proto-oncogene apoptosis in sperm.

PURPOSE: Pentoxifylline (PTX), a methylxanthine phosphodiesterase inhibitor reduces superoxide anions responsible for DNA apoptosis. The null hypothesis was that PTX was equally effective in reducing damage to specific cell genes. The objective was to determine the DNA integrity of the BRCA1 tumor suppressor gene and the c-myc proto-oncogene after PTX. METHODS: Sperm (64 samples, 4 patients) were preincubated in either 0 (control) or 3.6 mM PTX (30 min), washed and incubated for 4 h at either 37 or 40 degrees C heat shock activation. Single primer polymerase chain reactions (PCR) were carried out on lysed sperm targeting either BRCA1 exon 11 or c-myc exon 1. Control single-stranded DNA (ssDNA) were stained with 9 microM Hoechst 33342 (blue) while PTX-treated ssDNA were stained with SYBR Gold (green). Nytran membrane discs with control ssDNA were hybridized to PTX-derived ssDNA. Fluorescent images stored in a microarray design were analyzed using ANOVA and Students' t-test for (P < 0.05) significance. RESULTS: BRCA1 integrity was higher with PTX pretreatment (93.3 + 10.4 vs. control 50.5 + 9.2; mean + SEM). In contrast, there was no difference in c-myc integrity (56.8 + 9.0 vs. 41.7 + 6.4). Sense or antisense primers gave similar DNA fragmentation results. CONCLUSIONS: The data showed PTX pretreatment protected BRCA1 but not c-myc suggesting that PTX did not equally protect different cell genes. A possible explanation was that proto-oncogenes had more fragile sites. The study involved the DNA disc chip assay to assess separate PCR-amplified sense and antisense strands. The results suggested that both strands were equally affected by PTX pretreatment.

Apoptosis↗