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Synthesis and characterization of oligonucleotides containing a nitrogen mustard formamidopyrimidine monoadduct of deoxyguanosine.
Christov PP, Son KJ, Rizzo CJ
(2014) Chem Res Toxicol 27: 1610-8
MeSH Terms: Base Sequence, DNA Adducts, DNA Repair, DNA-Formamidopyrimidine Glycosylase, Deoxyguanosine, Deoxyribonuclease IV (Phage T4-Induced), Electrophoresis, Agar Gel, Escherichia coli, Escherichia coli Proteins, Kinetics, Mechlorethamine, Oligonucleotides, Organophosphorus Compounds, Pyrimidines
Show Abstract · Added January 7, 2016
N(5)-Substituted formamidopyrimidine adducts have been observed from the reaction of dGuo or DNA with aziridine containing electrophiles, including nitrogen mustards. However, the role of substituted Fapy-dGuo adducts in the biological response to nitrogen mustards and related species has not been extensively explored. We have developed chemistry for the site-specific synthesis of oligonucleotides containing an N(5)-nitrogen mustard Fapy-dGuo using the phosphoramidite approach. The lesion was found to be a good substrate for Escherichia coli endonuclease IV and formamidopyrimidine glycosylase.
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14 MeSH Terms
Evidence for a conjugation-like mechanism of DNA transfer in Helicobacter pylori.
Kuipers EJ, Israel DA, Kusters JG, Blaser MJ
(1998) J Bacteriol 180: 2901-5
MeSH Terms: Conjugation, Genetic, DNA, Bacterial, Deoxyribonuclease I, Drug Resistance, Microbial, Genetic Markers, Helicobacter pylori, Random Amplified Polymorphic DNA Technique, Transformation, Bacterial
Show Abstract · Added October 15, 2015
Many strains of Helicobacter pylori are naturally competent for transformation in vitro. Since there is a high degree of genetic variation among H. pylori strains, we sought to determine whether mechanisms of DNA exchange other than transformation exist in these organisms. Studies were done with H. pylori cells that each were resistant to two different antibiotics; the procedure used involved mating of cells on plates or in broth, in the absence or presence of DNase. In each experiment, such matings produced progeny with the markers of both parents. Examination of the full resistance profile and random arbitrarily primed DNA PCR (RAPD-PCR) profiles of the progeny indicated that DNA transfer was bidirectional. DNase treatment reduced but did not eliminate transfer; only the presence of both DNase and a membrane separating the cells did so. For progeny derived from matings in the presence of DNase, antibiotic resistance and RAPD profiles indicated that transfer was unidirectional. DNase-treated cell-free supernatants also did not transform, ruling out transduction. These experiments indicate that both a DNase-sensitive mechanism (transformation) and a DNase-resistant conjugation-like mechanism involving cell-to-cell contact may contribute to DNA transfer between H. pylori cells.
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8 MeSH Terms
The largest (70 kDa) product of the bacteriophage T4 DNA terminase gene 17 binds to single-stranded DNA segments and digests them towards junctions with double-stranded DNA.
Franklin JL, Haseltine D, Davenport L, Mosig G
(1998) J Mol Biol 277: 541-57
MeSH Terms: Adenosine Triphosphatases, Amino Acid Sequence, Bacteriophage T4, Base Sequence, DNA, Single-Stranded, Deoxyribonuclease I, Endodeoxyribonucleases, Molecular Sequence Data, Peptides, Recombinant Fusion Proteins, Sepharose, Substrate Specificity, Viral Proteins
Show Abstract · Added March 20, 2014
Bacteriophage terminases are oligomeric multifunctional proteins that bind to vegetative DNA, cut it and, together with portal proteins, translocate the DNA into preformed heads. Most terminases are encoded by two partially overlapping genes. In phage T4 they are genes 16 and 17. We have shown before that the larger of these, gene 17, can yield, in addition to a full-length 70 kDa product, several shorter peptides. At least two of these, gene product (gp) 17' and gp17", are initiated in the same reading frame as the 70 kDa gp17 from internal ribosome binding sites. Most of the shorter gp17 s contain predicted ATPase motifs, but only the largest (70 kDa) peptide has a predicted single-stranded DNA binding domain. Here we describe the DNA binding and cutting properties of the purified 70 kDa protein, expressed from two different clones containing gene 17 but no other T4 gene. Epitope-specific antibodies, which recognize several different gene 17 products in extracts of induced clones or of T4-infected cells, precipitate the purified 70 kDa gp17. When Mg2+ is chelated by EDTA this 70 kDa protein binds to single-stranded DNA, preferentially to junctions of single- and double-stranded DNA segments. It does not bind to blunt-ended double-stranded DNA. When Mg2+ is present the purified 70 kDa gp17 digests single-stranded segments preferentially up to junctions with double-stranded DNA. A 70 kDa gp17 from a P379L temperature sensitive (ts) mutant, which has lost the nuclease and ATPase activities, retains the single-stranded DNA binding activity. Taken together with earlier findings these results support a model for packaging of T4 DNA from single-stranded regions in recombinational or replicative intermediates, which occur at nearly random positions of the genome. This mechanism may be an alternative to site-specific initiation of packaging proposed by other investigators.
Copyright 1998 Academic Press Limited.
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13 MeSH Terms
Induction of the glucokinase gene by insulin in cultured neonatal rat hepatocytes. Relationship with DNase-I hypersensitive sites and functional analysis of a putative insulin-response element.
Parsa R, Decaux JF, Bossard P, Robey BR, Magnuson MA, Granner DK, Girard J
(1996) Eur J Biochem 236: 214-21
MeSH Terms: Animals, Animals, Newborn, Base Sequence, DNA Footprinting, Deoxyribonuclease I, Embryo, Mammalian, Enzyme Induction, Gene Expression Regulation, Enzymologic, Glucokinase, Insulin, Liver, Molecular Sequence Data, Promoter Regions, Genetic, RNA, Messenger, Rats, Rats, Wistar, Regulatory Sequences, Nucleic Acid, Simplexvirus, Thymidine Kinase
Show Abstract · Added February 23, 2011
Previous, in vivo experiments have shown that an appropriate hormonal environment (high plasma insulin, low plasma glucagon) was unable to induce the accumulation of glucokinase mRNA in term fetal rat liver, whereas it was very efficient in the newly born rat. We have confirmed in the present study that insulin induced the accumulation of glucokinase mRNA in cultured hepatocytes from 1-day-old newborn rats, but not in cultured hepatocytes from 21-day-old fetuses. To identify regulatory regions of the glucokinase gene involved in the insulin response, we have scanned the glucokinase locus for DNase I hypersensitive sites in its in vivo conformation. We confirmed the presence of four liver-specific DNase I hypersensitive sites located in the 5' flanking region of the gene. Moreover, two additional hypersensitive sites, located at 2.5 kb and 3.5 kb upstream of the cap site were found but none of these new sites displayed inducibility by insulin. Finally, an increase of the sensitivity of hypersensitive site-1 and hypersensitive site-2 to DNase I correlates with the ability of insulin to induce glucokinase gene expression in cultured hepatocytes from 1-day-old rats, as observed in previous in vivo studies. This suggests that neither a prior exposure to insulin nor a simple aging of the fetal cells in the presence of the hormone in culture are instrumental for the full DNase-I hypersensitivity of the two proximal sites necessary for the neonatal response of the glucokinase gene to insulin. The proximal hypersensitive site-1, which is close to the transcription start site in the liver, does coincide with a sequence (designated IRSL) that is 80% identical to the phosphoenolpyruvate carboxykinase IRS and with a DNase-I footprint that has been identified overlapping this sequence. Nevertheless, functional analysis of this sequence suggested that it is unlikely that the insulin-response sequence like alone is sufficient to mediate the transcriptional effect of insulin on the hepatic glucokinase gene.
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19 MeSH Terms
Cloning and characterization of the mouse glucokinase gene locus and identification of distal liver-specific DNase I hypersensitive sites.
Postic C, Niswender KD, Decaux JF, Parsa R, Shelton KD, Gouhot B, Pettepher CC, Granner DK, Girard J, Magnuson MA
(1995) Genomics 29: 740-50
MeSH Terms: Animals, Base Sequence, Biological Evolution, Chromosome Mapping, Cloning, Molecular, Conserved Sequence, DNA, DNA Primers, Deoxyribonuclease I, Exons, Gene Expression Regulation, Enzymologic, Gene Library, Glucokinase, Humans, Liver, Mice, Molecular Sequence Data, Organ Specificity, Polymerase Chain Reaction, Promoter Regions, Genetic, RNA, Messenger, Rats, Recombinant Proteins, Sequence Homology, Nucleic Acid, Transcription, Genetic
Show Abstract · Added February 23, 2011
We cloned and characterized an 83-kb fragment of mouse genomic DNA containing the entire glucokinase (GK) gene. The 11 exons of the gene span a total distance of 49 kb, with exons 1 beta and 1L being separated by 35 kb. A total of 25,266 bp of DNA sequence information was determined: from approximately -9.2 to approximately +15 kb (24,195 bp), relative to the hepatocyte transcription start site, and from -335 to +736 bp (1071 bp), relative to the transcription start site in beta cells. These sequences revealed that mouse GK is > 94% identical to rat and human GK. Mouse hepatic GK mRNA is regulated by fasting and refeeding, as also occurs in the rat. Alignment of the upstream and downstream promoter regions of the mouse, rat, and human genes revealed several evolutionarily conserved regions that may contribute to transcriptional regulation. However, fusion gene studies in transgenic mice indicate that the conserved regions near the transcription start site in hepatocytes are themselves not sufficient for position-independent expression in liver. Analysis of the chromatin structure of a 48-kb region of the mouse gene using DNase I revealed eight liver-specific hypersensitive sites whose locations ranged from 0.1 to 36 kb upstream of the liver transcription start site. The availability of a single, contiguous DNA fragment containing the entire mouse GK gene should allow further studies of cell-specific expression of GK to be performed.
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25 MeSH Terms
Search for androgen response elements in the proximal promoter of the canine prostate arginine esterase gene.
Dubé JY, Chapdelaine P, Guérin S, Leclerc S, Rennie PS, Matusik RJ, Tremblay RR
(1995) J Androl 16: 304-11
MeSH Terms: Androgens, Animals, Base Sequence, Binding, Competitive, Carboxylic Ester Hydrolases, DNA Footprinting, Deoxyribonuclease I, Dogs, Gene Deletion, Humans, Male, Mice, Molecular Sequence Data, Oligonucleotides, Point Mutation, Promoter Regions, Genetic, Prostate, Protein Structure, Tertiary, Rats, Transcription, Genetic, Transfection
Show Abstract · Added June 11, 2010
We have demonstrated the binding of the recombinant DNA binding domain of the rat androgen receptor to a DNA sequence of the canine prostate arginine esterase gene and have determined the functional significance of this sequence in transient transfection experiments. One of the binding sites was localized to a region (-172 to -148 bp) containing the sequence AGGACAACAGGTGTT that has 73% homology with the prostate-specific antigen (PSA) androgen response element (ARE) found at a similar position in the PSA promoter. Competition experiments showed that the androgen receptor had an approximately 100-fold more affinity for the PSA ARE than for the arginine sequence at -172 to -148. Transient cotransfection of 5'-deletion mutants of the arginine esterase promoter and 5'-flanking sequences driving the activity of the reporter gene along with the rat androgen receptor expression vector yielded only negligible inductions of chloramphenicol acetyl transferase (CAT) activity when dihydrotestosterone (DHT) was added to the culture medium. The introduction of one to four repeats of the -172 to -148 sequence of the arginine esterase gene upstream of the basal promoter of the mouse p12 gene in p12.108 also resulted in a minimal induction of CAT activity compared with a 10-fold induction of PSA AREs under similar conditions. These results suggest that the regulation of the canine arginine esterase gene by androgens is most probably achieved by mechanisms that differ from the ones prevailing with the human PSA and kallikrein-2 (hKLK2) genes.
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21 MeSH Terms
Simultaneous visualization of G- and F-actin in endothelial cells.
Haugland RP, You W, Paragas VB, Wells KS, DuBose DA
(1994) J Histochem Cytochem 42: 345-50
MeSH Terms: Actins, Animals, Antibodies, Monoclonal, Blotting, Western, Cattle, Cells, Cultured, Deoxyribonuclease I, Electrophoresis, Polyacrylamide Gel, Endothelium, Vascular, Fluorescent Dyes, Microscopy, Fluorescence, Phalloidine
Show Abstract · Added January 17, 2014
We developed site-specific fluorescent probes that permit simultaneous microscopic observation of G- and F-actin in bovine endothelial cells. G-actin distribution was visualized with fluorescein-deoxyribonuclease I (DNAse I). F-actin was labeled with phalloidin conjugated to the new long-wavelength fluorophore BODIPY 581/591 (581-nm excitation, 591-nm emission), which is spectrally similar to Texas Red. The G-actin appeared as pervasive green fluorescence that was more intense in the nuclear region, where cell thickness is greater and stress fibers are less frequent. In addition, we observed a punctate fluorescein pattern around the nuclei and in other parts of the cells, suggesting that some G-actin is localized to small discrete sites. F-actin was observed as red fluorescent filaments. Unlabeled DNAse I effectively prevented staining of G-actin by the fluorescent DNAse I conjugates. The specificity of DNAse I for G-actin was confirmed by the presence of a single labeled band with molecular weight corresponding to actin in a Western blot of total cytoplasmic endothelial proteins reacted with biotin-DNAse I-streptavidin-alkaline phosphatase. Anti-actin antibody, which associates with both G- and F-actin, in conjunction with fluorescent secondary antibody produced a pattern similar to that obtained by simultaneous visualization with fluorescein-DNAse I and BODIPY 581/591- or rhodamine-phalloidin.
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12 MeSH Terms
Cell specific differences in DNase I hypersensitivity between the two promoters of the rat glucokinase gene.
Williams CP, Granner DK, Magnuson MA, Chalkley R
(1995) Biochem Biophys Res Commun 215: 272-9
MeSH Terms: Animals, Binding Sites, Blotting, Southern, Cell Nucleus, Chromatin, DNA, Deoxyribonuclease EcoRI, Deoxyribonuclease I, Fibrosarcoma, Glucokinase, Islets of Langerhans, Liver, Liver Neoplasms, Experimental, Promoter Regions, Genetic, Rats, Tumor Cells, Cultured
Show Abstract · Added February 23, 2011
Glucokinase (GK) gene transcription occurs in the liver and the beta cell of the endocrine pancreas where it is subject to different modes of regulation. This is accomplished largely through the use of two linked, cell-specific promoters separated by at least 12 kbp. We have used DNase I hypersensitivity to explore the chromatin structure surrounding the two promoters in cells that express either the liver or beta cell form of the GK gene, as well as cells that do not express GK. In RIN38 cells, a beta-cell-derived cell line, hypersensitive sites are detected over both the proximal and distal promoters. In liver, hypersensitive sites are present in the proximal promoter but not the distal promoter. Interestingly, in H4IIEC3 cells, a hepatoma cell line that has lost the ability to express GK, hypersensitive sites are also found in the proximal promoter but not the distal promoter.
1 Communities
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16 MeSH Terms
Purification and in vitro DNA-binding specificity of the Bacillus subtilis phage phi 105 repressor.
Van Kaer L, Van Montagu M, Dhaese P
(1989) J Biol Chem 264: 14784-91
MeSH Terms: Bacillus subtilis, Bacteriophages, DNA-Binding Proteins, Deoxyribonuclease I, Escherichia coli, Hydroxides, Hydroxyl Radical, Methylation, Molecular Weight, Mutation, Nucleotide Mapping, Operator Regions, Genetic, Repressor Proteins, Sulfuric Acid Esters, Transcription Factors
Show Abstract · Added December 10, 2013
The Bacillus subtilis phage phi 105 repressor, a lambda repressor-like transcriptional regulatory protein, was overproduced in Escherichia coli and purified to near homogeneity in order to examine its in vitro DNA-binding properties. The active form of repressor appears to be a tetramer. DNase I protection experiments demonstrate that repressor can specifically bind to six distinct sites, all located within the phi 105 EcoRI-F immunity region (immF). Three of these sites had been identified earlier as functional operators by genetic analysis. They share a common 14-base pair, asymmetric "core" sequence, 5'-GACGGAAATACAAG-3', termed OR. The three additional sites show significant homology with OR. For an individual binding site, hydroxyl-radical footprinting reveals symmetrical repressor-DNA interactions established via one side of the helix. Dimethyl sulfate protection indicates that guanines at the conserved OR base pair positions 1, 3, and 4 may participate in sequence-specific interactions with repressor in agreement with a previously proposed recognition model. However, since the OR sequence is not symmetrical with respect to this GNCG motif, at present it remains difficult to completely understand the molecular basis of this interaction.
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15 MeSH Terms
A lipopolysaccharide-induced DNA-binding protein for a class II gene in B cells is distinct from NF-kappa B.
Gravallese EM, Boothby MR, Smas CM, Glimcher LH
(1989) Mol Cell Biol 9: 3184-92
MeSH Terms: Animals, B-Lymphocytes, Base Sequence, Cell Nucleus, DNA, DNA-Binding Proteins, Deoxyribonuclease I, Histocompatibility Antigens Class II, Lipopolysaccharides, Mice, Mice, Nude, Molecular Sequence Data, NF-kappa B, RNA, Spleen, Transcription Factors
Show Abstract · Added December 10, 2013
Class II (Ia) major histocompatibility complex molecules are cell surface proteins normally expressed by a limited subset of cells of the immune system. These molecules regulate the activation of T cells and are required for the presentation of antigens and the initiation of immune responses. The expression of Ia in B cells is determined by both the developmental stage of the B cell and by certain external stimuli. It has been demonstrated previously that treatment of B cells with lipopolysaccharide (LPS) results in increased surface expression of Ia protein. However, we have confirmed that LPS treatment results in a significant decrease in mRNA encoding the Ia proteins which persists for at least 18 h. Within the upstream regulatory region of A alpha k, an NF-kappa B-like binding site is present. We have identified an LPS-induced DNA-binding protein in extracts from athymic mice whose spleens consist predominantly of B cells. Binding activity is present in low levels in unstimulated spleen cells and is increased by LPS treatment. This protein binds to two sites in a regulatory region of the Ia A alpha k gene, one of which contains the NF-kappa B-like binding site. DNA fragments containing these sites cross-compete for protein binding. Analysis by DNase I footprinting identified a target binding sequence, named the LPS-responsive element. Although this target sequence contains an NF-kappa B-like binding site, competition with a mutant oligonucleotide demonstrated that bases critical for NF-kappa B binding are not required for binding of the LPS-inducible protein. Therefore, we hypothesized that this inducible protein represents a new mediator of LPS action, distinct from NF-kappa B, and may be one mechanism to account for the decrease in mRNA encoding the Ia proteins.
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16 MeSH Terms