Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: DrugBank:BIOD00001 (DNase I)
 8,324 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The diphtheria toxin repressor gene (dtxR) encodes a protein (DtxR) that regulates transcription of the diphtheria toxin gene (tox) by an iron-dependent mechanism. Cloned dtxR was expressed in Escherichia coli from the phage T7 gene 10 promoter, and DtxR was purified. Specific binding of DtxR to the tox+ operator was dependent on reduction of DtxR and the presence of ferrous ions. DtxR protected a sequence of approximately 30 nucleotide pairs, partially overlapping the tox promoter and containing a region of dyad symmetry, from digestion by DNase I. DtxR exhibited very little binding to the mutant tox-201 operator region and failed to bind to the promoter/operator region of the ferric uptake regulation (fur) gene of E. coli.
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PMID:Purification and characterization of the diphtheria toxin repressor. 150 69

A class of triplex-forming oligodeoxyribonucleotides (TFOs) is described that can bind to naturally occurring sites in duplex DNA at physiological pH in the presence of magnesium. The data are consistent with a structure in which the TFO binds in the major groove of double-stranded DNA to form a three-stranded complex that is superficially similar to previously described triplexes. The distinguishing features of this class of triplex are that TFO binding apparently involves the formation of hydrogen-bonded G.GC and T.AT triplets and the TFO is bound antiparallel with respect to the more purine-rich strand of the underlying duplex. Triplex formation is described for targets in the promoter regions of three different genes: the human c-myc and epidermal growth factor receptor genes and the mouse insulin receptor gene. All three sites are relatively GC rich and have a high percentage of purine residues on one strand. DNase I footprinting shows that individual TFOs bind selectively to their target sites at pH 7.4-7.8 in the presence of millimolar concentrations of magnesium. Electrophoretic analysis of triplex formation indicates that specific TFOs bind to their target sites with apparent dissociation constants in the 10(-7)-10(-9) M range. Strand orientation of the bound TFOs was confirmed by attaching eosin or an iron-chelating group to one end of the TFO and monitoring the pattern of damage to the bound duplex DNA. Possible hydrogen-bonding patterns and triplex structures are discussed.
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PMID:Binding of triple helix forming oligonucleotides to sites in gene promoters. 189 32

Transcriptional linkage of the enterobactin gene cluster entCEBA (P15) was confirmed by ent-lacZ gene fusion analysis. Control sequences directing iron-regulated expression of this polycistronic message were localized to the fepB-entC bidirectional promoter region. Transcriptional initiation sites defined by primer extension analysis were located 103 base-pairs apart for the divergent fepB and entC messages. Within this divergent regulatory region, strongly consensus -35 and -10 promoter determinants and potential Fur repressor-binding sequences were identified. A vector containing divergently oriented indicator gene fusions was constructed to monitor regulatory effects of mutations within this iron-responsive control region. The fepB-entC promoter-operator elements were confirmed by mutation, using the dual gene fusion system in multicopy and low copy number states. Mutations in the -35 and -10 regions of the fepB and entC promoters that decreased their similarity to consensus resulted in reduced promoter activity. Mutations in the Fur-controlled operators reduced induction ratios (iron-deficient levels/iron-rich levels) for the respective fusion gene activities by approximately sevenfold. Although operator mutants retained some degree of inducibility, complete relief of repression was observed for double operator mutants, suggesting that only minor regulatory influence is exerted by Fur occupation of the opposing operator site. DNase I footprinting experiments were performed to characterize the sequence-specific Fur interactions at the operator sequences. At the fepB operator, a 31 base-pair Fur-protected region was identified, corresponding to positions -19 to +12 with respect to the transcriptional start site. Similarly, Fur protected a 31 base-pair region in entC, corresponding to positions +1 to +31 in the message. A contiguous and sequentially occupied secondary Fur-binding site in entC was protected at higher Fur concentrations, extending the protected region to +49, and sequestering the putative Shine-Dalgarno sequence. Operator positional effects and co-operativity are discussed.
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PMID:Regulation of divergent transcription from the iron-responsive fepB-entC promoter-operator regions in Escherichia coli. 213 73

The DNase I footprinting analysis shows binding sites of approximately two or three base pairs, in particular 5'-XGC sequences, for the green-colored Co(III) and fully oxidized Fe(III) complexes of bleomycin (BLM). In contrast to covalent attachment of guanine N-7 with aflatoxin B1 or dimethyl sulfate, the modification of guanine 2-amino group with anthramycin remarkably inhibits the DNA cleavages at 5'-GC and 5'-GT sites by the iron and cobalt complex systems of BLM. The present results strongly indicate that metallobleomycin binds in minor groove of B-DNA and that the 2-amino group of guanine adjacent to 5'-side of the cleaved pyrimidine base is one key element of specific 5'-GC or 5'-GT recognition by metallobleomycin. On the basis of these experimental data, possible binding mode of metallobleomycin in B-DNA helix has been proposed by computer-constructed model building.
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PMID:Molecular biological analysis of sequence-specific DNA recognition and cleavage by metallobleomycins. 246 37

Four 25-nt oligonucleotides consisting of sequences of dA and dT (D1-4) have been synthesized. As shown in a companion paper (Rippe et al., 1989), the two combinations D1.D3 and D2.D4 form normal antiparallel duplexes, whereas the pairs D1.D2 and D3.D4 constitute duplexes with the same sequences, but with the two strands parallel to each other. The activities of the following DNA processing enzymes and chemical reagents on the parallel stranded (ps) and antiparallel stranded (aps) duplexes were tested. (i) The restriction endonucleases DraI, SspI, and MseI do not cut the ps duplexes. (ii) DNase I and exonuclease III exhibit a much lower activity with the ps duplexes. (iii) The nuclease activities of S 1 nuclease, micrococcal nuclease (S 7), phage lambda 5'-exonuclease, and the 3'-5' nuclease activity of Escherichia coli DNA polymerase I and its large fragment are higher with the ps than with the aps substrates. (iv) Bal 31 nuclease and the chemical nuclease 1,10-phenanthroline-copper ion [(OP)2Cu+] degrade ps-DNA and aps-DNA at approximately the same rate but show preferred cutting sites only with the aps molecules. (v) The iron(II)-EDTA complex has equivalent nuclease activities with the ps and the aps molecules. (vi) The ps duplex is not a substrate for blunt-end ligation with phage T4 DNA ligase.
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PMID:Substrate properties of 25-nt parallel-stranded linear DNA duplexes. 255 23

The molecular basis for the greatly elevated expression of the cir gene (encoding the colicin I receptor) in cells unable to maintain a critical supply of intracellular iron was investigated by genetic and biochemical means. Deletion analysis of the cloned promoter region allowed delineation of sequences necessary for control of transcription initiating at the two promoters, P1 and P2. Gel retardation assays were used to demonstrate both binding of purified Fur (ferric uptake regulation) protein to the iron control region and lack of binding to DNA fragments which are not involved in cir regulation. An operator sequence spanning 43 to 47 base pairs and completely encompassing the two promoters was identified by DNase I protection experiments (footprinting), with binding occurring in a metal-dependent fashion. Thus, during iron-replete growth, Fur appears to act as a repressor of transcription by blocking formation of a DNA-RNA polymerase complex, analogous to the mechanism previously described for regulation of the aerobactin operon (V. de Lorenzo, S. Wee, M. Herrero, and J.B. Neilands, J. Bacteriol. 169:2624-2630, 1987). Characterized and putative Fur recognition sites from several genes were analyzed and classified by statistical methods.
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PMID:Mechanism for iron-regulated transcription of the Escherichia coli cir gene: metal-dependent binding of fur protein to the promoters. 264 21

A fusion between the fur (ferric uptake regulation) gene, known to mediate negative regulation of iron absorption in Escherichia coli, and lacZ was constructed in vitro. beta-Galactosidase levels of cells harboring this fusion were under the control of sequences contained in a 185-bp DNA fragment located upstream of the fur structural gene. The fusion was prepared in multicopy (pVLN102 plasmid) and low-copy-number states, the latter constructed as a lambda phage lysogen carrying a fur'-'lacZ insert. DNase I footprinting experiments with purified Fur protein, performed on a 250-bp restriction fragment carrying the promoter region of the fusion, showed the presence of a single Fur-protected site overlapping the -10 region of a potential promoter sequence. Examination of the DNA sequences located upstream of the fur gene revealed a possible binding site for the catabolite-activator protein (CAP). beta-Galactosidase synthesis of E. coli cells harboring the fusion were measured in fur, crp and cya genetic backgrounds and compared with the corresponding levels in wild-type strains. The data obtained indicate a moderate autoregulation of fur expression by its gene product and also a significant stimulation by the cAMP-CAP system. Transcription start sites were mapped by primer-extension experiments with total RNA obtained in vivo from cells harboring pVLN102. The results show that transcription of the fur gene is initiated from at least two different sites separated by 6 bp, which appear to originate from two overlapping promoters sensitive to catabolic activation.
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PMID:Fur (ferric uptake regulation) protein and CAP (catabolite-activator protein) modulate transcription of fur gene in Escherichia coli. 283 93

We investigated in detail the structural changes that occur in nuclear chromatin upon activation of the four small heat shock protein genes in D. melanogaster. Both the chemical cleavage reagent methidiumpropyl-EDTA X iron(II) [MPE X Fe(II)] and the nuclease DNase I revealed a complex pattern of four or five hypersensitive sites upstream of each gene before activation. In addition, MPE X Fe(II) detected a short positioned array of nucleosomes located on each coding region. Upon heat shock activation a number of changes in the patterns occurred. For each gene, at least one of the upstream hypersensitive regions was eliminated or substantially shifted in position. Regions were established which became highly refractile to digestion by either MPE X Fe(II) or DNase I and, as such, appeared as small "footprints" in the pattern. The location of these refractile regions relative to the cap site varied for each gene examined. The coding regions themselves became highly accessible to DNase I. The nucleosomal arrays detected by MPE X Fe(II) were characterized by a considerable loss of detail and significantly enhanced accessibility, the extent of which probably reflected the relative transcription rate of each gene. Careful mapping of the location and extent of each upstream footprint and comparison with the DNA sequence revealed the presence at each location of two (or more) contiguous or overlapping segments that bear high homology to the heat shock consensus sequence C-T-N-G-A-A-N-N-T-T-C-N-A-G. A specific protein factor (or factors) is most likely bound at or near these sequence in heat-shocked Drosophila cells.
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PMID:Nucleosomal instability and induction of new upstream protein-DNA associations accompany activation of four small heat shock protein genes in Drosophila melanogaster. 302 29

Transcription of the iron-controlled aerobactin operon of the enterobacterial plasmid pColV-K30 is negatively regulated through the interaction of a Fe2+-binding repressor (the Fur protein) with operator sequences within the promoter region of the operon. The DNA sequences essential for interaction with the repressor were located by site-directed mutagenesis of specific regions within the 31 base-pair protected by the repressor from DNase I nicking. Occupation of two contiguous repressor-binding sites appears to be required for the complete repression of the system. Contacts of the Fur repressor with the corresponding operator sequences were analyzed with hydroxyl radical footprint and methylation protection experiments. These indicate that DNA-protein contacts approach a symmetrical mode and take place at all sides of the DNA helix.
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PMID:Metal ion regulation of gene expression. Fur repressor-operator interaction at the promoter region of the aerobactin system of pColV-K30. 306 82

Multiple copies of a human interferon-beta gene introduced into a mouse host cell line can be activated by induction with double-stranded RNA. Several induction-dependent changes of the chromatin structure could be traced by mapping techniques using four different agents [DNase I, micrococcus nuclease, bromoacetaldehyde and methidiumpropyl-EDTA X iron(II)]. Our data show that all copies of the interferon gene have adopted a very similar conformation in the host cell and respond to the inducing stimulus in a highly synchronous fashion. Detailed induction-specific changes were observed best with the chemical reagents which disclose a specific hypersensitive site within a sequence that has been shown to be required for the induction process (around position -80) and three other regions which, in addition to the transcribed region itself, gain single-strand character by an auxiliary process which can be mimicked by the addition of butyrate to the medium and may therefore involve histone hyperacetylation. Six discrete 'phased' nucleosomes are present upstream from the gene and are modulated by induction. At least four nucleosomes are located downstream. The interferon genes are largely protected from micrococcus nuclease in the inactive state. Gene activation increases access to micrococcus nuclease and DNase I indicating gross conformational changes on a higher level of chromatin structure.
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PMID:Chromatin structure and induction-dependent conformational changes of human interferon-beta genes in a mouse host cell. 308 85


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