Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound   Target Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound

---

Query: EC:3.1.25.1 (deoxyribonuclease)
1,471 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The glycosylase/abasic lyase T4 endonuclease V initiates the repair of ultraviolet light-induced pyrimidine dimers. This enzyme forms an imino intermediate between its N-terminal alpha-NH2 group and C-1' of the 5'-residue within the dimer. Sodium borohydride was used to covalently trap endonuclease V to a 49-base pair oligodeoxynucleotide containing a site-specific cyclobutane thymine dimer. The bound and free oligonucleotides were then subjected to nuclease protection assays using DNase I and a complex of 1,10-phenanthroline-copper. There was a large region of protection from both nucleases produced by endonuclease V evident on the strand opposite and asymmetrically opposed to the dimer. Little protection was seen on the dimer-containing strand. The existence of a footprint with the 1,10-phenanthroline-copper cleavage agent indicated that endonuclease V was interacting with the DNA predominantly via the minor groove. Methylation by dimethyl sulfate yielded no areas of protection when endonuclease V was covalently attached to the DNA, indicating that the protein may closely approach the DNA without direct contact with the bases near the thymine dimer. The Escherichia coli proteins Fpg and photolyase display a very different pattern of nuclease protection on their respective substrates, implying that endonuclease V recognizes pyrimidine dimers by a novel mechanism.
...
PMID:T4 endonuclease V protects the DNA strand opposite a thymine dimer from cleavage by the footprinting reagents DNase I and 1,10-phenanthroline-copper. 787 17

The globular cytoskeletal protein G-actin was isolated from the crude extract of soluble proteins from cress (Lepidium sativum L.) roots. The crude extract was loaded onto a deoxyribonuclease (DNase) I-affinity chromatography column and subsequently eluted with EGTA and urea. The fraction eluted with 2 mM EGTA was characterized by molecular weight determination, binding to DNase I, isoelectric focusing, and immunoblotting. These samples clearly showed one main 43,000 dalton protein with a pI value between 5.5 and 5.7. This polypeptide is an isoform of actin. It was stained using commercially available monoclonal and polyclonal actin antibodies. We used the EGTA fraction as plant actin antigen to produce a monoclonal cress root actin antibody. Antibodies (CRA) showed specific labelings on Western immunoblots against a 43,000 dalton protein of the cress root crude extract. Under the fluorescence microscope CRA detected actin in fixed statenchyma cells of cress roots. This antibody also demonstrated intact bundles of actin filaments in unfixed internodal cells of Chara australis. On the basis of these results we concluded that we had obtained a new monoclonal antibody (CRA) against actin from cress roots. We also found a cress root actin-binding protein antibody (CRAB) showing a filament staining pattern in internodal cells of Chara.
...
PMID:Monoclonal antibody CRA against a fraction of actin from cress roots recognizes its antigen in different plant species. 795 4

An alkaline endodeoxyribonuclease from rat brain has been purified to near homogeneity. The purified enzyme showed a M.Wt. of 54 Kd on SDS-PAGE and does not require metal ion for activity and thus differs from classical DNase I. No preference towards any particular form of calf thymus DNA (native, denatured, undamaged and damaged by exposure to UV, H2O2 and OsO4 and depurination) was noticed. However, with supercoiled pBR 322 plasmid DNA as substrate, higher activity was exhibited towards UV irradiated and depurinated forms. It is suggested that this DNase may be a 'housekeeping' enzyme to detect any conformational distortion in DNA and initiate excision repair.
...
PMID:A broad-specific alkaline DNase from rat brain with a putative role in DNA excision repair. 822 Feb 62

With the availability of direct genomic footprinting techniques the study of native genomes has been greatly facilitated. This review provides an overview of the techniques involved and gives also a description of the mode of action of different DNA modifying agents which can be used for such methods. These include exonuclease III, deoxyribonuclease, DNase I, micrococcal nuclease, dimethyl sulfate, diethyl sulfate, ethyl methanesulphonate, ethylnitrosourea, diethylpyrocarbonate, bromoacetaldehyde, potassium permanganate, osmium tetroxide, methidiumpropyl-EDTA-iron(II), formaldehyde, psoralen, 1,10 phenanthroline-copper and UV light. We also describe the limitations of the currently existing techniques and give some potential developments.
...
PMID:Approaches to characterize protein-DNA interactions in vivo. 843 8

During B cell development, the onset of DNA rearrangements, expression, and somatic hypermutation of Ig genes are regulated through the complex interaction of cis-acting elements with trans-acting factors. Our aim is to identify DNA elements required during activation of the human Ig lambda light chain genes. Determination of deoxyribonuclease (DNase) I-hypersensitive sites in complex regulated genes can lead to the identification of sequence elements which would have been overlooked by employing transient transfection protocols. We have therefore investigated the chromatin structure of human J-C lambda genes and identified three DNase I-hypersensitive sites (HSS-1, -2, and -3) within an 8-kb region downstream of the J-C lambda 7 gene. HSS-2 and HSS-3 are B cell specific. The DNase I-hypersensitive sites are also present in kappa-producing cell lines which have not rearranged the Ig lambda locus and produce germ-line J-C lambda transcripts. We conclude that in mature B cells, both kappa and lambda loci are in an active structure regardless of the type of light chain they produce. This suggests that the chromatin structure of both loci is opened early in B cell development and that the active structure persists in mature B cells. The observed temporal order (first kappa, then lambda) of activation can be explained by consecutive synthesis of the appropriate regulating factors and the tight regulation of the recombination machinery through the products of L chain gene rearrangements.
...
PMID:Tissue-specific deoxyribonuclease I-hypersensitive sites in the vicinity of the immunoglobulin C lambda cluster of man. 856 57

We have used a defined-sequence nucleosome to concomitantly investigate the generation and location of DNA lesions in nucleosomes and their influence on nucleosome positioning (translational and rotational setting). A 134 bp HISAT sequence from the yeast DED1 promoter, containing a polypyrimidine region (40 bp) with a T6-tract, two T5-tracts, and a T9-tract, was reconstituted in nucleosomes with a defined rotational setting. T-tracts adopt unusually rigid DNA structures in solution ("T-tract structure") and are hot spots of cyclobutane pyrimidine dimer (CPD) formation by UV light (254 nm). DNA was irradiated with UV light before or after reconstitution. The CPD yields and distribution were analyzed by cleavage with T4 endonuclease V. The rotational setting of nucleosomal DNA was characterized by DNase I digestion. With the exception of one T5-tract (1T5), the T6-, the 2T5-, and the T9-tracts formed T-tract structure in solution. T-tract structure was lost upon folding in nucleosomes, demonstrating a dominant constraint of DNA folding in nucleosomes over that of T-tract structure. CPD formation was strongly modulated by the nucleosome structure, but the CPD distribution differed from that reported for mixed-sequence DNA. CPD formation in the nucleosome had no effect on the rotational setting of nucleosomal DNA, but the rotational setting was affected when nucleosomes were assembled on damaged DNA. The toleration of DNA distortions imposed by CPDs in nucleosomes may have important implications for the recognition and repair of these damages in chromatin.
...
PMID:Modulation of cyclobutane pyrimidine dimer formation in a positioned nucleosome containing poly(dA.dT) tracts. 867 71

The rat androgen-binding protein (ABP) gene is transcriptionally regulated from two promoters: the P1 promoter regulates expression of transcripts starting at exon 1, whereas P(A) regulates transcripts containing exon A. The P1 promoter directs cell-specific gene regulation of ABP secreted by Sertoli cells. In this study, the Sertoli cell-regulatory sequences of P1 were further examined using a luciferase reporter system with three cell lines, including a Sertoli cell line (MSC-1) that expresses the ABP gene. Deletion mapping experiments determined that the sequences required for full activity in MSC-1 cells were included within 619 bp of the start site and identified several regions that demonstrated increased luciferase activity: the -583 bp to -564 bp, -503 bp to -484 bp, and -114 bp to -65 regions. The activities contributed by each region were much higher (up to 120-fold) in MSC-1 cells than in MA10 Leydig or NIH3T3 fibroblast cells. Nuclear-binding proteins and their binding sequences were identified using several molecular biology techniques. Complexes formed by nuclear proteins of MSC-1, MA10, and NIH3T3 cells, which bind specifically to the -114 to -65-bp region, were identified using gel retardation assays. Furthermore, the inverted repeat sequence in this region, 5'-AGGGTCAGTGTCCCT-3' was identified by deoxyribonuclease (DNase) I footprinting. The regulatory element contained within the -503 to -484-bp region was identified by scanning mutagenesis, but no protein was found that bound to this sequence by gel retardation or DNase I protection assays. This element is characterized by the core sequence, 5'-GGAGGC-3'. The third regulatory region (residues -583 to -564) bound a protein complex that retarded mobility of the free DNA probe in a gel shift assay. Using several techniques, the binding sequence was identified as 5'-TTCATAGTATCCATTAAAC-3'. In summary, these data have identified several transcriptional regulatory sequences and their binding proteins, which appear to play a role in the Sertoli cell-specific expression of the ABP gene.
...
PMID:DNA sequences and their binding proteins required for Sertoli cell-specific transcription of the rat androgen-binding protein gene. 925 28

The coreceptors CD4 and CD8 play a crucial role during thymocyte development and T cell effector function, and their expression is developmentally regulated. To determine the underlying molecular mechanisms of CD8 gene regulation we cloned the murine CD8 gene locus from genomic libraries and analyzed this region for deoxyribonuclease (DNase I) hypersensitive sites (HSS). Here we report, using transgenic mice, deletion analysis of one of the identified clusters of DNase I hypersensitivity, consisting of three DNase I-HSS and located in the intergenic region between the CD8alpha and CD8beta genes. Our data show that at least two of the DNase I-HSS constituting this cluster are individually sufficient to direct CD8alpha or heterologous transgene expression to the mature CD8 single-positive T cell subset and that this expression coincides temporally with the appearance of positively selected T cells.
...
PMID:A region in the CD8 gene locus that directs expression to the mature CD8 T cell subset in transgenic mice. 935 73

We have cloned and sequenced novel cDNAs that encode human and murine DNase II, the acidic deoxyribonuclease. Sequence analysis predicts that huDNase II contains an N-terminal signal sequence and that mature DNase II has 344 residues with a calculated molecular mass of 38 032 Da. DNase II is a novel enzyme with no homologies to proteins of known function. Surprisingly, C. elegans appears to possess a family of DNase II homologs. Unlike DNase I-like enzymes that have tissue-specific expression patterns, huDNase II is ubiquituously expressed at low levels. When huDNase II is expressed in human 293 cells, we observe secretion of a novel 42-44 kDa glycoprotein; approximately 20-30% of recombinant human DNase II activity is secreted in this system. The secreted enzyme possesses DNA hydrolytic activity and shares biochemical properties with purified DNase II obtained from other species. We also show that the mechanism by which DNase II cuts DNA is similar to DNase I in that the enzyme produces nicks rather than double-strand cuts.
...
PMID:Molecular cloning and characterization of human and murine DNase II. 971 27

This report demonstrates that Gadd45, a p53-responsive stress protein, can facilitate topoisomerase relaxing and cleavage activity in the presence of core histones. A correlation between reduced expression of Gadd45 and increased resistance to topoisomerase I and topoisomerase II inhibitors in a variety of human cell lines was also found. Gadd45 could potentially mediate this effect by destabilizing histone-DNA interactions since it was found to interact directly with the four core histones. To evaluate this possibility, we investigated the effect of Gadd45 on preassembled mononucleosomes. Our data indicate that Gadd45 directly associates with mononucleosomes that have been altered by histone acetylation or UV radiation. This interaction resulted in increased DNase I accessibility on hyperacetylated mononucleosomes and substantial reduction of T4 endonuclease V accessibility to cyclobutane pyrimidine dimers on UV-irradiated mononucleosomes but not on naked DNA. Both histone acetylation and UV radiation are thought to destabilize the nucleosomal structure. Hence, these results imply that Gadd45 can recognize an altered chromatin state and modulate DNA accessibility to cellular proteins.
...
PMID:Gadd45, a p53-responsive stress protein, modifies DNA accessibility on damaged chromatin. 1002 55


<< Previous 1 2 3 4 Next >>

---