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

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Query: EC:3.1.30.2 (endonuclease)
18,621 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Mitochondrial DNA has been studied in a number of eukaryotic organisms. Differences in inter- and intraspecies mitochondrial DNA restriction patterns have been shown to be due to differences in nucleotide sequences and have been used to study evolutionary relationships and the mode of inheritance of the mitochondrial genome. A relatively rapid and efficient method for the extraction of mitochondrial DNA from Candida parapsilosis and other Candida species was developed. Zymolyase was used to induce yeast protoplasts and mitochondrial DNA was extracted from DNase I-treated mitochondrial preparations. Digestion with the restriction endonucleases Eco RI, Hind III and Bam HI yielded the most definitive restriction patterns. The results of the restriction endonuclease analysis were in agreement with the current identification of these organisms. Candida parapsilosis, Candida albicans and Candida kefyr showed different restriction patterns. Eight Candida parapsilosis strains were compared and all had identical fragment patterns. The molecular size was approximately 30 kilobase pairs and the GC content was 33.2%. The results of these experiments demonstrate the potential of a simple molecular technique for the differentiation of yeast species.
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PMID:Restriction endonuclease analysis of mitochondrial DNA from Candida parapsilosis and other Candida species. 266 67

We have developed an affinity technique to obtain active gene domains from murine erythroleukemia cell nuclei, based on the differential sensitivity of potentially active and inactive chromatin to DNase I. Nuclei isolated from potentially active noninduced cells and transcriptionally active induced MEL cells were treated with DNase I at concentrations which did not digest the beta-globin gene, followed by repair using a typical nick translation reaction during which a cleavable biotinylated nucleotide analog, 5-[N-biotinamido)hexanoamido-ethyl-1,3-dithiopropionyl -3-aminoallyl]-2'- deoxyuridine 5'-triphosphate (Bio-19-SS-dUTP), was inserted into DNA sequences. Following purification and digestion with EcoRI restriction endonuclease, biotinylated sequences were affinity isolated by sequential binding to streptavidin and biotincellulose. The streptavidin/biotin-cellulose complex bound up to 80% of the nick-translated DNA, which comprised a small percentage of the total nuclear DNA. Cleavage of the disulfide bond in the linker arm of the biotinylated nucleotide resulted in elution of virtually all of the affinity isolated sequences. Hybridization analysis of this fraction of DNA revealed up to a 16-fold enrichment for the active beta-globin gene, as compared with DNA which did not bind to the biotincellulose. Conversely, the inactive alpha-fetoprotein gene was barely detectable in affinity isolated DNA from noninduced cells and was 2-fold depleted in samples from induced cells.
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PMID:Affinity isolation of transcriptionally active murine erythroleukemia cell DNA using a cleavable biotinylated nucleotide analog. 275 91

Nuclei isolated from Djungarian hamster fibroblasts transformed by SV40 were treated with restriction endonuclease Bsp RI, fixed on Celite columns and underwent successive gradients of dissociating agents, such as NaCl, LiCl-urea, and temperature. This procedure leads to fractionation of DNA fragments in accordance with the tightness of DNA-protein bonds in situ. The fractions obtained were analysed by agarose gel electrophoresis and dot-hybridization technique with the use of various DNA probes. The results received are as follows: a) a DNA fragment size is not a factor determining the chromatographic position, the latter is probably stipulated by DNA-protein interactions; b) an analysis of cells synchronized at the G1/S border shows that the distribution of specific DNA sequences, such as actin, histone, hsp 70, and c-Ha-ras genes as well as reiterated DNA sequences, does not coincide with that of total genomic DNA; the nuclear matrix-attached fragments of those sequences are enriched to various extents. By nick-translation labeling in situ, DNase I-sensitive and hypersensitive regions were tentatively identified among subdomain chromatin fragments.
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PMID:[Comparative analysis of subdomain fragments of chromatin]. 277 Jul 45

Using DNase I and Alu I endonuclease analysis of a site-directed CC-1065-[N3-adenine]DNA adduct in a 117-base-pair fragment from M13mp1 DNA, we have demonstrated that CC-1065 produces an asymmetric effect on DNA conformation that extends more than one helix turn to the 5' side of the covalently modified adenine. CC-1065 is a potent antitumor antibiotic produced by Streptomyces zelensis, which is believed to mediate its cytotoxic effects through covalent binding to DNA. Previous studies have demonstrated that CC-1065 binds covalently to N3 of adenine and lies within the minor groove of DNA spanning a 4-base-pair sequence to the 5' side of the modified adenine. DNase I footprinting of this site-directed CC-1065-DNA adduct on the noncovalently modified strand shows that inhibition of cleavage occurs over a 12-base region, which is bordered on the 3' side by a site of 2-fold enhancement of cleavage. On the covalently modified strand a much less pronounced inhibition/enhancement pattern of cleavage occurs as far as 11 bases to the 5' side of the covalently modified adenine. While Hae III is able to cleave the DNA on both strands on the 3' side of the covalently modified adenine, Alu I is only able to cleave the covalently modified strand on the 5' side of the adduct. By taking into account the recently published structure of DNase I, we are able to interpret these results and develop a model for the effect of CC-1065 on local DNA structure. In this model, we propose selective drug-induced distortion of the covalently modified strand as a consequence of the alkylation of adenine by CC-1065.
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PMID:Demonstration of the asymmetric effect of CC-1065 on local DNA structure using a site-directed adduct in a 117-base-pair fragment from M13mp1. 281 75

Enzymes such as pancreatic deoxyribonuclease (DNase I) nick the single strands of double-stranded DNA. Two nicks sufficiently close on opposite strands will lead to breakage of the DNA molecule. This paper gives a mathematical model for the breakage of circular, supercoiled DNA under the action of an enzyme which nicks at random sites (or at preferred sites, these being in abundance and randomly positioned around the circle). After the first nick the DNA loses its supercoiled structure; after many nicks it breaks to become topologically linear; further nicks lead to fragmentation of this linear form. Formulae are given for the proportions of DNA molecules in each of the four classes: supercoiled; nicked but still circular; linear; fragmented. Formulae are also presented for the case when there is, in addition to nicking, simultaneous action of an endonuclease which produces direct double-stranded breaks in the DNA. Finally, a general theory is given for the case where a third type of enzyme, topoisomerase I, is operative, with all three DNA modifications taking place simultaneously.
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PMID:Breakage of double-stranded DNA due to single-stranded nicking. 282 26

Chromatin fragmentation of bovine peripheral blood lymphocytes from normal animals and the ones suffering from chronic lympholeucosis (CLL) by DNase I, micrococcal nuclease and purified Ca/Mg-dependent endonuclease from nuclei of human splenocytes was studied. The lymphocytes chromatin from CLL animals was shown to be more resistant to nucleases, than the one from normal animals. It was found that difference between fragmentation of chromatin samples from normal and CLL bovines was more dramatic when Ca/Mg- dependent endonuclease was used versus traditionally exploited DNase I and micrococcal nuclease. The data suggest that purified Ca/Mg-dependent endonuclease can be a useful enzymatic probe for detection of lymphocytes chromatin changes during CLL.
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PMID:[Ca/Mg-dependent endonuclease as a probe for detecting chromatin changes in lymphocytes in chronic lymphoid leukemia]. 282 38

We have used enzymic and chemical probes to search for altered DNA conformations in the 5' flanking region of the gene for a high mobility group protein (HMG-T) from trout. This search was conducted in order to identify potential genetic elements that might be involved in the transcriptional control of the HMG-T gene. We identified, in supercoiled plasmid DNA molecules containing a 900 base pair insert of the 5' region of the gene, an S1-sensitive site situated within an (AT)12 sequence approximately 120 base pairs upstream from the start of the HMG-T gene. Chemical modification of supercoiled DNA with the single-strand-selective reagent bromoacetaldehyde was limited to a region coincident with the S1 nuclease site. T7 endonuclease I, a probe highly specific for four-way helical junctions, cleaved predominantly at the boundaries of the (AT)12 stretch. These data are most consistent with the interpretation that the (AT)12 sequence adopts a cruciform structure when torsionally stressed by negative supercoiling. DNase I footprinting analyses demonstrated that HMG-T protects two regions almost equidistant from the center of the (AT)12 sequence, indicating that HMG-T is a sequence-specific DNA binding protein.
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PMID:Induction by torsional stress of an altered DNA conformation 5' upstream of the gene for a high mobility group protein from trout and specific binding to flanking sequences by the gene product HMG-T. 283 70

DNA sequences of the X-chromosome-linked hypoxanthine phosphoribosyltransferase (HPRT) and glucose 6-phosphate dehydrogenase (G6PD) genes have revealed the presence of clusters of CpG dinucleotides, raising the possibility that such clusters are involved in the control of expression of these genes, which are expressed in all tissues. Although CpG clusters are not exclusive features of the X chromosome, the analysis of X-linked genes provides the means to determine whether CpG clusters are control elements; one of the two homologous X loci in female mammals is not expressed, so that active and inactive versions of the gene can be compared. In fact, it has been shown that these CpG clusters are undermethylated when the gene is active and extensively methylated when the gene is inactive. In addition to hypomethylation, chromatin hypersensitivity to endonuclease digestion is a known hallmark of regulatory sequences in eukaryotic genes. We report here that the CpG clusters of the active hprt and g6pd genes are not only undermethylated, but also hypersensitive to MspI, DNase I and S1 nuclease, further supporting the suggestion that they are involved in the control of expression of these genes.
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PMID:Clusters of CpG dinucleotides implicated by nuclease hypersensitivity as control elements of housekeeping genes. 298 78

The mechanism of chromosome banding induced by restriction endonucleases was analyzed by measuring the amount of radioactivity extracted from [14C]thymidine-labeled chromosomes digested first with restriction enzymes and subsequently with proteinase K and DNase I. Restriction enzymes with a high frequency of recognition sites in the DNA produced a large number short DNA fragments, which were extracted from chromosomes during incubation with the enzyme. This loss of DNA resulted in decreased chromosomal staining, which did not occur in regions resistant to restriction enzyme digestion and thus led to banding. Subsequent digestion of chromosomes with proteinase K produced a further loss of DNA, which probably corresponded to long fragments retained in the chromosome by the proteins of fixed chromatin. Restriction enzymes induce chromatin digestion and banding in G1 and metaphase chromosomes, and they induce digestion and the appearance of chromocenters in interphase nuclei. This suggests that the spatial organization and folding of the chromatin fibril plays little or no role in the mechanism of chromosome banding. It was confirmed that the pattern of chromosome banding induced by AluI, MboI, HaeIII, DdeI, RsaI, and HinfI is characteristic for each endonuclease. Moreover, several restriction banding polymorphisms that were not found by conventional C-banding were detected, indicating that there may be a range of variability in the frequency and distribution of restriction sites in homologous chromosome regions.
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PMID:The mechanism and pattern of banding induced by restriction endonucleases in human chromosomes. 298 44

The in-vitro nick translation reaction used to label DNA to high specific activity also produces aberrant DNA structures known as "snapback" hairpin loops. Hairpin structures are precluded from participating in precise DNA-DNA hybridization interactions. Three nick translation systems were all found to yield significant quantities of snapback hairpins, as determined by their resistance to S1 endonuclease digestion following denaturation. The relative quantities of hairpins produced correlated with both the mass average size of the final DNA probe product synthesized as well as the overall rate of the nick translation reaction. Decreases in the amount of exogenous DNase I used in nick translation reactions produced significant decreases in the amount of hairpin loop structures formed. Hairpins could be effectively removed from nick-translated DNAs by employing hydroxylapatite column chromatography. Strategies to reduce hairpin formation during nick translation and the removal of hairpins from nick-translated DNAs are presented.
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PMID:Molecular assessment of S1 endonuclease-resistant snapback hairpin loops generated by DNA polymerase I during the in-vitro nick translation reaction. 299 Mar 35


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