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)

The DNA homology relationships of 25 micrococci (15 strains of Micrococcus, eight strains of Sarcina and two strains of Staphylococcus) were studied by the deoxyribonucleic acid hybridization method using nuclease S1, an endonuclease specific for single-stranded DNA molecules. Nineteen of the strains were classified into three groups. Group I contained Micrococcus lysodeikticus IAMI056, M. luteus IAMI1010, M. flavus IAMI2005 and IAMI2006, Sarcina flava IAMI2007 and IAMI1006. S. subflava IAMI2009, S. lutea ATCC381, and ATCC382, and M. luteus IAMI1006. Group II contained M. roseus IAMI315, ATCC412, ATCC185 and IAMI295. Group III contained S. lutea IAMI099, IFO3232 and ATCC383, M. varians ATCC399 and Staphylococcus lactis ATCC15306. Micrococcus luteus IAMI097, M. varians ATCC19099 and ATCC19100, M. conglomeratus IAMI459 and IAMI470, and St. aureus IAMI011 could not be assigned to any of the three groups. The grouping corresponds to that derived from the results of differential lysis by lysozyme, 'lytic enzyme 2' from Cytophaga sp., or Streptomyces albus G enzyme; and to types of peptidoglycan in the cell walls and genetic transformation. The usefulness of classification based on sensitivity to various lytic enzymes was demonstrated. Group I probably coincides with M. luteus of Bergey's Manual of Determinative Bacteriology (1974), and groups II and III with M. roseus and M. varians respectively.
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PMID:Classification of micrococci on the basis of deoxyribonucleic acid homology. 18 Feb 38

Double-stranded chicken lysozyme cDNA was synthesized from an oviduct mRNA fraction enriched for lysozyme mRNA. The ds-cDNA was inserted into the BamHI site of plasmid pBR322 using chemically synthesized DNA linker molecules containing the BamHI restriction endonuclease cleavage site. After bacterial transformation, colonies carrying lysozyme DNA were identified by hybridization with highly purified lysozyme cDNA. The 555 base pairs long cloned DNA fragment of one recombinant plasmid was isolated and characterized by restriction endonuclease digestion. The DNA sequence of selected parts of the inserted DNA is as predicted from the amino acid sequence of prelysozyme. The sequence data allows the unambiguous location of the coding region within lysozyme mRNA.
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PMID:Cloning of chicken lysozyme structural gene sequences synthesized in vitro. 56 56

The functions of the promoter of the chicken-lysozyme-encoding gene (Lsz) are complex, since, on the one hand, the promoter serves to mediate the effects of five upstream regulatory elements and, on the other, it contains itself important regulatory sequences. To analyze this interplay we first monitored protein-DNA interactions at the Lsz promoter in hormonally regulated oviducts and in constitutively expressing HD11 cells by in vivo genomic footprinting. Two regions of strong protein-DNA interactions shared by both HD11 and oviduct cells were localized between nucleotides (nt) -105 and -119 and between nt -61 and -74, respectively. A third region of protein-DNA contacts was found selectively in HD11 cells from nt -199 to -204; this region corresponds in position with a previously identified HD11 cell-specific enhancer element. Furthermore, we determined the sites hypersensitive to an endogenous endonuclease in isolated nuclei using the genomic sequencing protocol. These sites fall into two regions: one encompasses the in vivo localized protein-DNA contacts between nt -105 and -119 and between nt -61 and -74; the other was found in a sequence largely devoid of in vivo protein-DNA interactions. We hypothesize that hypersensitive cleavage sites are generated by protein-induced changes in the DNA conformation.
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PMID:Genomic footprinting of proteins interacting with the chicken lysozyme promoter. 224 77

A simple technique is proposed for detection of bacterial restriction endonucleases. Analysis is performed directly in the cells from colonies cultivated on Petri dishes. The cells collected with an inoculation loop are treated with lysozyme and Triton X-100. After centrifugation the supernatant is tested for endonuclease activity. The technique enables up to 100 colonies to be tested for 3-4 h.
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PMID:[A method for detecting restriction endonucleases in bacterial colonies]. 283 59

A method for the isolation of DNA from mycobacteria propagated in vitro is described that utilizes organic solvents to extract lipoidal components from the outer membrane, and digestion with a protease (nagarse) and lysozyme to penetrate the cell wall. The mycobacterial cells were lysed by the addition of detergent and the DNA was purified by digestion with pronase, sequential phenol and chloroform extractions, and digestion with RNAase A. The isolated DNA, which was obtained in good yields, was of a relatively high Mr and could be readily digested by restriction endonucleases. By this method, the genomes of Mycobacterium avium, M. intracellulare, M. lepraemurium, 'M. lufu', M. marinum, M. phlei, M. scrofulaceum, M. smegmatis and M. tuberculosis were isolated and the restriction endonuclease digestion patterns analysed. Each species could be distinguished by the digestion patterns, indicating that this approach can be used for identifying mycobacterial species. This approach is also sufficiently sensitive to differentiate strains since we were able to distinguish two independently isolated strains of M. tuberculosis, H37 and H4. In addition, no evidence was obtained for the presence of methylcytosine residues in the sequences 5'.CCGG.3',5'.CCCGGG.3',5'.CC(A/T) GG.3' or for methyladenine at 5'.GATC.3' in the DNA of the nine mycobacterial species examined using pairs of restriction enzymes that recognize and cleave at the same nucleotide sequence but differ in their sensitivity to 5-methylcytosine or 6N-methyladenine.
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PMID:Isolation and restriction endonuclease analysis of mycobacterial DNA. 301 65

During nonpermissive infection by a T7 amber mutant in gene 1 (phage RNA polymerase-deficient), synthesis of the products of the phage genes 3 (endonuclease), 3, 5 (lysozyme), 5 (DNA polymerase), and 17 (serum blocking power) was shown to occur at about half the rate as during wild-type infection. This relatively high rate of expression of "late" genes (transcribed normally by the phage RNA polymerase) seems to be a general feature of all T7 mutants in gene 1 from our collection. In contrast, T3 gene 1 mutants and a T7 gene 1 mutant from another collection showed late protein synthesis at very reduced rates. Synthesis of the gene 3 endonuclease by T7 gene 1 mutants was very sensitive to the addition of rifampin 2 min after infection, conditions under which there was very little inhibition during wild-type infection. This supports the notion that late gene expression during nonpermissive infection by gene 1 mutants is dependent on the transcription of the T7 genome by the host RNA polymerase. In contrast to T3 gene 1 mutants, the T7 gene 1 mutants of our collection directed the synthesis of phage DNA during nonpermissive infection. This DNA accumulated as a material sedimenting faster than mature T7 DNA.
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PMID:Synthesis of bacteriophage-coded gene products during infection of Escherichia coli with amber mutants of T3 and T7 defective in gene 1. 457 63

Cells of Escherichia coli treated with lysozyme and Brij-58 become permeable to proteins, but do not release their DNA. I incubated permeable cells with an endonuclease that produces single-strand breaks in DNA-containing pyrimidine dimers. The enzyme entered the permeable cells, and, if they had been irradiated with ultraviolet light, caused breaks in their DNA. The frequency of breaks was estimated from the sedimentation pattern of the DNA in alkaline sucrose gradients. The procedure is sensitive enough to detect the dimers produced by a dose of 10 erg/mm(2) at 254 nm, or about 50 dimers per E. coli genome. This method exemplifies and extends the use of permeabilized cells for examining biological processes at the molecular level.
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PMID:A method for detecting pyrimidine dimers in the DNA of bacteria irradiated with low doses of ultraviolet light. 458 22

Based on the results of a systematic study of factors affecting plasmid yield and purity, a procedure suitable for the rapid screening for and isolation of covalently closed circular DNA from Streptomyces lividans and Escherichia coli was developed. The method consists of lysis of lysozyme-treated bacteria combined with alkaline denaturation of DNA at high temperature. Renaturation of CCC DNA and precipitation of single-stranded DNA together with protein is achieved by the addition of a minimal amount of phenol/chloroform. The screening procedure uses only a single tube and the samples can be analyzed by agarose gel electrophoresis about 30 min after lysis. Removal of phenol and further purification of the plasmid preparation is achieved by consecutive precipitations with isopropanol and spermine, followed by extraction with ethanol, producing samples suitable for restriction endonuclease digestion, ligation, and transformation of S. lividans protoplasts or competent E. coli cells in about 2 h. All steps of the procedure are explained in detail with information about the effects of changing parameters. This should help the experimenter to obtain reproducible results and may be useful if the method has to be adapted to new strains or plasmids.
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PMID:Factors affecting the isolation of CCC DNA from Streptomyces lividans and Escherichia coli. 638 33

This study evaluated the Promega Magic Minipreps (MM) (Promega Corporation, Madison, WI) DNA purification system for use in plasmid analysis of common nosocomial bacterial pathogens. The MM system is a kit that includes lysis solutions and buffers and incorporates a minicolumn of DNA binding resin for recovery of plasmid DNA. The MM system was used according to the manufacturer's directions to recover plasmids for agarose gel electrophoresis from clinical isolates of Acinetobacter calcoaceticus, Enterobacter cloacae, and Klebsiella pneumoniae. For Salmonella enteritidis and Staphylococcus aureus, lysozyme and lysostaphin, respectively, were used for pretreatment. Plasmid DNA from ten isolates could be recovered in approximately one hour with very little manipulation and no phenol/chloroform extractions and was suitable for restriction endonuclease digestion. Compared with a standard miniprep protocol, the MM system was much easier to perform and resulted in significant cost savings due to a 50% reduction in technologist time. The authors conclude that the MM system is a convenient and cost-effective method for clinical microbiology laboratories for recovering plasmid DNA from nosocomial bacterial pathogens.
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PMID:Evaluation of a commercial DNA purification system for plasmid analysis of nosocomial bacterial pathogens. 837 41

The lack of simple and efficient methods for extraction of DNA from Nocardia spp. has hampered molecular manipulation of the DNA for diagnostic purposes. In the present study, a method for the rapid extraction of undegraded genomic nocardial DNA was established. Briefly, 14 pathogenic Nocardia strains were grown at 37 degrees C for 3 to 5 days in Sauton broth containing 0.05% Tween 80. Subsequently, the cultures were treated for 48 h with 1.2 mg of cycloserine per ml (final concentration). Cells were then harvested by centrifugation and treated with a lysis solution containing 3 mg of lysozyme per ml. This was followed by the addition of proteinase K and sodium dodecyl sulfate to final concentrations of 0.2 mg/ml and 0.5%, respectively, and incubation for 1 h at 50 degrees C. DNA was precipitated with isopropanol after phenol-chloroform-isoamyl alcohol extractions and RNase treated before being quantitated and analyzed by agarose gel electrophoresis. The average undegraded DNA yields obtained were 101 micrograms for Nocardia brasiliensis and 121 micrograms for N. asteroides. This DNA was suitable for restriction endonuclease digestion and PCR amplification, which are methods being applied to the characterization and diagnosis of slowly growing organisms such as Nocardia spp.
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PMID:A rapid and gentle method for isolation of genomic DNA from pathogenic Nocardia spp. 887 44


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