• Restorative Dentistry and Endodontics
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• v.22 no.1
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• pp.413-427
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• 1997

Porphyromonas endodontalis and Prevotella intermedia are black-pigmented anaerobic gram negative rods which have been isolated from infected root canals and submucous abscesses of endodontic origin. And they are associated with clinical symptoms such as pain, percussion, and foul odor. It has been reported that there are 3 serotypes according to capsule membrane in P. endodontalis and 2 DNA homology groups and 3 serotypes in P. intermedia, but there is no data available regarding genetic diversity for the species P. endodontalis and P. intermedia. The purpose of this study is to investigate genetic diversities between individual strains of P. endodontalis and P. intermedia which are indistinguishable by serotyping and biotyping using bacterial DNA restriction endonuclease analysis. 45 teeth with at least one clinical symptoms, with single canal, and with pulp necrosis were sampled. For sampling bacteria, access cavity was prepared after disinfecting tooth and its surroundings. Then the paper point was inserted to the apex of the canal, leave there for 15 seconds, and finally it was placed into PRAS Ringer's solution and PBS solution. P. endodontalis and P. intermedia were identified by biochemical test and IIF after subculturing black and brown colonies which were produced after 7 days of incubation on BAP in anaerobic chamber. P. endodontalis and P. intermedia strains were grown in BHI broth and whole genomic DNA was extracted by phenol-chloroform extraction technique and digested by restriction endonuclease, Eco RI and Pst I. The resulting DNA fragments were separated by agarose gel electrophoresis, stained with EtBr and photographed under UV light. The results were as follows : 1. In both P. endodontalis and P. intermedia, different serotypes could be found within a root canal of same patient. 2. There were obvious genetic heterogeneity within a patient and within a serotype in both P. endodontalis and P. intermedia. 3. P. endodontalis serotype c, isolated from different patients, exhibited limited genotypic diversity.

• Journal of Microbiology
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• v.42 no.2
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• pp.99-102
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• 2004

Bacteriophage PM2 has a closed circular form of double stranded DNA as a genome. This DNA from the phage is a useful source for nick-circle endonuclease assay in the fmol range. Due to difficulties in the maintenance of viral infectivity, storage conditions of the phage should be considered for the puri-fication of PM2 DNA. The proper condition for a short-term storage of less than 2 months is to keep the PM2 phage at 4$^{\circ}C$; whereas the proper condition for a long-term storage of the PM2 phage for over 2 months is to keep it under liquid nitrogen in 7.5 ％ glycerol. The optimal conditions for a high yield of phage progeny were also considered with the goal to achieve a successful PM2 DNA preparation. A MOI(Multiplicity Of Infection) of 0.03, in which the OD$\sub$600/ of the host bacteria was between 0.3 and 0.5, turned out to be optimal for the mass production of PM2 phage with a burst size of about 214. Considerations of PM2 genome size, and the concentrations and radiospecific activities of purified PM2 DNA, are required to measure the endonuclease activity in the fmol range. This study reports the proper quantitation of radioactivity and the yield of purified DNA based on these conditions.

• Korean Journal of Veterinary Research
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• v.32 no.4
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• pp.597-603
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• 1992

To elucidate the molecular genetical properties of the canine parvoviruses isolated from the diseased puppies in the regions of Kyunggi and Chungnam provinces, the replicative form (RF) DNA of four field isolates were compared with those of two attenuated vaccine strains and a reference strains of CPV by restriction endonuclease analysis (REA). REA by Hinf I showed that three CPV isolates except CPV-V15 had an identical banding pattern with two vaccine strains, one standard strain and feline panleukopenia virus (FPLV). In CPV-V15 strain the fourth fragment of DNA with 800 bp was deleted. REA by Bgl II and Pst I indicated that CPV-V15 and FPLV had a bigger second fragment than those of the other strains of CPV. Meanwhile REA by Bam HI revealed that all the field isolates and vaccine strains used in this experiment showed similar banding patterns.

• Journal of Microbiology and Biotechnology
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• v.15 no.3
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• pp.484-490
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• 2005

Human ribosomal protein S3 (rpS3), which has a DNA repair endonuclease activity, is a multifunctional protein. This protein is involved in DNA repair, translation, and apoptosis. In particular, rpS3 has a lyase activity, which cleaves the phosphodiester bond of damaged sites such as cyclobutane pyrimidine dimers and AP sites. Here, using deletion analysis, we identified that the repair endonuclease domain resides in the C-terminal region (165-243 aa) of rpS3. We also found that ectopic expression of GST-rpS3 in bacterial strain BL21 promoted the resistance of these cells to ultraviolet (UV) radiation and hydrogen peroxide ($H_{2}O_{2}$) treatment. The repair domain of rpS3 was sufficient to exhibit the resistance to UV irradiation and recover cell growth and viability, showing that the repair activity of rpS3 is responsible for the resistance to UV irradiation. Our study suggests that rpS3 is able to process DNA damage in bacteria via its repair domain, showing the resistance to genotoxic stress. This implies that rpS3-like activity could be operative in bacteria.

• Korean Journal of Microbiology
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• v.24 no.1
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• pp.18-23
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• 1986

A new type II restriction endonuclease, Bdi I, has been isolated from Brenibacterium divaricatum FERM 5948 by procedures of ammonium sulfate fractionation, DEAE-cellulose chromatography and heparin agarose chromatography. The purified Bdi I restriction endonudlease had the same cleavage patterns of Cla I whose recognition sequence is 5' ATCGAT 3'. From the result that ${\lambda}-Cla$ I DNA frahment could be cloned in pBR 322 digested with Bdi I, it has been proven that Bdi I cuts between T and C(5' AT/CGAT3') within the recognition sequence and produces 5'pCG cohesive end. The optimal temperature for the Bdi I restriction endonuclease activity was $37^{\circ}C$, and optimal salt (NaCl) concentration was 50-100 mM.

• Korean Journal of Microbiology
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• v.32 no.4
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• pp.285-290
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• 1994

About 500 bacterial and fungal strains from a wide variety of natural habitats were screened for a new type II restriction endonuclease. Among the 500 species, we selected one species that produced a new restriction endonuclease. This strain has an optimum temperature of $30^{circ}C$ for growth. Morphological, cultural, and physiological characteristics were examined for identification of the isolated strain J-482. This strain was found to belong to the genus Alcaligenes. The restriction endonuclease was named as AspJI and partially purified from Alcaligenes sp. J-482 by DEAE-Sephadex A-50 column chromatography and gel filtration. Most of other nucleases were removed by the purification steps. The AspJI has a substrate specificity to ${lambda}$ DNA, pBR322 and Adenovirus-2 DNA. For its maximal activity, the isolated enzyme requires $MgCl_2$, which should be at least 12.5 mM and it does not need any other cofactors. It is maximally active in the absence of NaCl and is completely inactivated at 100 mM NaCl. The pH and temperature optima for activity were pH 7.5 and $37^{circ}C$, respectively. The DNA fragments generated by digesting ${lambda}$ DNA, pBR322, and Adenovirus-2 DNA with AspJI were the same as that produced by AatII. This suggests that AspJI is an isoschizomer of AatII.

• Proceedings of the Zoological Society Korea Conference
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• 1995.10b
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• pp.340.1-340
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• 1995

• Bulletin of the Korean Chemical Society
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• v.20 no.1
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• pp.109-111
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• 1999

• Korean Journal of Microbiology
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• v.24 no.2
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• pp.86-90
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• 1986

The DNA methylated by Hpa II methylase was not cleaved by Sma, I, Ava I and Nae I endonucleases. This experimental data could be interpreted as strong evidences that Sma I, Ava I and Nae I methylases which yet to be isolated would methylate on the inmost cytosine nucleotide within their hexameric recognition sequences. The facts that Sma I, Ava I and Nae I endonucleases can not cleave the DNA methylated by Hpa II methylase are the valuable informations for protecting DNAs upon cleavage reactions by Sma I, Ava I and NAe I endonucleases especially for cDNA insertion experiments into vector DNAs using Sma I, Ava I and Nae I oligonucleotide linkers. In the case of Xma I endonuclease, partially cleaved DNA fragments were observed although the reaction rate was greatly decreased. This result implies that the methylation site of Xma I methylase which yet to be isolated would not be the same as that of Hpa II methylase in Xma I sequence.

• BMB Reports
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• v.39 no.2
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• pp.140-144
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• 2006

A deoxyriboendonuclease has been purified to near homogeneity from a fast growing mycobacterium species, M. smegmatis and characterized to some extent. The size of enzyme is about 43 kDa as determined by a denaturing gel analysis. It shows optimum activity at $32^{\circ}C$ in Tris-HCl buffer (pH 7.2) containing 2.5 mM of $MgCl_2$. Both EDTA and $K^+$ but not $Na^+$ inhibit its activity. Evidences show that the enzyme is not a restriction endonuclease but catalyzes the endonucleolytic cleavage of both the double- as well as the single-strand DNA non-specifically. It has been shown that the cleavage by this enzyme generates DNA fragments carrying phosphate groups at 5' ends and hydroxyl group at the 3' ends, respectively. Analysis reveals that no endonuclease having size and property identical to our deoxyriboendonuclease had been purified from M. smegmatis before. The property of our enzymes closely matches with the deoxyriboendonucleases purified from diverse sources including bacteria.