Joon Kim

Sookmyung Women's University, Seoul, Seoul, South Korea

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Publications (63)215.13 Total impact

  • Article: Probing the local conformational change of alpha1-antitrypsin.
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    ABSTRACT: The native form of serpins (serine protease inhibitors) is a metastable conformation, which converts into a more stable form upon complex formation with a target protease. It has been suggested that movement of helix-F (hF) and the following loop connecting to strand 3 of beta-sheet A (thFs3A) is critical for such conformational change. Despite many speculations inferred from analysis of the serpin structure itself, direct experimental evidence for the mobilization of hF/thFs3A during the inhibition process is lacking. To probe the mechanistic role of hF and thFs3A during protease inhibition, a disulfide bond was engineered in alpha(1)-antitrypsin, which would lock the displacement of thFs3A from beta-sheet A. We measured the inhibitory activity of each disulfide-locked mutant and its heat stability against loop-sheet polymerization. Presence of a disulfide between thFs3A and s5A but not between thFs3A and s3A caused loss of the inhibitory activity, suggesting that displacement of hF/thFs3A from strand 5A but not from strand 3A is required during the inhibition process. While showing little influence on the inhibitory activity, the disulfide between thFs3A and s3A retarded loop-sheet polymerization significantly. This successful protein engineering of alpha(1)-antitrypsin is expected to be of value in clinical applications. Based on our current studies, we propose that the reactive-site loop of a serpin glides through between s5A and thFs3A for the full insertion into beta-sheet A while a substantial portion of the interactions between hF and s3A is kept intact.
    Protein Science 10/2007; 16(9):1842-50. · 2.80 Impact Factor
  • Article: Low-dose of ionizing radiation enhances cell proliferation via transient ERK1/2 and p38 activation in normal human lung fibroblasts.
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    ABSTRACT: This study shows the human cellular responses and the mechanism of low-dose ionizing radiation in CCD 18 Lu cells, which are derived from normal human lung fibroblasts. Cell proliferation and viability assay were measured for the cells following gamma-irradiation using trypan blue, BrdU incorporation, and Wst-1 assay. We also examined genotoxicity using a micronuclei formation assay. The activation of the MAPKs pathway was determined by Western blot analysis, and the siRNA system was used to inhibit the expression of ERK1/2 and p38. We found that 0.05 Gy of ionizing radiation stimulated cell proliferation and did not change Micronuclei frequencies. In addition, 0.05 Gy of ionizing radiation activated ERK1/2 and p38, but did not activate JNK1/2 in cells. A specific ERK1/2 inhibitor, U0126, decreased the phosphorylation of ERK1/2 proteins induced by 0.05 Gy of ionizing radiation, and a similar suppressive effect was observed with a p38 inhibitor, PD169316. Suppression of ERK1/2 and p38 phosphorylation with these inhibitors decreased cell proliferation, which was stimulated by 0.05 Gy of ionizing radiation. Furthermore, downregulation of ERK1/2 and p38 expression using siRNA blocked the cell proliferation that had been increased by 0.05 Gy of ionizing radiation. These results suggest that 0.05 Gy of ionizing radiation enhances cell proliferation through the activation of ERK1/2 and p38 in normal human lung fibroblasts.
    Journal of Radiation Research 10/2007; 48(5):407-15. · 1.68 Impact Factor
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    Article: Proteomic analysis of gamma-butyrolactone-treated mouse thalamus reveals dysregulated proteins upon absence seizure.
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    ABSTRACT: Absence seizure has been of interest because the symptom is related to sensory processing. However, the mechanism that causes the disease is not understood yet. To better understand the molecular mechanism related to the disease progress at protein level, we performed proteomic studies using the thalamus of mice for which absence seizure was induced by gamma-butyrolactone (GBL). Differential proteome expression between GBL-treated mice and control mice was examined by fluorescence 2D difference gel electrophoresis (DIGE) at three different time points (5, 10, and 30 min) after GBL-administration. We identified 16 proteins differentially expressed by >1.4-fold at any of the three time points. All proteins besides the serine protease inhibitor EIA were down-regulated in absence seizure-induced mice. The down-regulated proteins can be classified into five groups by their biological functions: cytoskeleton rearrangement, neuroprotection, neurotransmitter secretion, calcium binding, and metabolism. The maximum level of change was reached by 10 min after GBL-treatment, with the expression level returning back to the original at 30 min when mice were awakened from absence seizure thereby demonstrating the proteomic response is reversible. Our results suggest that absence seizures are associated with restricted functional sets of proteins, whose down-regulation may interfere with general function of neuronal cells.
    Journal of Neurochemistry 09/2007; 102(3):646-56. · 4.06 Impact Factor
  • Article: A new method for the construction of a mutant library with a predictable occurrence rate using Poisson distribution.
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    ABSTRACT: A yeast transcriptional activator, Gcn4p, induces the expression of genes that are involved in amino acid and purine biosynthetic pathways under amino acid starvation. Gcn4p has an acidic activation domain in the central region and a bZIP domain in the C-terminus that is divided into the DNA-binding motif and dimerization leucine zipper motif. In order to identify amino acids in the DNA-binding motif of Gcn4p which are involved in transcriptional activation, we constructed mutant libraries in the DNA-binding motif through an innovative application of random mutagenesis. Mutant library made by oligonucleotides which were mutated randomly using the Poisson distribution showed that the actual mutation frequency was in good agreement with expected values. This method could save the time and effort to create a mutant library with a predictable mutation frequency. Based on the studies using the mutant libraries constructed by the new method, the specific residues of the DNA-binding domain in Gcn4p appear to be involved in the transcriptional activities on a conserved binding site.
    Journal of Microbiological Methods 07/2007; 69(3):442-50. · 2.09 Impact Factor
  • Article: Rpn13p and Rpn14p are involved in the recognition of ubiquitinated Gcn4p by the 26S proteasome.
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    ABSTRACT: The 26S proteasome, composed of the 20S core and 19S regulatory complexes, is important for the turnover of polyubiquitinated proteins. Each subunit of the complex plays a special role in proteolytic function, including substrate recruitment, deubiquitination, and structural contribution. To assess the function of some non-essential subunits in the 26S proteasome, we isolated the 26S proteasome from deletion strains of RPN13 and RPN14 using TAP affinity purification. The stability of Gcn4p and the accumulation of ubiquitinated Gcn4p were significantly increased, but the affinity in the recognition of proteasome was decreased. In addition, the subcomplexes of the isolated 26S proteasomes from deletion mutants were less stable than that of the wild type. Taken together, our findings indicate that Rpn13p and Rpn14p are involved in the efficient recognition of 26S proteasome for the proteolysis of ubiquitinated Gcn4p.
    FEBS Letters 06/2007; 581(13):2567-73. · 3.54 Impact Factor
  • Article: Human PEP-1-ribosomal protein S3 protects against UV-induced skin cell death.
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    ABSTRACT: The consequences of ultraviolet (UV) exposure are implicated in skin aging and cell death. The ribosomal protein S3 (rpS3) is one of the major proteins by which cells counteract the deleterious effects of UV and it plays a role in the repair of damaged DNA. In the present study, we investigated the protective effects of PEP-1-rpS3 fusion protein after UV-induced cell injury. A human rpS3 gene was fused with PEP-1 peptide in a bacterial expression vector to produce a genetic in-frame PEP-1-rpS3 fusion protein. The expressed and purified fusion proteins were efficiently transduced into skin cells in a time- and dose-dependent manner. Once inside the cells, transduced PEP-1-rpS3 fusion protein was stable for 48h. We showed that transduced PEP-1-rpS3 fusion protein increased cell viability and dramatically reduced DNA lesions in the UV exposed skin cells. Immunohistochemical analysis revealed that PEP-1-rpS3 fusion protein efficiently penetrated the epidermis as well as the dermis of the subcutaneous layer when sprayed on animal skin. These results suggest that PEP-1-rpS3 fusion protein can be used in protein therapy for various disorders related to UV, including skin aging and cancer.
    FEBS Letters 01/2007; 580(30):6755-62. · 3.54 Impact Factor
  • Article: Reduction of invasion in human fibrosarcoma cells by ribosomal protein S3 in conjunction with Nm23-H1 and ERK.
    Sang Hwa Kim, Joon Kim
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    ABSTRACT: RpS3 is a component of the 40S ribosomal subunit of eukaryotes and also plays a role as a base damage endonuclease. Nm23-H1 encodes nucleoside diphosphate kinase A and acts as a suppressor of metastasis in certain human tumors. RpS3 interacted with nm23-H1, and the two proteins were colocalized in the cell periphery and cytoplasm. The 190th leucine of rpS3, and the 118th histidine and the 120th serine of nm23-H1 play key roles in the interaction of two proteins, respectively. The expression of rpS3 reduced the secretion of MMP-9 and the invasive potential in HT1080 cells. Additionally, the phosphorylated ERK was reduced by the expression of rpS3. In MCF7 cells, where the ERK pathway is inactivated and MMPs are not secreted and the ERK pathway can be activated by PMA, the PMA-induced ERK phosphorylation was reduced by the expression of rpS3. However, the L190A mutant of rpS3, which did not interact with nm23-H1, did not inhibit the invasive potential, the secretion of MMP-9, and the activation of the ERK pathway in HT1080 cells and PMA-activated MCF7 cells. These results suggest that rpS3 inhibits invasion via blocking the ERK pathway and MMP-9 secretion; the results also suggest that the interaction of rpS3 and nm23-H1 appears to be critical in this inhibition.
    Biochimica et Biophysica Acta 09/2006; 1763(8):823-32. · 4.66 Impact Factor
  • Article: Negative regulation of hepatitis B virus replication by cellular Hsp40/DnaJ proteins through destabilization of viral core and X proteins.
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    ABSTRACT: The hepatitis B virus core protein consists of an amino-terminal capsid-assembly domain and a carboxyl-terminal RNA-binding domain. By using the yeast two-hybrid system, two Hsp40/DnaJ chaperone-family proteins, Hdj1 and hTid1, that interact with the carboxyl-terminal region (aa 94-185) of the core protein were identified. Hdj1 is the prototype member of the family and hTid1 is the human homologue of the Drosophila tumour-suppressor protein Tid56. Binding of the viral core protein with the Hsp40 proteins was confirmed by affinity chromatography and immunoprecipitation of transiently expressed proteins. Moreover, in a sucrose gradient, the precursor form of hTid1 co-sedimented with capsid-like particles composed of the full-length core protein. Unlike the general perception of the role of the cellular chaperone proteins in assisting viral protein folding and thus enhancing virus replication, ectopic expression of Hdj1 and hTid1 suppressed replication of HBV in transfected human hepatoma cells. Conversely, RNA interference-mediated knock-down of hTid1 resulted in increased HBV replication. It was found that both Hsp40 proteins specifically accelerated degradation of the viral core and HBx proteins. Our results suggest that the cellular chaperones, through destabilization of viral proteins, exert inhibitory functions on virus replication and hence may play suppressive roles in hepatocellular carcinoma.
    Journal of General Virology 08/2006; 87(Pt 7):1883-91. · 3.36 Impact Factor
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    Article: Genomic structure and transcriptional studies on the mouse ribosomal protein S3 gene: expression of U15 small nucleolar RNA.
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    ABSTRACT: Ribosomal protein S3 (rpS3) is a multifunctional ribosomal protein (RP) which is known to function as a DNA repair endonuclease as well as an RP. Recently, it was reported that rpS3 is involved in apoptosis. We identified the complete 4760 base pair genomic structure of the mouse rpS3 gene, which is composed of 7 exons and 6 introns. Promoter study revealed that transcription of the mouse rpS3 gene started at two C residues embedded in the 5'-terminal oligopyrimidine tract (5'-TOP); this was then compared with the human counterpart. Functional U15 small nucleolar RNAs (snoRNAs) were expressed from the first and the fifth introns. About 300 base pairs (bps) upstream of the 5'-untranslated region (5'-UTR) of the mouse rpS3 gene was sufficient to show maximum transcription activity. This report shows the conservation of the genomic structure of the rpS3 gene in vertebrates and characteristics of its promoter similar to those of promoters of other mammalian RPs.
    Gene 04/2006; 368:12-20. · 2.34 Impact Factor
  • Article: Immunohistochemical studies of human ribosomal protein S3 (rpS3).
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    ABSTRACT: The human ribosomal protein S3 (rpS3) was expressed in E. coli using the pET-15b vector and the monoclonal antibodies (mAbs) were produced and characterized. A total of five hybridoma cell lines were established and the antibodies recognized a single band of molecular weight of 33 kDa on immunoblot with purified rpS3. When the purified rpS3 was incubated with the mAbs, the UV endonuclease activity of rpS3 was inhibited up to a maximum of 49%. The binding affinity of mAbs to rpS3 determined by using a biosensor technology showed that they have similar binding affinities. Using the anti-rpS3 antibodies as probes, we investigated the cross-reactivities of various other mammalian brain tissues and cell lines, including human. The immunoreactive bands on Western blots appeared to be the same molecular mass of 33 kDa in all animal species tested. They also appear to be extensively cross-reactive among different organs in rat. These results demonstrated that only one type of immunologically similar rpS3 protein is present in all of the mammalian brain tissues including human. Furthermore, these antibodies were successfully applied in immunohistochemistry in order to detect rpS3 in the gerbil brain tissues. Among the various regions in the brain tissues, the rpS3 positive neurons were predominantly observed in the ependymal cells, hippocampus and stantia nigra pars compacta. The different distributions of rpS3 in brain tissues reply that rpS3 protein may play an important second function in the neuronal cells.
    Journal of biochemistry and molecular biology 04/2006; 39(2):208-15. · 2.02 Impact Factor
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    Article: Interaction of Hsp90 with ribosomal proteins protects from ubiquitination and proteasome-dependent degradation.
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    ABSTRACT: Heat-shock protein 90 (Hsp90) is a molecular chaperone that plays a key role in the conformational maturation of various transcription factors and protein kinases in signal transduction. Multifunctional ribosomal protein S3 (rpS3), a component of the ribosomal small subunit, is involved in DNA repair and apoptosis. Our data show that Hsp90 binds directly to rpS3 and the functional consequence of Hsp90-rpS3 interaction results in the prevention of the ubiquitination and the proteasome-dependent degradation of rpS3, subsequently retaining the function and the biogenesis of the ribosome. Interference of Hsp90 activity by Hsp90 inhibitors appears to dissociate rpS3 from Hsp90, associate the protein with Hsp70, and induce the degradation of free forms of rpS3. Furthermore, ribosomal protein S6 (rpS6) also interacted with Hsp90 and exhibited a similar effect upon treatment with Hsp90 inhibitors. Therefore, we conclude that Hsp90 regulates the function of ribosomes by maintaining the stability of 40S ribosomal proteins such as rpS3 and rpS6.
    Molecular Biology of the Cell 03/2006; 17(2):824-33. · 4.94 Impact Factor
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    Article: Gamma-irradiation and doxorubicin treatment of normal human cells cause cell cycle arrest via different pathways.
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    ABSTRACT: Ionizing radiation and doxorubicin both produce oxidative damage and double-strand breaks in DNA. Double-strand breaks and oxidative damage are highly toxic and cause cell cycle arrest, provoking DNA repair and apoptosis in cancer cell lines. To investigate the response of normal human cells to agents causing oxidative damage, we monitored alterations in gene expression in F65 normal human fibroblasts. Treatment with g-irradiation and doxorubicin altered the expression of 23 and 68 known genes, respectively, with no genes in common. Both agents altered the expression of genes involved in cell cycle arrest, and arrested the treated cells in G2/M phase 12 h after treatment. 24 h after g-irradiation, the percentage of G1 cells increased, whereas after doxorubicin treatment the percentage of G2/M cells remained constant for 24 h. Our results suggest that F65 cells respond differently to g-irradiation- and doxorubicin-induced DNA damage, probably using entirely different biochemical pathways.
    Molecules and Cells 01/2006; 20(3):331-8. · 2.18 Impact Factor
  • Article: Erk phosphorylates threonine 42 residue of ribosomal protein S3.
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    ABSTRACT: The ribosomal protein S3 (rpS3) is involved in ribosome biogenesis as a member of ribosomal small subunit and also plays a role in the repair of damaged DNA. Extracellular signal-regulated kinase (Erk), a MAP kinase, is known to play important roles in the regulation of cell growth, differentiation, and apoptosis. In this study, the sequence analysis of rpS3 protein revealed that this protein has a putative FXFP motif which is believed to be an Erk binding site. Indeed, the motif was demonstrated as an Erk binding site by co-immunoprecipitation. In addition to this, it was revealed that Erk specifically phosphorylated Thr 42 residue of rpS3 in vitro and in vivo using the various mutants of rpS3. Taken together, rpS3 appears to be phosphorylated by activated Erk in proliferating cells, resulting in the decreased interaction between two proteins.
    Biochemical and Biophysical Research Communications 08/2005; 333(1):110-5. · 2.48 Impact Factor
  • Article: Characterization of a wide range base-damage-endonuclease activity of mammalian rpS3.
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    ABSTRACT: Mammalian rpS3, a ribosomal protein S3 with a DNA repair endonuclease activity, nicks heavily UV-irradiated DNA and DNA containing AP sites. RpS3 calls for a novel endonucleolytic activity on AP sites generated from pyrimidine dimers by T4 pyrimidine dimer glycosylase activity. This study revealed that rpS3 cleaves the lesions including AP sites, thymine glycols, and other UV damaged lesions such as pyrimidine dimers. This enzyme does not have a glycosylase activity as predicted from its amino acid sequence. However, it has an endonuclease activity on DNA containing thymine glycol, which is exactly overlapped with UV-irradiated or AP DNAs, indicating that rpS3 cleaves phosphodiester bonds of DNAs containing altered bases with broad specificity acting as a base-damage-endonuclease. RpS3 cleaves supercoiled UV damaged DNA more efficiently than the relaxed counterpart, and the endonuclease activity of rpS3 was inhibited by MgCl2 on AP DNA but not on UV-irradiated DNA.
    Biochemical and Biophysical Research Communications 04/2005; 328(4):962-7. · 2.48 Impact Factor
  • Article: Kinetic mechanism of protease inhibition by alpha1-antitrypsin.
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    ABSTRACT: The native form of serine protease inhibitor (serpin) is kinetically trapped in a metastable state. Metastability in these proteins is critical to inhibit target protease by forming a stable covalent complex. Despite recent determination of the crystal structures of a Michaelis protease-serpin complex as well as a stable covalent complex, details on the kinetic mechanism remain unsolved. In this report, we examined the reaction mechanism of alpha1-antitrypsin toward elastase by a combination of stopped-flow experiments via fluorescence resonance energy transfer and rapid-quench studies. The results suggest a non-covalent complex intermediate other than Michaelis complex as an intermediate before the cleavage of P1-P1' scissile bond, whose formation is the rate-determining step of the overall reaction. This rate-limiting step represents rearrangement of the reactive site loop, and is regulated by a salt bridge between E354 and R196. The ionic interaction is unique to alpha1-antitrypsin, which suggests that protease inhibition mechanisms are varied among serpins.
    Biochemical and Biophysical Research Communications 11/2004; 323(2):409-15. · 2.48 Impact Factor
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    Article: Biochemical quantitation of PM2 phage DNA as a substrate for endonuclease assay.
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    ABSTRACT: 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 purification of PM2 DNA. The proper condition for a short-term storage of less than 2 months is to keep the PM2 phage at 4 degrees 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 OD600 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.
    The Journal of Microbiology 07/2004; 42(2):99-102. · 1.10 Impact Factor
  • Article: RpS3, a DNA repair endonuclease and ribosomal protein, is involved in apoptosis.
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    ABSTRACT: It is known that mammalian rpS3 functions as a DNA repair endonuclease and ribosomal protein S3. It was also observed that several ribosomal proteins or DNA repair enzymes are related to apoptosis. We report here a third function of rpS3, induction of apoptosis. The localization of green fluorescent protein (GFP)-rpS3 is changed to the nuclear membrane when lymphocytic cells undergo rpS3-induced apoptosis. Transient expression of GFP-rpS3 activates caspase-8/caspase-3 and sensitizes cytokine-induced apoptosis. Deletion analysis reveals that the two functions of rpS3, DNA repair and apoptosis, use independent functional domains.
    FEBS Letters 03/2004; 560(1-3):81-5. · 3.54 Impact Factor
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    Article: Hepatitis B virus core protein stimulates the proteasome-mediated degradation of viral X protein.
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    ABSTRACT: Hepatitis B virus (HBV) X protein (HBx) plays an essential role in viral replication and in the development of hepatocellular carcinoma. HBx has the ability to transactivate the expression of all HBV proteins, including the viral core protein HBc. Consistent with its regulatory role, HBx is relatively unstable and is present at low levels in the cell. We report here that the level of HBx was significantly reduced by the coexpression of HBc in cultured human hepatoma cells, whereas the level of HBx mRNA was unaffected. The repression of HBx by HBc was relieved by treating cells with the proteasome inhibitor MG132, indicating that HBc acts by stimulating the proteasome-mediated degradation of HBx. Moreover, the inhibitory effect of HBc was specific to HBx and did not affect other proteins, including p53, a known target of the proteasome. Although no direct physical interaction between HBc and HBx could be demonstrated, mutational analysis indicated that the C-terminal half of HBc is responsible for its inhibitory effect. These results suggest that HBc functions as a novel regulator of the HBV life cycle and of hepatocellular carcinogenesis through control of the HBx level via an inhibitory feedback type of mechanism.
    Journal of Virology 08/2003; 77(13):7166-73. · 5.40 Impact Factor
  • Article: New preparation of PM2 phage DNA and an endonuclease assay for a single-strand break.
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    ABSTRACT: PM2 is a bacteriophage which has closed circular double-stranded DNA as a genome, which is the sole source for endonuclease assay for a single strand break in the fmol range. Therefore, it is important to isolate PM2 DNA with low control nicks for the endonuclease assay. Usually, the isolation method of phage DNA is to use ultracentrifugation which takes at least 4 days. In this report, a fast and effective method which takes only 2 days was developed to purify DNA using polyethylene glycol (PEG) 8000 and the yields of phage DNA isolated by these two methods were compared. The method using PEG 8000 increased the yield of PM2 DNA from 31.2% to 45.2%, and decreased the nick from 17.1% to 13.1%. Recently, the complete PM2 DNA genome sequence of 10,079 bp was published. The exact number of nucleotides of PM2 DNA is important for the correct enzyme assay which measures nicks generated by an endonuclease. The correct calculation of endonuclease activity of rpS3 for nick-circle assay was performed to measure single-strand breaks in this report.
    Antonie van Leeuwenhoek 02/2003; 83(3):223-9. · 2.09 Impact Factor
  • Article: Critical chain dynamics near the interdigitated–noninterdigitated chain configurational phase transition in decylammonium chloride
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    ABSTRACT: We have carried out a 1H nuclear magnetic resonance line shape analysis near the irreversible interdigitated-to-noninterdigitated chain configurational phase transition in decylammonium chloride (C10H21NH3Cl), a model biomembrane. The splitting parameter corresponding to the nematic order of the hydrocarbon chain shows a two-dimensional Ising behavior and indicates a chain defect motion in addition to the chain reorientational motion. The origin of the low-frequency critical fluctuation is attributed to a critical slowing down of the collective gear-like reorientation of the rigid hydrocarbon chain. © 2002 American Institute of Physics.
    The Journal of Chemical Physics 10/2002; 117(17):8004-8007. · 3.33 Impact Factor

Institutions

  • 2012
    • Sookmyung Women's University
      Seoul, Seoul, South Korea
  • 2007–2012
    • Radiation Health Research Institute
      Seoul, Seoul, South Korea
  • 2006–2012
    • Hallym University
      • College of Medicine
      Seoul, Seoul, South Korea
  • 2002–2012
    • Korea University
      Seoul, Seoul, South Korea
  • 2004–2010
    • Korea Institute of Science and Technology
      Seoul, Seoul, South Korea
  • 2008
    • Pusan National University
      • Department of Biological Sciences
      Pusan, Busan, South Korea