• Molecules and Cells
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• v.23 no.2
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• pp.239-245
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• 2007

DnaK is a major antigen in Streptococcus pneumoniae, and is induced by a minor shift in temperature (30 to $37^{\circ}C$) but not by ethanol shock. Although HrcA in the presence of $Ca^{{+}{+}}$ represses the expression of both groEL and hrcA, the control of transcription of the dnaK operon is not completely understood. In this study, the dnaK operon of S. pneumoniae (5' hrcA-grpE-dnaK-dnaJ) was cloned and analyzed. It contains large intergenic regions in grpE/dnaK and dnaK/dnaJ. Pulse labeling with [$^{35}S$]-methionine and immunoblot analyses revealed the presence of higher levels of DnaK than of HrcA even in the presence of $Ca^{{+}{+}}$ after heat shock suggesting that $Ca^{{+}{+}}$ differentially regulates the heat shock responses of hrcA and dnaK. By blocking de novo mRNA synthesis with rifampin it was shown that neither the hrcA nor the groEL transcripts were stabilized by heat shock even though dnaK transcripts were stabilized. We conclude that S. pneumoniae uses fine regulation of the transcription of the individual genes of the tetracistronic dnaK operon to cope with the various stresses experienced during infections.

• Journal of the Korea Computer Graphics Society
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• v.2 no.2
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• pp.61-68
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• 1996

In this paper we propose a new visualization technique to characterize qualitative information of a large DNA sequence. While a long DNA sequence has huge information, it is not easy to obtain genetic information from the DNA sequence. We transform DNA sequences into a polygon to compute their homology in image domain rather than text domain. Our program visualizes DNA sequences with colored random walk plots and simplify them k-convex hulls. A random walk plot represents DNA sequence as a curve in a plane. A k-convex hull simplifies a random work plot by removing some parts of its insignificant information. This technique gives a biologist an insight to detect and classify DNA sequences with easy. Experiments with real genome data proves our approach gives a good visual forms for long DNA sequences for homology analysis.

• Journal of Microbiology and Biotechnology
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• v.17 no.6
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• pp.945-951
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• 2007

DNA-DNA hybridization has been established as an important technology in bacterial species taxonomy and phylogenetic analysis. In this study, we analyzed how the efficiency with which the genomic DNA from one species hybridizes to the genomic DNA of another species (DNA-DNA hybridization) in microarray analysis relates to the similarity between two genomes. We found that the predicted DNA-DNA hybridization based on genome sequence similarity correlated well with the experimentally determined microarray hybridization. Between closely related strains, significant numbers of highly divergent genes (>55% identity) and/or the accumulation of mismatches between conserved genes lowered the DNA-DNA hybridization signal, and this reduced the hybridization signals to below 70% for even bacterial strains with over 97% 16S rRNA gene identity. In addition, our results also suggest that a DNA-DNA hybridization signal intensity of over 40% indicates that two genomes at least shared 30% conserved genes (>60% gene identity). This study may expand our knowledge of DNA-DNA hybridization based on genomic sequence similarity comparison and further provide insights for bacterial phylogeny analyses.

• Journal of Radiation Protection and Research
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• v.33 no.2
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• pp.53-59
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• 2008

We observed DNA damages as a function of mean absorbed dose to identify the indirect effect of high-energy radiation such as x-ray. Monolayer films of lyophilized pGEM-3Zf(-) plasmid DNA deposited on tantalum foils were exposed to Al $K{\alpha}$ X-ray (1.5 keV) for 0, 3, 7 and 10 min, respectively, in a condition of ultrahigh vacuum state. We compared DNA damages by X-ray irradiation with those by 3 eV electron irradiation. X-ray photons produced low-energy electrons (mainly below 20 eV) from the tantalum foils and DNA damage was induced chiefly by these electrons. For electron beam irradiation, DNA damage was directly caused by 3 eV electrons. Irradiated DNA was analyzed by agarose gel electrophoresis and quantified by ImagaQuant program. The quantities of remained supercoiled DNA after irradiation were linearly decreased as a function of mean absorbed dose. On the other hand, the yields of nicked circular (single strand break, SSB) and interduplex crosslinked form 1 DNA were linearly increased as a function of mean absorbed dose. From this study, it was confirmed that DNA damage was also induced by low energy electrons ($0{\sim}10\;eV$) even below threshold energies for the ionization of DNA.

• The Korean Journal of Zoology
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• v.18 no.1
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• pp.41-49
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• 1975

Dose response and time dependence of DNA repair synthesis were investigated to determine the possible relationship between DNA repair synthesis and chromosome exchanges in $\\gamma$-ray irradiated BHK-21 and KB cell lines. DNA repair synthesis induced by $\\gamma$-ray was dose dependent up to 5kR, then leveling off occurred until 50 kR was reached. Time dependence of DNA repair synthesis was continued for up to 1$\\sim$2 hours after irradiation although the initial dose responses were cell line specific. Chromosome exchanges induced by $\\gamma$-ray showed different radiosensitivities in these cell lines and did not show a correlation with the DNA repair synthesis.

• Bulletin of the Korean Chemical Society
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• v.26 no.3
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• pp.379-383
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• 2005

This research aims to develop DNA chip array without an indicator. We fabricated microelectrode array by photolithography technology. Several DNA probes were immobilized on an electrode. Then, indicator-free target DNA was hybridized by an electrical force and measured electrochemically. Cyclic-voltammograms (CVs) showed a difference between DNA probe and mismatched DNA in an anodic peak. Immobilization of probe DNA and hybridization of target DNA could be confirmed by fluorescent. This indicator-free DNA chip microarray resulted in the sequence-specific detection of the target DNA quantitatively ranging from $10^{-18}\;M\;to\;10^{-5}$ M in the buffer solution. This indicator-free DNA chip resulted in a sequence-specific detection of the target DNA.

• Journal of the Korean Magnetic Resonance Society
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• v.20 no.3
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• pp.66-70
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• 2016

The replication protein A (RPA), is a heterotrimer with 70, 32 and 14 kDa subunits and plays a crucial role in DNA replication, recombination, and repair. The largest subunit, RPA70, binds to single-stranded DNA (ssDNA) and mediates interactions with many cellular and viral proteins. In this study, we performed nuclear magnetic resonance experiments on the complex of the DNA binding domain A of human RPA70 (RPA70A) with ssDNA, d(CCCCC), at various temperatures, to understand the temperature dependency of ssDNA binding affinity of RPA70A. Essential residues for ssDNA binding were conserved while less essential parts were changed with the temperature. Our results provide valuable insights into the molecular mechanism of the ssDNA binding of human RPA.

• KIEE International Transactions on Electrophysics and Applications
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• v.4C no.4
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• pp.133-136
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• 2004

This research aims to develop a DNA chip array without an indicator. We fabricated a microelectrode array through photolithography technology. Several DNA probes were immobilized on an electrode. Then, target DNA was hybridized and measured electrochemically. Cyclic-voltammograms (CVs) showed a difference between the DNA probe and mismatched DNA in an anodic peak. This indicator-free DNA chip resulted in a sequence-specific detection of the target DNA.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.20 no.6
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• pp.569-572
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• 1987

The DNA damage by linoleic acid hydroperoxide (LHPO) was investigated in a DNA-LHPO system at $37^{\circ}C$ to elucidate the DNA damage mechanism by lipid peroxidation products. LHPO shelved a great DNA damage with the increase of its concentrations. DNA was completely damaged in a LHPO-DNA(weight ratio, 2:3) system after incubation for 2 days. The degree of DNA ,damage by LHPO was greated than that of linoleic acid. In the quantitative analysis of DNA damage, the decreasing ratio of DNA content was $60\%$ in $84{\mu}g$ LHPO system incubated for 1 day compared to the control solution marked $30\%$. There were no participation of active oxygens on the DNA damage by LHPO.

• Proceedings of the Korean Vacuum Society Conference
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• 2016.02a
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• pp.140.1-140.1
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• 2016

We have measured DNA translocation through a nanocapillary functionalized with probe DNA. These DNA-functionalized nanocapillaries selectively facilitate the translocation of target ssDNAs that are complementary to the probe ssDNAs. In addition, translocation of the complementary target ssDNA exhibits two tendencies to translocation speed, such as fast and slow translocation, whereas that of non-complementary target ssDNA yields only one tendency, fast translocation. These observations suggest that the complementary and non-complementary target ssDNAs may be discriminated due to different interaction strengths between target and probe ssDNAs. The temperature dependence measurements of DNA translocation show that slow translocation events are ascribed to the complementary interaction between probe and target ssDNA. This confirms that their dwell time is dependent on the base-pair binding strength. These results demonstrate that mere single-base different target DNA can be selectively detectable by using the probe DNA-functionalized nanocapillaries.