• 한국진공학회:학술대회논문집
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• 한국진공학회 2013년도 제45회 하계 정기학술대회 초록집
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• pp.155.1-155.1
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• 2013

The goals of this study are to elucidate the plasma effects on DNA molecules to apply some plasma based applications and also to find out the mechanisms of plasma-induced DNA damage in biomolecule. Nonthermal atmospheric pressure plasma has much potential for medical, agricultural and food applications for the future. The atmospheric pressure plasma jet (APPJ) contains radicals, charged particles, low energy electrons, excited molecules and UV light. It has been started doing experiments using APPJ at the early 21th. And some recent results showed that APPJ has a possibility to apply to new fields like mentioned above. But it is kind of at the very early stages of plasma based application. It is definitely necessary much of theoretical and experimental studies to further understanding to use nonthermal atmospheric pressure plasma in biomedical, agriculture and food parts. Here we introduce a new experimental system to study plasma effects on biomolecules. And we will show some recent results of LEE-induced DNA damage using electron irradiation apparatus under ultra-high vacuum.

• International Journal of Oral Biology
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• 제33권4호
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• pp.149-154
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• 2008

Porphyromonas gingivalis, a major periodontal pathogen, has been implicated in the initiation and progression of periodontal disease. Endothelial dysfunction (Editor note: Aberrant and dysfunction are somewhat redundant. The authors may want to choose one or the other.) contributes to chronic periodontal inflammation. Using cDNA-representational difference analysis, we found that P.gingivalis lipopolysaccharide differentially induces a number of genes in human microvascular endothelial cells. Among these upregulated genes, we focused on intercellular adhesion molecule-1 (VCAM-1), which is crucial for leukocyte recruitment during vascular inflammation. P. gingivalis LPS significantly increased the expression of vascular cell adhesion molecule-1 (VCAM-1) as well as ICAM-1. Promoter assays revealed that the transcription of these cell adhesion molecules was mainly regulated by nuclear factor-${\kappa}B$ (NF-${\kappa}B$) in endothelial cells. Furthermore, P. gingivalis LPS significantly increased leukocyte adhesiveness to microvascular endothelial cells and to aortic endothelium. Taken together, our results demonstrate that P. gingivalis LPS activates microvascular endothelial cells through NF-${\kappa}B$-dependent expression of cell adhesion molecules.

• Journal of Industrial and Engineering Chemistry
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• 제68권
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• pp.79-86
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• 2018

Although the intrinsic characteristics of DNA molecules and carbon nanotubes (CNT) are well known, fabrication methods and physical characteristics of CNT-embedded DNA thin films are rarely investigated. We report the construction and characterization of carboxyl (-COOH) group-modified multi-walled carbon nanotube (MWCNT-COOH)-embedded DNA and cetyltrimethyl-ammonium chloride-modified DNA (DNA-CTMA) composite thin films. Here, we examine the structural, compositional, chemical, spectroscopic, and electrical characteristics of DNA and DNA-CTMA thin films consisting of various concentrations of MWCNT-COOH. The MWCNT-COOH-embedded DNA and DNA-CTMA composite thin films may offer a platform for developing novel optoelectronics, energy harvesting, and sensing applications in physical, chemical, and biological sciences.

• Molecules and Cells
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• 제45권1호
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• pp.33-40
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• 2022

The various DNA-protein interactions associated with the expression of genetic information involve double-stranded DNA (dsDNA) bending. Due to the importance of the formation of the dsDNA bending structure, dsDNA bending properties have long been investigated in the biophysics field. Conventionally, DNA bendability is characterized by innate averaging data from bulk experiments. The advent of single-molecule methods, such as atomic force microscopy, optical and magnetic tweezers, tethered particle motion, and single-molecule fluorescence resonance energy transfer measurement, has provided valuable tools to investigate not only the static structures but also the dynamic properties of bent dsDNA. Here, we reviewed the single-molecule methods that have been used for investigating dsDNA bendability and new findings related to dsDNA bending. Single-molecule approaches are promising tools for revealing the unknown properties of dsDNA related to its bending, particularly in cells.

• Molecules and Cells
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• 제19권2호
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• pp.167-179
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• 2005

The cells of metazoans respond to DNA damage by either arresting their cell cycle in order to repair the DNA, or by undergoing apoptosis. This response is highly conserved across species, and many of the genes involved in this DNA damage response have been shown to be inactivated in human cancers. This suggests the importance of DNA damage response with regard to the prevention of cancer. The DNA damage checkpoint responses vary greatly depending on the developmental context, cell type, gene expression profile, and the degree and nature of the DNA lesions. More valuable information can be obtained from studies utilizing whole organisms in which the molecular basis of development has been well established, such as Drosophila. Since the discovery of the Drosophila p53 orthologue, various aspects of DNA damage responses have been studied in Drosophila. In this review, I will summarize the current knowledge on the DNA damage checkpoint response in Drosophila. With the ease of genetic, cellular, and cytological approaches, Drosophila will become an increasingly valuable model organism for the study of mechanisms inherent to cancer formation associated with defects in the DNA damage pathway.

• 한국지능시스템학회:학술대회논문집
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• 한국퍼지및지능시스템학회 2001년도 추계학술대회 학술발표 논문집
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• pp.225-228
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• 2001

DNA computing has been applied to the problem of getting an optimal solution since Adleman's experiment. DNA computing uses strings with various length and four-type bases that makes more useful for finding a global optimal solutions of the complex multi-modal problems. This paper presents DNA coding method for finding optimal solution of the multi-modal function and compares the efficiency of this method with the genetic algorithms (GA). GA searches effectively an optimal solution via the artificial evolution of individual group of binary string and DNA coding method uses a tool of calculation or Information store with DNA molecules and four-type bases denoted by the symbols of A(Ademine), C(Cytosine), G(Guanine) and T(Thymine). The same operators, selection, crossover, mutation, are applied to the both DNA coding algorithm and genetic algorithms. The results show that the DNA based algorithm performs better than GA.

• 대한의생명과학회지
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• 제10권2호
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• pp.65-73
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• 2004

I report that single-stranded antisense as a part of large circular (LC-) genomic DNA of recombinant M13 phage exhibits enhanced stability, sequence specific antisense activity, and no need for target site search. A cDNA fragment (708 bp) of rat TNF-$\alpha$ was inserted into a phagemid vector, and TNF-$\alpha$ antisense molecules (TNF$\alpha$-LCAS) were produced as single-stranded circular DNA. When introduced into a rat monocyte/macrophage cell line, WRT7/P2, TNF$\alpha$-LCAS was able to ablate LPS-induced TNF-$\alpha$ mRNA to completion. The antisense effect of TNF$\alpha$-LCAS was shown to be sequence-specific because expressions of three control genes ($\beta$-actin, GAPDH and IL-1$\beta$) were not significantly altered by the antisense treatment. Further, TNF$\alpha$-LCAS was found to be highly efficacious as only 0.1 $\mu$g (0.24 nM) of TNF$\alpha$-LCAS was sufficient to block TNF-$\alpha$ expression in 1$\times10^5$ WRT7/P2 cells. I have also observed specific antisense activity in reduction of NF-$\kappa$B gene expression. The results suggest that an antisense sequence as a part of single-stranded circular genomic DNA has a specific antisense activity.

• Molecules and Cells
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• 제20권3호
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• pp.423-428
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• 2005

Immediately after fertilization, a chromatin remodeling process in the oocyte cytoplasm extracts protamine molecules from the sperm-derived DNA and loads histones onto it. We examined how the histone H3-lysine 9 methylation system is established on the remodeled sperm chromatin in mice. We found that the paternal pronucleus was not stained for dimethylated H3-K9 (H3-$m_2K9$) during pronucleus development, while the maternal genome stained intensively. Such H3-$m_2K9$ asymmetry between the parental pronuclei was independent of $HP1{\beta}$ localization and, much like DNA methylation, was preserved to the two-cell stage when the nucleus appeared to be compartmentalized for H3-$m_2K9$. A conspicuous increase in H3-$m_2K9$ level was observed at the four-cell stage, and then the level was maintained without a visible change up to the blastocyst stage. The behavior of H3-$m_2K9$ was very similar, but not identical, to that of 5-methylcytosine during preimplantation development, suggesting that there is some connection between methylation of histone and of DNA in early mouse development.

• Bulletin of the Korean Chemical Society
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• 제12권2호
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• pp.214-219
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• 1991

To study the effect of solvents and counterions in Z-DNA crystal of d(5BrC-G-5BrC-G-5BrC-G), we performed the local energy analysis and then molecular dynamics simulations. Since counterions raise serious caging problems in crystal simulations, it is very important to search for the possible positions before simulations. For this purpose, the local energy analysis was done for the whole crystal volume. It is shown from our simulation that counterions along with water molecules play a bridging role to bind adjacent oligomers so as to form the crystal. In this crystal, each water molecule bound to Gua-N2H, either directly or indirectly, hydrates the adjacent anionic phosphate oxygen, and thus assists Gua to be in a syn position. From the simulation, the average root-mean-square deviation of allthe DNA heavy atom coordinates from the X-ray data is $0.99{\AA}$ . The bases are less deviated from the X-ray positions than the phosphates. The temperature factors from the simulation are consistent with those from the X-ray refinement, showing that the phosphates are more mobile than the bases.

• Molecules and Cells
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• 제28권3호
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• pp.149-154
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• 2009

Faithful and accurate replication of the DNA molecule is essential for eukaryote organisms. Nonetheless, in the last few years it has become evident that inheritance of the chromatin states associated with different regions of the genome is as important as the faithful inheritance of the DNA sequence itself. Such chromatin states are determined by a multitude of factors that act to modify not only the DNA molecule, but also the histone proteins associated with it. For instance, histones can be posttranslationally modified, and it is well established that these posttranslational marks are involved in several essential nuclear processes such as transcription and DNA repair. However, recent evidence indicates that posttranslational modifications of histones might be relevant during DNA replication. Hence, the aim of this review is to describe the most recent publications related to the role of histone posttranslational modifications during DNA replication.