• Korean Journal of Food Science and Technology
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• v.51 no.2
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• pp.188-191
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• 2019

In this study, the poor electro-transformant yield of large DNA in bifidobacteria was improved by increasing the DNA concentration, which was amplified by enhancing electroporation conditions: treating the cell wall weakening agent and cell membrane permeabilizing molecule as well as changing the electrical parameter. In the enhanced conditions, the electroporation frequency increased from 15 to 71 times compared to the initial conditions at the same DNA concentration. As the DNA concentration increased, the difference in the electroporation frequency between the two conditions became greater, and the curve of the enhanced conditions seemed to be saturated with a DNA concentration over $4{\mu}g$. The present study provided a clue to the recovery of the electroporation frequency with large DNA and formulated the relationship between the DNA concentration, the DNA size and the electroporation frequency in bifidobacteria. Therefore, this study will contribute to the expansion of molecular genetic studies of bifidobacteria.

• Proceedings of the Korean Institute of Electrical and Electronic Material Engineers Conference
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• 2008.06a
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• pp.143-143
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• 2008

Nanowires are promising options for building nanoscale electronic structures coming from high conductivity of nanowires. In particular, Deoxyribonucleic acid (DNA), which is structurally nanowire, can obtain highly ordered electronic components for nanocircuitry and/or nanodevices because of its very flexible length controllability, nanometer-size diameter, about 2 nm, and self-assembling properties. In this work, we used the method to form DNA-Nanowires (NWs) by using chemical treatment on Silicon (Si) surface, and Aminopropyl-triethoxysilane (APTES) was used as inducer of DNA sequence to modify the characteristics of Si surface. Moreover, we performed tilting technique to align DNA by the direction of flow of DNA solution. We investigated the assembly process between DNA molecules and APTES - coated Si surface according to the APTES concentration, from $1.2{\mu}\ell$ to $120{\mu}\ell$. Atomic Force Microscopy (AFM) images showed the combination rate of DNA molecules by the change of APTES concentration. As APTES concentration becomes thicker, aggregation of DNA molecules occurs, and this makes a kind of DNA networks. In this respect, we confirmed that there's a positive relationship between the concentration of APTES and the formation rate of DNA nanowires. Since there have been lots of research preceded to utilize DNA nanowires as template, so by using this positive relationship with proper alignment technique, realization of nano electronic devices with DNA nanowires might be feasible.

• Bulletin of the Korean Chemical Society
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• v.33 no.11
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• pp.3719-3726
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• 2012

Formation of Z-DNA, a left-handed double helix, from B-DNA, the canonical right-handed double helix, occurs during important biological processes such as gene expression and DNA transcription. Such B-Z transitions can also be induced by high salt concentration in vitro, but the changes in the relative stability of B-DNA and Z-DNA with salt concentration have not been fully explained despite numerous attempts. For example, electrostatic effects alone could not account for salt-induced B-Z transitions in previous studies. In this paper, we propose that the B-Z transition can be explained if counterion entropy is considered along with the electrostatic interactions. This can be achieved by conducting all-atom, explicit-solvent MD simulations followed by MM-PBSA and molecular DFT calculations. Our MD simulations show that counterions tend to bind at specific sites in B-DNA and Z-DNA, and that more ions cluster near Z-DNA than near B-DNA. Moreover, the difference in counterion ordering near B-DNA and Z-DNA is larger at a low salt concentration than at a high concentration. The results imply that the exclusion of counterions by Z-DNA-binding proteins may facilitate Z-DNA formation under physiological conditions.

• Current Applied Physics
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• v.18 no.11
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• pp.1294-1299
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• 2018

In this paper, we demonstrate the feasibility of constructing DNA nanostructures (i.e. DNA rings and double-crossover (DX) DNA lattices) with appropriate doxorubicin hydrochloride (DOX) concentration and reveal significant characteristics for specific applications, especially in the fields of biophysics, biochemistry and medicine. DOX-intercalated DNA rings and DX DNA lattices are fabricated on a given substrate using the substrateassisted growth method. For both DNA rings and DX DNA lattices, phase transitions from crystalline to amorphous, observed using atomic force microscopy (AFM) occurred above a certain concentration of DOX (at a critical concentration of DOX, $30{\mu}M$ of $[DOX]_C$) at a fixed DNA concentration. Additionally, the coverage percentage of DNA nanostructures on a given substrate is discussed in order to understand the crystal growth mechanism during the course of annealing. Lastly, we address the significance of optical absorption and photoluminescence characteristics for determining the appropriate DOX binding to DNA molecules and the energy transfer between DOX and DNA, respectively. Both measurements provide evidence of DOX doping and $[DOX]_C$ in DNA nanostructures.

• Rapid Communication in Photoscience
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• v.3 no.4
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• pp.81-84
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• 2014

To examine the microenvironmental effect of DNA on the photosensitized reaction, the electron-donor-connecting porphyrin, meso-(9-phenanthryl)-tris(N-methyl-p-pyridinio) porphyrin (Phen-TMPyP), was synthesized. Phen-TMPyP can bind to oligonucleotides with two binding modes, depending on the DNA concentration. The fluorescence lifetime measurement of Phen-TMPyP shows a shorter component than that of the reference porphyrin without the phenanthryl moiety. However, the observed value is much longer than those of previously reported similar types of electron-donor-connecting porphyrins, suggesting that electron-transfer quenching by the phenanthryl moiety is not sufficient. The fluorescence quantum yield of Phen-TMPyP ($5{\mu}M$) decreased with an increase in DNA concentration of up to $5{\mu}M$ base pair (bp), possibly due to self-quenching through an aggregation along the DNA strand, increased with an increase in DNA concentration of more than $5{\mu}M$ bp and reached a plateau. The fluorescence quantum yield of Phen-TMPyP with a sufficient concentration of DNA was larger than that of the reference porphyrin. The singlet oxygen ($^1O_2$) generating activity of Phen-TMPyP was confirmed by the near-infrared emission spectrum measurement. The quantum yield of $^1O_2$ generation was decreased by a relatively small concentration of DNA, possibly due to the aggregation of Phen-TMPyP, and recovered with a sufficient concentration of DNA. The recovered quantum yield was rather smaller than that without DNA, indicating the quenching of $^1O_2$ by DNA. These results show that a DNA strand can stabilize the photoexcited state of a photosensitizer and, in a certain case, suppresses the $^1O_2$ generation.

• Asian-Australasian Journal of Animal Sciences
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• v.13 no.10
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• pp.1367-1372
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• 2000

The present study was conducted to evaluate the efficiency of transgenic rabbit production by DNA microinjection using EGFP (Enhanced Green Fluorescent Protein) gene. In this experiment EGFP coding sequences fused to CMV promoter were microinjected into rabbit one-cell embryos, and then GFP expression and gene integration were evaluated in preimplantation embryos and fetuses recovered on day 15 of pregnancy to determine efficiency of transgenic rabbit production. Effect of DNA concentration was also tested on development in vitro following microinjection and transgene integration in fetuses. Development of embryos in vitro was decreased by DNA microinjection, but the rates of pregnancy and implantation were not significantly affected by microinjection. As development progressed in vitro percentage of GFP expression in rabbit embryos was decreased, resulting GFP expression detected in 37.5% of blastocysts. The efficiencies for production of transgenic fetuses were 4.0% and 7.6%, respectively, when $10ng/{\mu}l$ and $20ng/{\mu}l$ of DNA concentration were microinjected. Transgenic fetuses were confirmed by GFP expression and PCR analysis of fetus genomic DNA. These results indicated that DNA microinjection itself damaged embryo development and DNA concentration affected the efficiency of transgenic rabbit production.

• Proceedings of the Korean Institute of Electrical and Electronic Material Engineers Conference
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• 2007.11a
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• pp.105-106
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• 2007

M-DNAs based on zinc and cobalt ions were formed at the conditions of $26^{\circ}C$, 76% humidity, atmosphere, and pH 8.0. Some process parameters in synthesis of M-DNA such as synthetic temperature, concentration of metal ions, and synthetic time were varied and the electrical properties were investigated by changes of the parameters. The electrical properties of M-DNA showed the dependences on synthetic temperature, concentration of metal ions and synthetic time. The I-V characteristics rapidly increased with each increase of the parameters.

• Journal of Life Science
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• v.14 no.2
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• pp.255-262
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• 2004

We applied nuclear DNA content stained with 4'-6'-diamidino-2-phenylindole (DAPI) and total protein concentration to predict the existence of Cochlodinium polykrikoides before huge blooms occurred, based on a short-term survey at sites in the South Sea. Fluctuations in environmental conditions and nutrients (nitrate, nitrite, and phosphate) were of a similar range, regardless of sampling sites or early and middle field observations. However, C. polykrikoides abundance was significantly different depending on the station, with a higher cell density of 34, 62, and 57 cells L$^{-1}$ at Stn C2, C5, and C6, respectively than what was found in early August, 2000. In mid August, 2000, the highest cell density of 547 cells L$^{-1}$ at Stn C3 was observed. The relationship between C. polykrikoides abundance, DAPI-stained DNA content, and total protein concentration was a positive correlation coefficient, in particular a higher positive correlation was exposed to even a smaller abundance of C. polykrikoides. These results suggest that DNA stained by DAPI and total protein concentration could play an important index in easily predicting the presence of C. polykrikoides before blooms.

• Korean Journal of Microbiology
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• v.14 no.3
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• pp.135-145
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• 1976

Confluent AGMK cells were infected by large plaque SV40 virus. Levels of DNA polymeras $({\alpha}\;and\;{\beta})$ were measured in the cytoplasm and the cell nucleus. The activities of DNA $polymerase-{\alpha}$ which found in both the cell nucleus and the cytoplasm were increased approximately eight folds at 48 hours after infection of SV40 virus. Only insignificant but constant amounts of DNA $polymerase-{\beta}$ were found either in the nucleus of the SV40 infected cell or of the uninfected cell. The characteristics of the SV40 virus induced DNA polymerases were compared with that of the uninfected cellular DNA polymerase in regard of the effects of pH, salt concentration, NEM concentration and temperature on those enzyme activities. No differential effect was found between both enzymes. Endouclease activities wre examined in the purified DNA $polymerase-{\alpha}\;and\;{\beta}$. The low level of endonuclease activity which might cut SV40 DNA 1 at one site was observed in the DNA $polymerase-{\alpha}$ whereas high but nonspecific endonuclease activities were found in the DNA $polymerase-{\beta}$.

• Clinical and Experimental Reproductive Medicine
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• v.36 no.1
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• pp.35-43
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• 2009

Objectives: Seminal concentration of tumor necrosis factor-alpha (TNF-${\alpha}$) relevant to sperm nuclear DNA integrity has not been studied. The present study aimed to evaluate seminal concentration of TNF-${\alpha}$ in correlation with sperm parameters and nuclear DNA integrity in asymptomatic healthy donors. Methods: Semen samples were obtained by masturbation from forty-five healthy donors. Results: Sperm quality was assessed by computer-assisted semen analysis and nuclear DNA integrity measured by the TUNEL assay in raw semen. TNF-${\alpha}$ concentrations were measured by ELISA in frozen-thawed seminal plasmas. Sperm DNA fragmentation rates were ranged between 1.9% and 53.0% (mean${\pm}$SD, 12.4${\pm}$9.6%). Univariate analysis revealed that DNA fragmentation rate was not associated with sperm concentration or motility but had a correlation with linearity negatively (r=-0.325, p=0.03) and age positively (r=0.484, p=0.001). The mean seminal concentration of TNF-${\alpha}$ was 4.9 pg/mL with a range from 1.1 to 22.6 pg/mL. The TNF-${\alpha}$ concentration had no correlation with clinically relevant parameters of sperm quality or nuclear DNA fragmentation rate. Conclusion: Our results indicate that sperm nuclear DNA fragmentation may be not associated with seminal TNF-${\alpha}$ level or sperm quality in asymptomatic healthy donors.