• Korean Journal of Clinical Laboratory Science
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• v.36 no.1
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• pp.33-37
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• 2004

In order to study the effect of temperature of denaturation, annealing and extension and cycles on amplification of DNA by PCR method, We isolated the hepatitis B virus DNA from hepatitis B patient blood and compared the density of DNA amplified by Reference PCR Program (denaturation at $94^{\circ}C$ for 30 sec., annealing at $60^{\circ}C$ for 1 min., extension at $72^{\circ}C$ for 1 min., holding at $72^{\circ}C$ for 5min., 30 cycles) that is usually used in laboratory to the density of DNA amplified by PCR program changed only the denaturation temperature or annealing temperature or extension temperature. We amplified about 341bp of hepatitis B virus DNA by Reference PCR Program from hepatitis patient blood, but the DNAs denatured at $72^{\circ}C$ or $60^{\circ}C$ were not detectable on photoradiography film. The DNA amplified at $37^{\circ}C$ of annealing temperature was not detectable, but the DNA annealed at $72^{\circ}C$ was detectable the lower density of DNA than the DNA amplified by Reference PCR Program. Each DNA amplified by PCR program changed only the extension temperature to $37^{\circ}C$ or $60^{\circ}C$ was almost same density as DNA amplified by Reference PCR Program. We compared the density of hepatitis B virus DNA amplified by Reference PCR Program for 30 cycles, 20 cycles, 10 cycles, and 5 cycles. The DNA cycled for 20 cycles was not amplified well as cycled for 30 cycles, but the DNA was detectable on the photoradiography film. The DNAs amplified for 10 cycles or 5 cycles were not detectable on photoradiorgaphy film. The concentration of hepatitis B virus DNA amplified in Reference PCR condition for 30 cycles, 20 cycles, 10 cycles, and 5 cycles were $72{\mu}g/m{\ell}$, $83{\times}10^{-3}{\mu}g/m{\ell}$, $27{\times}10^{-6}{\mu}g/m{\ell}$, and nondetectable, respectively.

• Environmental Mutagens and Carcinogens
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• v.22 no.3
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• pp.199-204
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• 2002

It has been known that Ganoderma lucidum and Lentinus edodes have anticancer activity and immune enhancing activity. These two mushrooms were grown in liquid culture and harvested. From these mycelia, DNA was isolated and EtBr-CsCl density gradient ultracentrifugation was performed to purify it further. Then mitochondrial DNA was isolated by bisbenzimide-CsCl density ultracentrifugaton. Mitochondrial DNA of Ganoderma lucidum was digested by restriction enzymes, EcoR I, Hind Ⅲ, and Pst I, then electrophoresed. It showed 12, 22, 4 fragments. Mitochondrial DNA of Lentinus edodes was digested by EcoR I. Electric pattern showed 6 fragments. 4 fragments had appeared by Pst 1 digested mitochondrial DNA. Hind ill couldn't digest mitochondrial DNA of Lentinus edodes. Mitochondrial DNA of fusants was isolated to compare to those of parents. The results showed that fusant P₂S₄has new, recombined mitochondrial DNA. But P₂S₄had the same DNA that Ganoderma lucidum had.

• Clinical and Experimental Reproductive Medicine
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• v.46 no.1
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• pp.8-13
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• 2019

Objective: Density gradient centrifugation (DGC) is frequently used to isolate high-motility fractions of spermatozoa. We compared the efficacy of four DGC media in terms of the percentage of morphologically normal spermatozoa, DNA fragmentation level, and hyaluronic acid (HA) binding ability. Methods: Thirty men with a total motile spermatozoa count > 80 million participated. Semen samples were divided into four aliquots, which were processed using PureSperm, PureCeption, Sidney, and SpermGrad media, respectively. The DNA fragmentation level was measured using the Halosperm assay kit and HA binding ability was measured using the HBA assay kit. Results: The mean percentage of morphologically normal spermatozoa was significantly enhanced after DGC using all four media (10.3%, 9.9%, 9.8%, and 10.7%, respectively; p< 0.05 for each when compared with 6.9% in raw semen). The DNA fragmentation level was significantly reduced after DGC using PureSperm, PureCeption, and SpermGrad media (6.0%, 6.5%, and 4.9%, respectively; p< 0.05 for each when compared with 11.2% in raw semen), but not after DGC using Sidney media (8.5%, p> 0.05). HA binding ability did not change after DGC using any of the four media. Conclusion: The four media were equally effective for obtaining a sperm fraction with highly motile, morphologically normal sperm. PureSperm, PureCeption, and SpermGrad media were equally effective for acquiring a sperm fraction with less DNA fragmentation.

• Journal of Microbiology and Biotechnology
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• v.10 no.1
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• pp.21-26
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• 2000

A microarrayer system was developed mainly for manufacturing DNA chips. The 3-axis robot was designed to automatically collect samples from 96-or 384-well microtiter plates using up to 16 simultaneously moving pens and to deposit them on a surface-modified slide glass. This is followed by a wash/dry operation in a clean station. The cycle is repeated with a new set of samples, This system can deposit cDNA or oligonucleotides with spot intervals of $150{\;}\mu\textrm{m}$ and the spot size of $80\mu\textrm{m}$, thus allowing a high density DNA chip containing about 5,000 spots per $\textrm{cm}^2$. The entire procedure is controlled by the Visual C++ program that was written in our laboratory by using a personal computer with Pentium 100 CPU.

• Korean Journal of Microbiology
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• v.42 no.1
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• pp.62-66
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• 2006

To study the packaging mechanism of the bacteriophage P2-P4 system which is a useful experimental tool for the study of viral capsid assembly, we analyzed the DNA contents of P4 sid- mutant, P4 ash8 sid71's phage particles. Two kind of particles having different density were separated by the CsCl buoyant equilibrium density gradient experiment with fresh made stock of P4 ash8 sid71. The DNA from each particles was prepared and its conformations was analyzed by electrophoresis. Unexpectedly, both particles contain not only dimeric and trimeric but also monomeric P4 DNA.

• Bulletin of the Korean Chemical Society
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• v.25 no.11
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• pp.1667-1670
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• 2004

In DNA microarray produced by DNA-deposition technology, DNA-immobilization and -hybridization yields on a solid support are most important factors for its accuracy and sensitivity. We have developed a dendrimeric support using silylated aldehyde slides and polyamidoamine (PAMAM) dendrimers. An oligonucleotide array was prepared through a crosslinking between the dendrimeric support and an oligonucleotide. Both DNAimmobilization and -hybridization yields on the solid support increased by the modification with the dendrimers. The increase of the immobilization and hybridization efficiency seems to result from a threedimensional arrangement of the attached oligonucleotide. Therefore, our dendrimeric support may provide a simple and efficient solution to the preparation of DNA microarrays with high-density DNA-deposition and high hybridization efficiency.

• The Korean Journal of Food And Nutrition
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• v.8 no.4
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• pp.307-317
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• 1995

The purity of mtDNAs isolated from Archicitrus and Metacitrus leaves was higher in percoll density gradient centrifugation than differential and sucrose density gradient centrifugation. The most clear mtDNAs were obtained from mitochondria included in the Interface band of between 21% and 45% under isomotic, low viscosity conditions in the three step discontinuous percoll density gradient centrifugation. DNase treatment to the crude mitochondrlal suspension still more increased purity of mtDNA by the effective removal of the nuclear and chloroplast DNA and mtDNAs were appeared as a single band at middle position of tube by EtBr /cscl density gradient centrifugation. Agarose gel electrophoresis of mtDNAs resolved a single, broad band containing high molecular weight DNAs In all preparation. Yield of mtDNAs was about 110 and 2 ug Per 2009 in mature and immature leaves respectively. The mtDNA fragment patterns showed by EcoR I treatment were indistinguishable with respect to nom bet and position of bands in Archicitrus and Metacitrus. In the pattern of Hind E restriction, the Metacitrus displayed the unique band between 5.0 and 4.0kb, in addition to four fragments about 5.0, 2.4, 2.15, and 2.0kb, respectively, different from Archicitrus. Also the pattern of total mtDNAs fragment by the treatment of Pst I showed that the distinguishable fragment pat tern was not appeared in Archicitrus(C. iyo Tanaka), but about 6.0, 5.5, 5.0 and 2.Bkb fragments were appeared only in Metacitrus(C. junos Sieb). Therefore it was indicated that two species in intra-subgenus were identical each other, whereas considerable difference was revealed for inter-subgenus.

• Journal of Microbiology and Biotechnology
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• v.14 no.4
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• pp.836-843
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• 2004

Nontypeable H. influenzae (NTHi), a Gram-negative obligate human pathogen, causes pneumonia, chronic bronchitis, and otitis media, and the respiratory epithelium is the first line of defense that copes with the pathogen. In an effort to identify transcriptional responses of human respiratory epithelial cells to infection with NTHi, we examined its differential gene expression using high density cDNA microarrays. BEAS-2B human bronchial epithelial cells were exposed to NTHi for 3 hand 24 h, and the alteration of mRNA expression was analyzed using microarrays consisting of 8,170 human cDNA clones. The results indicated that approximately 2.6% of the genes present on the microarrays increased in expression over 2-fold and 3.8% of the genes decreased during the 24-h infection period. Upregulated genes included cytokines (granulocyte-macrophage colony stimulating factor 2, granulocyte chemotactic protein 2, IL-6, IL-10, IL-8), transcription factors (Kruppel-like factor 7, CCAAT/enhancer binding protein $\beta$, E2F-1, NF-$\kappa$B, cell surface molecules (CD74, ICAM-1, ICAM-2, HLA class I), as well as those involved in signal transduction and cellular transport. Selected genes were further confirmed by reverse-transcription-PCR. These data expand our knowledge of host cellular responses during NTHi infection and should provide a molecular basis for the study of host-NTHi interaction.

• Journal of the Korean Institute of Electrical and Electronic Material Engineers
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• v.24 no.6
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• pp.510-514
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• 2011

Based on first-principles LCAO method, we study the electronic and atomic structures of DNA nucleobases adenine (A), thymine (T), guanine (G), and cytosine (C) adsorbed on graphene surfaces. The ${\pi}-{\pi}$ stacking interactions between graphene and nucleobases lead to the bilayer geometries similar to the Bernal stacked graphite. Through the density of states and charge density analyses, it is found that nucleobases are physisorbed on graphene by dispersive interactions with negligible charge exchange. Our calculations reproduce the atomic structures obtained in previous plane wave calculations accurately with much less computation, and well describe the delocalized ${\pi}-{\pi}$ interactions in graphene-nucleobases system, indicating that the LCAO method is very efficient for investigating graphene-bio systems.

• Bulletin of the Korean Chemical Society
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• v.31 no.7
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• pp.2107-2109
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• 2010