• 약학회지
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• 제54권1호
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• pp.62-66
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• 2010

Benzopyrene is known to be one of the most powerful carcinogens which can build intercalated motif between base pairs in damaged DNA. The dimension of benzopyrene itself is much bigger than any of the DNA bases and thus the question whether the lesion of some base pair by insertion of benzopyrene can happen with or without a dramatic distortion of the helical structure is a highly interesting theme. In this work we used a molecular mechanics simulation using AMBER program package to go into the conformational characteristics. The condition of the insertion process of the benzopyrene motif from minor groove of the starting structure between the base pairs in the internal area of double helix was investigated using the molecular dynamics simulation at elevated temperature.

• Applied Microscopy
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• 제22권2호
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• pp.66-74
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• 1992

In an attempt to produce transgenic amphibia, bacteriophage ${\lambda}-DNA$ was microinjected into fertilized eggs of Xenopus laevis, and the effect on early embryogenesis and the ultrastructural behavior of exogenous DNA were investigated. The effect of microinjected gene on embryonic development showed differences according to the concentration of injected DNA and the incubation temperature. Various concentrations of ${\lambda}-DNA$ were tested. Among those, microinjection of 1-2 ng DNA dissolved in 20 nl TE buffer was not shown to disturb normal embryonic development and was recorded the highest survivability to the late tadpole stage (Stage 43); however, injection of increased concentrations of DNA than above provoked irregular cleavages or abnormal appearances, which resulted in reduced survivability. When the injected embryos were incubated at low temperatures (e.g., $12^{\circ}C$), 54.5% of the embryos developed to Stage 43, whereas 42.4% survived when incubated at room temperature. The survivability showed also differences according to the injection site. 58.0% of the embryos developed to Stage 43 when microinjected into the vegetal pole, whereas 44.9% survived when microinjected into the animal pole. To understand the structural fate or behavior of injected DNA a combined light and electron microscopical study was applied. The nucleus-like structure was observed in the ${\lambda}$ DNA-injected embryos, which was quite a similar to the interphase nuclei of normal Xenopus laevis. The nucleus-like structure showed the typical double-layered nuclear membrane and nuclear complexes; however, it consisted of unusual structures such as furrows of nuclear envelope into the nucleoplasm.

• BMB Reports
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• 제34권6호
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• pp.489-495
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• 2001

DNA damage by UV and environmental agents are the major cause of genomic instability that needs to be repaired, otherwise it give rise to cancer. Accordingly, mammalian cells operate several DNA repair pathways that are not only responsible for identifying various types of DNA damage but also involved in removing DNA damage. In mammals, nucleotide excision repair (NER) machinery is responsible for most, if not all, of the bulky adducts caused by UV and chemical agents. Although most of the proteins involved in NER pathway have been identified, only recently have we begun to gain some insight into the mechanism by which proteins recognize damaged DNA. Binding of Xeroderma pigmentosum group C protein (XPC)-hHR23B complex to damaged DNA is the initial damage recognition step in NER, which leads to the recruitment of XPA and RPA to form a damage recognition complex. Formation of damage recognition complex not only stabilizes low affinity binding of XPA to the damaged DNA, but also induces structural distortion, both of which are likely necessary for the recruitment of TFIIH and two structure-specific endonucleases for dual incision.

• 대한화학회지
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• 제34권6호
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• pp.539-547
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• 1990

DNA base인, Adenine, Guanine 그리고 Cytosine과 diaminecytosineplatinum(DCP)의 상호작용을 SC-MEH 방법에 의하여 계산한 결과, DNA base와 DCP 결합력의 크기는 guanine > adenine > cytosine임을 알 수 있었고, cis-백금(II)착물이 trans-백금(II) 착물보다 안정화에너지가 더 크게 나타남을 adenine-DCP 착물계에서 볼 수 있었다. DNA bases ring의 atomic charge는 백금(II)착물의 배위에 의해 많은 charge 변화가 있음을 관찰하였고, 이 효과에 의하여 백금(II)착물의 항암성 메카니즘을 설명할 수 있었다.

• Journal of the Korean Association of Oral and Maxillofacial Surgeons
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• 제34권5호
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• pp.509-517
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• 2008

DNA 손상 치유 유전자 연구를 기초로 한 임상적 접근이 새로운 치료방법으로 떠오르고 있다. 많은 연구들이 중요한 DNA 수복유전자의 다형성을 찾아내어 각각의 단백질의 활동성에 대한 영향을 알아내고 특정한 치료법을 찾아내고 임상적 적용을 시도하고 결과를 평가하였다. 그 결과 암 치료에서 정상 세포와 암세포에서 DNA 수복 유전자의 발현 분석은 화학요법이나 방사선 치료에서 개인맞춤형 치료법을 가능하게 하고 있다. 예를 들어, NER이 결핍된 종양은 cisplatin 치료에 민감성을 나타내고, MMR 결핍세포는 알킬화 화학요법 약제에 높은 내성을 나타낸다. 선천성 비폴립성 결장암과 같은 MMR 결손종양 또한 알킬화 화학요법 약제에 의한 치료에 내성을 가진다. 신경교종(glioma)에서 MGMT 유전자 프로모터가 흔히 메틸화되는데 이것은 유전자 발현이 억제되고 알킬화 화학요법제에 대한 반응성을 증가시킨다. 향후 구강악안면외과 영역에서도 구강암의 발생의 위험성을 증가시킬 수 있는 더 많은 DNA 수복 유전자의 다형성을 발굴하고 임상적으로 개인맞춤형 치료법을 개발하고 적용할 수 있는 많은 연구가 필요할 것으로 사료된다.

• Clinical and Experimental Reproductive Medicine
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• 제44권4호
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• pp.201-206
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• 2017

Objective: The aim of this study was to compare the efficacy of swim-up and density gradient centrifugation (DGC) for reducing the amount of sperm with fragmented DNA, sex chromosome aneuploidy, and abnormal chromatin structure. Methods: Semen samples were obtained from 18 healthy male partners who attended infertility clinics for infertility investigations and were processed with swim-up and DGC. The percentages of sperm cells with fragmented DNA measured by the sperm chromatin dispersion test, normal sex chromosomes assessed by fluorescence in situ hybridization, and abnormal chromatin structure identified by toluidine blue staining were examined. Results: The percentage of sperm cells with fragmented DNA was significantly lower in the swim-up fraction (9.7%, p= 0.001) than in the unprocessed fraction (27.0%), but not in the DGC fraction (27.8%, p= 0.098). The percentage of sperm cells with normal X or Y chromosomes was comparable in the three fractions. The percentage of sperm cells with abnormal chromatin structure significantly decreased after DGC (from 15.7% to 10.3%, p= 0.002). The swim-up method also tended to reduce the percentage of sperm cells with abnormal chromatin structure, but the difference was not significant (from 15.7% to 11.6%, p= 0.316). Conclusion: The swim-up method is superior for enriching genetically competent sperm.

• Molecules and Cells
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• 제38권9호
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• pp.789-795
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• 2015

A chromosome territory is composed of chromosomal subdomains. The internal structure of chromosomal subdomains provides a structural framework for many genomic activities such as replication and DNA repair, and thus is key to determining the basis of their mechanisms. However, the internal structure and regulating proteins of a chromosomal subdomain remains elusive. Previously, we showed that the chromosome territory expanded after BAF53 knockdown. Because the integrity of chromosomal subdomains is a deciding factor of the volume of a chromosome territory, we examined here the effect of BAF53 knockdown on chromosomal subdomains. We found that BAF53 knockdown led to the disintegration of histone H2B-GFP-visualized chromosomal subdomains and BrdU-labeled replication foci. In addition, the size of DNA loops measured by the maximum fluorescent halo technique increased and became irregular after BAF53 knockdown, indicating DNA loops were released from the residual nuclear structure. These data can be accounted for by the model that BAF53 is prerequisite for maintaining the structural integrity of chromosomal subdomains.

• 환경생물
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• 제23권4호
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• pp.379-382
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• 2005

The new cationic meso-substituted N-quarternized 4-pyridylporphyrins and their metal derivatives were synthesized as novel chemotherapeutics. The level of DNA damage induced by porphyrins TOBut4PyP, TOBut4PyP, TOEt4PyPMn and TOBut4PyPMn and its dependence on the chemical structure of compounds were analyzed by the Comet-assay. On the base of data obtained, the investigated porphyrins may be arranged by their genotoxic activity in the following order: TOEt4PyP>TOEt4PyPMn>TOBut4PyP>TOBut4PyPMn. Thus, i) the genotoxicity of the Mn-derivatives of TOEt4PyP and TOBut4PyP is higher than the original porphyrins and ii) the genotoxicity of TOEt4PyP and TOEt4PyPMn is increased after substitution of a butyl radical for ethyl one. The applied Comet-assay permits to reveal the dependence of DNA damage induction on the chemical structure of porphyrins.

• BMB Reports
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• 제33권3호
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• pp.268-275
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• 2000

In contrast to the pyrimidine (6-4)pyrimidone photoproduct [(6-4) adduct], its Dewar valence isomer (Dewar product) is low mutagenic and produces a broad range of mutations with a 42 % replicating error frequency. In order to determine the origin of the mutagenic property of the Dewar product, we used experimental NMR restraints and molecular dynamics to determine the solution structure of a Dewar·lesion DNA decamer duplex, which contains a mismatched base pair between the 3'-T residue and an opposed G residue. The 3'-T of the Dewar lesion forms stable hydrogen bonds with the opposite G residue. The helical bending and unwinding angles of the DW/GA duplex, however, are much higher than those of the DW/AA duplex. The stable hydrogen bonding of the G 15 residue does not increase the thermal stability of the overall helix. It also does not restore the distorted backbone conformation of the DNA helix that is caused by the forming of a Dewar lesion. These structural features implicate that no thermal stability, or conformational benefits of G over A opposite the 3'-T of the Dewar lesion, facilitate the preferential incorporation of an A. This is in accordance with the A rule during translesion replication and leads to the low frequent $3'-T{\rightarrow}C$ mutation at this site.

• 한국미생물학회:학술대회논문집
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• 한국미생물학회 2002년도 추계학술대회
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• pp.15-21
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• 2002

Terminal-restriction fragment length polymorphism (T-RFLP) analysis has been optimized by using in vitro model community composed of genomic DNAs of known bacterial strains and has been applied to assess the bacterial community structure in marine sediments. The specific fluorescence-labeled terminal restriction fragments (T-RFs) between 39 and 839 base long specifying each strain were precisely measured for known bacterial strains. The addition of a co-solvent (dimethylsulfoxide or glycerol) into PCR reactions has reduced differential PCR amplification. Comparative bacterial community structure was investigated for pristine and polluted sediments. A complex T-RFLP pattern showing complex bacterial community structure was obtained in the pristine sediment, whereas simple T-RFLP pattern (low bacterial diversity) was shown in polluted sediments where caged aquaculture has been conducted for several years. The results of T-RFLP analysis were compared with that of cloning and sequencing 16S rDNA clones from the same sediments. Sequence analysis of 16S rDNA clones (72) of the pristine sediment revealed a diverse collection of lineages, largely of the class Proteobacteria ($6\%$ alpha subdivision, $46\%$ gamma subdivision, $13\%$ delta subdivision, and $3\%$ epsilon subdivision), Nitrospina $(8\%)$, high G+C gram positive $(8\%)$, Verrucomicrobia $(7\%)$, and Planctomycetes $(6\%)$. In the contaminated sediments, 17 $(59\%)$ of the 16S rDNA clones (29) were related to Campylobacter and symbiont of Rimicaris exoculata belonging to epsilon subdivision of Proteobacteria. The results obtained indicated that T-RFLP analysis is a rapid and precise technique for comparative bacterial community analysis.