• Molecules and Cells
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• v.42 no.1
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• pp.67-78
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• 2019

Methylation of HBV cccDNA has been detected in vivo and in vitro; however, the mechanism and its effects on HBV replication remain unclear. HBx derived from a 1.2-mer HBV replicon upregulated protein levels and enzyme activities of DNA methyltransferase 1 (DNMT1), 3a, and 3b, resulting in methylation of the negative regulatory region (NRE) in cccDNA, while none of these effects were observed with an HBx-null mutant. The HBx-positive HBV cccDNA expressed higher levels of HBc and produced about 4-fold higher levels of HBV particles than those from the HBx-null counterpart. For these effects, HBx interrupted the action of NRE binding protein via methylation of the C-1619 within NRE, resulting in activation of the core promoter. Treatment with 5-Aza-2′dC or DNMT1 knock-down drastically impaired the ability of HBx to activate the core promoter and stimulate HBV replication in 1.2-mer HBV replicon and in vitro infection systems, indicating the positive role of HBx-mediated cccDNA methylation in HBV replication.

• Journal of Microbiology and Biotechnology
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• v.8 no.1
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• pp.89-91
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• 1998

Cryptotanshinone induced topoisomerase I-mediated DNA cleavage in vitro as strongly as camptothecin, whereas topoisomerase II-mediated DNA cleavage was not induced by this agent. In DNA relaxation assay using calf thymus DNA topoisomerase I and supercoiled pBR322 DNA, cryptotanshinone inhibited topoisomerase I-mediated DNA relaxation in a dose-dependent manner. In unwinding assay, cryptotanshinone ($50{\mu}M$) did not shift the topoisomers of DNA. These results suggest that cryptotanshinone exerted a preferential inhibition of topoisomerase I without intercalating into DNA.

• Korean Journal of Microbiology
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• v.42 no.1
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• pp.1-6
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• 2006

Saccharomyces cerevisiae Dna2 helicase/endonuclease plays an essential role in removing DNA primers during Okazaki fragment processing in eukaryotic DNA replication. Genome-wide scale co-immunoprecipitation experiments predicted that Dna2 interacts with a novel protein YHR122W (1). In this study, we observed that overexpression of YHR122W gene suppressed the temperature-sensitive phenotype of $dna2\Delta405N$ mutation. To investigate direct interaction between these two proteins, a histidine-tagged recombinant YHR122W protein was expressed and purified from E. coli. Physical interaction between the purified YHR122W and Dna2 proteins was detected by enzyme-linked immunosorbent assays. Further more, the complex formation was most efficient at physiological salt concentration, 150 mM NaCl. The genetic and physical interactions between YHR122W and Dna2 shown in this study suggest that the biological functions of these two proteins may be closely related each other.

• BMB Reports
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• v.43 no.4
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• pp.250-256
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• 2010

Natural phosphodiester bond CpG-DNA that contains immunomodulatory CpG motifs (PO-DNA) upregulates the expression of proinflammatory cytokines and induces an Ag-driven Th1 response in a CG sequence-dependent manner in mice. In humans, only phosphorothioate backbone-modified CpG-DNA (PS-DNA) and not PO-DNA has immunomodulatory activity. In this study, we found that liposome-encapsulated PO-DNA upregulated the expression of human $\beta$-defensin-2 (hBD-2) and major histocompatibility class II molecules (HLA-DRA) in a CG sequence-dependent and liposome- dependent manner in human B cells. Of the three different liposomes, DOTAP has the unique ability to enhance the immunomodulatory activity of PO-DNA. In contrast, HLA-DRA and hBD-2 promoter activation can be induced by liposome-encapsulated PS-DNA in a CG sequence-independent manner, depending on the CpG-DNA species. Our observations demonstrate that, when encapsulated with a proper liposome in the immune system, natural PO-DNA has the potential to be a useful therapy for the regulation of the innate immune response.

• Natural Product Sciences
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• v.21 no.3
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• pp.185-191
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• 2015

Comparative molecular analysis has been frequently adopted for the authentication of herbal medicines as well as the identification of botanical origins. Roots and rhizomes of the family Umbelliferae have been used as traditional herbal medicines to relieve various symptoms such as inflammation, neuralgia and paralysis in countries of East Asia. Since most herbal medicines of the Umbelliferae roots or rhizomes are generally supplied in the form of dried slices, morphological examination does not often provide sufficient evidence to identify the botanical origin. Using species-specific probes developed by the comparative analysis of nrDNA ITS sequences, a DNA chip was developed to identify herbal medicines for 13 species in the Umbelliferae. The developed DNA Chip proves its potential as a rapid, sensitive and effective tool for authenticating herbal medicines in future.

• Natural Product Sciences
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• v.8 no.4
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• pp.162-164
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• 2002

The methanol extracts of 42 Korean indigenous plants were evaluated for the DNA strand-scission activity. As a result, the 17 extracts were found to be active in the criteria of $IC_{50}$}<$25\;{\mu}g/ml$. Among others, the MeOH extracts of Caesalpinia sappan and Mucuna birdwoodiana showed the most potent DNA strand-scission activity with $IC_{50}$ values of 5.9 and $4.9\;{\mu}g/ml$, respectively. Therefore, the partition and fractionation for C. sappan were performed and tested in the DNA strand-scission assay system for further bioassay-guided fractionation.

• BMB Reports
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• v.55 no.11
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• pp.541-546
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• 2022

The repair of DNA double-strand breaks (DSBs) by homologous recombination (HR) is crucial for maintaining genomic integrity and is involved in numerous fundamental biological processes. Post-translational modifications by proteins play an important role in regulating DNA repair. Here, we report that the methyltransferase SET7 regulates HR-mediated DSB repair by methylating TIP60, a histone acetyltransferase and tumor suppressor involved in gene expression and protein stability. We show that SET7 targets TIP60 for methylation at K137, which facilitates DSB repair by promoting HR and determines cell viability against DNA damage. Interestingly, TIP60 demethylation is catalyzed by LSD1, which affects HR efficiency. Taken together, our findings reveal the importance of TIP60 methylation status by SET7 and LSD1 in the DSB repair pathway.

• Journal of the Korean Magnetic Resonance Society
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• v.18 no.2
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• pp.52-57
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• 2014

The TCP domain is a DNA-binding domain present in plant transcription factors and plays important roles in various biological functions. The hydrogen exchange rate constants of the imino protons were determined for the three DNA duplexes containing the DNA-binding sites for the TCP11, TCP15, and TCP20 transcription factors using NMR spectroscopy. The M11 duplex displays unique hydrogen exchange property of the five base pairs in the first binding site (5'-GTGGG-3'). However, the M15 and M20 duplexes lead to clear changes in thermal stabilities of these five base pairs. The unique dynamic features of the five base pairs in the first binding site might play crucial roles in the sequence-specific DNA binding of the class I TCP transcription factors.

• BMB Reports
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• v.43 no.2
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• pp.133-139
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• 2010

We have performed analyses using ancient DNA extracted from 25 excavated human bones, estimating around the 1st century B.C. Ancient human bones were obtained from Nukdo Island, which is located off of the Korean peninsula of East Asia. We made concerted efforts to extract ancient DNA of high quality and to obtain reproducible PCR products, as this was a primary consideration for this extensive kind of undertaking. We performed PCR amplifications for several regions of the mitochondrial DNA, and could determine mitochondrial haplogroups for 21 ancient DNA samples. Genetic information from mitochondrial DNA belonged to super-haplogroup M, haplogroup D or its sub-haplogroups (D4 or D4b), which are distinctively found in East Asians, including Koreans or Japanese. The dendrogram and principal component analysis based on haplogroup frequencies revealed that the Nukdo population was close to those of the East Asians and clearly distinguished from populations shown in the other regions. Considering that Nukdo is geologically isolated in the southern part of the Korean peninsula and is a site of commercial importance with neighboring countries, these results may reflect genetic continuity for the habitation and migration of ethnic groups who had lived in a particular area in the past. Therefore, we suggest that phylogenetic analyses of ancient DNA have significant advantages for clarifying the origins and migrations of ethnic groups, or human races.

• Environmental Analysis Health and Toxicology
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• v.22 no.4
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• pp.349-355
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• 2007

장수풍뎅이 유충(Allomyrina dichotoma larva, ADL)은 중국의 전통 약재로서, 특히 항산화 효과가 우수하여 항당료 제재로 사용되고 있다. 본 연구에서는 이러한 ADL의 추출물을 이용하여 헴스터 췌장의 ${\beta}$-세포(HIT-T15)에서 Streptozotocin에 의해 유발된 산화적 손상에 대한 보호효과 및 그 작용기전을 조사하였다. ADL추출물은 처리농도 의존적으로 Streptozotocin에 의해 유발된 지질과산화 및 세포 내 자유산 소종의 양을 억제함으로서 ${\beta}$-세포의 산화적 스트레스에 의한 손상을 보호하였다. 또한 DNA laddering 방법을 사용하여 Streptozotocin에 의해 유발된 DNA 손상을 조사한 결과, ADL추출물 처리농도에 비례하여 Streptozotocin에 의해 유발된 DNA 손상이 감소하였다. 이러한 산화적 손상의 억제능 관련 작용 기전을 조사하기 위해 DPPH free radical 소거능을 실시하였다. 그 결과 ADL추출물 자체가 DPPH 자유 레디컬 소거능이 있음을 확인하였으며, 또한 플라스미드를 이용한 Single-strand break 방법을 통한 DNA 손상 보호능을 측정한 결과도 $Fe^{3+}$ 및 $H_2O_2$에 의해 유발된 DNA 손상이 ADL추출물 처리농도에 비례하여 감소하였다. 이러한 결과들을 종합하여 볼 때, 장수풍뎅이 유충의 추출물들이 자체의 레디컬 소거능 및 산화적 손상에 의한 DNA손상을 억제함으로써, Streptozotocin에 의해 유발된 산화적 손상을 억제할 수 있을 것이라 사료된다.