• Journal of the Korean Chemical Society
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• v.58 no.2
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• pp.153-159
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• 2014

Herein, the cyclic voltammetric (CV) investigations of structurally similar bisnitrocompounds (N3, N4, N5, N6, having different-$CH_2$-spacer length) is presented. CV study offered interesting interactional possibilities of bisnitrocompounds with chicken blood ds.DNA at physiological pH 4.7 and human body temperature, 310 K. The results indicated strong interaction by these symmetric molecules with ds.DNA and strength of binding is found to depend on length of $CH_2$ spacer group in their molecular structure. Thermodynamics derived from electrochemical binding parameters also favored the irreversible interactions. Moreover, threading intercalation mode of binding is suggested based on thermodynamic and kinetic binding parameters extracted from CV studies.

• Journal of Microbiology
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• v.33 no.2
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• pp.165-170
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• 1995

The 356 amino acid long lambda integrase protein of bacteriophage .lambda. constains two autonomous DNA binding domains with distinct sequence specificities. The amino terminal domain of integrase is implicated to bind to the arm-type sequences and the carboxyl domain interacts with the coretype sequencess. As a first step to understand the molecular mechanism of the integrase-DNA interaction at the arm-type site, the int(am)94 gene carrying an amber mutation at the 94th codon of the int was cloned under the control of the P$\_$tac/ promoter and the lacI$\_$q/ gene. The Int(am)94 mutant protein of amino terminal 93 amino acid residues can be produced at high level from a suppressor free strain harboring the plasmid pInt(am)94. The arm-type binding activity of Int(am)94 were measured in vivo and in vitro. A comparison of the arm-type binding properties of the wild-type integrase and the truncated Int(am)94 mutant indicated that the truncated fragment containing 93 amino acid residues carry all the determinants for DNA binding at the arm-type sites.

• BMB Reports
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• v.38 no.6
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• pp.690-694
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• 2005

Transcription termination of the human mitochondrial genome requires specific binding to termination factor mTERF. In this study, mTERF was produced in E. coli and purified by two-step chromatography. mTERF-binding DNA sequences were isolated from a pool of randomized sequences by the repeated selection of bound sequences by gel-mobility shift assay and polymerase chain reaction. Sequencing and comparison of the 23 isolated clones revealed a 16-bp consensus sequence of 5'-GTG$\b{TGGC}$AGANCCNGG-3' in the light-strand (underlined residues were absolutely conserved), which nicely matched the genomic 13-bp terminator sequence 5'-$\b{TGGC}$AGAGCCCGG-3'. Moreover, mTERF binding assays of heteroduplex and single-stranded DNAs showed mTERF recognized the light strand in preference to the heavy strand. The preferential binding of mTERF with the light-strand may explain its distinct orientation-dependent termination activity.

• Bulletin of the Korean Chemical Society
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• v.28 no.4
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• pp.607-612
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• 2007

Relationship between charge transfer mechanism and quantum coherence has been investigated using a realtime quantum dynamics approach. In the on-the-fly filtered propagator functional path integral simulation, by separating paths that belong to different mechanisms and by integrating contributions of correspondingly sorted paths, it was possible to accurately obtain quantitative contribution of different transport mechanisms. For a 5'-GAGGG-3' DNA sequence, we analyze charge transfer processes quantitatively such that the governing mechanism alters from coherent to incoherent charge transfer with respect to the friction strength arising from dissipative environments. Although the short DNA sequence requires substantially strong dissipation for completely incoherent hopping transfer mechanism, even a weak system-environment interaction markedly destroys the coherence within the quantum mechanical system and the charge transfer dynamics becomes incoherent to some degree. Based on the forward-backward path deviation analysis, the coherence variation depending on the environment is investigated numerically.

• Bulletin of the Korean Chemical Society
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• v.25 no.8
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• pp.1211-1216
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• 2004

The interaction of the antitumour agent doxorubicin with calf thymus DNA is investigated in an aqueous solution at a pH level of 6-7 with molar ratios of 1/10. A UV-resonance Raman spectroscopy and surface enhanced Raman spectroscopy are used to determine the doxorubicin binding sites and the structural variations of doxorubicin-DNA complexes in an aqueous solution. Doxorubicin intercalates with adenine and guanine via a hydrogen bond formation between the N7 positions of purine bases and the hydroxyl group of doxorubicin.

• Bulletin of the Korean Chemical Society
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• v.32 no.7
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• pp.2217-2221
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• 2011

We investigated the selective deoxyribonucleic acid (DNA) adsorption on layered double hydroxide (LDH) nanoparticles via studying the interaction between positively charged LDH nanoparticle as adsorbent and negatively charged adsorbates such as methyl orange (MO), fluorescein (FL), and DNA strands. The size controlled LDH $(Mg_{0.78}Al_{0.22}(OH)_2(CO_3)_{0.11}{\cdot}mH_2O)$ was prepared by conventional coprecipitation method, followed by the hydrothermal treatment. According to the adsorption isotherms, the adsorbed amounts of MO and FL were similar, however, that of DNA were much larger. The adsorption behaviors were well fitted to Freundlich adsorption model. The concentration dependent adsorption behavior on LDH surface was described in order to verify the selective DNA separation ability. The result showed that the LDH has advantages in selective adsorption of DNA competing with single molecular anions.

• Bulletin of the Korean Chemical Society
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• v.15 no.5
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• pp.364-368
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• 1994

Growth inhibition potency of the anthraquinones, anthraquinone-1,5-disulfonic acid and carminic acid, for Sarcoma 180 and L1210 leukemia cells in vivo and in vitro, was induced by the divalent transition metal ion, $Cu^{2+}$. On the other hand spectroscopic titration data show that the anthraquinone drugs form $Cu2^+$ chelate complexes (carminic acid : $Cu^{2+}$ = 1 : 6; anthraquinone-1,5-disulfonic acid : $Cu^{2+}$ = 1 : 3). Furthermore the $Cu^{2+}$-drug complexes associate with DNA to form the $Cu^{2+}$-anthraquinone-DNA ternary complexes. The formation of the complexes was further supported by the $H_2O_2-dependent$ DNA degradation, which can be inhibited by ethidium bromide, caused by the $Cu^{2+}$-drug complexes. It is likely that the $Cu^{2+}$-mediated cytotoxicity of the anthraquinone drugs is related with the $Cu^{2+}-mediated$ binding of the anthraquinone drugs to DNA and DNA degradation.

• Proceedings of the Korean Information Science Society Conference
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• 2004.04b
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• pp.265-267
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• 2004

생명체의 기본 정보가 저장된 DNA에서 생성되는 단백질은 생명 현상의 중요한 기능적 역할을 수행하기 때문에 단백질과 관련된 다양한 연구가 진행되고 있다. 본 논문에서는 단백질간 상호작용(protein-protein interaction)을 예측하기 위해 시스템을 통계학적 모델인 Support Vector Machine(SVM)을 사용하였다. SVM 시스템은 상호작용이 있는 데이터(긍정예제)와 상호작용이 없는 데이터(부정예제)를 입력으로 하여 모델링 생성과 테스트를 하는데, 상호작용이 있는 데이터는 DIP에 있는 interaction list로 해결이 가능하지만 상호작용이 없는 데이터는 현재 존재하지 않기 때문에 이를 생성하기 위한 생성방법이 필요하다. 이 논문에서는 shuffling, non-interaction list, 그리고 앞의 두 방법을 보완하는 non-interaction list ＋ shuffling이라는 방법을 제시하고 기존의 실험 결과를 상회하는 부정예제 생성방법을 제시한다.

• Korean Journal of Animal Reproduction
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• v.19 no.2
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• pp.95-104
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• 1995

Mouse mammary epithelial cells(NMuMG) were maintained onto 6-well plates (3$\times$105 cells/well) or chambered slide (1$\times$104 cells/well), in DMEM supplemented with 10% fetal calf serum. After serum starvation for 24 hours, DMNB (1$\mu$M) was added and exposed to UV light (300nm, 3 second pulse) after 2 hours from DMNB addition in order to activate DMNB which induces a rapid transient increase in intracellular cAMP upon UV irradiation. EGF (100ng/ml) and/or IGF-I (10ng/ml) were treated at the time of UV irradiation. Nuclear labeling index was estimated as percent of nuclear labeled cells(percent of S phase of cells) by incorporation of 3H-thymidine into DNA(1 hour pulse with 1$\mu$Ci/ml). DMNB(1$\mu$M), EGF (100ng/ml) and/or IGF-I (10ng/ml) signifciantly increased nuclear labeling index than those of control (P<0.05). Addition of DMNB＋EGF or DMNB＋EGF＋IGF-I showed the interaction effect in nuclear labeling index (P<0.05). Protein kinase A activities by addition of EGF, IGF-I or EGF＋IGF-I were 10.5, 9.8 or 9.4 unit/mg protein, respectively, and no statistical difference was found in comparison with control (P>0.05). Additon of DMNB＋EGF showed the moderate interaction effect on tyrosyl kinase activity (P<0.1). In the fluorography analysis, there were no specific protein phosphorylation patterns were found at 1 or 15 minute by addition of DMNB. EGF and/or IGF-I. These results suggest that the interaction effect in nuclear labeling index by addition DMNB and EGF could be mediated through the modulation of tyrosyl kinase activity by cAMP.

• The Korean Journal of Physiology and Pharmacology
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• v.7 no.1
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• pp.9-14
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• 2003

Recent studies indicated that cancer cells become resistant to ionizing radiation (IR) and chemotherapy drugs by enhanced DNA repair of the lesions. Therefore, it is expected to increase the killing of cancer cells and reduce drug resistance by inhibiting DNA repair pathways that tumor cells rely on to escape chemotherapy. There are a number of key human DNA repair pathways which depend on multimeric polypeptide activities. For example, Ku heterodimer regulatory DNA binding subunits (Ku70/Ku80) on binding to double strand DNA breaks (DSBs) are able to interact with 470-kDa DNA-dependent protein kinase catalytic subunit (DNA-PKcs), and are essential for DNA-dependent protein kinase (DNA-PK) activity. It has been known that DNA-PK is an important factor for DNA repair and also is a sensor-transmitting damage signal to downstream targets, leading to cell cycles arrest. Our ultimate goal is to develop a treatment of breast tumors by targeting proteins involved in damage-signaling pathway and/or DNA repair. This would greatly facilitate tumor cell cytotoxic activity and programmed cell death through DNA damaging drug treatment. Therefore, we designed a domain of Ku80 mutants that binds to Ku70 but not DNA end binding activity and used the peptide in co-therapy strategy to see whether the targeted inhibition of DNA-PK activity sensitized breast cancer cells to irradiation or chemotherapy drug. We observed that the synthesized peptide (HNI-38) prevented DNA-PKcs from binding to Ku70/Ku80, thus resulting in inactivation of DNA-PK activity. Consequently, the peptide treated cells exhibited poor to no DNA repair, and became highly sensitive to IR or chemotherapy drugs, and the growth of breast cancer cells was inhibited. Additionally, the results obtained in the present study also support the physiological role of resistance of cancer cells to IR or chemotherapy.