• 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.

• BMB Reports
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• v.29 no.1
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• pp.1-10
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• 1996

The binding interaction of ethidium to a series of synthetic deoxyoligonucleotides containing a B-Z junction between left-handed Z-DNA and right-handed B-DNA, was studied. The series of deoxyoligonucleotides was designed so as to vary a dinucleotide step immediately adjacent to a B-Z junction region. Ethidium binds to the right-handed DNA forms and hybrid B-Z forms which contain a B-Z junction, in a highly cooperative manner. In a series of deoxyoligonucleotides, the binding affinity of ethidium with DNA forms which were initially hybrid B-Z forms shows over an order of magnitude higher than that with any other DNA forms, which were entirely in B-form DNA The cooperativity of binding isotherms were described by an allosteric binding model and by a neighbor exclusion model. The binding data were statistically compared for two models. The conformation of allosterically converted DNA forms under binding with ethidium is found to be different from that of the initial B-form DNA as examined by CD spectra. The ratio of the binding constant was interestingly correlated to the free energy of base unstacking and the conformational conversion of the dinucleotide. The more the base stacking of the dinucleotide is unstable, or the harder the conversion of B to A conformation, the higher the ratio of the binding constant of ethidium with the allosterically converted DNA forms and with the initial B-Z hybrid forms. DNA sequence around a B-Z junction region affects the binding affinity of ethidium. The results in this study demonstrate that ethidium could preferentially interact with unusual DNA structures.

• YAKHAK HOEJI
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• v.40 no.6
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• pp.697-704
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• 1996

Quinolone derivatives, SJ5b (ethyl 5,12-dihydro-5-dihydro-5-oxobenzoxazolo[3,2-a]quinoline-6-carboxylate) and SQ7b (3-fluoro-2-(4-methylpiperazin-1-yl)-5.12-dihydro-5-oxobenzoxa zolo[3,2-a]quinoloine carboxylic acid) showed in vitro cytotoxicities against various tumor cell lines. SJ5b and SQ7b completely inhibited the DNA relaxation activities of human placental topoisomerase II at the concentration of 15.63 and 1.95 ${\mu}$g/ml, respectively. However, unlike etoposide which stabilize the topoisomerase II-DNA complex, SQ7b did not cause topoisomerase II-mediated DNA cleavage and SJ5b weakly stabilized the topoisomerase II-DNA cleavable complex. Through both experiments. DNA relaxation assay by the increment of topoisomerase II concentration and DNA unwinding assay, it was shown that SJ5b and SQ7b did not interact with topoisomerase II itself but bound to DNA. Therefore, it was concluded that DNA binding of SJ5b and SQ7b caused the inhibition of topoisomerase II related to DNA relaxation but no or very weak stabilization of topoisomerase II-DNA cleavable complex. In addition, SJ5b and SQ7b prevented whole cell nucleic acid syntheses in HL60 cells.

• The Korean Journal of Physiology and Pharmacology
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• v.27 no.5
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• pp.427-436
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• 2023

Mitotic arrest deficient 2 like 2 (Mad2L2, also known as Mad2B), the human homologue of the yeast Rev7 protein, is a regulatory subunit of DNA polymerase ζ that shares high sequence homology with Mad2, the mitotic checkpoint protein. Previously, we demonstrated the involvement of Mad2B in the cisplatin-induced DNA damage response. In this study, we extend our findings to show that Mad2B is recruited to sites of DNA damage in human cancer cells in response to cisplatin treatment. We found that in undamaged cells, Mad2B exists in a complex with Polζ-Rev1 and the APC/C subunit Cdc27. Following cisplatin-induced DNA damage, we observed an increase in the recruitment of Mad2B and Cdc20 (the activators of the APC/C), to the complex. The involvement of Mad2B-Cdc20-APC/C during DNA damage has not been reported before and suggests that the APC/C is activated following cisplatin-induced DNA damage. Using an in vitro ubiquitination assay, our data confirmed Mad2B-dependent activation of APC/C in cisplatin-treated cells. Mad2B may act as an accelerator for APC/C activation during DNA damage response. Our data strongly suggest a role for Mad2B-APC/C-Cdc20 in the ubiquitination of proteins involved in the DNA damage response.

• Environmental Mutagens and Carcinogens
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• v.19 no.1
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• pp.34-38
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• 1999

Fumonisin B1 is a secondary metabolite of Fusarium moniliforme, a contaminant of corn and corn product. Fumonisin B1 has been shown to be responsible for major toxicological effects of the fungus in rats, horses, and pigs. Fumonisin B1 induced λ DNA fragmentation, which was increased with incubation time, reducing agent NADPH and metal ion (Cu2+). The DNA damage was inhibited by dimethyl sulfoxide (DMSO) or mannitol as radical scavenger for free radicals. DNA fragmentation, induced by fumonisin B1 in the presence of 1 mM NADPH and 0.1 mM CuCl2, was inhibited by 100 mM DMSO. By the in vitro reaction of fumonisin B1 with supercoiled plasmid pBR322 DNA, plasmid DNA was relaxed, eventually linearized in the agarose gel electrphoresis. From rifampicin sensitive E. coli CSH138 in bacterial mutagenesis system, the rifampicin resistant E. coli mutants were obtained by fumonisin B1. These results suggest that fumonisin B1 may be a possible environmental mutagen in bacterial mutagen assay system.

• Biomolecules & Therapeutics
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• v.31 no.3
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• pp.340-349
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• 2023

Mad2B (Mad2L2), the human homolog of the yeast Rev7 protein, is a regulatory subunit of DNA polymerase ζ that shares sequence similarity with the mitotic checkpoint protein Mad2A. Previous studies on Mad2B have concluded that it is a mitotic checkpoint protein that functions by inhibiting the anaphase-promoting complex/cyclosome (APC/C). Here, we demonstrate that Mad2B is activated in response to cisplatin-induced DNA damage. Mad2B co-localizes at nuclear foci with DNA damage markers, such as proliferating cell nuclear antigen and gamma histone H2AX (γ-H2AX), following cisplatin-induced DNA damage. However, unlike Mad2A, the binding of Mad2B to Cdc20 does not inhibit the activity of APC/C in vitro. In contrast to Mad2A, Mad2B does not localize to kinetochores or binds to Cdc20 in spindle assembly checkpoint-activated cells. Loss of the Mad2B protein leads to damaged nuclei following cisplatin-induced DNA damage. Mad2B/Rev7 depletion causes the accumulation of damaged nuclei, thereby accelerating apoptosis in human cancer cells in response to cisplatin-induced DNA damage. Therefore, our results suggest that Mad2B may be a critical modulator of DNA damage response.

• Korean Journal of Food Science and Technology
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• v.24 no.4
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• pp.367-370
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• 1992

Aflatoxins are highly carcinogenic agents consistantly found as contaminants in human food supplies in many areas of the world and epidemiologically linked to incidence of human liver cancer. To examine the carcinogenic action of aflatoxin $B_1$, aflatoxin $B_1-DNA$ adducts were chemically synhtesized with the reaction of 20 mg calf thymus DNA, and 8 mg standard aflatoxin $B_1$. Since DNA molecule was too large for analysis, it was fragmented by acid hydrolysis and heat. The fragmented aflatoxin $B_1-DNA$ adducts were selectively concentrated by immunoaffinity column procedure and confirmed by HPLC method. The main component was aflatoxin $B_1-guanine$ adduct, which was quantatively measured as 5.2 mg aflatoxin $B_1$.

• Microbiology and Biotechnology Letters
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• v.4 no.4
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• pp.166-178
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• 1976

Taxonomic study of 11 strains of Bacillus coagulans and 14 strains of 13 spccies of Bacillus by deoxyribonucleic acid (DNA)-DNA hybridization were conducted. Among the 11 strains of B. coagulans, 6 were isolated from soil and the rest were the authentic strains obtained from American Type culture collection (ATCC) or the Institute for Fermentation, Osaka (IFO). All strains were examined to confirm as they are expected species of B. coagulans by the methods of Cordon et al. according to Bergey's Manual (8th ed.). The intraspecific DNA homology indexes among the 11 strains of B. coagulans using strain ATCC 7050 as the standard ($^3$H labeled input DNA) showed 76％ or, more, respectively. These findings accorded well with the results of the conventional taxonomic study according to the Bergey's Manual. The interspecific DNA homology indexes between B. coagulant strain ATCC 7050 and the type cultures of B. subtilis (168), B. licheniformis (IFO 12107), B. pumilus (IFO 12110), B. firmus (ATCC 14575), B. lentus (ATCC 10840), B. circulans (ATCC 4513), B. macelans (ATCC 8244), B. polymyxa (ATCC 842), B. sphaericus (ATCC 14577), B. brevis (ATCC 8246, IFO 12334), B. laterosporus (ATCC 64), and B. pantothenticus (ATCC 14576) respectively, showed 2 to 4％, while that of between B. coagulans ATCC 7050 and Escherichia coli K-12 was less than 1 ％.

• Environmental Mutagens and Carcinogens
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• v.18 no.2
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• pp.77-82
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• 1998

In order to compare the suppressive effect of galangin on the genotoxicity by N-methyl-N-nitrosourea (MNU) or benzo[a]pyrene B(a)P, in vivo micronycleus test using mouse peripheral blood and in vitro sister chromatid exchange(SCE) test using mouse spleen lymphocytes were performed. MNU or B(a)P-induced micronucleated reticulocytes in vivo was decreased by the simultaneous treatment of galangin. MNU or B(a)P-induced SCEs in vitro was also decreased by the simultaneous treatment of galangin. On the other hand, the determinations of [$^3$H]MNU-induced total DNA binding and methylated DNA were performed to find out the mechanism of action. [$^3$H]MNU-induced total DNA binding was inhibited by the treatment of galangin in calf thymus DNA. HPLC analysis of DNA hydrolysates showed that galangin caused a decrease of 7-methyl guanine and $O^{6}$-methyl guanine in calf thymus DNA. To elucidate the action mechanism of galangin against B(a)P, alteration of B(a)P metabolism was studied. Galangin inhibited B(a)P metabolism in the presence of S-9 mix and decreased B(a)P-DNA binding in calf thymus DNA with S-9 mix.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.15
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• pp.6535-6539
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• 2015

This study was designed to assess, whether a new chemotherapeutic microtubule inhibitor, Epothilone B (EpoB, Patupilone), can induce DNA damage in normal ovarian cells (MM14.Ov), and to evaluate if such damage could be repaired. The changes were compared with the effect of paclitaxel (PTX) commonly employed in the clinic. The alkaline comet assay technique and TUNEL assay were used. The kinetics of DNA damage formation and the level of apoptotic cells were determined after treatment with IC50 concentrations of EpoB and PTX. It was observed that PTX generated significantly higher apoptotic and genotoxic changes than EpoB. The peak was observed after 48 h of treatment when the DNA damage had a maximal level. The DNA damage induced by both tested drugs was almost completely repaired. As EpoB in normal cells causes less damage to DNA it might be a promising anticancer drug with potential for the treatment of ovarian tumors.