• Journal of the Korean Chemical Society
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• v.38 no.1
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• pp.21-25
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• 1994

The proton affinities of substituted imidazoles, relevant to the binding of lexitropsins that contain imidazole ring to the base pair (G-C sequence) of minor groove of DNA, are studied with the aid of EHT calculations. It is shown that proton affinity of imidazole substituted at position $\alpha$ to the basic nitrogen is slightly larger than that of imidazole substituted at N for the methylimidazole. Proton affinities of N-substituted imidazoles are found to be larger than those of imidazoles substituted at position ${\alpha}$ for a selected set of the other derivatives. As predicted the proton affinity increases when electron-donating group is attached at position N of imidazole.

• Bulletin of the Korean Chemical Society
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• v.21 no.10
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• pp.1052-1054
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• 2000

Binding geometries of $[Ru(II)(110-phenanthroline)_2L]^2+$, complexes (where L = dipyrido [3,2-a:2',3'-c]phena-zine (DPPZ) or benzodipyrido[3,2-a:2',3'-c] phenazine (BDPPZ)) to poly(dG)${\cdot}$poly(dC)${\cdot}$poly(dC) + triplex DNA (CGC + triplex) has been investigated by linear dichroism and normal absorption spectroscopy. Analysis of the linear dichroism for the CGC+ triplex and $[Ru(II)(phen)_2BDPPZ]^2+$ complex indicates that the extended ligand of the metal complex lie perpendicular to the polynucleotide helix axis. Together with strong hypochromism and red shift in the interligand absorption region, we concluded that the extended BDPPZ or DPPZ ligand in-tercalated between the bases of polynucleotide. The spectral properties of the metal complexes bound to CGC+ triplex are similar to those bound to $poly(dA)[poly(dT)]^2$ triplex (Choi et al., Biochemistry 1997, 36, 214), sug-gesting that the metal complex is located in the minor groove of the CGC+ triplex.

• Archives of Pharmacal Research
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• v.25 no.1
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• pp.11-24
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• 2002

The antitumor antibiotic (+)-CC-1065 can alkylate N3 of guanine in certain sequences. A previous high-field $^1H$ NMR study on the$(+)-CC-1065d[GCGCAATTG*CGC]_2$ adduct ($^*$ indicates the drug alkylation site) showed that drag modification on N3 of guanine results in protonation of the cross-strand cytosine [Park, H-J.; Hurley, L. H. J. Am. Chem. Soc.1997, 119,629]. In this contribution we describe a further analysis of the NMR data sets together with restrained molecular dynamics. This study provides not only a solution structure of the (+)-CC-1065(N3- guanine) DNA duplex adduct but also new insight into the molecular basis for the sequence- specific interaction between (+)-CC-1065 and N3-guanine in the DNA duplex. On the basis of NOESY data, we propose that the narrow minor groove at the 7T8T step and conformational kinks at the junctions of 16C17A and 18A19T are both related to DNA bending in the drugDNA adduct. Analysis of the one-dimensional $^1H$ NMR (in $H_2O$) data and rMD trajectories strongly suggests that hydrogen bonding linkages between the 8-OH group of the (+)-CC-1065 A-sub-unit and the 9G10C phosphate via a water molecule are present. All the phenomena observed here in the (+)-CC-1065(N3-guanine) adduct at 5'$-AATTG^*$are reminiscent of those obtained from the studies on the (+)-CC-1065(N3-adenine) adduct at $5'-AGTTA^*$, suggesting that (+)-CC-1065 takes advantage of the conformational flexibility of the 5'-TPu step to entrap the bent structure required for the covalent bonding reaction. This study reveals a common molecular basis for (+)-CC-1065 alkylation at both $5'-TTG^*$ and $5'-TTA^*$, which involves a trapping out of sequence-dependent DNA conformational flexibility as well as sequence-dependent general acid and general base catalysis by duplex DNA.

• Proceedings of the Korean Society for Applied Microbiology Conference
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• 2001.06a
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• pp.27-31
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• 2001

Previous biochemical assays and a structural model indicated that the dimer interface of the Hin recombinase is composed of the two a-helices. To elucidate the structure and function of the helix, amino acids in the N-terminal end of the helix, where the two helices contact most, were randomized, and inversion-incompetent mutants were selected. To investigate why the mutants lost their inversion activities, the DNA binding, hix-pairing, invertasome formation, and DNA cleavage activities were assayed using in vivo and in vitro methodologies. Results indicated that the mutants could be divided into 4 classes based on their DNA binding activity. We proposed that the a-helices might place a DNA binding motif of Hin properly to the minor DNA groove of the recombination site. All the mutants except the non-binders were able to perform hix-pairing and invertasome formation, suggesting that the dimer interface is not involved in the process of hix-pairing or invertasome formation. The inversion-incompetent phenotype of the binders was caused by the inability of mutants to perform the DNA cleavage activity. The less binders exhibited wild-type level of hix-pairing activity because the hix-pairing activity overcomes the DNA binding defect of the less binders. This phenotype of the less binders suggests that the binding domains of Hin could mediate Hin-Hin interaction during hix-pairing..

• Molecular & Cellular Toxicology
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• v.4 no.2
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• pp.144-149
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• 2008

Despite versatile activity (cancericidal, antimicrobial, hypoxia inducible factor (HIF) inhibition, immune deactivation of DNA bis-intercalation agent, echinomycin, its specific mechanism has been elusive. Of these novel mechanisms, we reported that using human colon cancer cells (HT-29), apoptotic machinery induced by echinomycin might be dependent of caspase-3 pathway. Despite a partial enlightenment of prototypic signal path triggered by echinomycin, the role of Bcl-2 in this signaling pathway is unclear. To address this issue, we explored whether or not echinomycin would overcome the anti-apoptotic impact of Bcl-2 in HT-29 cells by the controlled Bcl-2 overexpression. Prior to this proof, we confirmed that echinomycin induces mitochondrial depolarization, then triggering the mitochondrial pathway of apoptosis with an involvement of upstream cas-pases-3. Transiently transfection with inactive Bax-DNA failed to prevent echinomycin-induced apoptosis in HT-29 cells. To dissect the role of Bcl-2 in echinomycin-induced apoptosis, HT-29 cells were transiently transfected with Bcl-2 DNA for overexpression and then treated with echinomycin for 24h. Combined analyses of DNA fragmentation and flow cytometric analysis clearly verified that echinomycin-induced apoptosis was drastically attenuated by Bcl-2 overexpression, whereas a control vector rarely affected echinomycin-induced apoptosis. Collectively, these data verify that Bcl-2 regulates echinomycin-induced apoptosis in HT-29 cells. To my knowledge, this is the first evidence that of diverse, structured minor groove binders (MGB), the prototypic echinomycin might control the apoptotic signaling via Bcl-2-mitochondrial pathway.

• Animal cells and systems
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• v.2 no.4
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• pp.539-543
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• 1998

Hrp1, of Schizosaccharomyces pombe, is a new member of the SW12/SNF2 protein family that contains a chromodomain and a DNA binding domain as well as ATPase/7 helicase domains. This configuration suggests that Hrp1 could be a homolog of mouse CHD1, which is thought to function in altering the chromatin structure to facilitate gene expression. To understand the enzymatic nature of Hrp1 we purified the 6-Histidine-tagged Hrp1 protein (6$\times$His-Hrp1) to homogeneity from a S. pombe Hrp1-overexpressing strain and hen examined its biochemical properties. We demonstrate that the purified 6$\times$His-Hrp1 protein exhibited a DNA-binding activity with a moderate preference to the (A＋T)-rich tract in double-stranded NA via a minor groove interaction. However, we failed to detect any intrinsic DNA helicase activity from the purified Hrp1 like other SW12/SNF2 proteins. These observations suggest that the DNA binding activities of Hrp1 may be involved in the remodeling of the chromatin structure with DNA-dependent ATPase. We propose that Hrp1 may function in heterochromatins as other proteins with a chromo- or ATPase/helicase domain and play an important role in the determination of chromatin architecture.

• Journal of the Korean Chemical Society
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• v.44 no.1
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• pp.45-51
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• 2000

The binding mode of anthryl derivatives to synthetic polynucleotides were investigated by various spectroscopic methods. The spectroscopic properties of anthracence with metbylamine and methylethylenediamine side chains, complexed with $poly[d(A-T)_2]$ and $poly[d(G-C)_2]$, can be summarized as a red-shift, with a strong hypochromism in the absortion spectrum, similar induced CD spectra, and a strong negative LD spectrum with an $LD^r$ magnitude comparable to the DNA absorption region. These observations indicate that anthracene moiety is intercalated between the nucleo-bases of $poly[d(A-T)_2]$ and $poly[d(G-C)_2]$. The side chains did not alter the spectroscopic properties, demonstrating that the binding mode was not affected by them. A strong energy transfer was observed from poly[d(A-T),] and $poly[d(I-C)_2]$ but not from $poly[d(G-C)_2]$, as reported by Kumar et al. (J. Am. Chem. Soc.(1993) 115, 8547). Since the binding mode is the same for all the polynucleotides, the amine group of the guanine base, which protrudes into the minor groove of $poly[d(G-C)_2]$, is concluded to disrupt the energy transfer.

• Korean Journal of Head & Neck Oncology
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• v.18 no.1
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• pp.11-17
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• 2002

Objectives: Expression of HMGI(Y), a nucleoprotein that binds to A/T rich sequences in the minor groove of the DNA helix, is observed in neoplastically transformed cells but not in normal cells. We have analyzed HMGI(Y), p53 expression and Ki-67 labelling index in squamous cell carcinomas of the head and neck, and evaluated its clinicopathologic significance. Materials and Methods: 40 cases of squamous cell carcinoma of the head and neck were entered on the study of immunohistochemical stains for HMGI(Y), p53 and Ki-67. We analyzed the relationship between HMGI(Y), p53, Ki-67 expression and age, sex, primary tumor site, stage, survival rate, recurrence. Results: HMGI(Y) expression evidenced by immunohistochemical staining was observed in 35 of 40 (87.5%) squamous cell carcinoma of the head and neck. But no significant correlation was observed between HMGI(Y) expression and other clinical factors such as primary site, tumor stage, differenciation, cervical lymph node, metastasis, recurrence and immunohistochemical status of p53. The Ki-67 labelling index was significantly correlated with recurrence and HMGI(Y) expression (p<0.05). Conclusion: This results suggest the Ki-67 is a good prognostic factor and the HMGI(Y) expression plays some roles in carcinogenesis and cellular proliferation of squamous cell carcinoma of the head and neck. HMGI(Y) gene can be used as a cancer marker, the correlation between the gene expression and the prognosis of the cancer patient should be proved in the future studies.