• Bulletin of the Korean Chemical Society
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• 제32권5호
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• pp.1669-1678
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• 2011

Six new binuclear copper(II) complexes have been prepared by template condensation of the dialdehydes 1,8-[bis(3-formyl-2-hydroxy-5-methyl)benzyl]-l,4,8,11-tetraazacyclotetradecane (PC-a) and 1,8-[bis(3-formyl-2-hydroxy-5-bromo)benzyl]-l,4,8,11-tetraazacyclotetradecane (PC-b) with appropriate aliphatic diamines, and copper(II) perchlorate. The structural features of the complexes have been confirmed by elemental analysis, IR, UV-vis and mass spectra etc. The electrochemical behavior of all the copper(II) complexes show two irreversible one electron reduction process. The room temperature magnetic moment studies depict the presence of an antiferromagnetic interaction in the binuclear complexes. The catechol oxidation and hydrolysis of 4-nitrophenylphosphate were carried out by using the complexes as catalyst. The antimicrobial screening data show good results. The binding of the complexes to calf thymus DNA (CT DNA) has been investigated with absorption and emission spectroscopy. The complex [$Cu_2L^{1a}$] displays significant cleavage property of circular plasmid pBR322 DNA in to linear form. Spectral, electrochemical, magnetic and catalytic studies support the distortion of the copper ion geometry that arises as the macrocyclic ring size increases.

• Journal of Microbiology and Biotechnology
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• 제11권6호
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• pp.940-945
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• 2001

Symbiobacterium toebii has been previously reported as a novel commensal thermophile exhibiting a commensal interaction with thermophilic Geobacillus sp. SK-1. We investigated the distribution of this commensal thermophile in various soils using molecular methods, such as quantitative PCR and terminal restriction fragment polymorphism analysis. Based on a nested competitive quantitative PCR the 16S rDNA of the commensal thermophile was only detected in compost soils at about $1.0{\times}10^4$ cpoies per gram of soil, corresponding to $0.25{\times}10^4$ cells per gram of soil. However, in an enrichment experiment at $60^{\circ}C$, about $1.0{\times}10^8$ copies of 16S rDNA molecules were detected per ml of enriched culture broth for all the soils, and more than 0.1 mM indole accumulated as the product of commensal bacterial growth. When incubated at $30^{\circ}C$, neither the 16S rDNA of the commensal bacterium nor any indole accumulation was detected. Accordingly, even though the 16S rDNA of the bacterium was only detected in the compost soils by a nested PCR, the presence of the 16S rDNA molecules of commensal thermophile and accumulation of indole in all the enriched cultures appeared to indicate that the commensal thermophile is widely distributed in various soils.

• Bulletin of the Korean Chemical Society
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• 제28권12호
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• pp.2203-2208
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• 2007

Three possible binding modes of cationic meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (TMPyP) to d[(GCATATATGC)2] duplex were investigated by the molecular dynamics (MD) simulation. Among the three binding modes namely, “along the groove”, “across the groove” and “face on the groove”, the “across the groove” model exhibited the largest negative binding free energy and the DNA backbone remained as the B form. In this model, the molecular plain of the TMPyP tilts 45o with respect to the DNA helix axis and is largely exposed to the solvent. TMPyP was stabilized mainly by the interaction between the positively charged neighboring pyridinium moieties of TMPyP and negatively charged phosphate groups of DNA. The result obtained in this work by MD and the report (Jin, B. et al., J. Am. Chem. Soc. 2005, 127, 2417.) that the spectral properties of poly[d(A-T)2] bound TMPyP in the presence and absence of the minor groove binding drug 4',6- diamidino-2-phenylindole are similar, we propose that TMPyP bind across the minor groove of the AT rich- DNA.

• Bulletin of the Korean Chemical Society
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• 제34권3호
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• pp.810-814
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• 2013

The thermodynamic parameters for the intercalative interaction of structurally related well known intercalators, 9-aminoacridine (9AA) and proflavine (PF) were determined by means of fluorescence quenching study. The fluorescence intensity of 9AA decreased upon intercalation to DNA, poly[$d(A-T)_2$] and poly[$d(G-C)_2$]. A van't Hoff plot was constructed from the temperature-dependence of slope of the ratio of the fluorophore in the absence and presence of a quencher molecule with respect to the quencher concentration, which is known as a Stern-Volmer plot. Consequently, the thermodynamic parameters, enthalpy and entropy change, for complex formation was calculated from the slope and y-intercept of the van't Hoff plot. The detailed thermodynamic profile has been elucidated the exothermic nature of complex formation. The complex formation of 9AA with DNA, poly[$d(A-T)_2$] and poly[$d(G-C)_2$] was energetically favorable with a similar negative Gibb's free energy. On the other hand, the entropy change appeared to be unfavorable for 9AA-poly[$d(G-C)_2$] complex formation, which was in contrast to that observed with native DNA and poly[$d(A-T)_2$] cases. The equilibrium constant for the intercalation of PF to poly[$d(G-C)_2$] was larger than that to DNA, and was the largest among sets tested despite the most unfavorable entropy change, which was compensated for by the largest favorable enthalpy. The favorable hydrogen bond contribution to the formation of the complexes was revealed from the analyzed thermodynamic data.

• Animal cells and systems
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• 제2권4호
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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.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2003년도 제2차 연례학술대회 발표논문집
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• pp.17-25
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• 2003

Determining the binding sites in protein-nucleic acid complexes is essential to the complete understanding of protein-nucleic acid interactions and to the development of new drugs. We have developed a set of algorithms for analyzing protein-nucleic acid interactions and for predicting potential binding sites in protein-nucleic acid complexes. The algorithms were used to analyze the hydrogen-bonding interactions in protein-RNA and protein-DNA complexes. The analysis was done both at the atomic and residue level, and discovered several interesting interaction patterns and differences between the two types of nucleic acids. The interaction patterns were used for predicting potential binding sites in new protein-RNA complexes.

• 대한의생명과학회지
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• 제10권4호
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• pp.407-413
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• 2004

Heterotrimeric GTP binding proteins (G proteins) transduce signals of a variety of hormones and neurotransmitters. Go is one of the most abundant G proteins in the brain and classified as the Gi/Go family due to their sequence homology to Gi proteins. While the Gi proteins inhibit adenylyl cyclase and decrease the intracellular cAMP concentration, the functions of Go is not clearly understood despite their sequence homology to Gi. The promeylocytic leukemia zinc finger protein (PLZF) is a DNA binding transcription factor and is expressed highly in central nervous system (CNS). Several studies reported that PLZF may be involved in regulation segmentation/differentiation during CNS development. Here, I report that the alpha subunit of Go (Go ) interacts with PLZF. The interaction between Goa and PLZF was verified by using GST pulldown assay and co-immunoprecipitation. Our findings indicate that Goa could modulate gene expression via interaction with PLZF during neuronal or brain development.

• BMB Reports
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• 제47권2호
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• pp.92-97
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• 2014

We have examined the effect of bithorax complex genes on the expression of castor gene. During the embryonic stages 12-15, both Ultrabithorax and abdominal-A regulated the castor gene expression negatively, whereas Abdominal-B showed a positive correlation with the castor gene expression according to real-time PCR. To investigate whether ABD-B protein directly interacts with the castor gene, electrophoretic mobility shift assays were performed using the recombinant ABD-B homeodomain and oligonucleotides, which are located within the region 10 kb upstream of the castor gene. The results show that ABD-B protein directly binds to the castor gene specifically. ABD-B binds more strongly to oligonucleotides containing two 5'-TTAT-3' canonical core motifs than the probe containing the 5'-TTAC-3' motif. In addition, the sequences flanking the core motif are also involved in the protein-DNA interaction. The results demonstrate the importance of HD for direct binding to target sequences to regulate the expression level of the target genes.

• 한국식물병리학회:학술대회논문집
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• 한국식물병리학회 2003년도 정기총회 및 추계학술발표회
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• pp.29-29
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• 2003

Incompatible plant-pathogen interactions result in the rapid cell death response known as hypersensitive response (HR) and activation of host defense-related genes. To understand the molecular and cellular mechanism controlling defense response better, several approaches including isolation and characterization of novel genes, promoter analysis of those genes, protein-protein interaction analysis and reverse genetic approach etc. By using the yeast two-hybrid system a clone named Tsipl, Tsil -interacting protein 1, was isolated whose translation product apparently interacted with Tsil, an EREBP/AP2 type DNA binding protein. RNA gel blot analysis showed that the expression of Tsipl was increased by treatment with NaCl, ethylene, salicylic acid, or gibberellic acid. Transient expression analysis using a Tsipl::smGFP fusion gene in Arabidopsis protoplasts indicated that the Tsipl protein was targeted to the outer surface of chloroplasts. The targeted Tsipl::smGFP proteins were diffused to the cytoplasm of protoplasts in the presence of salicylic acid (SA) The PEG-mediated co-transfection analysis showed that Tsipl could interact with Tsil in the nucleus. These results suggest that Tsipl-Tsil interaction might serve to regulate defense-related gene expression. Basically the useful promoters are valuable tools for effective control of gene expression related to various developmental and environmental condition.(중략)

• Journal of Animal Science and Technology
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• 제60권6호
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• pp.11.1-11.7
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• 2018

After pubertal, cohort of small antral follicles enters to gonadotrophin-sensitive development, called recruited follicles. This study was aimed to identify candidate genes in follicular cyclic recruitment via analysis of protein-protein interaction (PPI) network. Differentially expressed genes (DEGs) in ovine granulosa cells of small antral follicles between follicular and luteal phases were accumulated among gene/protein symbols of the Ensembl annotation. Following directed graphs, PTPN6 and FYN have the highest indegree and outdegree, respectively. Since, these hubs being up-regulated in ovine granulosa cells of small antral follicles during the follicular phase, it represents an accumulation of blood immune cells in follicular phase in comparison with luteal phase. By contrast, the up-regulated hubs in the luteal phase including CDK1, INSRR and TOP2A which stimulated DNA replication and proliferation of granulosa cells, they known as candidate genes of the cyclic recruitment.