• KSBB Journal
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• v.17 no.1
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• pp.1-13
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• 2002

Label-free optical methods for the monitoring of interactions between biological molecules have become increasingly popular within the last decade. A rising number of publications have demonstrated the benefits of direct biomolecular interaction analysis(BIA) for biology and biochemistry, such as antigen-antibody Interactions, receptor-ligand interactions, protein-DNA, DNA- intercalator, and DNA-DNA interactions. This article gives an overview of the historical development, principle and application of label-free optical biosensor to examine the functional characteristics of biospecific interaction, such as kinetics, affinity, and binding position of biomolecular between an immobilized species at the transducer surface and its dissolved binding partner.

• Archives of Pharmacal Research
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• v.27 no.11
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• pp.1161-1167
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• 2004

Adriblastina, a cancerostatic anthracycline antibiotic, causes considerable oxidative damage to DNA molecules. The interaction of this compound with DNA was investigated using Osteryoung square wave stripping voltammetry (OSWSV) and cyclic voltammetry (CV) at an in situ mercury film electrode. It was found that the equilibrium constant of the bonded oxidized form of the drug was 63 times bigger more important than that of the bonded reduced form. Copper forms 1 metal: 2 drug stoichiometry complex which is highly stable compared to ssDNA-drug interaction and consequently inhibited the drug biochemical damaging effects. Copper complex offered sub-nanogram determination of adriblastina in aqueous and urine media.

• Proceedings of the Korean Institute of Electrical and Electronic Material Engineers Conference
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• 2006.06a
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• pp.404-405
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• 2006

Microarray-based DNA chips provide an architecture for multi-analyte sensing. In this paper, we report a new approach for DNA chip microarray fabrication. Multifunctional DNA chip microarray was made by immobilizing many kinds of biomaterials on transducers (particles). DNA chip microarray was prepared by randomly distributing a mixture of the particles on a chip pattern containing thousands of m-scale sites. The particles occupied a different sites from site to site. The particles were arranged on the chip pattern by the random fluidic self-assembly (RFSA) method, using a hydrophobic interaction for assembly.

• Journal of Life Science
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• v.6 no.3
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• pp.185-192
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• 1996

Bacteriophage T7 gene 2.5 protein, a single-stranded DNA binding protein, is required for T7 DNA replication, recombination, and repair. T7 gene 2.5 protein has two distinctive domains, DNA binding and C-terminal domain, directly involved in protein-protein interaction. Gene 2.5 protein participates in the DNA replication of Bacteriophage T7, which makes this protein essential for the T7 growth and DNA replication. What gene 2.5 protein makes important at T7 growth and DNA replication is its binding affinity to single-stranded DNA and the protein-protein important at T7 DNA replication proteins which are essential for the T7 DNA synthesis. We have constructed pGST2.5(WT) encoding the wild-type gene 2.5 protein and pGST2.5$\Delta $21C lacking C-terminal 21 amino acid residues. The purified GST-fusion proteins, GST2.5(WT) and GST2.5(WT)$\Delta$21C, were used for whether the carboxyl-terminal domain participates in the protein-protein interactions or not. GST2.5(WT) and GST2.5$\Delta$21C showed the difference in the protein-protein interaction. GST2.5(WT) interacted with T7 DNA polymerase and gene 4 protein, but GST2.5$\Delta$21C did not interact with either protein. Secondly, GST2.5(WT) interacts with gene 4 proteins (helicase/primase) but not GST2.5$\Delta$21C. these results proved the involvement of the carboxyl-terminal domain of gene 2.5 protein in the protein-protein interaction. We clearly conclude that carboxy-terminal domain of gene 2.5 protein is firmly involved in protein-protein interactions in T7 replication proteins.

• Bulletin of the Korean Chemical Society
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• v.30 no.9
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• pp.1973-1977
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• 2009

In the present study, at first, 2,4-Dihydroxy Salophen (2,4-DHS), has been synthesized by combination of 1, 2-diaminobenzene and 2,4-dihydroxybenzaldehyde in a solvent system. This ligand containing meta-quinone functional groups were characterized using UV-Vis and IR spectroscopies. Subsequently, the interaction between native calf thymus deoxyribonucleic acid (ct-DNA) and 2,4-DHS, was investigated in 10 mM Tris/HCl buffer solution, pH 7.2, using UV-visible absorption and fluorescence spectroscopies, thermal denaturation technique and viscosity measurements. From spectrophotometric titration experiments, the binding constant of 2,4-DHS with ct-DNA was found to be (1.1 ${\pm}\;0.2)\;{\times}\;10^4\;M^{-1}.$ The fluorescence study represents the quenching effect of 2,4-DHS on bound ethidium bromide to DNA. The quenching process obeys linear Stern-Volmer equation in extended range of 2,4-DHS concentration. Thermal denaturation experiments represent the increasing of melting temperature of DNA (about 3.5 ${^{\circ}C}$) due to binding of 2,4-DHS. These results are consistent with a binding mode dominated by interactions with the groove of ct-DNA.

• Journal of Microbiology
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• v.38 no.2
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• pp.113-116
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• 2000

Escherichia coli F plasmid partition apparatus is composed of two trans-acting proteins (SopA and SopB) and one cis-acting DNA sequence (sopC). The SopB-sopC complex has been suggested to serve a centromere-like function through its interaction with chromosomally encoded proteins which remain to be identified. In this paper, we are introducing a new yeast 1.5-hybrid system which assembles the two-hybrid and one-hybrid system as a mean to find and additional component of the F plasmid partition system, interacting with DNA (sopC)-bound SopB protein. The results indicates that this system is a promising one, capable of selecting an interacting component.

• Bioinformatics and Biosystems
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• v.2 no.1
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• pp.12-16
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• 2007

DNA repair means a collection of processes that a cell identifies and corrects damage to genome sequence. The DNA repair processes are important because a genome would not be able to maintain its essential cellular functions without the processes. In this research, we make some gene regulatory networks of DNA repair in S. cerevisiae to know how each gene interacts with others. Two approaches are adapted to make the networks; Bayesian Network and ARACNE. After construction of gene regulatory networks based on the two approaches, the two networks are compared to each other to predict which genes have important roles in the DNA repair processes by finding conserved interactions and looking for hubs. In addition, each interaction between genes in the networks is validated with interaction information in S. cerevisiae genome database to support the meaning of predicted interactions in the networks.

• Korean Journal of Environmental Biology
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• v.19 no.1
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• pp.19-24
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• 2001

Agricultural pesticides may cause certain biological risks since they are widely used to eradicate pests. Agricultural disasters may arise even from the possibility of their synergistic interaction with other harmful enviromnetal factors. The effect of pesticide on radiation-induced DNA damage in human blood lymphocytes was evaluated by the single cell gel electrophoresis (SCGE) assay. The lymphocytes, with or without pretreatment of the pesticide, were exposed to 0-2.0 Gy of $^60 CO$ gamma ray. Significantly increased tail moment, which was a marker of DNA strand breaks in SCGE assay, showed an excellent dose-response relationship. The present study confirms that the pesticide has the cytotoxic effect on lymphocytes and that it shows the synergistic interaction with radiation on DNA damage as well. The results may have a role of providing biological information necessary for the prevention of environmental disaster.

• BMB Reports
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• v.33 no.2
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• pp.155-161
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• 2000

The saccharomyces cerevisiae Rad27, a structure-specific endonuclease for the okazaski fragment maturation has been known to interact genetically and biochemically with Dna2, an essential enzyme for DNA replication. In an attempt to define the significance of the interaction between the two enzymes, we expressed and purified both Dna2 and Rad27 proteins. In this report, Rad27 could not form a complex with Dna2 in the three different analyses. The analyses included glycerol gradient sedimentation, protein-column chromatography, and coinfection of baculoviruses followed by affinity purification. This is in striking contrast to the previous results that used crude extracts. These results suggest that the interaction between the two proteins is not sufficiently stable or indirect, and thus requires an additional protein(s) in order for Rad27 and Dna2 to form a stable physical complex. This result is consistent with our genetic findings that Schizosaccharomyces pombe Dna2 is capable of interacting with several proteins that include two subunits of polymerase $\delta$, DNA ligase I, as well as Fen-1. In addition, we found that the N-terminal modification of Rad27 abolished its enzymatic activity. Thus, as suspected, we found that on the basis of the structure determination, N-terminal methionine indeed plays an important role in the nucleolytic cleavage reaction.

• Bulletin of the Korean Chemical Society
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• v.31 no.11
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• pp.3099-3102
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• 2010

A label-free DNA detection method was developed for a simple electrochemical DNA sensor with a short assay time. Self-assembled monolayers of peptide nucleic acid were used as a probe on gold electrodes. The formation of the self-assembled monolayers on the gold electrodes was successfully checked by means of cyclic voltammetry. The target DNA, hybridized with peptide nucleic acid, can be detected by the anodic peak current of ferrocene dendrimers, which interact electrostatically with the target DNA. This anodic peak current was measured by square wave voltammetry at 0.3 V to decrease the detection limit on the order of the nanomolar concentrations. As a result, the label-free electrochemical DNA sensor can detect the target DNA in concentrations ranging from 1 nM to $1\;{\mu}M$ with a detection limit of 1 nM.