• Title/Summary/Keyword: DNA interaction

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Study of Interaction of Native DNA with Iron(III)-(2,4-Dihydroxysalophen)chloride (천연 DNA와 2,4-디히드록시살로펜-염화철(III)과 의 상호작용 연구)

  • Azani, Mohammad-Reza;Hassanpour, Azin;Bordbar, Abdol-Khalegh
    • Journal of the Korean Chemical Society
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    • v.54 no.5
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    • pp.573-578
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    • 2010
  • In this study, iron(III)-2,4-dihydroxysalophen chloride (Fe(2,4-DHSalophen)Cl), has been synthesized by combination of 2,4-dihydroxysalophen (2,4-DHSalophen) with $FeCl_2$ in a solvent system. This complex combination was characterized using UV-vis and IR spectroscopies. Subsequently, the interaction between native calf thymus deoxyribonucleic acid (ct-DNA) and Fe(2,4-DHSalophen)Cl, 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 Fe(2,4-DHSalophen)Cl with ct-DNA was found to be $(1.6{\pm}0.2){\times}10^3\;M^{-1}$. The fluorescence study represents the quenching effect of Fe(2,4-DHSalophen)Cl on bound ethidium bromide to DNA. The quenching process obeys linear Stern-Volmer equation in extended range of Fe(2,4-DHSalophen)Cl concentration. Thermal denaturation experiments represent the increasing melting temperature of DNA (about $4.3^{\circ}C$) due to binding of Fe(2,4-DHSalophen)Cl. These results are consistent with a binding mode dominated by interactions with the groove of ct-DNA.

Functional and Physical Interaction between Human Lactate Dehydrogenase B and $Na^+/H^+$ Exchanger Isoform 1

  • Kim, Eun-Hee
    • Animal cells and systems
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    • v.13 no.3
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    • pp.283-288
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    • 2009
  • The ubiquitous plasma membrane $Na^+/H^+$ exchanger 1 (NHE1) is rapidly activated in response to various extracellular stimuli and maintains normal cytoplasmic pH. Yeast two-hybrid screening was used in order to identify proteins interacting with NHE1 using its cytoplasmic domain as a bait from HeLa cDNA library. One of the interacting cDNA clones was human Lactate dehydrogenase B (LDHB). In vitro translated LDHB was pulled down together with GST-NHE1.cd protein in the GST pull down assay, confirming the interaction in vitro. LDHB antibody immunoprecipitated endogenous LDHB together with NHE1 from H9c2 cells, validating cellular interaction between NHE1 and LDHB. Subsequent analysis revealed that the overexpression of LDHB increased intracellular PH, implying opening of the NHE1 transporter. Moreover, overexpression of LDHB activated caspase 3 and induced cell death, consistent with the expected phenotype of hyper-activation of NHE1. Collectively, our data indicate that LDHB modulates NHE1 activity via physical interaction.

Determination of Monoclonal Antibodies Capable of Recognizing the Native Protein Using Surface Plasmon Resonance

  • Kim, Deok-Ryong
    • BMB Reports
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    • v.34 no.5
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    • pp.452-456
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    • 2001
  • Surface plasmon resonance has been used for a biospecific interaction analysis between two macromolecules in real time. Determination of an antibody that is capable of specifically interacting with the native form of antigen is very useful for many biological and medical applications. Twenty monoclonal antibodies against the $\alpha$ subunit of E. coli DNA polymerase III were screened for specifically recognizing the native form of protein using surface plasmon resonance. Only four monoclonal antibodies among them specifically recognized the native $\alpha$ protein, although all of the antibodies were able to specifically interact with the denatured $\alpha$ subunit. These antibodies failed to interfere with the interaction between the $\tau$ and $\alpha$ subunits that were required for dimerization of the two polymerases at the DNA replication fork. This real-time analysis using surface plasmon resonance provides an easy method to screen antibodies that are capable of binding to the native form of the antigen molecule and determine the biological interaction between the two molecules.

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Interaction of Phenolic Compound-Specific Activator with Its Promoter using SPR-Based DNA Chip (SPR 근거 DNA 칩을 이용한 페놀 화합물 특이 CapR 조절 단백질과 촉진유전자와의 상호작용 연구)

  • 박선미;박후휘;임운기;신혜자
    • Journal of Life Science
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    • v.13 no.1
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    • pp.99-104
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    • 2003
  • Aromatic compounds are of major concern among environmental pollutants due to their toxicity and persistence. To monitor aromatic compounds in a real time with a better sensitivity, a new method of SPR (surface plasmon resonance) based on DNA chip (Biacore 3000) was developed here. It is thought that CapR regulatory protein as a complex with phenol, could bind to their corresponding promoter, Po. Biotinylated DNA oligomers for the promoter was synthesized by PCR and coupled onto streptoavidin-linked CM5-chip. CapR regulatory proteins were purified after cloning their genes in pET21a (+) vector and expressing proteins. The interaction was assessed by the system where the regulatory proteins flowed with or without phenol through the cells of DNA chip. CapR regulatory protein even in the presence of phenol had no response to its promoter, Po, suggesting that other factor(s) might be required for the activation of Po promoter. The present work reveals a promising possibility of the SPR-based DNA chip in monitoring specific environmental pollutants in a real time.

Current methodologies in construction of plant-pollinator network with emphasize on the application of DNA metabarcoding approach

  • Namin, Saeed Mohamadzade;Son, Minwoong;Jung, Chuleui
    • Journal of Ecology and Environment
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    • v.46 no.2
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    • pp.126-135
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    • 2022
  • Background: Pollinators are important ecological elements due to their role in the maintenance of ecosystem health, wild plant reproduction, crop production and food security. The pollinator-plant interaction supports the preservation of plant and animal populations and it also improves the yield in pollination dependent crops. Having knowledge about the plant-pollinator interaction is necessary for development of pesticide risk assessment of pollinators and conservation of endangering species. Results: Traditional methods to discover the relatedness of insects and plants are based on tracing the visiting pollinators by field observations as well as palynology. These methods are time-consuming and needs expert taxonomists to identify different groups of pollinators such as insects or identify flowering plants through palynology. With pace of technology, using molecular methods become popular in identification and classification of organisms. DNA metabarcoding, which is the combination of DNA barcoding and high throughput sequencing, can be applied as an alternative method in identification of mixed origin environmental samples such as pollen loads attached to the body of insects and has been used in DNA-based discovery of plant-pollinator relationship. Conclusions: DNA metabarcoding is practical for plant-pollinator studies, however, lack of reference sequence in online databases, taxonomic resolution, universality of primers are the most crucial limitations. Using multiple molecular markers is preferable due to the limitations of developed universal primers, which improves taxa richness and taxonomic resolution of the studied community.

Single Interaction Force of Biomolecules Measured with Picoforce AFM (원자 힘 현미경을 이용한 단일 생분자 힘 측정)

  • Jung, Yu-Jin;Park, Joon-Won
    • Journal of the Korean Vacuum Society
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    • v.16 no.1
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    • pp.52-57
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    • 2007
  • The interaction force between biomolecules(DNA-DNA, antigen-antibody, ligand-receptor, protein-protein) defines not only biomolecular function, but also their mechanical properties and hence bio-sensor. Atomic force microscopy(AFM) is nowadays frequently applied to determine interaction forces between biological molecules and biomolecular force measurements, obtained for example using AFM can provide valuable molecular-level information on the interactions between biomolecules. A proper modification of an AFM tip and/or a substrate with biomolecules permits the direct measurement of intermolecular interactions, such as DNA-DNA, protein-protein, and ligand-receptor, etc. and a microcantilever-based sensor appeared as a promising approach for ultra sensitive detection of biomolecular interactions.

The Role of Gene-environment Interaction in Environmental Carcinogenesis (환경성 발암 기전에서 유전자-환경 상호작용의 역할)

  • Han, So-Hee;Lee, Kyoung-Mu
    • Journal of Environmental Health Sciences
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    • v.36 no.1
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    • pp.1-13
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    • 2010
  • Evidences supporting gene-environment interaction are accumulating in terms of environmental exposure including lifestyle factors and related genetic variants. One form of defense mechanism against cancer development involves a series of genes whose role is to metabolize (activation/detoxification) and excrete potentially toxic compounds and to repair subtle mistakes in DNA. The purpose of this article is to provide a brief review of the notion of gene-environment interaction, environmental/occupational carcinogens and related cancers, and previous studies of gene-environment interaction on cancers caused by exposure to carcinogenesis. With a number of studies on the interaction between lifestyle factors (e.g., smoking and diet) and genetic polymorphisms in genes involved in xenobiotic metabolism and DNA repair excluded, only several studies have been conducted on the interactive effects between polymorphisms of CYPs, GSTs, ERCCs, XRCCs and environmental/occupational carcinogens such as vinyl chloride, benzo[a]pyrene, and chloroform on carcinogenesis or genotoxicity. Future studies may need to be conducted with sufficient number of subjects and based on occupational cohorts to provide useful information in terms of advanced risk assessment and regulation of exposure level.

The MO Study about Interaction of cis-Diamminedichloroplatinum (cis-DDP) Complexes with DNA base, 1-Methylcytosine, for Development of Anti-Tumor Drugs (항암성물질의 개발을 위한 cis-Diamminedichloroplatinum (cis-DDP) 류와 DNA base인 1-Methylcytosine의 Interaction에 관한 분자궤도함수론적 연구)

  • Kim, Ui Rak;Kim, Sang Hae;Edward A. Boudreaux
    • Journal of the Korean Chemical Society
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    • v.34 no.4
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    • pp.331-339
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    • 1990
  • It has been studied that relations between electronic structure and anti-tumor activity by variation of amine group in cis-diamminedichloroplatinum (Ⅱ) complexes. We were also interested in these Pt (Ⅱ) complexes interaction with 1-methylcytosine of DNA base and the electronic structure of these complexes in order to understand the mechanism of the metal-nucleobases interaction. The results showed that net charge of center metal in Pt complexes effect anti-tumor activity. The mechanisgm of the bonding between metal and ligands largely based on charge transfer from ligand to metal atom. Furthermore, the established molecular orbitals showed that metal 6p-orbitals played an important role in the bonding scheme for the interactions between platinum (Ⅱ) complexes and 1-methylcytosine. We also found that the stronger Pt-N3 bonding strength became, the better anti-tumor agents were.

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