• BMB Reports
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• v.46 no.4
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• pp.225-229
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• 2013

Methylglyoxal (MG) is an endogenous metabolite which is present in increased concentrations in diabetics and reacts with amino acids to form advanced glycation end products. In this study, we investigated whether ferritin enhances DNA cleavage by the reaction of MG with lysine. When plasmid DNA was incubated with MG and lysine in the presence of ferritin, DNA strand breakage was increased in a dose-dependent manner. The ferritin/MG/lysine system-mediated DNA cleavage was significantly inhibited by reactive oxygen species (ROS) scavengers. These results indicated that ROS might participate in the ferritin/MG/lysine system-mediated DNA cleavage. Incubation of ferritin with MG and lysine resulted in a time-dependent release of iron ions from the protein molecules. Our data suggest that DNA cleavage caused by the ferritin/MG/lysine system via the generation of ROS by the Fenton-like reaction of free iron ions released from oxidatively damaged ferritin.

• Biotechnology and Bioprocess Engineering:BBE
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• v.8 no.4
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• pp.221-226
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• 2003

With the current rapid development of nanotechnology and synthesis technology for designed oligonucleotides or oligonucleotide-modified nanoparticle conjugates, the combined strategies have become one of the most valuable methods in detection technology for DNA analysis. Using the uniquely recognizable interactions of pre-designed DNA molecules in assembling nanoparticles, various novel approaches have been recently developed towards detecting specific DNA sequences. Here we describe the key fundamentals and issues of this promising strategies ranging from the initial findings of rationally designed DNA-based assembly of nanoparticles to the extended chip-based detection system. Some limitations of these new strategies and possible approaches will be also discussed for the practical application in the area of DNA microarray detection.

• Molecules and Cells
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• v.38 no.8
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• pp.669-676
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• 2015

Genome instability, primarily caused by faulty DNA repair mechanisms, drives tumorigenesis. Therapeutic interventions that exploit deregulated DNA repair in cancer have made considerable progress by targeting tumor-specific alterations of DNA repair factors, which either induces synthetic lethality or augments the efficacy of conventional chemotherapy and radiotherapy. The study of Fanconianemia (FA), a rare inherited blood disorder and cancer predisposition syndrome, has been instrumental in understanding the extent to which DNA repair defects contribute to tumorigenesis. The FA pathway functions to resolve blocked replication forks in response to DNA interstrand cross-links (ICLs), and accumulating knowledge of its activation by the ubiquitin-mediated signaling pathway has provided promising therapeutic opportunities for cancer treatment. Here, we discuss recent advances in our understanding of FA pathway regulation and its potential application for designing tailored therapeutics that take advantage of deregulated DNA ICL repair in cancer.

• Bulletin of the Korean Chemical Society
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• v.30 no.12
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• pp.2873-2874
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• 2009

• 한국생물공학회:학술대회논문집
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• 2005.04a
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• pp.88-92
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• 2005

Aptamer is the single-stranded oligonucleotide which binds to various target molecules such as proteins, peptides, lipids and small organic molecules with high affinity and specificity. DNA aptamers specific for the $17{\beta}-estradiol$ were selected by SELEX (Systematic Evolution of Ligands by EXponential enrichment) process from a random DNA library. These DNA aptamers have a high affinity to $17{\beta}-estradiol$ as an endocrine disrupting chemical. Nanowell and $200{\mu}m$ gold electrode were used as substrate for DNA aptamer immobilization and electrochemical analysis. Especially, nanowell gold electrode was fabricated by e-beam lithography. The size of single nanowell is 130nm and 40,000 nanowells were deposited on one gold electrode. The immobilization method was based on the interaction between the biotinylated aptamer and streptavidin deposited on gold electrode previously. Immobilization procedure was optimized by surface plasma resonance (SPR) and electrochemical analysis. After the immobilization of DNA aptamer on streptavidin modified gold electrode, $17{\beta}-estradiol$ solution was treated on aptamer immobilized gold electrode. The current of gold electrode was decreased by the binding of $17{\beta}-estradiol$ to DNA aptamer immobilized on gold electrode. However, in negative control experiments of 1-aminoanthraquinone and 2-methoxynaphthalene, the current was rarely decreased. And more sensitive data was obtained from nanowell gold electrode comparing with $200{\mu}m$ gold electrode.

• Journal of Life Science
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• v.9 no.1
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• pp.1-4
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• 1999

Large-scale deletions of mitochondrial DNA(mtDNA) have been documented in patients with mitochondrial myopathies and seem to be especially frequent in patients with Kearns-Sayre syndrome (KSS). About one third of all patients shows a 4,977 bp deletion, known as the "common deletion", that removes a segment of DNA that includes several genes encoding for respiratory chain subunits. In this disorder, the population of deleted mtDNA molecules coexists with population of normal, wild-type full length mtDNAs, a situation known as heteroplasmy. We have performed polymerase chain reaction (PCR) on paraffin-embedded muscle tissues from two korean KSS patients. The PCR analysis revealed the existence of two amplified fragments, the deleted fragments, the deleted fragment of 123 bp characteristic for common deletion and the wild-type fragment of 152 bp.of 152 bp.

• Molecules and Cells
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• v.40 no.8
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• pp.533-541
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• 2017

Engineered DNA-binding domains provide a powerful technology for numerous biomedical studies due to their ability to recognize specific DNA sequences. Zinc fingers (ZF) are one of the most common DNA-binding domains and have been extensively studied for a variety of applications, such as gene regulation, genome engineering and diagnostics. Another novel DNA-binding domain known as a transcriptional activator-like effector (TALE) has been more recently discovered, which has a previously undescribed DNA-binding mode. Due to their modular architecture and flexibility, TALEs have been rapidly developed into artificial gene targeting reagents. Here, we describe the methods used to design these DNA-binding proteins and their key applications in biomedical research.

• Molecules and Cells
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• v.46 no.4
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• pp.200-205
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• 2023

DNA-dependent protein kinase catalytic subunit (DNA-PKcs), a member of the phosphatidylinositol 3-kinase-related kinase family is a well-known player in repairing DNA double-strand break through non-homologous end joining pathway. This mechanism has allowed us to understand its critical role in T and B cell development through V(D)J recombination and class switch recombination, respectively. We have also learned that the defects in these mechanisms lead to the severely combined immunodeficiency (SCID). Here we highlight some of the latest evidence where DNA-PKcs has been shown to localize not only in the nucleus but also in the cytoplasm, phosphorylating various proteins involved in cellular metabolism and cytokine production. While it is an exciting time to unveil novel functions of DNA-PKcs, one should carefully choose experimental models to study DNA-PKcs as the experimental evidence has been shown to differ between cells of defective DNA-PKcs and those of DNA-PKcs knockout. Moreover, while there are several DNA-PK inhibitors currently being evaluated in the clinical trials in an attempt to increase the efficacy of radiotherapy or chemotherapy, multiple functions and subcellular localization of DNA-PKcs in various types of cells may further complicate the effects at the cellular and organismal level.

• The Korean Journal of Physiology and Pharmacology
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• v.20 no.4
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• pp.367-378
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• 2016

Recently, it was reported that the role of mitochondria-reactive oxygen species (ROS) generating pathway in cisplatin-induced apoptosis is remarkable. Since a variety of molecules are involved in the pathway, a comprehensive approach to delineate the biological interactions of the molecules is required. However, quantitative modeling of the mitochondria-ROS generating pathway based on experiment and systemic analysis using the model have not been attempted so far. Thus, we conducted experiments to measure the concentration changes of critical molecules associated with mitochondrial apoptosis in both human mesothelioma H2052 and their ${\rho}^0$ cells lacking mitochondrial DNA (mtDNA). Based on the experiments, a novel mathematical model that can represent the essential dynamics of the mitochondrial apoptotic pathway induced by cisplatin was developed. The kinetic parameter values of the mathematical model were estimated from the experimental data. Then, we have investigated the dynamical properties of this model and predicted the apoptosis levels for various concentrations of cisplatin beyond the range of experiments. From parametric perturbation analysis, we further found that apoptosis will reach its saturation level beyond a certain critical cisplatin concentration.

• Molecules and Cells
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• v.23 no.2
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• pp.239-245
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• 2007

DnaK is a major antigen in Streptococcus pneumoniae, and is induced by a minor shift in temperature (30 to $37^{\circ}C$) but not by ethanol shock. Although HrcA in the presence of $Ca^{{+}{+}}$ represses the expression of both groEL and hrcA, the control of transcription of the dnaK operon is not completely understood. In this study, the dnaK operon of S. pneumoniae (5' hrcA-grpE-dnaK-dnaJ) was cloned and analyzed. It contains large intergenic regions in grpE/dnaK and dnaK/dnaJ. Pulse labeling with [$^{35}S$]-methionine and immunoblot analyses revealed the presence of higher levels of DnaK than of HrcA even in the presence of $Ca^{{+}{+}}$ after heat shock suggesting that $Ca^{{+}{+}}$ differentially regulates the heat shock responses of hrcA and dnaK. By blocking de novo mRNA synthesis with rifampin it was shown that neither the hrcA nor the groEL transcripts were stabilized by heat shock even though dnaK transcripts were stabilized. We conclude that S. pneumoniae uses fine regulation of the transcription of the individual genes of the tetracistronic dnaK operon to cope with the various stresses experienced during infections.