• Journal of the Korean Institute of Electrical and Electronic Material Engineers
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• v.24 no.6
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• pp.510-514
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• 2011

Based on first-principles LCAO method, we study the electronic and atomic structures of DNA nucleobases adenine (A), thymine (T), guanine (G), and cytosine (C) adsorbed on graphene surfaces. The ${\pi}-{\pi}$ stacking interactions between graphene and nucleobases lead to the bilayer geometries similar to the Bernal stacked graphite. Through the density of states and charge density analyses, it is found that nucleobases are physisorbed on graphene by dispersive interactions with negligible charge exchange. Our calculations reproduce the atomic structures obtained in previous plane wave calculations accurately with much less computation, and well describe the delocalized ${\pi}-{\pi}$ interactions in graphene-nucleobases system, indicating that the LCAO method is very efficient for investigating graphene-bio systems.

• Journal of the Korean Society of Food Science and Nutrition
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• v.12 no.1
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• pp.1-6
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• 1983

Nucleobases and nucleosides in Panax and Acanthopanax genus were determined by high-performance liquid chromatography. Chromatography was performed on a reversed-phase system with ${\mu}$ Bondapak $C_{18}$ column using phosphate buffer and 80% methanol gradient. Content of each nucleobase in two genera was about 0-2mg/100g. Panax was contained guanosine and/or adenosine ca. 15-22mg/100g;and Acanthopanax guanosine ca. 3-8mg/100g and adenosine ca. 2-7mg/100g. Considerable amounts of cytidine, uridine, inosine, and thymidine were also detected in two genera.

• Asian-Australasian Journal of Animal Sciences
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• v.4 no.2
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• pp.161-164
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• 1991

A rapid and accurate method is described for the determination of nucleo-bases in rumen micro-organisms. A procedure to satisfactorily hydrolyse the micro-organisms involving reaction with a mixture of readily volatile organic acids (acetic and formic acids) under high pressure, is proposed, and optimal conditions for an analytical procedure with reversed phase HPLC is described. The following nucleobases contents (mmol/kg DM) of rumen micro-organisms were found: Adenine (Ade), 82.62; Guanine (Gua), 61.34; Cytosine (Cyt), 84.61; Thymine (Thy), 35.74; Uracil (Ura), 68.62; Hypoxanthine (Hxn), 13.06; Xanthine (Xn), 8.35. Total purine-N content (g/kg N) of rumen micro-organisms were 99.60. The nucleic acid N content (g/kg N) of microbial isolates were: RNA-N, 109.9; DNA-N, 50.9.

• Bulletin of the Korean Chemical Society
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• v.31 no.12
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• pp.3794-3796
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• 2010

• Bulletin of the Korean Chemical Society
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• v.32 no.spc8
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• pp.2906-2910
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• 2011

A fluorescent nucleoside analogue, $^AC$, featuring two non-complementary nucleobases linked through an ethynyl group, was synthesized. The extended ${\pi}$-conjugation imparts $^AC$ with red-shifted absorbance (relative to adenine and cytosine) and pale-blue fluorescence. It spontaneously forms nanoparticles, which exhibit considerably enhanced fluorescence, without the help of any additional stabilizing agent. The DMSO/water ratio was an important factor influencing the construction of the NPs. X-ray crystallography confirmed the structure of $^AC$; dynamic light scattering and scanning electron microscopy confirmed the existence of the nanoparticles.

• Analytical Science and Technology
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• v.8 no.3
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• pp.313-319
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• 1995

Surface-enhanced Raman scattering(SERS) spectroscopy was employed to analyze the genotoxic nucleobase adducts of benzo[a]pyrene(BP) formed through one-electron oxidation pathway. SERS spectroscopy provided sufficient resolution to distinguish if BP intermediate was bound to different nucleobases(e. g. adenine or guanine). Furthermore, SERS specroscopy was also able to detect the difference in the binding position of the adduct to the various sites of the nucleobase. The linearity of the calibration curve for N7Ade-BP ranged from 20 picogram to 800 nanogram per microliter and the detection limit under the current conditions was determined 20 picogram per microliter in a solution volume of 20 microliter.

• Bulletin of the Korean Chemical Society
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• v.31 no.12
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• pp.3658-3662
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• 2010

A new bis-Ru(II) complex, in which two [Ru(1,10-phenanthroline)$_2$dipyrido[3,2-a:2',3'-c]phenazine]$^{2+}$ were tethered by a 1,3-bis(4-pyridyl)propane linker, was synthesized and its binding mode and stoichiometry to DNA was investigated by optical spectroscopy including linear dichroism (LD) and fluorescence intensity measurement. The magnitude of the negatively reduced LD signal of the bis-Ru(II) complex in the dipyrido[3,2-a:2',3'-c]phenazine (DPPZ) ligand absorption region appeared to be similar compared to that in the DNA absorption region, which is considered to be a diagnostic for DPPZ ligand intercalation. The binding stoichiometry measured from its LD magnitude and enhanced fluorescence intensity corresponds to one ligand per three DNA bases, effectively violating the nearest neighbouring site exclusion model for classical DNA intercalation. This observation is in contrast with monomer analogue [Ru(1,10-phenanthroline)$_2$dipyrido[3,2-a:2',3'-c]phenazine]$^{2+}$, which is saturated at the DPPZ ligand to DNA base ratio of 0.25, or one DPPZ ligand per four nucleobases.

• 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.

• Bulletin of the Korean Chemical Society
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• v.31 no.6
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• pp.1519-1526
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• 2010

The behavior of peptide or protein solutes in saline aqueous solution is a fundamental topic in physical chemistry. Addition of ions can strongly alter the thermodynamic and physical properties of peptide molecules in solution. In order to study the effects of added ionic salts on protein conformation and dynamics, we have used the molecular dynamics (MD) simulations to investigate the behavior of Staphylococcus aureus Hfq protein under two different ionic concentrations: 0.1 M NaCl and 1.0 M NaCl in presence and absence of RNA (a hepta-oligoribonucleotide AU5G). Hfq, a global regulator of gene expression is highly conserved and abundant RNA-binding protein. It is already reported that in vivo the increase of ionic strength results in a drastic reduction of Hfq affinity for $Q{\beta}$ RNA and reduces the tendency of aggregation of Escherichia coli host factor hexamers. Our results revealed the crucial role of 0.1 M NaCl Hfq system on the bases with strong hydrogen bonding interactions and by stabilizing the aromatic stacking of Tyr42 residue of the adjacent subunits/monomers with the adenine and uridine nucleobases. An increase in RNA pore diameter and weakened compactness of the Hfq-RNA complex was clearly observed in 1.0 M NaCl Hfq system with bound RNA. Aggregation of monomers in Hfq and the interaction of Hfq with RNA are greatly affected due to the presence of high ionic strength. Higher the ionic concentration, weaker is the aggregation and interaction. Our results were compatible with the experimental data and this is the first theoretical report for the experimental study done in 1980 by Uhlenbeck group for the present system.