• 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.9
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• pp.2724-2726
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• 2010

• 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.

• Proceedings of the Korean Vacuum Society Conference
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• 2015.08a
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• pp.109.1-109.1
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• 2015

Understanding the reaction mechanisms and structures underlying the adsorption of biomolecules on semiconductors is important for functionalizing semiconductor surfaces for various bioapplications. Herein, we describe the characteristic behavior of a primary nucleobase adsorbed on the semiconductor Ge(100). The adsorption configuration of guanine, a primary nucleobase found in DNA and RNA, on the semiconductor Ge(100) at an atomic level was investigated using scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. When adsorbed on Ge(100) at room temperature, guanine appears dark in STM images, indicating that the adsorption of guanine on Ge(100) occurs through N-H dissociation. In addition, DFT calculations revealed that "N(1)-H dissociation through an O dative bonded structure" is the most favorable adsorption configuration of all the possible ones. We anticipate that the characterization of guanine adsorbed on Ge(100) will contribute to the development of semiconductor-based biodevices.

• 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.

• Bulletin of the Korean Chemical Society
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• v.31 no.7
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• pp.2011-2014
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• 2010

The fluorescence intensity of a single-stranded oligonucleotide containing a fluorene-labeled deoxyuridine $(U^{Fl})$ unit increases by only 1.5-fold upon formation of its perfectly matched duplex. To increase the fluorescence signal during hybridization, we positioned a quencher strand containing a deoxyguanine (dG) nucleobase, functioning as an internal quencher, opposite to the $U^{Fl}$ unit to reduce the intrinsic fluorescence upon hybridization with a probe. From an investigation of the optimal length of the quencher strand and the effect of the neighboring base sequence, we found that a short strand (five-nucleotide) containing all natural nucleotides and dG as an internal quencher was effective at reducing the intrinsic fluorescence of a linear beacon; it also exhibited high total discrimination factors for the formation of perfectly matched and single base-mismatched duplexes. Such assays that function based on clear changes in fluorescence in response to single-base nucleotide mutations would be useful tools for accelerating diagnoses related to various diseases.

• Proceedings of the Korean Vacuum Society Conference
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• 2014.02a
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• pp.415.1-415.1
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• 2014

Carrying out first-principles calculations, we study N-doped capped carbon nanotube (CNT) electrodes applied to DNA sequencing. While we obtain for the face-on nucleobase junction configurations a conventional conductance ordering where the largest signal results from guanine according to its high highest occupied molecular orbital (HOMO) level, we extract for the edge-on counterparts a distinct conductance ordering where the low-HOMO thymine provides the largest signal. The edge-on mode is shown to operate based on a novel molecular sensing mechanism that reflects the chemical connectivity between N-doped CNT caps that can act both as electron donors and electron acceptors and DNA functional groups that include the hyperconjugated thymine methyl group[1].

• Journal of Photoscience
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• v.9 no.2
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• pp.488-490
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• 2002

DNA photodamage mediated by photosensitizers are believed to play an important role in solar UVA carcinogenesis. We investigated the relationship between the DNA-damaging abilities of photoexcited xanthone analogues (as photosensitizers) and their highest occupied molecular orbital (HOMO) energies. DNA damage was examined using /sup 32/P-labeled DNA fragments obtained from the p53 tumor suppressor gene. These compounds induced DNA photodamage in a similar manner, and the extents of DNA damage were following order: xanthone> thioxanthone > acridone. Photoexcited xanthone caused nucleobase oxidation specifically at 5'-G of GG sequence in double-stranded DNA. An oxidative product of 2'-deoxyguanosine, 8-hydroxy-2'-deoxyguanosine (8-OHdG), was detected, and the amount was decreased by DNA denaturation. These findings suggest that photoexcited xanthone generates 8-OHdG at 5'-G of GG in double-stranded DNA through electron transfer. The calculated HOMO energies of these photosensitizers decreased in the following order: xanthone> thioxanthone > acridone. This study has demonstrated that DNA-damaging abilities of these photosensitizers increased exponentially with an increase in their HOMO energies.

• Journal of Microbiology and Biotechnology
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• v.26 no.11
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• pp.1972-1982
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• 2016

Influenza A virus is a single-stranded RNA virus with a genome of negative polarity. Owing to the antigenic diversity and cross concrete shift, an immense number of novel strains have developed astronomically over the years. The present work deals with the codon utilization partialness among five different influenza A viruses isolated from human hosts. All the subtypes showed the homogeneous pattern of nucleotide utilization with a little variation in their utilization frequencies. A lower bias in codon utilization was observed in all the subtypes as reflected by higher magnitudes of an efficacious number of codons. Dinucleotide analysis showed very low CpG utilization and a high predilection of A/T-ending codons. The H5N1 subtype showed noticeable deviation from the rest. Codon pair context analysis showed remarkable depletion of NNC-GNN and NNT-ANN contexts. The findings alluded towards GC-compositional partialness playing a vital role, which is reflected in the consequential positive correlation between the GC contents at different codon positions. Untangling the codon utilization profile would significantly contribute to identifying novel drug targets that will pacify the search for antivirals against this virus.

• Bulletin of the Korean Chemical Society
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• v.35 no.9
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• pp.2649-2654
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• 2014

Synthesis of north-5'-methylbicyclo[3.1.0]hexyl adenine and hypoxanthine nucleosides with an ethenyl group at C3' position was successfully achieved by a highly facile method. Methylbicyclo[3.1.0]hexanone (${\pm}$)-7 with three contiguous chiral centers and its epimer (${\pm}$)-6 was remarkably simply constructed only by four steps involving a carbenoid insertion reaction in the presence of rhodium (II) acetate dimer as a metal catalyst, giving a correct relative stereochemistry of the generated three chiral centers. Due to steric hindrance from the concave face of the bicyclo[3.1.0]hexanone system, a Grignard reaction of (${\pm}$)-7 with ethenylmagnesium bromide showed exclusive diastereoselectivity towards the b-face. The Grignard reaction chemoselectively proceeded without reacting with ester functionality. Coupling reaction of glycosyl donor (${\pm}$)-11 with 6-chloropurine nucleobase afforded only the desired $N^9$-alkylated nucleoside without the formation of $N^7$-regioisomer. By the conventional method, 6-chloro group was converted into 6-amino and 6-hydroxy groups to give the desired adenine and hypoxanthine bicyclo[3.1.0]hexyl carbanucleosides with 3'-ethenyl group, respectively.