• Proceeding of EDISON Challenge
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• 2015.03a
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• pp.151-155
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• 2015

The molecular interactions between the nucleic acid bases and water molecules are important in organism. Despite Adenine-Thymine Hoogsteen base pair and Guanine-Cytosine Watson-Crick base pair have been demonstrated to be most stable in a gas phase, the effect of water on the stability of these base pairs remains elusive. Here we report the structural and thermodynamic characteristics on possible Adenine-Thymine and Guanine-Cytosine base pairs in a gas phase as well as in an aqueous phase by using quantum mechanical method and statistical mechanical calculations. First, we optimized the direct base-pair interaction energies of four Adenine-Thymine base pairs (Hoogsteen base pair, reverse Hoogsteen base pair, Watson-Crick base pair, and reverse Watson-Crick base pair) and three Guanine-Cytosine base pairs (GC1 base pair, GC2 base pair, and Watson Crick base pair) in a gas phase at the $B3LYP/6-31+G^{**}$ level. Then, the effect of solvent was quantified by the electronic reorganization energy and the solvation free energy by statistical mechanical calculations. Thereby, we discuss the effect of water on the stability of Adenine-Thymine and Guanine-Cytosine base pairs, and argue why Adenine-Thymine Watson-Crick base pair and Guanine-Cytosine Watson-Crick base pair are most stable in an aqueous environment.

• Bulletin of the Korean Chemical Society
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• v.29 no.3
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• pp.539-540
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• 2008

• Mass Spectrometry Letters
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• v.2 no.3
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• pp.73-75
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• 2011

In the collisionally-activated dissociation of the proton-bound cluster ions of DNA base guanine (G) and cytosine (C), $G{\bullet}{\bullet}H^+{\bullet}{\bullet}C$, the abundance of [$CH^+$] ions was found to be higher than that of [$GH^+$] despite the fact that G has a higher proton affinity than C. This unexpected observation seems to demonstrate another example that the simple kinetic method scheme does not work. We suggest that a kinetic factor or detailed dynamics governing the proton transfer and dissociation should be carefully considered in the applications of the kinetic method to the proton affinity measurements.

• Korean Chemical Engineering Research
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• v.48 no.1
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• pp.88-92
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• 2010

DNA structure studies attract many interests in pharmaceutical, biochemical and medical disciplines. Among them, base pairs play a vital role in biological information transfer. Therefore, they need to be analyzed in various ways and the pair of guaninine and cytosine is the present analytical object. Separation of guanine and cytosine was researched by Aspen chromatography simulator and HPLC(High Performance Liquid Chromatography) experiments. Aspen chromatography simulation resulted in various chromatograms with changes of sample concentration, eluent flow rate and number of plate. The resolutions and yields of guanine and cytosine were calculated to obtain a best separation condition. $C_{18}$ HPLC column and water/methanol/acetic acid mixture(90/10/0.2) were used for separation of guanine and cytosine. HPLC parameters(resolution and number of theoretical plate) were calculated under different flow rates and sample concentrations. Aspen chromatography simulation and HPLC experimental results were compared with fair agreement.

• Journal of the Korean Chemical Society
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• v.24 no.4
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• pp.280-287
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• 1980

The interactions of chemical carcinogens, such as polycyclic aromatic hydrocarbons, dimethylaminoazobenzene (DAB) and its derivatives and heterocyclic compounds with tissue components, especially with deoxyribonucleic acid (DNA), were examined by means of simple Huckel method. Assuming that the formations of a loose molecular complex between the carcinogens and the tissue components are the first step of chemical carcinogenesis, the most proble orientation between the chemical carcinogens and adenine-thymine (A=T) pair or guanine-cytosine $(G\equivC)$ pair is determined. It has been found that, in the case of the formation of molecular complex between chemical carcinogens and A=T pair, the two atoms of K-region of the carcinogens and the atom of L-region in the proximity of their K-region are combined correspondingly with C-l' carbon atom in the sugar that is attached to thymine, N-1 nitrogen atom and C-5 carbon atom in the thymine part of A=T pair, while, in the case of that between the carcinogens and $G\equivC$ pair, the above three atoms of the carcinogens are combined correspondingly with C-8 carbon atom, N-9 nitrogen atom and N-3 nitrogen atom in the guanine part of $G\equivC$ pair.

• Journal of Animal Science and Technology
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• v.64 no.3
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• pp.599-602
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• 2022

A new bacteriocin-producing lactic acid bacteria isolated from kimchi was identified as Lactococcus lactis JNU 534, presenting preservative properties for foods of animal origin. In this study, we present the complete genome sequence of the bacterial strain JNU 534. The final complete genome assembly consists of one circular chromosome (2,443,687 bp [base pair]) with an overall GC (guanine-cytosine) content of 35.2%, one circular plasmid sequence (46,387bp) with a GC content of 34.5%, and one circular contig sequence (7,666 bp) with a GC content of 36.2%.

• Journal of Animal Science and Technology
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• v.65 no.2
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• pp.473-477
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• 2023

Lactobacillus amylovorus CACC736 was originated from swine feces in Korea. The complete genome sequences of the strain contained one circular chromosome (2,057,809 base pair [bp]) with 38.2% guanine-cytosine (GC) content and two circular plasmids, namely, pCACC736-1 and pCACC736-2. The predicted protein-coding genes, which are encoding the clustered regularly interspaced short palindromic repeats (CRISPR)-associated proteins, biosynthesis of bacteriocin (helveticin J), and the related proteins of the bile, acid tolerance. Notably, the genes related to vitamin B-group biosynthesis (riboflavin and cobalamin) were also found in L. amylovorus CACC736. Collectively, the complete genome sequence of the L. amylovorus CACC736 will aid in the development of functional probiotics in the animal industry.

• Journal of Animal Science and Technology
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• v.65 no.6
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• pp.1341-1344
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• 2023

In this study, we report the complete genome sequence of Lactiplantibacillus plantarum L55, a probiotic strain of lactic acid bacteria isolated from kimchi. The genome consists of one circular chromosome (2,077,416 base pair [bp]) with a guanine cytosine (GC) content of 44.5%, and two circular plasmid sequences (54,267 and 19,592 bp, respectively). We also conducted a comprehensive analysis of the genome, which identified the presence of functional genes, genomic islands, and antibiotic-resistance genes. The genome sequence data presented in this study provide insights into the genetic basis of L. plantarum L55, which could be beneficial for the future development of probiotic applications.

• Microbiology and Biotechnology Letters
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• v.22 no.2
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• pp.134-142
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• 1994

The neucleotide sequences of the xylA gene encoding $\beta $-xylosidase of Bacillus stearothermophilus and is its flanking regions were datermined. Three open reading frame(ORFs) were found, one of which(ORF1) appeared to code for the $\beta $-xylosidase. The 1830 base pair ORF1 encoded 609 amino acids starting from a TTG initiation codon. The molecular weight deduced from the nucleotide sequence(68 KD) was in agreement with that estimated by SDS-polyacrylamide gel electrophoresis of the purified enzyme(66 KD). The Shine-Dalgarno sequence(5'-AGGAGG-3') was found 11 bp upstream of the initiation codon. Further 15 bp upstream, there observed a potential transcription initiation signals. The putative -10 sequence(CATAAT) and -35 sequence(TTGTTA) coresponded closely to the consensus sequences for Bacillus subtilis RNA polymerase with major sigma factor. The guanine-plus-cytosine content of the coding region of the xylA gene was 56mol% while that of the third position of the codons was 63 mol%. Based on the comparison with the amino acid sequences of several other carbohydrate degrading enzymes, two conserved regions, possibly participating in the catalytic mechamism of $\beta $-xylosidase xylA, were identified in 278-298 and 329-350 regions of the translated xylA gene. The nucleotide sequence of the xylA was found to exhibit no homology to any other genes so far reproted.

• Bulletin of the Korean Chemical Society
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• v.28 no.3
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• pp.386-390
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• 2007

By use of a simple two-point extrapolation scheme estimating the correlation energies of the molecules along with the basis sets specifically targeted for extrapolation, we have shown that the MP2 basis set limit binding energies of large hydrogen-bonded complexes can be accurately predicted with relatively small amount of computational cost. The basis sets employed for computation and extrapolation consist of the smallest correlation consistent basis set cc-pVDZ and another basis set made of the cc-pVDZ set plus highest angular momentum polarization functions from the cc-pVTZ set, both of which were then augmented by diffuse functions centered on the heavy atoms except hydrogen in the complex. The correlation energy extrapolation formula takes the (X+1)-3 form with X corresponding to 2.0 for the cc-pVDZ set and 2.3 for the other basis set. The estimated MP2 basis set limit binding energies for water hexamer, hydrogen fluoride pentamer, alaninewater, phenol-water, and guanine-cytosine base pair complexes of nucleic acid by this method are 45.2(45.9), 36.1(37.5), 10.9(10.7), 7.1(6.9), and 27.6(27.7) kcal/mol, respectively, with the values in parentheses representing the reference basis set limit values. A comparison with the DFT results by B3LYP method clearly manifests the effectiveness and accuracy of this method in the study of large hydrogen-bonded complexes.