• BMB Reports
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• v.33 no.2
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• pp.126-132
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• 2000

The hepadnaviruses replicate their nucleic acid through a reverse transcription step. The MBP-fused HBV polymerase was expressed in E. coli and purified by using amylase affinity column chromatography. The purified protein represented DNA-dependent DNA polymerase activity. In this report, the MBP-HBV polymerase was shown to lack 3'$\rightarrow$5' exonuclease activity, like other retroviral RTs. The ratio of the insertion efficiency for the wrong versus right vase pairs indicates the misinsertion frequency (f). The nucleotide insertion fidelity (1/f), observed with the MBP-HBV polymerase and HIV-1 RT, was between 60 and 54,000, and between 50 and 73,000, respectively, showing that they are in close range. A relatively efficient nucleotide incorporation by the MBP-HBV polymerase was observed with a specificity of three groups: (1) A : T, T : A>C : G, G : C (matched pairs), (2) A : C, C : A>G: T, T : G (purine-pyrimidine and pyrimidine-purine mispairs), and (3) C : C, A : A, G : G, T : T>T : C, C : T>A : G, G : A (purine-purine or pyrimidine-pyrimidine mispairs), and their order is (1)>(2)>(3). The data from the nucleotide insertion fidelity by the MBP-HBV polymerase suggest that the HBV polymerase may be as error-prone as HIV-1 RT.

• Environmental Mutagens and Carcinogens
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• v.23 no.1
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• pp.16-22
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• 2003

Single nucleotide polymorphisms (SNPs) are alterations in DNA base that occur most frequently throughout the human genome. The SNPs of DNA repair genes, hMLH1, hMSH2 and ATM, among 100 Korean people were analyzed using Dynamic Allele specific Hybridization (DASH) techniques. Mutation at the position of exon 38 (GA) and exon 10 (CG) of ATM gene, mutation at the position of exon 8 (AG), and exon 1 (AG) of hMLH1 gene and exon 14 (AG) of hMSH2 gene were investigated. No mutation at the selected position of ATM gene and hMSH1 gene was found. However, while there was no mutation at the position of exon of hMSH2 gene, mutation was found at the promotion region (CT) with the frequency of 24% CC, 36% CT and 62% TT genotyes. This results might be used as baseline data for research on SNP of Korean population.

• BMB Reports
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• v.32 no.5
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• pp.492-496
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• 1999

We have investigated the biochemical properties of the herpes simplex virus type 1 (HSV-1) DNA polymerase without the UL42 protein (Pol), purified from insect cells infected with a recombinant baculovirus containing the UL30 gene. BSA and DTT have inhibitory effects on dAMP incorporation. Pol showed a greater turnover rate of steady-state single nucleotide incorporation at 12 mM $MgCl_2$ than at 2 mM $MgCl_2$. However, it showed a greater processivity of DNA synthesis at lower $MgCl_2$ concentration (1 mM, 2 mM) than at a higher $MgCl_2$ concentration (12.5 mM). These results are consistent with a slow DNA dissociation at lower $MgCl_2$ concentrations. Pol does not incorporate a correct nucleotide into the primer with an incorrect nucleotide at the end; instead, it preferentially excises the incorrect nucleotide at the 3' end of the primer. Pol has DNA polymerase activity at pHs 6.5 and 7.5 but little at pHs 5.5, 8.5, and 9.5. It has exonuclease activity at pHs 6.5, 7.5, and 8.5 but little at pHs 4.5, 5.5, and 9.5. The finding that Pol has exonuclease activity but not DNA polymerase at pH 8.5 suggests that DNA binds to Pol, but deoxynucleotide binding or incorporation does not occur at pH 8.5.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.9
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• pp.1235-1243
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• 2015

The goat Capra hircus is one of several economically important livestock in China. Advances in molecular genetics have led to the identification of several single nucleotide variation markers associated with genes affecting economic traits. Validation of single nucleotide variations in a whole-transcriptome sequencing is critical for understanding the information of molecular genetics. In this paper, we aim to develop a large amount of convinced single nucleotide polymorphisms (SNPs) for Cashmere goat through transcriptome sequencing. In this study, the transcriptomes of Cashmere goat skin at four stages were measured using RNA-sequencing and 90% to 92% unique-mapped-reads were obtained from total-mapped-reads. A total of 56,231 putative SNPs distributed among 10,057 genes were identified. The average minor allele frequency of total SNPs was 18%. GO and KEGG pathway analysis were conducted to analyze the genes containing SNPs. Our follow up biological validation revealed that 64% of SNPs were true SNPs. Our results show that RNA-sequencing is a fast and efficient method for identification of a large number of SNPs. This work provides significant genetic resources for further research on Cashmere goats, especially for the high density linkage map construction and genome-wide association studies.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.2
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• pp.170-176
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• 2012

Genetic diversities, population genetic structures and demographic histories of the thread-sail filefish Stephanolepis cirrhifer were investigated by nucleotide sequencing of 336 base pairs of the mitochondrial DNA (mtDNA) control region in 111 individuals collected from six populations in Korean coastal waters. A total of 70 haplotypes were defined by 58 variable nucleotide sites. The neighbor-joining tree of the 70 haplotypes was shallow and did not provide evidence of geographical associations. Expansion of S. cirrhifer populations began approximate 51,000 to 102,000 years before present, correlating with the period of sea level rise since the late Pleistocene glacial maximum. High levels of haplotype diversities ($0.974{\pm}0.029$ to $1.000{\pm}0.076$) and nucleotide diversities (0.014 to 0.019), and low levels of genetic differentiation among populations inferred from pairwise population FST values (-0.007 to 0.107), support an expansion of the S. cirrhifer population. Hierarchical analysis of molecular variance (AMOVA) revealed weak but significant genetic structures among three groups ($F_{CT}$ = 0.028, p<0.05), and no genetic variation within groups (0.53%; $F_{SC}$ = 0.005, p = 0.23). These results may help establish appropriate fishery management strategies for stocks of S. cirrhifer and related species.

• Korean Journal of Veterinary Research
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• v.38 no.2
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• pp.319-327
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• 1998

The nucleotide sequences of spike (S) glycoprotein containing antigenic sites A and D of TGEV isolated in Korea were determined and compared with published sequences for TGEVs. The TGEV 133 and DAE5 strains had 97.40% nucleotide sequence similarity. The overall nucleotide sequence similarity of the 133 and DAE5 strains compared with other TGEV strains was between 96.86% and 99.15%. The similarity of the predicted amino acid sequence of the 133 and DAE5 strains was 94.93%. The TGEV 133 and DAE5 strains had 94.93-98.61% amino acid similarity with published sequences of other TGEV strains. The sequences of amino acid codons in the antigenic sites A and D were identical among all the viruses although there were several nucleotide changes in region containing antigenic sites A and D of Korean TGEV isolates. By phylogenetic analysis of the sequences, two Korean isolates 133 and DAE5 seemed to be derived from different lineages. These studies showed that a distinct difference in genome exists among TGEV field strains isolated in Korea.

• Bulletin of the Korean Chemical Society
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• v.32 no.9
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• pp.3233-3238
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• 2011

The fluorescence of norfloxacin was quenched by various nucleotides. The ratio of the fluorescence intensities in the absence and presence of nucleotide was linearly dependent on nucleotide concentration, suggesting that quenching occurred through the formation of nonfluorescent norfloxacin-nucleotide complexes. The gradient of the linear relationship represented the equilibrium constant of complex formation; it decreased with increasing temperature. The slopes of van't Hoff plots constructed from the temperature-dependent equilibrium constants were positive in all cases, indicating that complex formation was energetically favorable - i.e., exothermic, with negative Gibb's free energy. The equilibrium constant increased when triphosphate was used instead of monophosphate. It also increased when the oxygen at the $C'_2$ position of the nucleotide was removed. Both enhancements were due to entropic effects: entropy decreased when complexes with AMP or GMP formed, while it increased when norfloxacin complexed with ATP, GTP, dAMP and dGMP.

• The Plant Pathology Journal
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• v.24 no.3
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• pp.361-364
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• 2008

The complete nucleotide sequences of a Korean isolate of Potato virus X(PVX-Kr) has been determined. Full-length cDNA of PVX-Kr has been directly amplified by long template reverse transcription and polymerase chain reaction(RT-PCR) using virus specific 5'-end primer and 3'-end primer, and then constructed in a plasmid vector. Consecutive subclones of a full-length cDNA clone were constructed to identify whole genome sequence of the virus. Total nucleotide sequences of genome of PVX-Kr were 6,435 excluding one adenine at poly A tail, and genome organization was identical with that of typical PVX species. Comparison of whole genome sequence of PVX-Kr with those of European and South American isolates showed 95.4-96.8% and 77.4-77.9%, in nucleotide similarity, respectively. Sequenced PVX-Kr in this study and twelve isolates already reported could be divided into two subgroups in phylogeny based on their complete nucleotide sequences. Phylogenetic tree analysis demonstrated that PVX-Kr was clustered with European and Asian isolates(Taiwan, os, bs, Kr, S, X3, UK3, ROTH1, Tula) in the same subgroup and South American isolates(CP, CP2, CP4, HB) were clustered in the other subgroup.

• Biomedical Science Letters
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• v.11 no.2
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• pp.109-113
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• 2005

From the RT-PCR amplifications using mRNA templates isolated from Sprague-Dawley rat brains, we isolated a cDNA fragment of 1,524 bp which covered the full coding information of the rat brain CYP2El. Its nucleotide sequence was identical to the previously reported rat liver CYP2El mRNA except for the difference of one base (A to C at the nucleotide position 73). This difference also altered the amino acid Lys to GIn. However, no insertion or deletion of nucleotide(s) which could alter the reading frame was found within the structure of this rat brain CYP2El. This study should provide the molecular basis regarding the pathophysiological function of CYP2El in the brain.

• Korean Journal of Veterinary Research
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• v.46 no.4
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• pp.355-361
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• 2006

Porcine epidemic diarrhea virus (PEDV) strain Chinju99, which was previously isolated from piglets suffering from severe diarrhea was used to characterize the membrane (M) protein gene to establish the molecular information, and the results will be useful in elucidating concepts related to molecular pathogenesis and antigenic structures of PEDV isolates. The Chinju99 M gene generated by reverse transcription and polymerase chain reaction (RT-PCR) consisted of 681 bases containing 22.3% adenine, 22.3% cytosine, 23.1% guanine and 32.3% thymine nucleotides, and the GC content was 45.4%. It had some nucleotide mismatches from M gene of other PEDV strains, such as CV777, Br1/87, KPEDV-9, JMe2, JS2004-2 and LJB-03 with 97-99% nucleotide sequence homology to these strains. Also, it encoded a protein of 226 amino acids, which had some mismatches from those of CV777, Br1/87, KPEDV-9, JMe2, JS20004-2 and LJB-03, as the amino acid sequence homology showed a 97-98% to these strains. The Chinju99 had a very close relationship to the Japanese strain JMe2 for the nucleotide and amino acid sequences of the M gene. The amino acids predicted from Chinju99 M gene consisted of mostly hydrophobic residues and contained three potential sites for asparagine (N)-linked glycosylation, two serine (S)-linked phosphorylation sites by protein kinase C, and two S- or threonine (T)-linked phosphorylation sites by casein kinase II.