• Bulletin of the Korean Chemical Society
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• v.30 no.9
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• pp.1951-1955
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• 2009

A Thermodynamic study on the interaction of bovine calf thymus DNA with new designed Pd(II) complex (Ethylendiamine- 8-hydroxyquinolinato Palladium(II) chloride) was studied by using isothermal titration calorimetry (ITC) at 27 ${^{\circ}C}$ in Tris buffer solution at pH = 7.5. The enthalpies of Pd(II) complex + DNA interaction are reported and analysed in terms of the new solvation theory. It was indicated that there are three identical and non-cooperative sites for Pd(II) complex. The binding of a Pd(II) complex is endothermic with association equilibrium constants of 428.03 m$M^{-1}$ at 27 ${^{\circ}C}$. The binding of Pd(II) complex can cause some changes in the stability of the DNA at low and high Pd(II) complex concentrations. Our results suggested that this complex might interact with DNA as an intercalator, thus interfering with DNA replication and cell proliferation.

• Bulletin of the Korean Chemical Society
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• v.30 no.9
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• pp.1973-1977
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• 2009

In the present study, at first, 2,4-Dihydroxy Salophen (2,4-DHS), has been synthesized by combination of 1, 2-diaminobenzene and 2,4-dihydroxybenzaldehyde in a solvent system. This ligand containing meta-quinone functional groups were characterized using UV-Vis and IR spectroscopies. Subsequently, the interaction between native calf thymus deoxyribonucleic acid (ct-DNA) and 2,4-DHS, was investigated in 10 mM Tris/HCl buffer solution, pH 7.2, using UV-visible absorption and fluorescence spectroscopies, thermal denaturation technique and viscosity measurements. From spectrophotometric titration experiments, the binding constant of 2,4-DHS with ct-DNA was found to be (1.1 ${\pm}\;0.2)\;{\times}\;10^4\;M^{-1}.$ The fluorescence study represents the quenching effect of 2,4-DHS on bound ethidium bromide to DNA. The quenching process obeys linear Stern-Volmer equation in extended range of 2,4-DHS concentration. Thermal denaturation experiments represent the increasing of melting temperature of DNA (about 3.5 ${^{\circ}C}$) due to binding of 2,4-DHS. These results are consistent with a binding mode dominated by interactions with the groove of ct-DNA.

• Transactions of the Korean Society of Mechanical Engineers A
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• v.32 no.6
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• pp.459-464
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• 2008

We present a novel microcantilever device with nano-interdigitated electrodes (nano-IDEs) and DNA selective immobilization on the nano-IDEs for biosensing applications. Using the nano-IDEs and cyclic voltammetric methods, we have achieved selective immobilization of DNA with submicrometer spatial resolution on a freestanding microcantilever. $70{\sim}500\;nm$-wide gold (Au) nano-IDEs are fabricated on a low-stress SiNx microcantilever with dimensions of $100{\sim}600\;{\mu}m$ in length, and $15{\sim}60\;{\mu}m$ in width, with a $0.5\;{\mu}m$ thickness using electron beam lithography and bulk micromachining. Streptavidin is selectively deposited on one side of the nano-IDEs using cyclic voltammetry at a scan rate of 0.1 V/s with a range of $-0.2{\sim}0.7\;V$ during $1{\sim}5$ cycles. The selective deposition of dsDNA is confirmed by fluorescence microscopy after labeling with YOYO-1 dye.

• Reproductive and Developmental Biology
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• v.34 no.4
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• pp.283-288
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• 2010

During normal early embryonic development in mammals, the global pattern of genomic DNA methylation undergoes marked. changes. The level of methylation is high in male and female gametes. Thus, we cloned the cDNA of the porcine DNA methyltransferase 1 (Dnmt1) gene to promote the efficiency of the generation of porcine clones. In this study, porcine Dnmt1 cDNA was sequenced, and Dnmt1 mRNA expression was detected by reverse transcription-polymerase reaction (RT-PCR) in porcine tissues during embryonic development. The porcine Dnmt1 cDNA sequence showed more homology with that of bovine than human, mouse, and rat. The complete sequence of porcine Dnmt1 cDNA was 4,774-bp long and consisted of an open reading frame encoding a protein of 1611 amino acids. The amino acid sequence of porcine DNMT1 showed significant homology with those of bovine (91%), human (88%), rat (76%), and mouse (75%) Dnmt1. The expression of porcine Dnmt1 mRNA was detected during porcine embryogenesis. The mRNA was detected at stages of porcine preimplantation development (1-cell, 2-cell, 4-cell, 8-cell, morula, and blastocyst stages). It was also abundantly expressed in tissues (lung, ovary, kidney and somatic cells). Further investigations are necessary to understand the complex links between methyltransferase 1 and the transcriptional activity in cloned porcine tissues.

• Animal cells and systems
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• v.3 no.1
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• pp.79-87
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• 1999

Mitochondrial DNA (mtDNA) from 54 specimens of the blue mussel (Mytilus edulis) species complex sampled from the southern coast of Korea was assayed for polymorphism with a portion of the COIII gene (336 bp). Fifteen haplotypes were found. PAUP, one-step networks, and PHYLIP analyses revealed the presence of two clearly differentiated mitochondrial clades (termed clades B and E), separated by 3.6% of minimum sequence divergence. The distribution pattern of the species appears to be consistent with category II of the phylogeographic pattern sensu (Avise et al., 1987): the presence of two discontinuous and distinct mtDNA genotypes in the same geographic region. This unusual mitochondrial polymorphism was explained by the presence of the Mediterranean species, M. galloprovincialis, possessing mtDNA of both M. galloprovincialis and M. edulis.

• Food Science of Animal Resources
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• v.43 no.1
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• pp.101-112
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• 2023

This study aimed to assess whether genomic DNA (gDNA) extracted from Pediococcus acidilactici inhibits Porphyromonas gingivalis lipopolysaccharide (LPS)-induced inflammatory responses in RAW 264.7 cells. Pretreatment with gDNA of P. acidilactici K10 or P. acidilactici HW01 for 15 h effectively inhibited P. gingivalis LPS-induced mRNA expression of interleukin (IL)-1β, IL-6, and monocyte chemoattractant protein (MCP)-1. Although both gDNAs did not dose-dependently inhibit P. gingivalis LPS-induced mRNA expression of IL-6 and MCP-1, they inhibited IL-1β mRNA expression in a dose-dependent manner. Moreover, pretreatment with both gDNAs inhibited the secretion of IL-1β, IL-6, and MCP-1. When RAW 264.7 cells were stimulated with P. gingivalis LPS alone, the phosphorylation of mitogen-activated protein kinases (MAPKs) was increased. However, the phosphorylation of MAPKs was reduced in the presence of gDNAs. Furthermore, both gDNAs restored IκBα degradation induced by P. gingivalis LPS, indicating that both gDNAs suppressed the activation of nuclear factor-κB (NF-κB). In summary, P. acidilactici gDNA could inhibit P. gingivalis LPS-induced inflammatory responses through the suppression of MAPKs and NF-κB, suggesting that P. acidilactici gDNA could be effective in preventing periodontitis.

• Journal of Life Science
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• v.17 no.1 s.81
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• pp.39-44
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• 2007

The Rqh1 gene is essential for vegetative growth in fission Yeast. The rqh1 mutant showed that sensitivity of DNA damaging agent, a wild range of phenotype including abnormal gene expression and cell elongation. This result showed that the rqhl-overexpression cell was sensitivity to DNA damaging agent like rqhl mutant. When Rqh1 have an over-expression by $nmt1^+$ promoter of pREP vector, rqh1 mutant DNA damaging agent sensitivity could be compensated. We isolated two strong mutant containing complementation gene, rqh156 and rqh172, respectively. This result observed that the DNA damaging agent sensitivity of rqhl mutant was complemented by the expression of rqh156 and rqh172. They induced mRNA expression in a dose-dependent manner HU, MMS and UV. The HU sensitivity of the rqhl was complemented by the expression of rqh156 and rqh172. The mRNA expression of rqh156 decreased on HU dose dependent but the mRNA expression of rqh172 did not decrease on HU dose dependent. The MMS and W sensitivity of the rqhl was complemented by the expression of rqh156 and rqh172. These results indicate that the isolated rqhl gene may play an important role in DNA metabolism.

• Microbiology and Biotechnology Letters
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• v.13 no.3
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• pp.289-296
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• 1985

A simple procedure for rapid isolation of plasmid DNA from lactobacillus species and streptococcus species is described. Lactic acid bacteria were cultured in the TCM broth containing 0.5％ glycine and plasmid DNA was isolated from cells treated with mutanolysin by alkaline-detergent lysis method. Good results for releasing and isolating plasmid DNA from lactobacillus species were obtained by treatment of cells with 30$\mu\textrm{g}$ of mutanolysin per ml at 37$^{\circ}C$ for 5 to 10 min. For the streptococcus species, the optimum conditions were slightly different. The procedure could be used for rapid characterization of plasmid DNA in Lactobacillus casei, Lactobacillus acidophilus, Lactobacillus helveticus, Streptococcus lactis, Streptococcus faecalis, Streptococcus faecium, and Streptococcus cremoris strains. Using this procedure, plasmids isolated from $1.5m\ell$ cultures could readily be visualized in agarose gel.

• Applied Biological Chemistry
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• v.41 no.3
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• pp.219-223
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• 1998

We have established a transformation system for entomopathogenic fungus, Metarhizium anisopliae, in order to develop mycoinsecticide by recombinant DNA techniques. Protoplasts of M. anisopliae would be transformed to a benomyl-resistant by introducing pBRG-4 plasmid DNA, which contains a ${\beta}-tubulin$ gene of Aspergillus flavus conferring resistance to benomyl and a pyr4 gene of Neurospora crassa, in the presence of 5% polyethylene glycol and 10 mM calcium chloride. Transformants occuring at a frequency of 10 colonies per $50\;{\mu}g$ pBRG-4 DNA grew on the $5\;{\mu}g/ml$ concentrations of benamyl, while the wild type was inhibited by $2.5\;{\mu}g/ml$. From the Southern analysis using genomic DNAs isolated from M. anisopliae transformants, the positive signals suggested that the ${\beta}-tubulin$ gene had integrated in the M. anisopliae genome by homologous recombination.

• Journal of KIISE:Databases
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• v.36 no.6
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• pp.455-465
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• 2009

Suffix trees are widely used in similar sequence matching for DNA. They have several problems such as time consuming, large space usages of disks and memories and data skew, since DNA sequences are very large and do not fit in the main memory. Thus, in the paper, we present a space efficient indexing method called SENoM, allowing us to build trees without merging phases for the partitioned sub trees. The proposed method is constructed in two phases. In the first phase, we partition the suffixes of the input string based on a common variable-length prefix till the number of suffixes is smaller than a threshold. In the second phase, we construct a sub tree based on the disk using the suffix sets, and then write it to the disk. The proposed method, SENoM eliminates complex merging phases. We show experimentally that proposed method is effective as bellows. SENoM reduces the disk usage less than 35% and reduces the memory usage less than 20% compared with TRELLIS algorithm. SENoM is available to query efficiently using the prefix tree even when the length of query sequence is large.