• Journal of Microbiology and Biotechnology
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• v.32 no.8
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• pp.1026-1033
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• 2022

This study presents a novel DNA part characterization technique that increases throughput by combinatorial DNA part assembly, solid plate-based quantitative fluorescence assay for phenotyping, and barcode tagging-based long-read sequencing for genotyping. We confirmed that the fluorescence intensities of colonies on plates were comparable to fluorescence at the single-cell level from a high-end, flow-cytometry device and developed a high-throughput image analysis pipeline. The barcode tagging-based long-read sequencing technique enabled rapid identification of all DNA parts and their combinations with a single sequencing experiment. Using our techniques, forty-four DNA parts (21 promoters and 23 RBSs) were successfully characterized in 72 h without any automated equipment. We anticipate that this high-throughput and easy-to-use part characterization technique will contribute to increasing part diversity and be useful for building genetic circuits and metabolic pathways in synthetic biology.

• Journal of the Korean Magnetic Resonance Society
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• v.20 no.3
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• pp.66-70
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• 2016

The replication protein A (RPA), is a heterotrimer with 70, 32 and 14 kDa subunits and plays a crucial role in DNA replication, recombination, and repair. The largest subunit, RPA70, binds to single-stranded DNA (ssDNA) and mediates interactions with many cellular and viral proteins. In this study, we performed nuclear magnetic resonance experiments on the complex of the DNA binding domain A of human RPA70 (RPA70A) with ssDNA, d(CCCCC), at various temperatures, to understand the temperature dependency of ssDNA binding affinity of RPA70A. Essential residues for ssDNA binding were conserved while less essential parts were changed with the temperature. Our results provide valuable insights into the molecular mechanism of the ssDNA binding of human RPA.

• JSTS:Journal of Semiconductor Technology and Science
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• v.7 no.3
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• pp.133-139
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• 2007

Future MEMS systems will be composed of larger varieties of devices with very different functionality such as electronics, mechanics, optics and bio-chemistry. Integration technology of heterogeneous devices must be developed. This article first deals with the current development trend of new fabrication technologies; those include self-assembling of parts over a large area, wafer-scale encapsulation by wafer-bonding, nano imprinting, and roll-to-roll printing. In the latter half of the article, the concept towards the heterogeneous integration of devices and functionality into micro/nano systems is described. The key idea is to combine the conventional top-down technologies and the novel bottom-up technologies for building nano systems. A simple example is the carbon nano tube interconnection that is grown in the via-hole of a VLSI chip. In the laboratory level, the position-specific self-assembly of nano parts on a DNA template was demonstrated through hybridization of probe DNA segments attached to the parts. Also, bio molecular motors were incorporated in a micro fluidic system and utilized as a nano actuator for transporting objects in the channel.

• Journal of the Korea Computer Graphics Society
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• v.2 no.2
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• pp.61-68
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• 1996

In this paper we propose a new visualization technique to characterize qualitative information of a large DNA sequence. While a long DNA sequence has huge information, it is not easy to obtain genetic information from the DNA sequence. We transform DNA sequences into a polygon to compute their homology in image domain rather than text domain. Our program visualizes DNA sequences with colored random walk plots and simplify them k-convex hulls. A random walk plot represents DNA sequence as a curve in a plane. A k-convex hull simplifies a random work plot by removing some parts of its insignificant information. This technique gives a biologist an insight to detect and classify DNA sequences with easy. Experiments with real genome data proves our approach gives a good visual forms for long DNA sequences for homology analysis.

• Korean Journal of Plant Resources
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• v.27 no.6
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• pp.714-719
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• 2014

This study investigated DNA damage protection and anti-inflammatory activity of different solvent fractions from Aruncus dioicus var. kamtschaticus (A. dioicus) aerial parts water extract. As for DNA damage protection, distilled water ($H_2O$) fraction displayed the most powerful protection for DNA damage at a concentration of 1 mg/ml. As for anti-inflammatory activity, dichloromethane ($CH_2Cl_2$) fraction exhibited the highest NO inhibition activity, ranging from 61% to 19% ($10-40{\mu}g/ml$). Furthermore, the levels of pro-inflammatory cytokines mRNA expressions and intracellular reactive oxygen species (ROS) were employed to verify the anti-inflammatory activity of the $CH_2Cl_2$ fraction on further researches. It could be concluded that A. dioicus had a significantly effect of DNA damage protection and anti-inflammatory activity which also as an essential edible vegetable and medicinal species.

• Biomolecules & Therapeutics
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• v.18 no.1
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• pp.1-15
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• 2010

Progress in the development of DNA vaccines and their delivery strategies has been made since their initial concept as a next generation vaccine. Since DNA vaccine includes non-infectious DNA parts of pathogens, it can't cause disease yet it closely mimic the natural process of infection and immune responses. Despite their early promising results of controlling infectious diseases and cancer in small animal models, DNA vaccines failed to display a level of immunogenicity required for combating these diseases in humans, possibly due to their lower protein expression levels. However, increasing evidence has shown that DNA vaccines are clinically well-tolerated and safe. Furthermore, one notable advantage of DNA vaccines includes convenient utilities of plasmid DNAs coding for antigens. For instance, any emerging pathogens could be prevented easily and timely by allowing the simple exchange of antigen-encoding genes. In this review, newly developed DNA vaccine strategies, including electroporation, which has emerged as a potent method for DNA delivery, targeting infectious diseases and cancer will be discussed with a focus on any on-going DNA vaccine trials or progress made pre-clinically and in clinics.

• Korean Journal of Ecology and Environment
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• v.54 no.3
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• pp.221-228
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• 2021

Recently, environmental DNA (eDNA)-based metabarcoding approaches have been proposed to evaluate the status of freshwater ecosystems owing to various advantages, including fast and easy sampling and minimal habitat disruption from sampling. Therefore, as a case study, we applied eDNA metabarcoding techniques to evaluate the effects of an abandoned mine land located near a headwater stream of Nakdonggang River, South Korea, by examining benthic macroinvertebrate diversity and compared the results with those obtained using the traditional Surber-net sampling method. The number of genera was higher in Surber-net sampling (29) than in the eDNA analysis (20). The genus richness tended to decrease from headwater to downstream in eDNA analysis, whereas richness tended to decrease at sites with acid-sulfated sediment areas using Surber-net sampling. Through cluster analysis and non-metric multidimensional scaling, the sampling sites were differentiated into two parts: acid-sulfated and other sites using Surber-net sampling, whereas they were grouped into the two lowest downstream and other sites using eDNA sampling. To evaluate freshwater ecosystems using eDNA analysis in practical applications, it is necessary to constantly upgrade the methodologies and compare the data with field survey methods.

• BMB Reports
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• v.33 no.5
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• pp.417-421
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• 2000

Mitochondrial DNA (mtDNA) mutation was investigated in a hepatoma patient using a polymerase chain reaction (PCR) and an in situ hybridization technique. Biotin-labeled probes for the subunit m of cytochrome c oxidase revealed differences in the in situ hybridization. A PCR assay using biopsied and microdissected tissues showed that common deletion (4,977 bp) was more pronounced in the cancer region than in the normal parts of the same patient. These results suggest that mtDNA deletion might be associated with tumorigenesis in hepatoma.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.11
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• pp.6791-6795
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• 2013

Apoptotic and cytotoxic activity of plant extracts obtaining from naturally growing Cynara syriaca in Turkey and cultivated C cardunculus against DLD1 colorectal cancer cells was determined. Extracts from wild and cultivated Cynara species were obtained from their vegetative parts and receptacles using hexane and applied with five different dose (0.1-1 mg/ml) as well as apigenin for MTT tests for three time periods (24, 48 and 72 hours). After cells were treated with $IC_{50}$ doses for each extract total DNA and RNA were isolated for determination of the cause of cell death. From isolated RNAs, cDNA were synthesized and amplification of p21, BCL-2 and BAX gene regions was carried out. Consequently, we found that pro-apoptotic (BAX) gene expression and a cell cycle inhibitor (p21) were induced in the presence of our artichoke extracts. In contrast, anti-apoptotic BCL-2 gene expression was reduced compared to the control group. In addition DNA fragmentation results demonstrated DLD1 cell death via apoptosis.

• Journal of Plant Biology
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• v.16 no.1_2
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• pp.23-29
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• 1973

The effect of phosphorus nutrition on the content of deoxyribonucleic acid(DNA), ribonucleic acid(RNA), crude protein and plant growth of soybean plant(Glycine max, Merr.) was studied. Yields of the above-and under-ground parts of the soybean plant in terms of dry weight, the amounts of crude protein, RNA and DNA continued to increase with increasing phosphorus supply. The amounts of RNA and crude protein were highest in the leaf tissues where most intensive growth was taking place. The relationships among DNA, RNA, crude protein and plant growth appeared to consist of the central dogma which has immortalized, while DNA in plant tissue was subject to charges cuased by external environmental facters such as phosphorus nutrition.