• Korean Journal of Microbiology
• /
• v.43 no.4
• /
• pp.250-255
• /
• 2007

The RecA protein of Deinococcus radiodurans is essential for the extreme radiation resistance of this organism. The central steps involved in recombinational DNA repair require DNA-dependent ATP hydrolysis by recA protein. Key feature of RecA protein-mediated activities is the interactions with ssDNA and dsDNA. The ssDNA is the site where RecA protein filament formation nucleates and where initiation of DNA strand exchange takes place. The effect of sequence heterogeneity of ssDNA was examined in this experiment. The rate of homopolymeric synthetic ssDNA-dependent ATP hydrolysis was constant or nearly so over a broader range of pHs. For poly(dT)-dependent ATP or dATP hydrolysis, rates were generally faster, with a broader optimum between pH 7.0 and 8.0. Activities of RecA protein were affected by the ionic environment. The ATPase activity was shown to have different sensitivity to anionic species. The presence of glutamate seemed to slimulate the hydrolytic activity. Dr RecA protein was shown to require $Mg^{2+}$ ion greater than 2 mM for binding to etheno ssDNA and the binding stoichiometry of 3 nucleotide for RecA protein monomer.

• Korean Journal of Environmental Biology
• /
• v.18 no.1
• /
• pp.53-61
• /
• 2000

In order to characterize the genetic diversity of bacterial community in groundwater, samples were collected from used for drinking water and polluted with heavy metal wastewater in Seoul city and natural cave of Kangwondo. The DNA was amplified with 165 rDNA-based primers by use of the PCR, and then analysed ARDRA (amplified ribosomal DNA restriction analysis). Restriction endonuclease analysis patterns of amplified 165 rDNA in drinking water and wastewater relatively showed high genetic diversity in situ and drinking groundwater. The number of DNA fragments varied with in situ and drinking water. This method of ARDRA of bacterial communities in groundwater could be used for a quick assessment of genotypic changes between different locations reflecting different environmental conditions and the diversity reflected pollution of groundwater (natural cave water>drinking water>waste water, as in order of grade). [Genetic diversity, Groundwater, 165 rDNA, PCR, ARDRA].

• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2006.02a
• /
• pp.11-18
• /
• 2006

바이오칩의 대표 주자인 DNA 칩은 점차 분자생물학의 주요 도구로 인식되고 있다. 쓰임새 또한 다양해져 기초 생물학, 기능 유전체학 연구뿐만 아니라 임상 현장에서의 적용을 위한 연구가 활발히 진행되고 있다. 임상분야에서 최근 주목 받고 있는 분야가 DNA 칩을. 이용한 질병진단 및 예후 측정이다. 개별 환자 세포의 분자유전학적 상태는 DNA 칩의 유전체 프로파일링(genome-wide profiling)으로 상세히 파악될 수 있으므로, DNA 칩은 질병의 세부아형 진단, 약물에 대한 개인 민감도 측정, 정확한 예후 측정을 통한 환자의 세심한 관리 등 미래 의료의 핵심이라 할 수 있는 개인별 맞춤 치료(personalized medicare)를 가능하게 하는데 지대한 역할을 할 것으로 기대되고 있다. 특히 수많은 질병 중에서 현대인의 난치병으로 손꼽히는 암은 DNA 칩 분석의 주요 적용 대상이다. 암에 연관된 복잡한 메커니즘을 기존의 단일 표지자로 진단하는 데는 한계가 있기 때문에, DNA 칩을 이용해 질병의 특정 phenotype과 관련 있는 암의 특이 패턴을 전사체 수준에서 분석하여 새로운 형태의 분자유전학적 표지자(transcriptional molecular signature)를 발굴하는 것이다 본 발표에서는 이러한 연구에 쓰이는 DNA 칩 분석 방법들과 실제 위암 데이터에 적용한 사례에 대해 논의하고자 한다. 연세의대 암전이 연구센터의 17K cDNA 칩을 이용하였으며, 진단 및 예후 측정을 위한 여러 분석 방법을 수행하였다.

• Korean Journal of Heritage: History & Science
• /
• v.41 no.1
• /
• pp.99-108
• /
• 2008

The paleogenetic analysis has become an increasingly important subject of archaeological, anthropological, biological as well as public interest. Recently, scientific research for human skeletal remains was more activated because of increasing awareness of the valuable archaeological information by the ancient DNA analysis. State of preservation of organic remains vary in different soil and burying environmental condition. Almost all available tissue disappear to analysis ancient DNA of bone in acidic soil caused by climate and geological features in Korea. Many preserved human remains excavated in the 'Heogwakmyo'(limelayered tomb of Chosun Dynasty Period) is able to explain through the relationship between burial conditions and bone survival form the burial method and ceremony. Ancient DNA analysis of excavated human bone form ancient tomb requires to remove contaminants such as microorganism's DNA and soil components that affect authentic results. Particularly, contamination control of contemporary human DNA is major serious problem and should verified by criteria of authenticity. In order to understand migration and culture of ancient population, when possible, ancient DNA studies needs to go abreast both radiocarbon and stable isotope studies because the dietary inferences will suggest ancient subsistence and settlement patterns. Also when the paleogenetic research supported with the arts and humanities research such as physical anthropology and archaeology, more valuable ancient genetic information is providing a unique results about evolutionary and population genetics studies to reconstruct the past.

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

• Analytical Science and Technology
• /
• v.24 no.1
• /
• pp.51-59
• /
• 2011

Genetic Identification has become an important forensic investigation method which discerns identity through analysis of physical samples discovered in various crime scenes. Recently more samples are being requested to undergo A-STR analysis of low copy number (LCN) DNA, which is known as touch evidence-type sample and left on various objects such as a pen briefly used by the criminal, the gear of the car used for driving, the handle, and various buttons inside a car. This research attempted to extract the LCN DNA of the touch evidencetype left on crushed fingerprints on firearms, etc. and examine the genotyping success rate. Four types of firearms (M16, K1A, COLT 45 Pistol, M29 Revolver) were fired individually and physical samples were gathered from four parts of each firearm. Subsequently, in order to extract the LCN DNA, Microkit and $Prepfiler^{TM}$ were used to compare and analyze the quantity of DNA extracted and the genotyping success rate. Analysis results showed that the quantity of DNA extracted by $Prepfiler^{TM}$ was on average 1.7 times higher than that of Microkit, and in genotype analysis success rate $Prepfiler^{TM}$ also demonstrated 24.9% on average in contrast to 0% for Microkit. In regards to the grip part of the K1A, $Prepfiler^{TM}$'s success rate was as high as 50.6%.

• The Korean Journal of Mycology
• /
• v.27 no.1 s.88
• /
• pp.20-26
• /
• 1999

The specific DNA band appeared in PCR-RAPD analysis using OPO-2 primer was a very important for the researching Korean pine-mushrooms, Tricholoma matsutake. This DNA band, sequenced to be the 770 base pairs, existed as only a single copy in the whole genomic DNA's of Korean pine-mushrooms. However, this band was not presenting from the PCR-RAPD bands of other ectomycorrhyzal fungi reacted with the OPO-2 primer or the dot blots. Also, this DNA sequence was not matched with those of the other genes known by NCBI and had low homology together with sequence of other proteins compared. Those results suggested that the specific DNA band can be used as probe for identification of T. matsutake and might be related to the informations rather than the gene for the proteins with analysis of protein sequence translated from the DNA sequence.

• Korean Journal of Fisheries and Aquatic Sciences
• /
• v.30 no.5
• /
• pp.804-808
• /
• 1997

The genetic differentiation and characteristics of two oyster populations (Crassostrea gigas) in Korea were assessed based on the restriction fragment length polymorphisms (RFLP) analysis and the restriction patterns of subcloned mtDNA. The restriction fragments of twenty individuals in West Sea revealed an identical pattern, determined by 8 restriction enzymes. On the other hand, two haplotypes having variation at the HindIII site were shown in the specimens from South Sea; minor haplotypes (4 of 20) were similar to the results obtained from individuals in West Sea while major haplotypes were different from those in West Sea. It was suggested that oysters (C. gigas) of West Sea might have been introduced to South Sea. Each mitochondrial DNA from two oyster populations in Korea and from one in Japan was divided to three parts and subcloned into pUC19 to use in genetic studies effectively. Restriction map was constructed based on the cleavage pattern by multiple restriction enzymes.

• Food Science of Animal Resources
• /
• v.25 no.2
• /
• pp.218-225
• /
• 2005

This study was performed to determine sequence variation and RFLP of the mt DNA D-loop region using Southern blot hybridization analysis and to develop mt DNA marker affecting milk production traits in Hanwoo cows. The PCR was used to amplify an 1142 bp fragment within the D-loop region of mt DNA using specific primers. Mt DNA were digested with seven restriction enzymes and hybridized using DIG-labeled D-loop probe. The mt DNA RFLP polymorphisms were observed in the four enzymes, BamHI, RsaI, XbaI and HpaII. Nucleotide substitutions were detected at positions 441 (G/C), 469 (T/C), 503 (C/T), 569 (G/A), 614 (C/A) and 644 (C/T) of the mt DNA D-loop region between two selected lines. Significant relationship between the XbaI RFLP type and breeding value was found(p<0.05). Cows with A type had higher estimated breeding values than those with B type (P<0.05) between high and low milk production lines. Therefore, the RFLP marker of mt DNA could be used as a selection assisted tool for individuals with high milk producing ability in Hanwoo.

• Applied Biological Chemistry
• /
• v.39 no.5
• /
• pp.403-408
• /
• 1996

Total bacterial community DNA, which was extracted from microcosm soil and field soil after 2,4-D amendments, was analyzed on Southern blots, using the tfdA gene probe derived from plasmid pJP4 and the Spa probe from Sphingomonas paucimobilis. Southern blot analyses with total bacterial DNA extracted from soils Inoculated with Pseudomonas cepacia/pJP4 revealed that DNA probe method could detect the 2,4-D degrading bacteria down to $10^5\;cells/g$ dry soil. In the microcosm experiment, there was a good correlation between 2,4-D degradation and banding patterns in hybridization analyses performed after each 2,4-D treatment using the two probes. When bacterial DNA extracted from microcosm soil was hybridized with the Spa probe, a change in the position of hybrid bands was observed over time in a Southern blot, suggesting that population change or possibly genetic rearrangement in 2,4-D degrading microbial populations occurred in this soil. With the Spa probe, one hybrid DNA band was persistently observed throughout the five 2,4-D additions. When bacterial DNA isolated from the field soil was probed with the tfdA and Spa, strong hybridization signal was observed in the 100 ppm-treated subplot, weak signal In the 10 ppm-treated subplot, and no significant signal in the 1 ppm-treated and control subplots. The data show that DNA probe analyses were capable of detecting and discriminating the indigenous 2,4-D degrading microbial populations in soil amended with 2,4-D under laboratory and field conditions.