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

• The Transactions of the Korean Institute of Electrical Engineers C
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• v.51 no.6
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• pp.265-270
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• 2002

The determination of DNA hybridization reaction can apply the molecular biology research, clinic diagnostics, bioengineering, environment monitoring, food science and application area. So, the improvement of DNA hybridization detection method is very important for the determination of this hybridization reaction. Several molecular biological techniques require accurate predictions of matched versus mismatched hybridization thermodynamics, such as PCR, sequencing by hybridization, gene diagnostics and antisense oligonucleotide probes. In addition, recent developments of oligonucleotide chip arrays as means for biochemical assays and DNA sequencing requires accurate knowledge of hybridization thermodynamics and population ratios at matched and mismatched target sites. In this study, we report the characteristics of the probe and matched, mismatched target oligonucleotide hybridization reaction using thermodynamic method. Thermodynamic of 5 oligonucleotides with central and terminal mismatch sequences were obtained by measured UV-absorbance as a function of temperature. The data show that the nearest-neighbor base-pair model is adequate for predicting thermodynamics of oligonucleotides with average deviations for $\Delta$H$^{0}$ , $\Delta$S$^{0}$ , $\Delta$G$_{37}$ $^{0}$ and T$_{m}$, respectively.>$^{0}$ and T$_{m}$, respectively.

• Proceedings of the Korean Society of Applied Pharmacology
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• 1993.04a
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• pp.59-59
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• 1993

비방사능물질인 Biotin을 DNA probe에 표지하여 nonisotopic hybridization 방법을 사용하여 감도를 높임으로써, 손쉽게 생물공학 의약품의 품질관리에 사용되도록 하였다. Bethesda Research Laboratories(BRL) 회사 제품인 biotinylated probes-avidin alkaline phosphatase를 이용한 chemiluminescene detection방법으로 행하여 λ phage DNA, yeast DNA, E.coil DNA의 한계 검출 농도를 알아내고, 생물 공학 제품에 적용하였다. Dot blot hybridization 방법으로 행하여 λ phage DNA는 0.1pg, Yeast DHA는 4.5pg, E. coli DNA는 8.9pg까지 검출되었고, 기존 생물공학 제품에서는 숙주 유래 DNA가 전혀 검출되지 않았다.

• Proceedings of the KIEE Conference
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• 2004.07c
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• pp.2128-2130
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• 2004

High throughput analysis using a DNA chip microarray is powerful tool in the post genome era. Less labor-intensive and lower cost-performance is required. Thus, this paper aims to develop the multi-channel type label-free DNA chip and detect SNP (Single nucleotide polymorphisms). At first, we fabricated a high integrated type DNA chip array by lithography technology. Various probe DNAs were immobilized on the microelectrode array. We succeeded to discriminate of DNA hybridization between target DNA and mismatched DNA on microarray after immobilization of a various probe DNA and hybridization of label-free target DNA on the electrodes simultaneously. This method is based on redox of an electrochemical ligand.

• Journal of Periodontal and Implant Science
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• v.32 no.2
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• pp.269-280
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• 2002

The purpose of this study is to develop species-specific DNA probes and polymerase chain reaction (PCR) primers for detection and identification of Prevotella nigrescens (P. nigrescens) 9336. This study procedure includes (1) whole-genomic DNA extraction of P. nigrescens 9336 (2) construction of the genomic DNA library, (3) screening of strain-specific DNA probe by reverse Dot Hybridization method, (4) confirmation of strain-specific DNA probe by Southern blot analysis, (5) determination of nucleotide sequences of strain-specific DNA probe. Thirty-five restriction fragments of P. nigrescens 9336 genomic DNA digested with the Hind III were obtained. Reverse dot hybridization and Southern blot analysis data showed that three of them, Pn10, Pn23, and Pn35, could be P. nigrescens 9336-specific DNA probes. These data indicated that these DNA probes could be useful in detection and identification of the P. nigrescens 9336.

• KIEE International Transactions on Electrophysics and Applications
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• v.4C no.4
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• pp.133-136
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• 2004

This research aims to develop a DNA chip array without an indicator. We fabricated a microelectrode array through photolithography technology. Several DNA probes were immobilized on an electrode. Then, target DNA was hybridized and measured electrochemically. Cyclic-voltammograms (CVs) showed a difference between the DNA probe and mismatched DNA in an anodic peak. This indicator-free DNA chip resulted in a sequence-specific detection of the target DNA.

• The Korean Journal of Mycology
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• v.25 no.4 s.83
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• pp.362-368
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• 1997

Five formae speciales of Fusarium oxysporum in Korea were examined using RFLP analysis to find the possibility for classification and analyze genetic variations. DNAs from F. oxysporum f. sp. lycopersici, cucumerinum, fragariae, garlic and sesami were used with three recombinant probes such as pFC46, pFC52 and pFC57. Distinct differences among five formae speciales of this fungus were detected in RFLP band patterns based on southern hybridization of genomic DNA using each recombinant clone, which was a repetitive copy probe. Strains belong to four formae speciales could be very stable in genetic variation except f. sp. sesami which has more variation than the others based on the RFLP analysis. They formed their own cluster which has high similarity within the same formae specialis resulted from the UPGMA analysis for genetic relationship analysis and each cluster represented its own formae specialis. The method using three recombinant DNA probes could be a good tool for classification of formae speciales in F. oxysporum.

• Korean Journal of Veterinary Research
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• v.39 no.1
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• pp.148-158
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• 1999

The purpose of this study was to establish a rapid, reliable diagnostic method detecting Encephalomyocarditis virus(EMCV) RNA in formalin-fixed, paraffin-embedded tissues of EMCV naturally infected pigs by cDNA probe of EMC $K_3$, the EMCV strain isolated from Korea. Using a biotin-labelled nick translated probe for the cDNA marker. We made up for some defects of radiolabeled method. In sits hybridization(ISH) technique, differently from the other nucleic acid hybridization methods, is able to detect the virus genome specifically in the state of the intact shapes of cells and/or tissues. We succeeded in performing the experiment to detect the EMCV within 1~2 hours using the $MicroProbe^{TM}$ capaillary action system. In this study, we observed highly specific positive signals of red color by staining the paraffin-embedded tissue sections of naturally EMCV-infected pig organs or tissues, including brain, heart, kidney and lacrimal gland with the Fast Red TR salt/Naphtol phosphate chromogen. The results suggested that this ISH method is considered as a highly sensitive and reliable tool for molecular biologic diagnosis of the EMC viral disease.

• The Korean Journal of Mycology
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• v.26 no.2 s.85
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• pp.135-143
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• 1998

Contour-clamped homogeneous electric field gel electrophoresis was used to establish electrophoretic karyotype for 10 species of Fusarium sections Sporotrichiella, Liseola, Gibbosum, Discolor and Martiella. Intact chromosomal DNA was isolated from fungal protoplast and separated under various conditions according to their size in order to improve DNA separation. The numbers of chromosome-sized DNA molecules for individual species ranged from 5-13, with individual chromosomes ranging from 0.78 Mb to 7.20 Mb in size. The total genome DNA size of each species was estimated at about 18.32 Mb to 48.20 Mb. Comparison of karyotype profiles following Southern hybridization analysis with a randomly selected genomic probe of F. oxysporum formae speciales litii was carried out.

• Reproductive and Developmental Biology
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• v.28 no.2
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• pp.133-137
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• 2004

Sexing from bovine embryos which were fertilized in vitro implicate a possibility of the sex-controlled cattle production. This study was carried out to investigate the possibility of determining of embryo sex by fluorescence in situ hybridization (FISH) technique. FISH was achieved in in vitro fertilized bovine embryos using a bovine Y-specific DNA probe which constructed from the btDYZ-1 sequences. To evaluate Y-chromosome specificity of the FISH probe, metaphase spreads of whole embryos and lymphocytes were prepared and tested. A male-specific signal was detected on 100% of Y chromosome bearing metaphase specimens. Using the FISH technique with a bovine Y-specific probe, 232 whole embryos of 8 cell- to blastocyst-stage were analyzed. Observing the presence of the Y-probe signal on blastomeres, 102 embryos were predicted as male, and 130 embryos as female. The determining rate of embryo sex by FISH technique was about 93% regardless of embryonic stages. In conclusion, the FISH using a bovine Y-specific DNA probe is an accurate, reliable and quick method for determining the sex of bovine embryos.