• KIEE International Transactions on Electrophysics and Applications
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• v.11C no.3
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• pp.85-90
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• 2001

The determination of DNA hybridization reaction can apply the molecular biology research, clinic diagnostics, bioengineering, environment monitoring, food science and other application area. So, the improvement of DNA detection system is very important for the determination of this hybridization reaction. In this study, we report the characterization of the probe and target oligonucleotide hybridization reaction using the evanescent field microscopy. First, we have fabricated DNA chip microarray. The particles which were immobilized oligonucleotides were arranged by the random fluidic self-assembly on the pattern chips, using hydrophobic interaction. Second, we have detected DNA hybridization reaction using evanescent field microscopy. The 5'-biotinylated probe oligonucleotides were immobilized on the surface of DNA chip microarray and the hybridization reaction with the Rhodamine conjugated target oligonucleotide was excited fluorescence generated on the evanescent field microscopy. In the foundation of this result, we could be employed as the basis of a probe olidonucleotide, capable of detecting the target oligonucleotide and monitoring it in a large analyte concentration range and various mismatching condition.

• BMB Reports
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• v.35 no.5
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• pp.532-535
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• 2002

To establish a method to evaluate the quality of the printed microarray and DNA fragments' immobilization. The target gene fragments that were made with the restriction display PCR (RD-PCR) technique were printed on a superamine modified glass slide, then immobilized with UV cross-linking and heat. This chip was hybridized with universal primers that were labeled with cy3-dUTP, as well as cDNA that was labeled with cy3-dCTP, as the conventional protocol. Most of the target gene fragments on the chip showed positive signals, but the negative control showed no signal, and vice versa. We established a method that enables an effective evaluation of the quality of the microarrays.

• Proceedings of the Korea Information Processing Society Conference
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• 2003.11b
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• pp.733-736
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• 2003

본 논문은 DNA microarray chip 을 사용한 실험 결과로 생산되는 대량의 데이터를 효율적으로 관리하기 위한 LIMS 개발에 대해 기술한다. 기존의 상용 LIMS 는 보편적 패턴과 방식을 정규화하여 제공하기 때문에 실험실의 고유한 방식을 포함하긴 어렵다. 본 논문에서는 유연성 있는 LIMS 를 개발하기 위해 특정 실험 중심으로 설계하면서 MAGE-OM 의 표준을 따르도록 디자인하였고, HYLIMS manager 라는 Local Application 과 검색을 주로 이용하는 사용자를 위하여 Web 검색 시스템을 구현하였다. 데이터베이스의 부하를 줄이기 위해 데이터 저장용 DB 와 검색용 DB 를 구분하였고, 데이터를 타입과 처리 형태에 따라 분류하여 관리하였으며 데이터 보안을 위해 실험 관리자가 사용자의 접근 제한을 설정 할 수 있도록 하였다.

• Environmental Mutagens and Carcinogens
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• v.22 no.1
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• pp.54-59
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• 2002

We have used cDNA microarray hybridization to identify gene regulated in response to gamma-irradiation in U-937 cell. The cDNA-chip was composed entirely of 1,000 human cancer related gene including apoptosis and angiogenesis etc. In gamma-irradiated U-937 cell, highly charged protein, ribosomal protein L32, four and a half LIM domains 3, lipocalin 2 (oncogene 24p3) and interleukin 15, ataxia telangiectasia mutated (includes complementation groups A, C and D) genes showed increased level of its transcription, and cell division cycle 25A, dihydrofolate reductase, topoisomerase (DNA) II beta(180kD), kinase suppressor of ras and strarigin genes showed reduced level of its transcription compared to untreated U-937 cell. The significant change of level of transcription was not found in well-known ionizing radiation(IR)-responsive gene, such as transcription factor TP53 and p53 related gene, except ataxia telangiectasia mutated gene.

• Proceedings of the Korea Society of Environmental Toocicology Conference
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• 2003.10a
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• pp.173-173
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• 2003

With the introduction of DNA microarrays, a high throughput analysis of gene expression is now possible as a replacement to the traditional time-consuming Southern-blot analysis. This cDNA microarray should be ahighly favored technology in the area of molecular toxicology or analysis of environmental stresses.In this study, therefore, we developed a novel cDNA microarray for analyzing stress-specific responses in japanese Medaka fish. In the design and fabrication of this stress specific functional cDNA microarray, 123 different genes in Medaka fish were selected from eighteen different stress responsive groups and spotted on a 25${\times}$75 mm glass surface. After exposure of the fish to bisphenol A which is the one of the well-known endocrine disrupting chemicals (EDCs), over 1 or 10 days, the responses of the DNA chip were found to show distinct expression patterns according to the mode of toxic actions from environmental toxicants. As a results, they showed specific gene expression pattern to bisphenol A, additionally, the chemical spesific biomarkers could be suggested based on the chip analysis data. Therefore, this chip can be used to monitor stress responses of unknown and/or known toxic chemicals using Medaka fish and may be used for the further development of biomarkers by utilizing the gene expression patterns for known contaminants.

• Proceedings of the Korean Statistical Society Conference
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• 2001.11a
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• pp.149-153
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• 2001

본 논문은 microarray를 분석하기위한 표준화에 대한 여러 방법들을 소개하고 비교해보았다. Microarray 연구는 Human Genome Project에서 파생된 여러 생명공학 기술 중 가장 널리 사용되는 기술로 기존에는 하지 못했던 총체적인 유전자의 발현상황을 탐색할 수 있다는 장점을 지니고 있으나, 자료들에 일정한 패턴이 나타나거나 잡음이 첨가되어 정보의 추출이 용의하지 않다는 단점을 지니고 있다. 특히 자료에 일정한 패턴이 있는 경우에 올바르지 못한 결론을 이끌어낼 수도 있기에 이 패턴을 제거하는 표준화작업은 microarray 분석에 있어서 매우 중요한 처리과정이다. 본 논문에서는 표준화방법들을 소개하고 각각 가지고 있는 장단점을 실제 국내에서 얻어진 자료를 통해 비교하였고, 그 결과 LOWESS 적합을 통한 표준화방법이 타 방법에 비해 유용한 점이 많음을 확인할 수 있었다.

• Bulletin of the Korean Chemical Society
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• v.26 no.3
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• pp.379-383
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• 2005

This research aims to develop DNA chip array without an indicator. We fabricated microelectrode array by photolithography technology. Several DNA probes were immobilized on an electrode. Then, indicator-free target DNA was hybridized by an electrical force and measured electrochemically. Cyclic-voltammograms (CVs) showed a difference between DNA probe and mismatched DNA in an anodic peak. Immobilization of probe DNA and hybridization of target DNA could be confirmed by fluorescent. This indicator-free DNA chip microarray resulted in the sequence-specific detection of the target DNA quantitatively ranging from $10^{-18}\;M\;to\;10^{-5}$ M in the buffer solution. This indicator-free DNA chip resulted in a sequence-specific detection of the target DNA.

• Microbiology and Biotechnology Letters
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• v.38 no.1
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• pp.70-76
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• 2010

The single-stranded large circular (LC)-sense DNA were utilized as probes for DNA chip experiments. The microarray experiment using LC-sense DNA probes found differentially expressed genes in A549 cells as compared to WI38VA13 cells, and microarray data were well-correlated with data acquired from quantitative real-time RT-PCR. A 5K LC-sense DNA microarray was prepared, and the repeated experiments and dye swap test showed consistent expression patterns. Subsequent functional analysis using LC-antisense library of overexpressed genes identified several genes involved in A549 cell growth. These experiments demonstrated proper feature of LC-sense molecules as probe DNA for microarray and the potential utility of the combination of LC-sense microarray and antisense libraries for an effective functional validation of genes.

• Journal of the Korean Institute of Electrical and Electronic Material Engineers
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• v.18 no.6
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• pp.560-570
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• 2005

In this paper, a microelectrode away DNA chip was fabricated on glass slide using photolithography technology. Several probe DNAs consisting of mercaptohexyl moiety at their 5' end were immobilized on the gold electrodes by DNA arrayer utilizing the affinity between gold and sulfu. Then target DNAs were hybridized and reacted with Hoechst 33258, which is a DNA minor groove binder and electrochemically active dye. Cyclic voltammetry in 5mA ferricyanide/ferrocyanide solution at 100 mV/s confirmed the immobilization of probe DNA on the gold electrodes. Linear sweep voltammetry or cyclic voltammetry showed a difference between target DNA and control DNA in the anodic peak current values. It was derived from Hoechst 33258 concentrated at the electrode surface through association with formed hybrid. It suggested that this DNA chip could recognize the sequence specific genes. It suggested that multichannel electrochemical DNA microarray is useful to develop a portable device for clinical gene diagnostic system.

• Korean Journal of Microbiology
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• v.41 no.2
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• pp.105-111
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• 2005

Streptomyces produces many kinds of secondary-metabolites including antibiotics. Screening of a new compound and elucidation of a biosynthetic pathway for the secondary metabolites are very important fields of biology, however, there is a main problem that most of the identified compounds are already researched compounds. To solve these problems, a microarray system that is based on the data related to the biosynthetic genes for secondary-metabolites was designed. For the main contents of DNA microarray, the important genes for the bio-synthesis of aminoglycosides, polyenes group, enediyne group, alpha-glucosidase inhibitors, glycopeptide group, and orthosomycin group were chosen. A DNA microarray with 69 genes that were involved in the bio-synthesis for the antibiotics mentioned above was prepared. The usability of the DNA microarray was confirmed with the chromosomal DNA and total RNA extracted from S. coelicolor whose genomic sequence had already been reported.