• Title, Summary, Keyword: cDNA Chip

Search Result 119, Processing Time 0.03 seconds

DNA Chip using Single Stranded Large Circular DNA: Low Background and Stronger Signal Intensity

  • Park, Jong-Gu
    • Biomedical Science Letters
    • /
    • v.10 no.2
    • /
    • pp.75-84
    • /
    • 2004
  • Massive identification of differentially expressed patterns has been used as a tool to detect genes that are involved in disease related process. We employed circular single stranded sense molecules as probe DNA for a DNA chip. The circular single stranded DNAs derived from 1,152 unigene cDNA clones were purified in a high throughput mode from the culture supernatant of bacterial transformants containing recombinant phagemids and arrayed onto silanized slide glasses. The DNA chip was examined for its utility in detection of differential expression profile by using cDNA hybridization. Hybridization of the single stranded probe DNA were performed with Cy3- or Cy5-labeled target cDNA preparations at $60^\circ$C. Dot scanning performed with the hybridized slide showed 29 up-regulated and 6 down-regulated genes in a cancerous liver tissue when compared to those of adjacent noncancerous liver tissue. These results indicate that the circular single stranded sense molecules can be employed as probe DNA of arrays in order to obtain a precious panel of differentially expressed genes.

  • PDF

Indicator-free DNA Chip Array Using an Electrochemical System

  • Park, Yong-Sung;Kwon, Young-Soo;Park, Dae-Hee
    • KIEE International Transactions on Electrophysics and Applications
    • /
    • v.4C no.4
    • /
    • pp.133-136
    • /
    • 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.

Development of Pattern Classifying System for cDNA-Chip Image Data Analysis

  • Kim, Dae-Wook;Park, Chang-Hyun;Sim, Kwee-Bo
    • 제어로봇시스템학회:학술대회논문집
    • /
    • /
    • pp.838-841
    • /
    • 2005
  • DNA Chip is able to show DNA-Data that includes diseases of sample to User by using complementary characters of DNA. So this paper studied Neural Network algorithm for Image data processing of DNA-chip. DNA chip outputs image data of colors and intensities of lights when some sample DNA is putted on DNA-chip, and we can classify pattern of these image data on user pc environment through artificial neural network and some of image processing algorithms. Ultimate aim is developing of pattern classifying algorithm, simulating this algorithm and so getting information of one's diseases through applying this algorithm. Namely, this paper study artificial neural network algorithm for classifying pattern of image data that is obtained from DNA-chip. And, by using histogram, gradient edge, ANN and learning algorithm, we can analyze and classifying pattern of this DNA-chip image data. so we are able to monitor, and simulating this algorithm.

  • PDF

Development of High-Intergrated DNA Array on a Microchip by Fluidic Self-assembly of Particles (담체자기조직화법에 의한 고집적 DNA 어레이형 마이크로칩의 개발)

  • Kim, Do-Gyun;Choe, Yong-Seong;Gwon, Yeong-Su
    • The Transactions of the Korean Institute of Electrical Engineers C
    • /
    • v.51 no.7
    • /
    • pp.328-334
    • /
    • 2002
  • The DNA chips are devices associating the specific recognition properties of two DNA single strands through hybridization process with the performances of the microtechnology. In the literature, the "Gene chip" or "DNA chip" terminology is employed in a wide way and includes macroarrays and microarrays. Standard definitions are not yet clearly exposed. Generally, the difference between macro and microarray concerns the number of active areas and their size, Macroarrays correspond to devices containing some tens spots of 500$\mu$m or larger in diameter. microarrays concern devices containing thousnads spots of size less than 500$\mu$m. The key technical parameters for evaluating microarray-manufacturing technologies include microarray density and design, biochemical composition and versatility, repreducibility, throughput, quality, cost and ease of prototyping. Here we report, a new method in which minute particles are arranged in a random fashion on a chip pattern using random fluidic self-assembly (RFSA) method by hydrophobic interaction. We intend to improve the stability of the particles at the time of arrangement by establishing a wall on the chip pattern, besides distinction of an individual particle is enabled by giving a tag structure. This study demonstrates the fabrication of a chip pattern, immobilization of DNA to the particles and arrangement of the minute particle groups on the chip pattern by hydrophobic interaction.ophobic interaction.

The Antioxidant Effect, Inhibition of Interleukin-4 and the Effect on the Gene Expression by Using cDNA Chip of Chungsangboha-tang(Qingshangbuxia-tang) (청상보하탕의 항산화 효과, Interleukin-4 억제 및 cDNA chip을 이용한 유전자발현에 미치는 영향)

  • 이동생;정희재;정승기;이형구
    • The Journal of Korean Medicine
    • /
    • v.24 no.2
    • /
    • pp.148-158
    • /
    • 2003
  • Backgrounds & Objectives: In many recent studies, molecular biological methods have been used to investigate the role of cytokines in pathogenesis and new therapeutic targets of asthma. Recently, as a method of research on the gene expression, they are applying another method which assays multiple gene expressions at the same time by the microarray. In this study, the antioxidant effect, the inhibitory effect against interleukin-4 and the effect on the CD/cytokine gene expression in PBMC (peripheral blood mononuclear cells) was evaluated by using cDNA microarray chip of Chungsangboha-tang. Methods: Experimental studies were performed for the antioxidant effect of Chungsangboha-tang on DPPH (1, 1-diphenyl-2-picrylhydrazyl) solution, for the IL-4-inhibiting effect on BALB/c mouse spleen, and for the gene expression effect on PBMC (peripheral blood mononuclear cells) with microarray. Results: Chungsangboha-tang showed antioxidant effect dose-dependently. Chungsangboha-tang inhibited interleukin-4 dose-dependently and showed significant difference in 10ug/ml and 100ug/ml of test groups. There was no 2 more times upregulated genes than in the control group by using cDNA microarray chip of Chungsangbohn-tang, but there were 140%-200% upregulated genes. There was no 2 more times downregulated genes than in the control group by using cDNA microarray chip of Chungsangboha-Tang, but there was 50%-75% downregulated genes. Conclusions: This study showed that Chungsangboha-tang has an antioxidant effect and inhibition of Interleukin-4, but further studies are necessary with microarray.

  • PDF

Electrochemical Detection of Single Nucleotide Polymorphism (SNP) Using Microelectrode Array on a DNA Chip (미소전극어레이형 DNA칩을 이용한 유전자다형의 전기화학적 검출)

  • 최용성;권영수;박대희
    • The Transactions of the Korean Institute of Electrical Engineers C
    • /
    • v.53 no.5
    • /
    • pp.286-292
    • /
    • 2004
  • In this study, an integrated microelectrode array was fabricated on glass slide using microfabrication technology. Probe DNAs consisting of mercaptohexyl moiety at their 5-end were spotted on the gold electrode using micropipette or DNA arrayer utilizing the affinity between gold and sulfur. Cyclic voltammetry in 5mM ferricyanide/ferrocyanide solution at 100 ㎷/s confirmed the immobilization of probe DNA on the gold electrodes. When several DNAs were detected electrochemically, there was a difference between target DNA and control DNA in the anodic peak current values. It was derived from specific binding of Hoechst 33258 to the double stranded DNA due to hybridization of target DNA. 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.

Analysis of Combined Yeast Cell Cycle Data by Using the Integrated Analysis Program for DNA chip (DNA chip 통합분석 프로그램을 이용한 효모의 세포주기 유전자 발현 통합 데이터의 분석)

  • 양영렬;허철구
    • KSBB Journal
    • /
    • v.16 no.6
    • /
    • pp.538-546
    • /
    • 2001
  • An integrated data analysis program for DNA chip containing normalization, FDM analysis, various kinds of clustering methods, PCA, and SVD was applied to analyze combined yeast cell cycle data. This paper includes both comparisons of some clustering algorithms such as K-means, SOM and furry c-means and their results. For further analysis, clustering results from the integrated analysis program was used for function assignments to each cluster and for motif analysis. These results show an integrated analysis view on DNA chip data.

  • PDF

Development of New DNA Chip and Genome Detection Using an Indicator-free Target DNA (비수식화 DNA를 이용한 유전자 검출 및 새로운 DNA칩의 개발)

  • Park, Yong-Sung;Park, Dae-Hee;Kwon, Young-Soo;Tomoji Kawai
    • The Transactions of the Korean Institute of Electrical Engineers C
    • /
    • v.52 no.8
    • /
    • pp.365-370
    • /
    • 2003
  • This research aims to develop an indicator-free DNA chip using micro-fabrication technology. At first, we fabricated a DNA microarray by lithography technology. Several probe DNAs consisting of thiol group at their 5-end were immobilized on the gold electrodes. Then indicator-free target DNA was hybridized by an electrical force and measured electrochemically in potassium ferricyanide solution. Redox peak of cyclic-voltammogram showed a difference between target DNA and mismatched DNA in an anodic peak current. Therefore, it is able to detect various genes electrochemically after immobilization of various probe DNAs and hybridization of indicator-free DNA on the electrodes simultaneously It suggested that this DNA chip could recognize the sequence specific genes.

Toxicogenomic analysis of Effects of Bisphenol A on Japanese Medaka fish using high density-functional cDNA microarray

  • Jiho Min;Park, Kyeong-Seo;Hong, Han-Na;Gu, Man-Bock
    • Proceedings of the Korea Society of Environmental Toocicology Conference
    • /
    • /
    • pp.173-173
    • /
    • 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.

  • PDF