2007 Fiscal Year Final Research Report Summary
Improvement of DNA chip system with probe-on-carriers for practical uses
| Project/Area Number |
18310135
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| Research Category |
Grant-in-Aid for Scientific Research (B)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
Applied genomics
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| Research Institution | Japan Advanced Institute of Science and Technology |
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Principal Investigator |
TSUKAHARA Toshifumi Japan Advanced Institute of Science and Technology, Center for Nano Materials and technology, Professor (60207339)
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| Co-Investigator(Kenkyū-buntansha) |
FUJIMOTO Kenzo Japan Advanced Institute of Science and Technology, School of Materials Science, Associate Professor (90293894)
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| Project Period (FY) |
2006 – 2007
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| Keywords | DNA Chin / Microarrav / Porous Glass / Synthesis of Nucleic Acids / Probe-on-Carrier / Genotype Analysis / Gene Expression Analysis / Order-Maid Medicine |
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| Research Abstract |
In this study, we are improving a method to generate DNA chips with "probe-on-carriers", immobilized oligonucleotide probes on the solid phase, for practical uses. In this DNA chip, each oligonucleotide was synthesized on porous glass as a solid phase-carrier, and can be used as an immobilized probe for the complementary target sequence. Therefore, high-quality DNA chips can be fabricated easily and economically.
First, we optimized synthesis of DNA probes on porous glass resins by using a new hydrophobic linker and a new non-aqueous reagent for the deprotection process. We also proposed a new strategy called "Protected DNA Probes (PDP) method" in which appropriately protected bases can bind highly selectively to the complementary bases even without removal of their base protecting groups. This PDP strategy could guarantee highly efficient synthesis of DNA probes on controlled porous glass with high purity and thereby could eliminate the time-consuming procedures for isolation of DNA pr
… More
obes. SNPs were successfully recognized each other by using PDPs immobilized on glass plates, suggesting its potential usefulness. Moreover, we succeeded to develop new method for the SNP analysis by using a chemical or photochemical ligation technique on plates with high coupling efficiency. These methods showed markedly high match/mismatch discrimination ability. Therefore, these technologies resulted in significant improvement of the base discrimination ability in DNA chip system with probe-on-carriers for practical uses.
We also tried to develop DNA microarrays with probe-on-carriers for gene expression analysis. The porous glass supports gave an excellent result for a 120 mer-long oligonucleotide synthesis. The yield was almost 20 times as much as by using cross-linked polystyrene, the most popular support for oligonucleotide synthesis. Therefore, by using probe-on-carriers with different probe lengths, an economical device, which could analyze not only SNPs but also gene expression at one time, could be developed. Less
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[Journal Article] 'Protected DNA Probes' capable of strong hybridization without removal of base protecting groups.2008
Author(s)
Ohkubo A, Kasuya R, Sakamoto K, Miyata K, Taguchi H, Nagasawa H, Tsukahara T, Watanobe T, Maki Y, Seio K, Sekine M
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Journal Title
Nucleic Acids Res. 36
Pages: 1952-1964.
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] 'Protected DNA Probes' capable of strong hybridization without removal of base protecting groups2008
Author(s)
Ohkubo, A., Kasuya, R., Sakamoto, K., Miyata, K., Taguchi, H., Nagasawa, H., Tsukahara, T., Watanobe, T., Maki, Y., Seio K., Sekine, M
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Journal Title
Nucleic Acids Res 36
Pages: 1952-1964
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] A New Hydrophobic Linker Effective for the in situ Synthesis of DNA-CPG Conjugates as Tools for SNP Analysis2007
Author(s)
Ohkubo, A., Taguchi, H., Seio, K., Nagasawa, H., Tsukahara, T., Sekine, M
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Journal Title
Tetrahedron Letters 48
Pages: 5147-5150
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] An effective method for the in situ synthesis of DNA-CPG conjugates using chemical ligation technology as tools for SNP analysis2007
Author(s)
Ohkubo, A., Tanaka, K., Taguchi, H., Seio, K., Nagasawa, H., Tsukahara, T., Sekine, M
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Journal Title
Biomg Med Chem Lett 17
Pages: 5969-5973
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] Aberrant neuromuscular junctions and delayed terminal muscle fiber maturation in α-dystroglycanopathies2006
Author(s)
Taniguchi M, Kurahashi H, Noguchi S, Fukudome T, Okinaga T, Tsukahara T, Tajima Y, Ozono K, Nishino I, Nonaka I, Toda T
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Journal Title
Hum. Mol. Genet 15
Pages: 1279-1289
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] Expression profiling of muscles from Fukuyama-type congenital muscular dystrophy and laminin-alpha2 deficient congenital muscular dystrophy; is congenital muscular dystrophy a primary fibrotic disease?2006
Author(s)
Taniguchi M, Kurahashi H, Noguchi S, Sese J, Okinaga T, Tsukahara T, Guicheney P, Ozono K, Nishino I, Morishita S, Toda T
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Journal Title
Biochem Biophys Res Commun. 342
Pages: 489-502
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] Okinaga T.,Tsukahara T., Tajima Y., Ozono K, Nishino I., Nonaka I., Toda T : Aberrant neuromuscular junctions and delayed terminal muscle fiber maturation in a -dystroglycanopathies2006
Author(s)
Taniguchi, M., Kurahashi, H., Noguchi, S., Fukudome, T
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Journal Title
Hum. Mot Genet 15
Pages: 1279-1289
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] Toda T : Expression profiling of muscles from Fukuyama-type congenital muscular dystrophy and laminin-alpha2 deficient congenital muscular dystrophy ; is congenital muscular dystrophy a primary fibrotic disease2006
Author(s)
Taniguchi, M., Kurahashi, H., Noguchi, S., Sese, J., Okinaga, T., Tsukahara, T., Guicheney, P., Ozono, K., Nishino, I., Morishita, S
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Journal Title
Biochem Biophys Res Commun 342
Pages: 489-502
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] Toshifumi Tsukahara, Shoichi Ishiura : Hesrl knockout mice exhibit behavioral alterations through the dopaminergic nervous system2006
Author(s)
Satoshi, Fuke, Natsumi, Minami, Hiroki, Kokubo, Ayumu, Yoshikawa, Hiroshi Yasumatsu, Noboru, Sasagawa, Yumiko, Saga
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Journal Title
J. Neurosci. Res 84
Pages: 1555-1563
Description
「研究成果報告書概要(欧文)」より
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[Presentation] Development of a next generation oligo-DNA microarray with probe-on-carriers2007
Author(s)
Tsukahara, T., Nagasawa, H., Ohkubo, A., Seio, K., Sekine, M., Suzuki, H
Organizer
Malaysia-Japan International Symposium on Advanced Technology 2007
Place of Presentation
Kuala Lumpur, Malaysia
Year and Date
2007-11-15
Description
「研究成果報告書概要(欧文)」より
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[Presentation] Development of a next generation oligo-DNA microarray with probe-on-carriers for SNPs analysis2006
Author(s)
Tsukahara, T., Nagasawa, H., Ohkubo, A., Seio, K., Sekine, M., Fuke, S
Organizer
20th IUBMB International Congress of Biochemistry and Molecular Biology
Place of Presentation
Kyoto Japan
Year and Date
2006-06-20
Description
「研究成果報告書概要(欧文)」より
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