| Project/Area Number |
09558090
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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 | 展開研究 |
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| Research Field |
Functional biochemistry
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| Research Institution | RIKEN Insutitute |
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Principal Investigator |
SARAI Akinori RIKEN, Insutitute, Senior Scientist, 分子遺伝学研究室, 副主任研究員 (20221286)
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| Co-Investigator(Kenkyū-buntansha) |
PICHIERRI Fabio RIKEN, Insutitute, Scientist, 情報伝達モデル化研究チーム, 研究員
TORIGOE Hidetaka RIKEN, Insutitute, Senior Scientist, 細胞生理学研究室, 先任研究員 (80227678)
YOKOYAMA Kazunari RIKEN, Insutitute, Senior Scientist, 遺伝子材料開発室, 副主任研究員 (80182707)
SINDO Heisaburo TOKYO UNIVERSITY OF PHARMACY, PROFESSOR, 薬学部, 教授 (80138966)
PICHIERRI Fa 理化学研究所, ジーンバンク室, 訪問研究員
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| Project Period (FY) |
1997 – 2000
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| Project Status |
Completed (Fiscal Year 2001)
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| Budget Amount *help |
¥11,600,000 (Direct Cost: ¥11,600,000)
Fiscal Year 2000: ¥3,000,000 (Direct Cost: ¥3,000,000)
Fiscal Year 1999: ¥2,700,000 (Direct Cost: ¥2,700,000)
Fiscal Year 1998: ¥2,500,000 (Direct Cost: ¥2,500,000)
Fiscal Year 1997: ¥3,400,000 (Direct Cost: ¥3,400,000)
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| Keywords | Triplex DNA / Thermodynamics / Computer simulation / Antisense |
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| Research Abstract |
In order to understand the mechanism of stability and specificity in triplex DNA formation, we performed experimental and computational analyses. We synthesized DNA with chemical modifications at different locations, and measured thermodynamic quantities such as dissociation constant and kinetic quantities such as association rate constant for the triplex formation. These results showed that the chemical modification, particularly at backbone, affected the thermodynamic and kinetic quantities of triplex formation. We attempted to investigate the molecular mechanism of that effect by computational analysis. We performed quantum-chemical calculations for the modified DNA to obtain partial atomic charges and conformation of DNA. We found that the phosphorothioation of DNA has significant effect on the charges and conformation. We also performed computer simulation of DNA to calculate its average conformation and fluctuation, by using a new algorithm for conformational sampling. The chemical modification affected the average conformation and fluctuation of DNA depending on the location of the modification. These results suggest that the chemical modification may affect the stability and specificity of triplex DNA formation through the changes in structure and property of DNA. In order to understand the biological role of triplex DNA in cell, we made biochemical and functional analyses of MAZ protein, which binds to triplex DNA. This protein acts as a transcription factor and regulates the expression of c-myc gene. We also examined the effect of chemical modification of DNA on the binding and transcriptional activities of an oncogene product, Myb. We found that the modification destabilized the DNA and abolished the Myb binding. The present experimental and computational studies of triplex DNA have laid a basis for the design of antisense DNA, which inhibits expression of genes.
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