| Project/Area Number |
21K05274
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Multi-year Fund |
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| Section | 一般 |
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| Review Section |
Basic Section 37010:Bio-related chemistry
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| Research Institution | Kyoto University |
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Principal Investigator |
A. Rajendran 京都大学, エネルギー理工学研究所, 講師 (90723122)
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| Project Period (FY) |
2021-04-01 – 2024-03-31
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| Project Status |
Completed (Fiscal Year 2023)
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| Budget Amount *help |
¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2023: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2022: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Fiscal Year 2021: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
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| Keywords | DNA origami / DNA nanotechnology / Structural biology / Nucleic acids chemistry / DNA-protein interaction / DNA origami stability / Topological DNA / DNA-protein interactions / Atomic force microscopy / Viral proteins / Topological structures / Minicircle DNA / Interlocked structures / DNA minicircles / HS-AFM / Viral inhibitor / Viral integrase / Drug screening |
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| Outline of Research at the Start |
The topologically-interlocked minicircle DNAs that mimic the structural features of nucleosomal DNA will be prepared inside a frame-shaped DNA origami. The structures will then be used as substrates to probe the role of DNA structure on retroviral integration. The efficiency and selectivity of integration will be evaluated on various DNA forms. Finally, the acquired knowledge will be used to develop and screen the integrase catalytic inhibitors by using the interlocked DNA substrates.
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| Outline of Final Research Achievements |
We explored how DNA structure impacts DNA-protein interactions by creating topologically interlocked DNA minicircles within a frame-shaped DNA origami. Using restriction enzymes, we found that interlocked minicircles were more resistant than linear DNAs, highlighting the importance of DNA topology. We also tested topology-specific proteins like topoisomerase on these structures, observing their relative instability under various biological conditions. To proceed with DNA-protein interaction studies and drug screening, we stabilized these structures using enzymatic and chemical methods. Our stabilization techniques improved the origami's stability under diverse biological conditions. Preliminary results suggest our platform's potential for analyzing viral proteins such as those from HIV. The current work involves investigating the interaction between nucleocapsid proteins and retroviral integration to further understand DNA topology's role in DNA-protein interactions.
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| Academic Significance and Societal Importance of the Research Achievements |
Knowledge obtained on the role of DNA topology is useful to understand the biological process taking place on topologically constrained DNA structure in nucleosomes. Stability improvement methods developed are useful for synthesizing stable DNA nanomaterials for drug delivery and virus inhibition.
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