2023 Fiscal Year Annual Research Report
Retroviral integration into topologically-interlocked DNAs to probe the role of DNA structure and screen viral inhibitors
| Project/Area Number |
21K05274
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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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| Keywords | DNA origami stability / DNA nanotechnology / Topological DNA / DNA-protein interactions / Atomic force microscopy / Viral proteins |
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| Outline of Annual Research Achievements |
In this study, we aimed to probe the role of DNA structure/topology in DNA-protein interactions. For this purpose, the topologically interlocked DNA minicircles inside a frame-shaped DNA origami were synthesized. At first, we probed the DNA-protein interactions using the restriction enzymes. Interestingly, the minicircles in the free and the topologically interlocked forms exhibited relatively higher resistance when compared to free linear DNAs of the same or similar sequence and length. This indicated the importance of DNA topology on DNA-protein interactions. Next, we also tested the DNA topology-specific proteins, such as topoisomerase, on these structures. During this study, we noticed that these interlocked minicircles and also the DNA origami frame are relatively unstable under various biological conditions. Thus, before the investigation of the DNA-protein interactions any further and drug screening, it was necessary to stabilize these structures. We then developed an enzymatic method and a chemical method to stabilize the DNA origami and incorporated functional DNA structures. Our stabilization method indicated that origami can now be used under diverse biological conditions with much better stability. Our preliminary results indicated that we could use our platform for the analysis of viral proteins (such as the HIV virus). We are now working on the interaction of nucleocapsid proteins and retroviral integration to further investigate the DNA topology on the DNA-protein interactions.
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| Remarks |
Our recent work on the DNA origami stability enhancement for the purpose of using them in biological samples such as cell, proteins/enzymes, and viruses was highlighted in several new reports.
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