akai Yusuke Sakai

    About Yusuke

    Yusuke Sakai, PhD is one of the youngest awardees of POLONEZ programme, a regional Marie Curie Fellowship co-funded by Polish National Science Centre (NCN) and Horizon 2020. Since 2016 he has been running his own project as a semi-independent postdoc researcher in the group of Prof. Jonathan Heddle at the Malopolska Centre of Biotechnology, Jagiellonian University in Krakow. Before moving from Japan to Poland, he investigated the mechanism of tRNA modification involved in bacterial decoding system and took a doctorate at the Department of Chemistry and Biotechnology, the Graduate School of Engineering, the University of Tokyo. At MCB, he expanded his field to DNA nanotechnology and is developing DNA based nanorobot aiming at smart drug delivery. After the POLONEZ programme, he is drawing a plan to bridge DNA nanotechnology and molecular biology by e.g. offering useful DNA/RNA based nano-tools those enable to elucidate challenging issues in basic science.

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    About the Project

    DNA is not only the blueprint of genetic information as all knows, but also can be material which has self-assembling nature. Once designing and synthesising a set of short oligo DNAs, a long scaffold DNA is folded to form multiple pattern of crossovering, forming single defined shape. This method, called DNA origami methodology has enabled us to design arbitrary shape of nanostructure efficiently. Here we are developing DNA origami based nanocapsule which can separate the hollow from surrounding. The structure can be connected or dissociated to each other, open and close by external signal, eventually have potential to be a component of novel and smart carrier for drug delivery.

    sakai origami


    Members

    • Joanna Markiewicz, MA, technician
    • Martyna Adamiak, master course student
    • Naoto Asai, MA, Internship PhD student from Ito lab in Kansai University

    Publications related to the project

    1. Yusuke Sakai, Md. Sirajul Islam, Martyna Adamiak, Simon Chi-Chin Shiu, Julian Alexander Tanner, Jonathan Gardiner Heddle,* “DNA Aptamers for Functionalisation of DNA Origami Nanostructures.” Genes, 9, 571 (2018). Open Access. (POLONEZ funded)
    2. Simon Chi-Chin Shiu, Andrew B Kinghorn, Yusuke Sakai, Yee-Wai Cheung, Jonathan G Heddle, and Julian A Tanner,* “The Three S's for Aptamer-Mediated Control of DNA Nanostructure Dynamics: Shape, Self-Complementarity, and Spatial Flexibility.” ChemBioChem, 19, 18, 1900–1906 (2018).
    3. Akinori Kuzuya,* Yusuke Sakai, Takahiro Yamazaki, Yan Xu, Yusei Yamanaka, Yuichi Ohya and Makoto Komiyama,* “Allosteric Control of Nanomechanical DNA Origami Pinching Devices for Enhanced Target Binding.” Chemical Communications, 53, 59, 8276–8279 (2017)
    4. Takahiro Yamazaki, Yuichiro Aiba, Kohei Yasuda, Yusuke Sakai, Yusei Yamanaka, Akinori Kuzuya,* Yuichi Ohya, and Makoto Komiyama*, “Clear-cut observation of PNA invasion using nanomechanical DNA origami devices.” Chemical Communications, 48, 11361–11363 (2012).
    5. Akinori Kuzuya,* Yusuke Sakai, Takahiro Yamazaki, Yan Xu, and Makoto Komiyama,* “Nanomechanical DNA origami ‘single-molecule beacons’ directly imaged by atomic force microscopy.” Nature Communications, 2, 449 (2011). Open Access.
    6. Other publications

    7. Yusuke Sakai,† Satoshi Kimura,† Tsutomu Suzuki,* “Dual pathways of tRNA hydroxylation ensure efficient translation by expanding decoding capability.” Nature Communications, 10, 2858 (2019). († equal contribution) Open Access
    8. Satoshi Kimura, Yusuke Sakai, Kenta Ishiguro, Tsutomu Suzuki,* “Biogenesis and iron-dependency of ribosomal RNA hydroxylation.” Nucleic Acids Research, 45, 22, 1–14 (2017). Open Access
    9. Yusuke Sakai, Kenjyo Miyauchi, Satoshi Kimura and Tsutomu Suzuki,* “Biogenesis and growth phase-dependent alteration of 5-methoxycarbonylmethoxyuridine in tRNA anticodons.” Nucleic Acids Research, 44, 509-523 (2016) (selected as NAR Breakthrough Article) Open Access

    10. Funding

      This project is supported by POLONEZ3 (2016/23/P/NZ1/04097) of Polish National Science Centre (NCN) co-funded by the Marie Skłodowska-Curie action of the European Union (665778).

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