最先端研究セミナー

講演者：　杉山　弘　（京都大学大学院理学研究科　化学専攻生物化学研究室  教授）

演題：　Chemical biology of nucleic acids: DNA origami and artificial genetic switch

Abstract

The DNA origami method developed for the preparation of fully addressable two-dimensional (2-D) structures has been utilized for the selective positioning of the functional molecules and nanoparticles.  We designed ”DNA frame” using the DNA origami method to investigate enzymatic action and DNA structural change.^[1] To observe the behaviors and reactions of DNA methyltransferase, DNA recombinase, Cas9, MOC1, and DNA repair enzymes, the substrate dsDNAs were incorporated into the cavity of the DNA frame, and the enzymes that bound to the target dsDNA were observed using HS-AFM.^[1,2]  We recently developed DNA nanocages and investigated the effect of confined space on the property of G-quadruplex and found that mechanical and thermodynamic stabilities of the G-quadruplex inside the nanocage are significantly increased.^[3] Also a strategy for lipid-bilayer-assisted self-assembly of various DNA origami tiles into 2-D lattices was developed.^[4]

We have been undertaking original research on the molecular recognition of DNA by antitumor antibiotics, and the analysis of atom-specific chemical reaction on DNA. By reconstituting such knowledge, various functionalized sequence-specific DNA binding pyrrole-imidazole polyamides (PIPs) were synthesized as an artificial genetic switch, which can switch on and switch off the gene expression on demand. We recently developed alkylating PIP that could switches off cancer related KRAS gene^[5] and RUNX 1-3 controling genes.^[6,7] To switch on the gene expression we need to consider Epigenetics. We developed a SAHA-PIP containing sequence-specific pyrrole-imidazole polyamides (PIPs) and HDAC inhibiting SAHA. Evaluation of the effect of SAHA-PIPs on genome-wide gene expression in human dermal fibroblasts (HDFs) divulged that each SAHA-PIP could differentially activate the therapeutically important genes.^[8] Conjugation of DNA binding domain of ‘I’ with HAT activating CTB remarkably activated identical cluster of genes as SAHA-PIP ‘I’ to substantiate the role of PIP in sequence-specific gene regulation.^[9] Recently we introduced Bromodomain inhibitor to PIP to activate gene expression in sequence-specific manner.^[10]  To extend recognition sequence, we introduce host-guest system to facilitate cooperative binding to target sequence. ^[11]  In this talk recent progress of DNA origami technology and regulation of the gene expression using designed PIPs will be discussed.

References: [1] Rajendran, A. et al., Chem. Rev. 2014, 114, 1493. [2]  Kobayashi, Y. et al.,  Science 2017, 356, 631. [3] Shresha, P.; Jonchhe, S.; Emura, T.et al. Nature Nanotech. 2017, 12, 582. [4] Suzuki, Y. et al., Nat Commun., 2015, 6, 8052. [5] Hiraoka, K. et al., Nature. Commun., 2015, 6, 6706.  [6] Morita, K. et al., J. Clin. Invest. 2017, 127, 2815. [7] Maeda R. et al., J. Am. Chem. Soc., 2019, 141, 4257. [8] Pandian, G. N. et al., Sci. Rep., 2014, 4, 3843. [9] Han, L. et al., Angew. Chem. Int. Ed. 2015, 54, 8700. [10] Taniguchi, J. et al., J. Am. Chem. Soc., 2018, 140, 7108. [11] Yu, Z et al. J. Am. Chem. Soc., 2018, 140, 2426.

担当分野：ゲノム神経学　塩田（内線：6633）

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