PLENARY LECTURE Ⅰ
Chemical Biology of Nucleic Acids: DNA Origami and Artificial Genetic Switches
Prof. Hiroshi Sugiyama
Kyoto University, Japan
The DNA origami method developed for the preparation of fully addressable two-dimensional (2-D) structures has been utilized for the selective positioning of functional molecules and nanoparticles. We designed a DNA frame using the DNA origami method to investigate enzymatic action and DNA structural change.[1] The substrate dsDNAs were incorporated into the cavity of the DNA frame to allow observation of the behaviors and/or reactions of transcription factors,[2] DNA methyltransferase, DNA recombinase, CRISPR-Cas9, MOC1,[3] and DNA repair enzymes. The proteins that bound to the target dsDNA in aqueous solution on a mica surface were visualized using a high-speed atomic force microscope (hs-AFM). We recently developed DNA nanocages using the DNA origami method and investigated the effect of confined space on the properties of G-quadruplex[4] and i-motif,[5] finding that the mechanical and thermodynamic stabilities of the G-quadruplex inside the nanocage were significantly increased. We also developed a strategy for lipid bilayer-assisted self-assembly of various DNA origami tiles into 2-D lattices.[6] Our results clearly demonstrated that the DNA origami method could provide a unique platform for the analysis of biomolecules at the single-molecule level.
Our group has also undertaken original research on the molecular recognition of DNA by antitumor antibiotics, and analyzed atom-specific chemical reactions on DNA. By integrating this information, we synthesized various functionalized sequence-specific DNA-binding pyrrole–imidazole polyamides (PIPs), which act as artificial genetic switches that can switch gene expression on and off on demand. We recently developed an alkylating PIP that could switch off the cancer-related KRAS gene[7] and RUNX 1–3 regulatory genes.[8,9] To switch on gene expression we needed to consider epigenetic factors. We also developed a SAHA–PIP complex that comprised a sequence-specific PIP and HDAC-inhibiting SAHA. Evaluation of the effect of SAHA–PIPs on genome-wide gene expression in human dermal fibroblasts demonstrated that each SAHA–PIP could differentially activate therapeutically important genes.[10] Conjugation of the DNA-binding domain "I" with HAT-activating CTB markedly activated the same cluster of genes as SAHA–PIP "I," substantiating the role of PIP in sequence-specific gene regulation.[11] Recently we introduced a bromodomain inhibitor to PIP to activate gene expression in a sequence-specific manner.[12] To extend the recognition sequence, we introduced a host–guest system to facilitate cooperative binding to the target sequence.[13] We can also control the forward/reverse orientation preference of PIP using a cyclic PIP with a chiral amino group.[14]
In this talk, I will discuss recent progress in molecular analysis using the DNA origami method and regulation of gene expression using specifically designed PIPs.
References
[1] Rajendran, A. et al., Chem. Rev. 2014, 114, 1493.
[2] Raghavan, G. et al., Angew. Chem. Int. Ed. 2019, 58, 7626.
[3] Kobayashi, Y. et al., Science 2017, 356, 631.
[4] Shresha, P.; Jonchhe, S.; Emura, T. et al. Nature Nanotech. 2017, 12, 582.
[5] Jonchhe, S et al., Proc. Natl. Acad. Sci. USA 2018, 115, 9539.
[6] Suzuki, Y. et al., Nature Commun., 2015, 6, 8052.
[7] Hiraoka, K. et al., Nature. Commun., 2015, 6, 6706.
[8] Morita, K. et al., J. Clin. Invest. 2017, 127, 2815.
[9] Maeda R. et al., J. Am. Chem. Soc., 2019, 141, 4257.
[10] Pandian, G. N. et al., Sci. Rep., 2014, 4, 3843.
[11] Han, L. et al., Angew. Chem. Int. Ed. 2015, 54, 8700.
[12] Taniguchi, J. et al., J. Am. Chem. Soc., 2018, 140, 7108.
[13] Yu, Z et al. J. Am. Chem. Soc., 2018, 140, 2426.
[14] Hirose, Y. et al. J. Am. Chem. Soc., in press.
Keywords
DNA nanotechnology; DNA origami; hs-AFM; PIP; genetic switch; epigenetic
JOIN
LOGIN
