論文 - 杉本 直己
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In-Cell Stability Prediction of RNA/DNA Hybrid Duplexes for Designing Oligonucleotides Aimed at Therapeutics. 査読あり 国際共著 国際誌
Dipanwita Banerjee, Hisae Tateishi-Karimata, Maria Toplishek, Tatsuya Ohyama, Saptarshi Ghosh, Shuntaro Takahashi, Marko Trajkovski, Janez Plavec, Naoki Sugimoto
Journal of the American Chemical Society 145 ( 43 ) 23503 - 23518 2023年11月
In cells, the formation of RNA/DNA hybrid duplexes regulates gene expression and modification. The environment inside cellular organelles is heterogeneously crowded with high concentrations of biomolecules that affect the structure and stability of RNA/DNA hybrid duplexes. However, the detailed environmental effects remain unclear. Therefore, the mechanistic details of the effect of such molecular crowding were investigated at the molecular level by using thermodynamic and nuclear magnetic resonance analyses, revealing structure-dependent destabilization of the duplexes under crowded conditions. The transition from B- to A-like hybrid duplexes due to a change in conformation of the DNA strand guided by purine-pyrimidine asymmetry significantly increased the hydration number, which resulted in greater destabilization by the addition of cosolutes. By quantifying the individual contributions of environmental factors and the bulk structure of the duplex, we developed a set of parameters that predict the stability of hybrid duplexes with conformational dissimilarities under diverse crowding conditions. A comparison of the effects of environmental conditions in living cells and in vitro crowded solutions on hybrid duplex formation using the Förster resonance energy transfer technique established the applicability of our parameters to living cells. Moreover, our derived parameters can be used to estimate the efficiency of transcriptional inhibition, genome editing, and silencing techniques in cells. This supports the usefulness of our parameters for the visualization of cellular mechanisms of gene expression and the development of nucleic acid-based therapeutics targeting different cells.
DOI: 10.1021/jacs.3c06706
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Theranostic approach to specifically targeting the interloop region of BCL2 i-motif DNA by crystal violet 査読あり 国際共著 国際誌
Sinjan Das , Shuntaro Takahashi , Tatsuya Ohyama, Sudipta Bhowmik , Naoki Sugimoto
Scientific Reports 13 2023年9月
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Quantification of the concentration in a droplet formed by liquid–liquid phase separation of G-quadruplex-forming RNA 査読あり
Kohei Yokosawa, Mitsuki Tsuruta, Shinji Kajimoto, Naoki Sugimoto, Daisuke Miyoshi, Takakazu Nakabayashi
Chemical Physics Letters 826 140634 2023年9月
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Nearest-neighbor parameters for the prediction of RNA duplex stability in diverse in vitro and cellular-like crowding conditions 査読あり 国際誌
S. Ghosh, S. Takahashi, D. Banerjee, T. Ohyama, T. Endoh, H. Tateishi-Karimata, and N. Sugimoto
Nucleic Acids Res. 51 4101 - 4111 2023年5月
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Simple and fast screening for structure-selective G-quadruplex ligands 査読あり 国際誌
Y. Hashimoto, Y. Imagawa, K. Nagano, R. Maeda, N. N.agahama, T. Torii, N. Kinoshita, N. Takamiya, K. Kawauchi, H. Tateishi-Karimata, N. Sugimoto and D. Miyoshi
Chem. Commun. 59 4891 - 4894 2023年4月
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Endogenous G-quadruplex-forming RNAs inhibit the activity of SARS-CoV-2 RNA polymerase 査読あり 国際誌
T. Endoh, S. Takahashi, and N. Sugimoto
Chem. Commun. 59 872 - 875 2023年1月
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Pressure-temperature control of activity of RNA polymerase ribozyme 査読あり 国際誌
S. Takahashi and N. Sugimoto
Biophys. Chem. 292 106914 2023年1月
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Cladogenetic Orthogonal Light-Up Aptamers for Simultaneous Detection of Multiple Small Molecules in Cells 査読あり 国際共著 国際誌
T. Endoh, J. H. Tan, S. B. Chen, and N. Sugimoto
Anal. Chem. 95 976 - 985 2022年12月
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High-temperature adaptation of an OsNRT2.3 allele is thermoregulated by small RNAs 査読あり 国際共著 国際誌
Y. Zhang, H. Tateishi-Karimata, T. Endoh, Q. J., Kexin Li, X. Fan, Y. Ma, L. Gao, H. Lu, Z. Wang, A. E. Cho, X. Yao, Ch. Liu, N. Sugimoto, S. Guo, X. Fu, Q. Shen, G. Xu, L. R. Herrera-Estrella, X. Fan
Science Advances 8 9785 2022年11月
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Controlling liquid-liquid phase separation of G-quadruplex-forming RNAs in a sequence-specific manner. 査読あり 国際誌
Mitsuki Tsuruta, Takeru Torii, Kazuki Kohata, Keiko Kawauchi, Hisae Tateishi-Karimata, Naoki Sugimoto, Daisuke Miyoshi
Chemical communications (Cambridge, England) 58 ( 93 ) 12931 - 12934 2022年11月
We constructed a minimum liquid-liquid phase separation model system to form liquid droplets using only G-quadruplex-forming oligonucleotides and R- and G-rich oligopeptides. We found that the G-quadruplex structure is an essential component for RNA to form droplets with the peptide. Based on this model system and our findings, droplet redissolution via structure transition from a G-quadruplex to a duplex was achieved in a sequence-specific manner.
DOI: 10.1039/d2cc04366a
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DNA methylation is regulated by both the stability and topology of G-quadruplex 査読あり 国際誌
S. Matsumoto, H. Tateishi-Karimata, N. Sugimoto
Chem. Commun., 58 12459 - 12462 2022年10月
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Volumetric strategy for quantitatively elucidating local hydration network around a G-quadruplex 査読あり 国際共著 国際誌
S. Matsumoto, S. Takahashi, S. Bhowmik, T. Ohyama, and N. Sugimoto
Anal. Chem 94 ( Selected as a Supplemental Cover ) 7400 - 7407 2022年5月
担当区分:最終著者
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Applicability of Nearest-neighbour Model for Pseudoknot RNAs 査読あり 国際誌
S. Satpathi, T. Endoh, and N. Sugimoto
Chem. Commun 58 ( [Selected as an Inside Back Cover] ) 5952 - 5955 2022年4月
担当区分:最終著者
DOI: 10.1039/d1cc07094k
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S. Takahashi, S. Bhowmik, S. Sato, S. Takenaka, and N. Sugimoto
Life 12 ( 4 ) 553 2022年4月
担当区分:最終著者
DOI: 10.3390/life12040553
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Ruthenium Polypyridyl Complex Bound to a Unimolecular Chair-Form G-Quadruplex 査読あり 国際共著 国際誌
Kane T. McQuaid, Shuntaro Takahashi, Lena Baumgaertner, David J. Cardin, Neil G. Paterson, James P. Hall, Naoki Sugimoto, and Christine J. Cardin
Journal of the American Chemical Society 144 ( 13 ) 5956 - 5964 2022年4月
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細胞内での核酸の挙動を明らかにする熱力学的解析 査読あり 国際誌
高橋俊太郎, 杉本 直己
熱測定 49 14 - 19 2022年1月
共著
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S. Takahashi, S. Matsumoto, P. Chilka, S. Ghosh, H. Okura, and N. Sugimoto
Scientific reports 12 1149 2022年1月
担当区分:最終著者
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Effect of DNA modifications on the transition bet and non-canoncial DNA stransures in CpG islands during senescence 査読あり 国際誌
S.Matsumoto, H. Tateishi-Karimata, T. Ohyama, and N. Sugimoto
RSC Advances 11 37205 - 37217 2021年12月
共著
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Intramolecular G-quadruplex-hairpin loop structure competition of a GC-rich exon region in the TMPRSS2 gen 査読あり 国際誌
W. Sugimoto, N. Kinoshita, M. Nakata, T. Ohyama, H. Tateishi-Karimata, T. Nishikata, N. Sugimoto, D. Miyoshi, and K. Kawauchi
Chem. Commun. 58 48 - 51 2021年11月
共著
DOI: 10.1039/d1cc05523b
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Correction to 'Improved nearest-neighbor parameters for the stability of RNA/DNA hybrids under a physiological condition'. 国際誌
Dipanwita Banerjee, Hisae Tateishi-Karimata, Tatsuya Ohyama, Saptarshi Ghosh, Tamaki Endoh, Shuntaro Takahashi, Naoki Sugimoto
Nucleic acids research 49 ( 18 ) 10796 - 10799 2021年10月