教員・研究者詳細 - 川上　純司

論文 - 川上　純司

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Sequence-Specific Free Energy Changes in DNA/RNA Induced by a Single LNA-T Modification in Antisense Oligonucleotides 査読あり

Elisa Tomita-Sudo, Tomoka Akita, Nae Sakimoto, Saori Tahara-Takamine, Junji Kawakami

International Journal of Molecular Sciences 25 13240 - 13240 2024年12月

DOI： 10.3390/ ijms252413240 Academic

Bioinformatic Analysis of Actin-Binding Proteins in the Nucleolus During Heat Shock 査読あり

Shinya Taniguchi, Takeru Torii, Toshiyuki Goto, Kohei Takeuchi, Rine Katsumi, Mako Sumida, Sunmin Lee, Wataru Sugimoto, Masaya Gessho, Katsuhiko Itoh, Hiroaki Hirata, Junji Kawakami, Daisuke Miyoshi, Keiko Kawauchi

genes 15 ( 12 ) 1580 2024年12月

DOI： 10.3390/genes15121580

その他リンク： https://www.mdpi.com/2073-4425/15/12/1580

L-Histidine Modulates the Catalytic Activity and Conformational Changes of the HD3 Deoxyribozyme 査読あり

Nae Sakimoto, Hirofumi Imanaka, Elisa Tomita-Sudo, Tomoka Akita, Junji Kawakami

genes 15 1481 2024年11月

DOI： 10.3390/genes15111481

異なるカチオン共存下におけるG4 アプタマーの構造変化のカロリメトリーを用いた検出招待あり査読あり

冨田恵麗沙，石垣卓，廣瀬雅子, 加藤眞紀, 川上純司

熱測定 51 ( 4 ) 148 - 152 2024年10月

担当区分：最終著者

Separation of the diastereomers of phosphorothioated siRNAs by anion-exchange chromatography under non-denaturing conditions 査読あり国際誌

Hiroyuki Togawa, Takashi Okubo, Kazuki Horiuchi, Takao Yamaguchi, Elisa Tomita-Sudo, Tomoka Akita, Junji Kawakami, Satoshi Obika

Journal of Chromatography A 1721 464847 2024年4月

共著

In recent years, several small interfering RNA (siRNA) therapeutics have been approved, and most of them are phosphorothioate (PS)-modified for improving nuclease resistance. This chemical modification induces chirality in the phosphorus atom, leading to the formation of diastereomers. Recent studies have revealed that Sp and Rp configurations of PS modifications of siRNAs have different biological properties, such as nuclease resistance and RNA-induced silencing complex (RISC) loading. These results highlight the importance of determining diastereomeric distribution in quality control. Although various analytical approaches have been used to separate diastereomers (mainly single-stranded oligonucleotides), it becomes more difficult to separate all of them as the number of PS modifications increases. Despite siRNA exhibits efficacy in the double-stranded form, few reports have examined the separation of diastereomers in the double-stranded form. In this study, we investigated the applicability of non-denaturing anion-exchange chromatography (AEX) for the separation of PS-modified siRNA diastereomers. Separation of the four isomers of the two PS bonds tended to improve in the double-stranded form compared to the single-stranded form. In addition, the effects of the analytical conditions and PS-modified position on the separation were evaluated. Moreover, the elution order of the Sp and Rp configurations was confirmed, and the steric difference between them, i.e., the direction of the anionic sulfur atom, appeared to be important for the separation mechanism in non-denaturing AEX. Consequently, all 16 peak tops of the four PS modifications were detected in one sequence, and approximately 30 peak tops were detected out of 64 isomers of six PS bonds, indicating that non-denaturing AEX is a useful technique for the quality control of PS-modified siRNA therapeutics.

DOI： 10.1016/j.chroma.2024.464847

Sequencing of Morpholino Antisense Oligonucleotides Using Electron Capture Dissociation Mass Spectrometry 査読あり国際誌

Kaoru Karasawa, Eva Duchoslav, Lyle Burton, Junji Kawakami, Takashi Baba

Analytical Chemistry 95 ( 44 ) 16352 - 16358 2023年10月

共著

We report the first sequencing of morpholino antisense oligonucleotides (phosphorodiamidate morpholino oligomers, PMOs) using electron capture dissociation (ECD) mass spectrometry. In this research, we found dissociation of the backbone of 18- to 25-mer PMOs to produce d and z ions as the major ions, and 100% cleavage coverage (sequence coverage) was obtained with these ions. This is a critical contrast with beam-type collision-induced dissociation, which dominantly induces base loss, so it is difficult to obtain sequence information. The results showed that an electron beam energy (typically 15 eV) can be used universally for PMOs with different sequences, lengths, and charge states so that no detailed optimization is required for multiprecursor targeting liquid chromatography coupled with tandem mass spectrometry measurements. We also confirmed that the ECD reaction speed was compatible with the high-performance liquid chromatography time scale. Finally, we demonstrated a liquid chromatography electron capture dissociation tandem mass spectrometry workflow to survey the modification sites of the emulated PMO impurities.

DOI： 10.1021/acs.analchem.3c03621

その他リンク： https://doi.org/10.1021/acs.analchem.3c03621

Mitochondrial Dynamics of Bcl-2 Family Proteins during 17-β-Estradiol-Induced Apoptosis Correlate with the Malignancy of Endometrial Cancer Cells 査読あり

Takahiro Yaguchi, Misaki Kameno, Hirofumi Taira, and Junji Kawakami

Biochemstry 62 ( 21 ) 3041 - 3049 2023年10月

DOI： 10.1021/acs.biochem.3c00064

その他リンク： https://pubs.acs.org/doi/10.1021/acs.biochem.3c00064

複数種の液体クロマトグラフ質量分析計を用いたモデル核酸医薬品の分析データの比較査読あり

Kenji Hirose, Tokuyuki Yoshida, Maki Terasaki, Hiroshi Sezaki, Kaoru Karasawa, Noriyuki Iwasaki, Kentaro Takahara, Naomi Takiguchi, Mitsuaki Sekiguchi, Hirokazu Nankai, Emi Saito, Hideaki Sato, Takashi Osawa, Takao Yamaguchi, Kosuke Ito, Junji Kawakami, Satoshi Obika, and Takao Inoue

54 439 - 454 2023年10月

Not all 2',4'-bridged modifications stabilize DNA/RNA duplexes 査読あり

Tomoka Akita, Elisa Tomita-Sudo, Shin Itoh, Nae Sakimoto, Takeshi Masuda, Akifumi Nakamura, Yoshiyuki Onishi, Makoto Koizumi Junji Kawakami

Nucleosides, Nucleotides & Nucleic Acids 2023年3月

共著

2’,4’-Bridged modifications such as 2’-O,4’-C-methylene-bridged nucleotides (LNAs) and 2’-O,4’-C-ethylene-bridged nucleotides (ENAs) provide high binding affinity for duplex formation. Stabilization by the introduction of the bridged nucleic acids is considered to be due to pre-organization. In this study, we found that the introduction of 2’,4’-C-bridged 2’-deoxynucleotides (CRNs; Conformationally Restricted Nucleotides) into DNA/RNA duplexes leads to destabilization, as opposed to the previously accepted notion that 2’,4’-bridged modifications always lead to stabilization.

その他リンク： https://www.tandfonline.com/doi/full/10.1080/15257770.2023.2232414

Actin Filament in the First Cell Cycle Contributes to the Determination of the Anteroposterior Axis in Ascidian Development 査読あり

Toshiyuki Goto, Shuhei Torii, Aoi Kondo, Kazumasa Kanda, Junji Kawakami, Yosky Kataoka, Takahito Nishikata

Journal of Developmental Biology 10 ( 1 ) 10 - 10 2022年2月

出版者・発行元：MDPI AG

In many animal species, the body axis is determined by the relocalization of maternal determinants, organelles, or unique cell populations in a cytoskeleton-dependent manner. In the ascidian first cell cycle, the myoplasm, including mitochondria, endoplasmic reticulum (ER), and maternal mRNAs, move to the future posterior side concomitantly (called ooplasmic segregation or cytoplasmic and cortical reorganization). This translocation consists of first and second phases depending on the actin and microtubule, respectively. However, the transition from first to second phase, that is, translocation of myoplasmic components from microfilaments to microtubules, has been poorly investigated. In this study, we analyzed the relationship between these cytoskeletons and myoplasmic components during the first cell cycle and their role in morphogenesis by inhibitor experiments. Owing to our improved visualization techniques, there was unexpected F-actin accumulation at the vegetal pole during this transition period. When this F-actin was depolymerized, the microtubule structure was strongly affected, the myoplasmic components, including maternal mRNA, were mislocalized, and the anteroposterior axis formation was disordered. These results suggested the importance of F-actin during the first cell cycle and the existence of interactions between microfilaments and microtubules, implying the enigmatic mechanism of ooplasmic segregation. Solving this mystery leads us to an improved understanding of ascidian early development.

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論文 - 川上　純司