Papers - KAWAKAMI Junji
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Sequence-Specific Free Energy Changes in DNA/RNA Induced by a Single LNA-T Modification in Antisense Oligonucleotides Reviewed
Elisa Tomita-Sudo, Tomoka Akita, Nae Sakimoto, Saori Tahara-Takamine, Junji Kawakami
International Journal of Molecular Sciences 25 13240 - 13240 2024.12
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Bioinformatic Analysis of Actin-Binding Proteins in the Nucleolus During Heat Shock Reviewed
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 2024.12
Other Link： https://www.mdpi.com/2073-4425/15/12/1580
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L-Histidine Modulates the Catalytic Activity and Conformational Changes of the HD3 Deoxyribozyme Reviewed
Nae Sakimoto, Hirofumi Imanaka, Elisa Tomita-Sudo, Tomoka Akita, Junji Kawakami
genes 15 1481 2024.11
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Detection of Conformational Changes of G4 Aptamer in the Presence of Different Cations using Calorimetry Invited Reviewed
Elisa Tomita-Sudo, Taku Ishigaki, Masako Hirose, Maki Kato, and Junji Kawakami
Netsu Sokutei 51 ( 4 ) 148 - 152 2024.10
Authorship：Last author
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Separation of the diastereomers of phosphorothioated siRNAs by anion-exchange chromatography under non-denaturing conditions Reviewed International journal
Hiroyuki Togawa, Takashi Okubo, Kazuki Horiuchi, Takao Yamaguchi, Elisa Tomita-Sudo, Tomoka Akita, Junji Kawakami, Satoshi Obika
Journal of Chromatography A 1721 464847 2024.4
Joint Work
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.
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Sequencing of Morpholino Antisense Oligonucleotides Using Electron Capture Dissociation Mass Spectrometry Reviewed International journal
Kaoru Karasawa, Eva Duchoslav, Lyle Burton, Junji Kawakami, Takashi Baba
Analytical Chemistry 95 ( 44 ) 16352 - 16358 2023.10
Joint Work
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
DOI： 10.1021/acs.analchem.3c03621
Other Link： https://doi.org/10.1021/acs.analchem.3c03621
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Mitochondrial Dynamics of Bcl-2 Family Proteins during 17-β-Estradiol-Induced Apoptosis Correlate with the Malignancy of Endometrial Cancer Cells Reviewed
Takahiro Yaguchi, Misaki Kameno, Hirofumi Taira, and Junji Kawakami
Biochemstry 62 ( 21 ) 3041 - 3049 2023.10
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Comparison of Analysis Data of Model Oligonucleotide Therapeutics Obtained with Different Types of Liquid Chromatograph- Mass Spectrometers Reviewed
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
Pharmaceutical and Medical Device Regulatory Science 54 439 - 454 2023.10
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Not all 2',4'-bridged modifications stabilize DNA/RNA duplexes Reviewed
Tomoka Akita, Elisa Tomita-Sudo, Shin Itoh, Nae Sakimoto, Takeshi Masuda, Akifumi Nakamura, Yoshiyuki Onishi, Makoto Koizumi Junji Kawakami
Nucleosides, Nucleotides & Nucleic Acids 2023.3
Joint Work
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.
Other Link： https://www.tandfonline.com/doi/full/10.1080/15257770.2023.2232414
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Toshiyuki Goto, Shuhei Torii, Aoi Kondo, Kazumasa Kanda, Junji Kawakami, Yosky Kataoka, Takahito Nishikata
Journal of Developmental Biology 10 ( 1 ) 10 - 10 2022.2
Publisher：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.
DOI： 10.3390/jdb10010010
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Miho Takagi-Sato, Koji Morita, Yoshiyuki Onishi, Yuuka Watahiki, Taku Ishigaki, Tomoka Akita, Erisa Tomita, Junji Kawakami, Makoto Koizumi
Nucleosides, Nucleotides & Nucleic Acids 39 ( 6 ) 838 - 852 2020.6
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Efficacy of Fermented Extract Obtained from Multiple-Processed Fermentation Technology of Thermophilic Bacteria and Yeast Reviewed
Daichi Kawano, Zhengzheng Liao, Jing Nie, Akira Date, Eduardo Perez, Jose Fernandez, Corey Webb, Kristen Huber, Jeffry B. Stock, Junji Kawakami, Zihua Fu
JOURNAL OF JAPANESE COSMETIC SCIENCE SOCIETY 44 ( 3 ) 194 - 202 2020
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Different reactivity of Sp and Rp isomers of phosphorothioate-modified oligonucleotides in a duplex structure Reviewed
Md Ariful Islam, Aki Fujisaka, Junji Kawakami, Takao Yamaguchi, Satoshi Obika
Bioorg. Med. Chem. Lett. 30 ( 14 ) 127166 - 127166 2020
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Enhancement of exon skipping activity by reduction in the secondary structure content of LNA-based splice-switching oligonucleotides Reviewed
T. Shimo, K. Tachibana, Y. Kawawaki, Y. Watahiki, T. Ishigaki, Y. Nakatsuji, T. Hara, J. Kawakami and S. Obika
Chem. Commun. 55 6850 - 6853 2019.4
Joint Work
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Influence of intracellular environment on allosteric ribozyme activity
Misaki Kameno, Mika Sawada, Nae Sakimoto and Junji Kawakami
Proc. 44th Intl. Symp. Nucleic Acid Chemistry 178 - 179 2017.11
Joint Work
Authorship：Lead author
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Quantification of stabilization effect of co-solutes on RNA tertiary interaction
Natsumi Sasaki, Daisuke Miyoshi and Junji Kawakami
Proc. 44th Intl. Symp. Nucleic Acid Chemistry 174 - 175 2017.11
Joint Work
Authorship：Lead author
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Quantitative relationship between chemical properties and bioactivities of anti-microRNA oligonucleotides targeted to tumor-associated microRNA-21 Reviewed
Koji Nagahama, Kenta Iseda, Daichi Kawano, Junji Kawakami
BIOCHIMIE 137 124 - 131 2017.6
Joint Work
Authorship：Last author, Corresponding author Publisher：ELSEVIER FRANCE-EDITIONS SCIENTIFIQUES MEDICALES ELSEVIER
Synthetic anti-microRNA oligonucleotides (AMOs) are promising drug candidates to inactivate disease related microRNAs because of their sequence-specific binding to their targets and the variety of chemical modifications available. Over the last decade, the qualitative relationships between the chemical properties of AMOs and bioactivity (inactivation of their target miRNAs) have been studied to enhance their bioactivity. On the other hand, in real-world drug development, drugs must be designed case-by case, taking many factors into account. Thus, in order to design AMOs that target specific miRNA, understanding the quantitative relationship between the chemical properties of AMOs and inactivation of their target miRNA is necessary. Here, we aimed to find the specific quantitative relationship of AMOs targeted to tumor-associated miR-21 through direct comparison of their inactivation efficacies with systematically varied chemical properties, including sequence-specific binding affinity, nuclease resistance, and RNase H activation. As a result, we newly found the quantitative relationships; (1) sequence specific binding affinity of AMOs against miR-21 is the main determining factor for inactivation efficacy, (2) nuclease resistance of AMOs impacts their miR-21 inactivation efficacy acting cooperatively with the binding affinity, although nuclease resistance alone does not affect the miRNA inactivation efficacy, and (3) RNase H activation is unnecessary. This study also demonstrates the utility of the obtained relationship for the design of AMO-based drugs targeted to miR-21, through cell-based analyses. Thus, the obtained quantitative relationship would make it possible to predict the miR-21 inactivation efficacy of AMOs which are newly designed. (C) 2017 Elsevier B.V. and Societe Francaise de Biochimie et Biologie Moleculaire (SFBBM). All rights reserved.
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Quantitative relationship between chemical properties and bioactivities of anti-microRNA oligonucleotides targeted to tumor-associated microRNA-21 Reviewed
Koji Nagahama, Kenta Iseda, Daichi Kawano, Junji Kawakami
Biochimie 137 124 - 131 2017.3
Joint Work
Authorship：Lead author
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Influence of intracellular environment on allosteric ribozyme activity
M. Kameno, M. Sawada, N. Sakimoto, J. Kawakami
Proc. 44th Intl. Symp. Nucleic Acid Chemistry 178 - 179 2017
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Quantification of stabilization effect of co-solutes on RNA tertiary interaction
N. Sasaki, D. Miyoshi, J. Kawakami
Proc. 44th Intl. Symp. Nucleic Acid Chemistry 174 - 175 2017