Papers - KAWAKAMI Junji
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A Comparative Study on the Relative Quantification of Oligonucleotide Impurities Using Several Different Types of Liquid Chromatography-Mass Spectrometers at Analytical Facilities of Multiple Institutions Reviewed
Ryutaro Takamine, Takao Yamaguchi, Kenji Hirose, Mitsuaki Sekiguchi, Kaoru Karasawa, Noriyuki Iwasaki, Kentaro Takahara, Hiroshi Sezaki, Yoshihiro Hayakawa, Hiroyuki Togawa, Takashi Okubo, Hiroo Nagano, Amane Sakurai, Nae Sakimoto, Elisa Tomita-Sudo, Tokuyuki Yoshida, Takao Inoue, Satoshi Obika, Junji Kawakami
Pharmaceutical and Medical Device Regulatory Science 57 ( 3 ) 2026.6
Authorship：Last author, Corresponding author
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Current Trends in Liquid Chromatography-Mass Spectrometry Analysis of Small Interfering RNAs: A Short Review Reviewed
Hiroyuki Togawa, Takao Yamaguchi, Junji Kawakami, Satoshi Obika
Journal of Chromatography A 1766 466550 2026.1
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Theoretical calculation of the amounts of nucleotide deletion impurities in oligonucleotides Reviewed
Yasunori Uchida, Tokuyuki Yoshida, Emi Saito, Hirokazu Nankai, Kaoru Karasawa, Chie Inagaki, Noriyuki Iwasaki, Daisuke Higo, Kentaro Takahara, Takashi Osawa, Takao Yamaguchi, Kosuke Ito, Junji Kawakami, Satoshi Obika, Takao Inoue
International Journal of Pharmaceutical 687 126364 2026.1
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Position-dependent stabilization of DNA/RNA duplexes by site-specific incorporation of LNA nucleosides Reviewed
Elisa Tomita-Sudo, Tomoka Akita, Nae Sakimoto, Saori Tahara-Takamine, Renshin Sano, Shigenori Iwai, Junji Kawakami
Journal of Nucleic Acids 2026
Authorship：Last author, Corresponding author
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Effects of N–1-mer impurities in antisense oligonucleotides on the target RNA suppression Reviewed
Tomoka Akita, Elisa Tomita-Sudo, Renshin Sano, Nae Sakimoto, Shigenori Iwai, Hirokazu Nankai, Satoshi Obika, Takao Inoue, Junji Kawakami
Nucleic Acid Therapeutics 2026
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Effects of acid-mediated deamination of cytidine and 5-methylcytidine on solid-phase synthesis of oligonucleotides Reviewed
Yusuke Isono, Chihiro Karasugi, Takuya Akisawa, Takashi Osawa, Qin Ren, Michiaki Tatsuno, Fumi Ito, Takao Inoue, Junji Kawakami, Satoshi Obika, Masaki Shinoda
Tetrahedron 185 134840 - 134840 2025.10
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Functional analysis of histidine-dependent self-cleaving RNAs obtained by in vitro selection Reviewed
Nae Sakimoto, Shoichiro Tanaka, Riki Hatakenaka, Yoshie Yamaguchi-Miyazaki, Elisa Tomita-Sudo, Tomoka Akita, Taku Ishigaki, Shigenori Iwai, Junji Kawakami
ChemBioChem e202500411 2025.9
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Bioinformatic Analysis of Actin-Binding Proteins in the Nucleolus During Heat Shock Reviewed
Shinya Taniguchi, Takeru Torii, Yoshiyuki 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 1580 2024.12
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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 2024.12
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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 Reviewed
Elisa Tomita-Sudo, Taku Ishigaki, Masako Hirose, Maki Kato, Junji Kawakami
Netsu Sokutei 51 ( 4 ) 148 - 152 2024.9
Authorship：Last author, Corresponding author
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Separation of the diastereomers of phosphorothioated siRNAs by anion-exchange chromatography under non-denaturing conditions Reviewed
Hiroyuki Togawa, Takashi Okubo, Kazuki Horiuchi, Takao Yamaguchi, Elisa Tomita-Sudo, Tomoka Akita, Junji Kawakami, Satoshi Obika
Journal of Chromatography A 1721 464847 - 464847 2024.4
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Changes in gene expression due to product-related impurities of nucleic acid therapeutics
ISHIDA Kazuya, UCHIDA Yasunori, YOSHIDA Tokuyuki, AKAHORI Yumi, SAITO Emi, NANKAI Hirokazu, KARASAWA Kaoru, INAGAKI Chie, IWASAKI Noriyuki, HIGO Daisuke, TAKAHARA Kentaro, KAWAKAMI Junji, OBIKA Satoshi, INOUE Takao
Annual Meeting of the Japanese Society of Toxicology 51.1 P-302 2024
Publisher：The Japanese Society of Toxicology
Nucleic acid therapeutics contain impurities derived from nucleotide deletion or insertion, such as N-1 (single nucleotide deletion) and N+1 (single nucleotide insertion) impurities. Although they can hybridize with off-target RNAs, it is unclear whether N-1/N+1 impurities alter gene expression and contribute to off-target toxicity.
In this study, we prepared samples of antisense oligonucleotides with varying impurity content. Then, we confirmed the accurate mass corresponding to each N-1/N+1 impurity and determined their relative amount by LC-MS. Next, samples were introduced into human cells for comprehensive gene expression analysis. The results showed that many genes fully complementary to the N-1/N+1 impurities were down-regulated. This was probably caused by the fully complementary binding of the N-1/N+1 impurities and/or the partially complementary binding of the desired product with one nucleotide incompatibility. For some genes, the knockdown efficiency became higher with increasing content of the fully complementary N-1/N+1 impurities, strongly suggesting that the knockdown was caused by the binding of the N-1/N+1 impurities.
These results indicate that N-1/N+1 impurities can change gene expression. Comprehensive gene expression analyses will enable us to estimate the genes whose expression is altered by the binding of the desired product and the N-1/N+1 impurities. By considering the toxicological risk when the expression of these genes is changed, it will be possible to evaluate the risk of the N-1/N+1 impurities together with the desired product. -
Sequencing of Morpholino Antisense Oligonucleotides Using Electron Capture Dissociation Mass Spectrometry Reviewed
Kaoru Karasawa, Eva Duchoslav, Lyle Burton, Junji Kawakami, Takashi Baba
Analytical Chemistry 95 ( 44 ) 16352 - 16358 2023.10
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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, Junji Kawakami
Biochemstry 62 ( 21 ) 3041 - 3049 2023.10
Authorship：Last author
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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, Takao INOUE
Pharmaceutical and Medical Device Regulatory Science 54 ( 5 ) 439 - 454 2023.7
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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 43 ( 1 ) 57 - 64 2023.3
Authorship：Last author, Corresponding author
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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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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
Bioorganic Medicinal Chemistry Letters 30 ( 14 ) 127166 - 127166 2020.7
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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