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Position |
Professor |
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Research Field |
Molecular biology, Structural biochemistry |
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Graduating School 【 display / non-display 】
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1985.04-1989.03
Osaka University Faculty of Pharmaceutical Science Graduated
Graduate School 【 display / non-display 】
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1991.04-1994.03
Hokkaido University Graduate School, Division of Pharmaceutical Sciences Doctor's Course Completed
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1989.04-1991.03
Osaka University Graduate School, Division of Pharmaceutical Sciences Master's Course Completed
Studying abroad experiences 【 display / non-display 】
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2001.03-2002.03
Yale University Visiting Scholar
Campus Career 【 display / non-display 】
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2009.04-Now
KONAN UNIVERSITYDepartment of Nanobiochemistry, FIRST Professor
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2007.04-2009.03
KONAN UNIVERSITYAssociate Professor
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2005.04-2007.03
KONAN UNIVERSITYAssociate Professor (as old post name)
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2001.04-2005.03
KONAN UNIVERSITYLecturer
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1996.04-2001.03
KONAN UNIVERSITYLecturer
Association Memberships 【 display / non-display 】
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2017.11
The Japan Society of Nucleic Acids Chemistry
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2015.04
Nucleic Acids Therapeutics Society of Japan
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2007.04
The RNA Society
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1996.04
American Association for the Advancement of Science
Published Papers 【 display / non-display 】
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Enhancement of exon skipping activity by reduction in the secondary structure content of LNA-based splice-switching oligonucleotides
T. Shimo, K. Tachibana, Y. Kawawaki, Y. Watahiki, T. Ishigaki, Y. Nakatsuji, T. Hara, J. Kawakami and S. Obika
Chem. Commun. 55 6850 - 6853 2019.04 [Refereed]
Joint Work
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Enhancement of exon skipping activity by reduction in the secondary structure content of LNA-based splice-switching oligonucleotides
T. Shimo, K. Tachibana, Y. Kawawaki, Y. Watahiki, T. Ishigaki, Y. Nakatsuji, T. Hara, J. Kawakami, S. Obika
Chem. Commun. 55 6850 - 6853 2019
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
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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
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Quantitative relationship between chemical properties and bioactivities of anti-microRNA oligonucleotides targeted to tumor-associated microRNA-21
Koji Nagahama, Kenta Iseda, Daichi Kawano, Junji Kawakami
BIOCHIMIE ( ELSEVIER FRANCE-EDITIONS SCIENTIFIQUES MEDICALES ELSEVIER ) 137 124 - 131 2017.06
Joint Work
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.
Books etc 【 display / non-display 】
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ゼロからはじめるバイオ実験マスターコース③ 細胞培養トレーニング
西方敬人, 川上純司, 藤井敏司, 長濱宏治, 川内敬子 (Part： Joint Work )
学研メディカル秀潤社 2015.04 ISBN: 9784780909036
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ゼロからはじめるバイオ実験マスターコース② 遺伝子組換え基礎実習
西方敬人, 川上純司, 藤井敏司, 長濱宏治 (Part： Joint Work )
学研メディカル秀潤社 2012.12 ISBN: 978-4-7809-0862-6
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ゼロからはじめるバイオ実験マスターコース① 実験の基本と原理
西方敬人, 川上純司, 藤井敏司, 長濱宏治 (Part： Joint Work )
学研メディカル秀潤社 2012.09 ISBN: 978-4-7809-0856-5
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ゼロからはじめるバイオ実験マスターコース1 実験の基本と原理
西方敬人, 川上純司, 藤井敏司, 長濱宏治 (Part： Other )
秀潤社 2012
Review Papers (Misc) 【 display / non-display 】
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Pyrrolidinyl peptide nucleic acid with α/β-peptide backbone - A conformationally constrained PNA with unusual hybridization properties
C. Vilaivan, C. Srisuwannaket, C. Ananthanawat, C. Suparpprom, J. Kawakami, Y. Yamaguchi, Y. Tanaka, T. Vilaivan
Artificial DNA: PNA & XNA 2 11 2011
Joint Work
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Triplet analysis that identifies unpaired regions of functional RNAs
Junji Kawakami, Yoshie Yamaguchi, Naoki Sugimoto
Journal of Nucleic Acids 2011 2011
Joint Work
We developed a novel method for analyzing RNA sequences, deemed triplet analysis, and applied the method in an in vitro RNA selection experiment in which HIV-1 Tat was the target. Aptamers are nucleic acids that bind a desired target (bait), and to date, many aptamers have been identified by in vitro selection from enough concentrated libraries in which many RNAs had an obvious consensus primary sequence after sufficient cycles of the selection. Therefore, the higher-order structural features of the aptamers that are indispensable for interaction with the bait must be determined by additional investigation of the aptamers. In contrast, our triplet analysis enabled us to extract important information on functional primary and secondary structure from minimally concentrated RNA libraries. As a result, by using our method, an important unpaired region that is similar to the bulge of TAR was readily predicted from a partially concentrated library in which no consensus sequence was revealed by a conventional sequence analysis. Moreover, our analysis method may be used to assess a variety of structural motifs with desired function. © 2011 Junji Kawakami et al.
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Comparative thermodynamic analysis of RNA-protein interaction on surface and in solution
Y. Tanaka, K. Ishidate, K. Kishimoto, N. Sugimoto, J. Kawakami
Proc. 37th Intl. Symp. Nucleic Acids Chemistry 276 2010
Joint Work
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Accurate curve fitting procedure for UV melting analysis of highly thermostable RNA hairpins
J. Kawakami, Y. Tanaka, K. Kishimoto
Nucleic Acids Symp. Ser. 53 227 2009
Joint Work
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Recognition of a flipped base in a hairpinloop DNA by a small peptide
Junji Kawakami, Shinji Okabe, Yoshiatsu Tanabe, Naoki Sugimoto
NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS ( TAYLOR & FRANCIS INC ) 27 ( 3 ) 292 - 308 2008.03
Joint Work
Two tiny hairpin DNAs, CORE (dAGGCTTCGGCCT) and AP2 (dAGGCTXCGGCCT,X:abasic nucleotide), fold into almost the same tetraloop hairpin structure with one exception, that is, the sixth thymine (T6) of CORE is exposed to the solvent water (Kawakami, J et al., Chem. Lett. 2001, 258-259). In the present study, we selected small peptides that bind to CORE or AP2 from a combinatorial pentapeptide library with 2.5 x 106 variants. On the basis of the structural information, the selected peptide sequences should indicate the essential qualifications for recognition of the hairpin loop DNA with and without a flipped base. In the selected DNA binding peptides, aromatic amino acids such as histidine for CORE and glutamine/aspartic acid for AP2 were found to be abundant amino acids. This amino acid preference suggests that CORE-binding peptides use)pi-pi stacking to recognize the target while hydrogen bonding is dominant for AP2-binding peptides. To investigate the binding properties of the selected peptide to the target, surface plasmon resonance was used. The binding constant of the interaction between CORE and a CORE-binding peptide (HWHHE) was about 1.1 x 10(6) M-1 at 25 degrees C and the resulting binding free energy change at 25 degrees C (Delta G(25)degrees) was - 8.2 kcal mol(-1). The binding of the peptide to AP2 was also analyzed and the resulting binding constant and Delta G(25)degrees were about 4.2 x 10(4) M-1 and -63 kcal mol(-1), respectively. The difference in the binding free energy changes (Delta Delta G(25)degrees) of 1.9 kcal mol(-1) was comparable to the values reported in other systems and was considered a consequence of the loss of pi-pi stacking. Moreover, the stabilization effect by stacking affected the dissociation step as well as the association step. Our results suggest that the existence Of an aromatic ring (T6 base) produces new dominant interactions between peptides and nucleic acids, although hydrogen bonding is the preferable mode of interaction in the absence of the flipping base. These findings regarding CORE and AP2 recognition are expected to give useful information in the design of novel artificial DNA binding peptides.
Conference Activities & Talks 【 display / non-display 】
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細胞内におけるASOのmRNA結合を検出するアプタセンサーの構築
綿引優花、石垣卓、谷口慎也、赤松由御、川上純司
日本核酸医薬学会 第5回年会 (大阪) 2019.07 - 2019.07 日本核酸医薬学会
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Locked nucleic acid (LNA) を導入した splice-switching oligonucleotides (SSO) の高次構造形成と活性の相関
中辻悠輔、下剛典、橘敬祐、川脇優希、綿引優花、石垣卓、原孝史、川上純司、小比賀聡
日本核酸医薬学会 第5回年会 (大阪) 2019.07 - 2019.07 日本核酸医薬学会
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好熱性細菌及び酵母菌による多段階培養発酵技術から得られた発酵エキスの有用性
川野大地、付子華、伊達朗、寥箏箏、聶菁、Eduardo Perez、Jose Fernandez、Corey Webb、Kristen Huber、Jeffry B. Stock、川上純司、孫培文
第44回日本香粧品学会 (東京) 2019.06 - 2019.06
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好熱性細菌と酵母の共培養発酵技術から得られた発酵エキスTIRACLEの機能評価
付子華、川野大地、伊達朗、寥箏箏、聶菁、Eduardo Perez、Jose Fernandez、Corey Webb、Kristen Huber、Jeffry B. Stock、川上純司、孫培文
日本薬学会第139年会 (千葉) 2019.03 - 2019.03 日本薬学会
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臨床試験中及び実用化された核酸医薬
谷口陽祐、川上純司、佐々木茂貴
日本薬学会第139年会 (千葉) 2019.03 - 2019.03 日本薬学会
Grant-in-Aid for Scientific Research 【 display / non-display 】
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Grant-in-Aid for Young Scientists(B)
Project Year： 2004.04 - 2006.03
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Grant-in-Aid for Young Scientists(B)
Project Year： 2004.04 - 2006.03
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Grant-in-Aid for Young Scientists(B)
Project Year： 2004.04 - 2006.03