Publications

55. Cecilia Cerretani, Mikkel Liisberg, Vanessa Rück, Jiro Kondo*, Tom Vosch*.

The effect of inosine on the spectroscopic properties and crystal structure of a NIR-emitting DNA-stabilized silver nanocluster.”

Nanoscale Adv., 12, in press (2022).

54. Takahiro Atsugi, Akira Ono*, Miho Tasaka, Natsumi Eguchi, Shoji Fujiwara and Jiro Kondo*.

“A novel Ag(I)-DNA rod comprising a one-dimensional array of 11 silver ions within a double helical structure.”

Angew. Chem. Int. Ed. 61, in press (2022).

53. Takenori Dairaku,* Rika Kawai, Kanako Nozawa-Kumada, Kentaro Yoshida, Yoshinori Kondo, Jiro Kondo, Akira Ono, Yoshiyuki Tanaka* and Yoshitomo Kashiwagi*.

“Chemical reduction of Ag+ to Ag employing organic electron donors: evaluation of the effect of Ag+-mediated cytosine–cytosine base pairing on the aggregation of Ag nanoparticles.”

Dalton Trans., 50, 12208-12214 (2021).

52. Takenori Dairaku,* Rika Kawai, Teppei Kanaba, Tetsuya Ono, Kentaro Yoshida, Hajime Sato, Kanako Nozawa-Kumada, Yoshinori Kondo, Jiro Kondo, Akira Ono, Yoshiyuki Tanaka* and Yoshitomo Kashiwagi*.

“Effect of cytosine–Ag+–cytosine base pairing on the redox potential of the Ag+/Ag couple and the chemical reduction of Ag+ to Ag by tetrathiafulvalene.

Dalton Trans. 50, 7633-7639 (2021).

51. Cecilia Cerretani, Jiro Kondo* and Tom Vosch*.

“Mutation of position 5 as a crystal engineering tool for a NIR-Emitting DNA-Stabilized Ag16 Nanocluster.”
CrystEngComm, 22, 8136-8141 (2020).

50. Cecilia Cerretani, Jiro Kondo* and Tom Vosch*.

“Removal of the A10 adenosine in a DNA-stabilized Ag16 nanocluster.”
RSC Adv., 10, 23854-23860 (2020).

49. Jiro Kondo* and Mai Koganei.

“Structural bases for the fitness cost of the aminoglycoside-resistance and lethal mutations at position 1408 of 16S rRNA.”
Molecules, 25, 159 (2020). 

48. Melanie Meyer, Helene Walbott, Vincent Olieric, Jiro Kondo, Maria Costa and Benoit Masquida*.

“Conformational adaptation of UNCG loops upon crowding”
RNA, 25, 1522-1531 (2019). 

47. Cecilia Cerretani, Hiroki Kanazawa, Tom Vosch and Jiro Kondo*.

“Crystal structure of a NIR‐Emitting DNA‐Stabilized Ag16 Nanocluster.”
Angew. Chem. Int. Ed., 58, 17153-17157 (2019). *Selected as Very Important Paper (VIP) and an Inside Back Cover Picture

46. Akira Ono*, Hiroki Kanazawa, Hikari Ito, Misato Goto, Koudai Nakamura, Hisao Saneyoshi and Jiro Kondo*.

“A Novel DNA Helical Wire Containing HgII‐Mediated T:T and T:G Pairs.”
Angew. Chem. Int. Ed., 58, 16835-16838 (2019). *Selected as Very Important Paper (VIP) 

45. Akira Ono*, Takahiro Atsugi, Misato Goto, Hisao Saneyoshi, Takahito Tomori, Kohji Seio, Takenori Dairaku and Jiro Kondo*.

“Crystal structure of a DNA duplex cross-linked by 6-thioguanine–6-thioguanine disulfides: reversible formation and cleavage catalyzed by Cu(II) ions and glutathione.”
RSC Adv., 9, 22859-22862 (2019).

44. Hiroki Kanazawa, Oscar M. Saavedra, Juan Pablo Maianti, Simon A. Young, Luis Izquierdo, Terry K. Smith*, Stephen Hanessian*, Jiro Kondo*.

“Structure-Based Design of a Eukaryote-Selective Antiprotozoal Fluorinated Aminoglycoside.”
ChemMedChem, 13, 1541-1548 (2018).

43. Hiroki Kanazawa, Fumika Baba, Mai Koganei & Jiro Kondo*.

“A structural basis of the antibiotic resistance conferred by an N1-methylation of A1408 in 16S rRNA.”
Nucleic Acids Res., 45, 12529-12535 (2017).

 

42. Jiro Kondo*, Toru Sugawara, Hisao Saneyoshi & Akira Ono*.

“Crystal structure of a DNA duplex containing four Ag(I) ions in consecutive dinuclear Ag(I)-mediated base pairs: 4-thiothymine-2Ag(I)-4-thiothymine.”
Chem. Commun., 53, 11747-11750 (2017).

 

41. Hiroki Kanazawa & Jiro Kondo*.

“Crystal structure of a novel RNA motif that allows for precise positioning of a single metal ion.”
J. Inorg. Biochem., 176, 140-143 (2017).

40. Jiro Kondo*, Yoshinari Tada, Takenori Dairaku, Yoshikazu Hattori, Hisao Saneyoshi, Akira Ono & Yoshiyuki Tanaka.

“A metallo-DNA nanowire with uninterrupted one-dimensional silver array.”
Nat. Chem., 9, 956-960 (2017).
プレスリリースはこちら)

 

39. Takenori Dairaku, Kyoko Furuita, Hajime Sato, Jakub Severa, Katsuyuki Nakashima, Jiro Kondo, Daichi Yamanaka, Yoshinori Kondo, Itaru Okamoto, Akira Ono, Vladimir Sychrovsky*, Chojiro Kojima* & Yoshiyuki Tanaka*.

“Structure determination of an AgI-mediated cytosine-cytosine base pair within DNA duplex in solution with 1H/15N/109Ag NMR spectroscopy.”
Chem. Eur. J., 22, 13028-13031 (2016).

 

38. Hiroki Kanazawa, Md. Mominul Hoque, Masaru Tsunoda, Kaoru Suzuki, Tamotsu Yamamoto, Gota Kawai, Jiro Kondo* & Akio Takénaka*.

“Structural insights into the catalytic reaction trigger and inhibition of D-3-hydroxybutyrate de-hydrogenase.”
Acta Crystallogr., F72, 507-515 (2016). * Selected as a Cover Picture

37. Satoshi Horikoshi, Kota Nakamura, Mari Kawaguchi, Jiro Kondo & Nick Serpone.

“Effect of microwave radiation on the activity of catalase. decomposition of hydrogen peroxide under microwave and conventional heating.”
RSC Adv., 6, 48237-48244 (2016).

36. Jiro Kondo*, Yusuke Nomura, Yukiko Kitahara, Satoshi Obika* & Hidetaka Torigoe*.

“Crystal structure of 2',4'-BNANC[N-Me]-modified antisense gapmer in complex with the target RNA.”
Chem. Commun., 52, 2354-2357 (2016).

35. Yoshiyuki Tanaka*, Jiro Kondo, Vladimir Sychrovsk, Jakub Šebera,Takenori Dairaku, Hisao Saneyoshi, Hidehito Urata, Hidetaka Torigoe & Akira Ono*.

“Structures, physicochemical properties, and applications of T-HgII-T, C-AgI-C, and other metallo-base pairs.”
Chem. Commun., 51, 17343-17360 (2015). * Selected as an Inside Cover Picture

 

34. Jiro Kondo*, Yoshinari Tada, Takenori Dairaku, Hisao Saneyoshi, Itaru Okamoto, Yoshiyuki Tanaka & Akira Ono

“High-resolution crystal structure of Silver(I)-RNA hybrid duplex containing Watson-Crick-like C-Silver(I)-C metallo-base pair”
Angew. Chem. Int. Ed., 54, 13323-13326 (2015).
プレスリリースはこちら)

 

33. Stephen Hanessian*, Oscar M. Saavedra, Miguel A. Vilchis-Reyes, Juan P. Maianti, Hiroki Kanazawa, Paola Dozzo, Rowena D. Matias, Alisa Serio & Jiro Kondo.

“Synthesis, broad spectrum antibacterial activity, and X-ray co-crystal structure of the decoding bacterial ribosomal A-site with 4'-deoxy-4'-fluoro neomycin analogs”
Chem. Sci., 5, 4621-4632 (2014).
報道記事12はこちら)

32. Juan Pablo Maianti, Hiroki Kanazawa, Paola Dozzo, Rowena D. Matias, Lee Ann Feeney, Eliana S. Armstrong, Darin J. Hildebrandt, Timothy R. Kane, Micah J. Gliedt, Adam A. Goldblum, Martin S. Linsell, James B. Aggen, Jiro Kondo & Stephen Hanessian*.

“Toxicity modulation, resistance enzyme evasion, and A-site X-ray structure of broad-spectrum antibacterial neomycin analogs”
ACS Chem. Biol., 9, 2067-2073 (2014).

 

31. Hiroshi Yamaguchi, Jakub Šebera, Jiro Kondo (Joint First Author), Shuji Oda, Tomoyuki Komuro, Takuya Kawamura, Takenori Dairaku, Yoshinori Kondo, Itaru Okamoto, Akira Ono, Jaroslav V. Burda, Chojiro Kojima, Vladimir Sychrovsky* & Yoshiyuki Tanaka*.

“The structure of metallo-DNA with consecutive thymine–HgII–thymine base pairs explains positive entropy for the metallo base pair formation”
Nucleic Acids Res., 42, 4094-4099 (2014).

 

30. Jiro Kondo*, Tom Yamada, Chika Hirose, Itaru Okamoto, Yoshiyuki Tanaka & Akira Ono.
“Crystal structure of metallo-DNA duplex containing consecutive Watson-Crick-like T-HgII-T base pairs” 
Angew. Chem. Int. Ed., 53, 2385-2388 (2014).
プレスリリース報道記事はこちら)

 

29. Nina Sesto, Marie Touchon, José Marques Andrade, Jiro Kondo, Eduardo P. C. Rocha, Cecilia Maria Arraiano, Cristel Archambaud, Eric Westhof, Pascale Romby* & Pascale Cossart*.

“A PNPase dependent CRISPR system in Listeria” 
PLoS Genet., 10, e1004065 (2014).

28. Moran Shalev, Jiro Kondo, Dmitry Kopelyanskiy, Charles L. Jaffe, Noam Adir* & Timor Baasov*.

“Identification of the molecular attributes required for aminoglycoside activity against Leishmania” 
Proc. Natl. Acad. Sci. USA., 110, 13333-13338 (2013).
報道記事はこちら)

 

27. Jiro Kondo*, Anne-Catherine Dock-Bregeon, Dagmar K. Willkomm, Roland K. Hartmann & Eric Westhof.

“Structure of an A-form RNA duplex obtained by degradation of 6S RNA in a crystallization droplet” 
Acta Crystallogr., F69, 634-639 (2013).

26. Jiro Kondo*, Mai Koganei, Juan Pablo Maianti, Vu Linh Ly & Stephen Hanessian*.

“Crystal structures of a bioactive 6'-hydroxy variant of sisomicin bound to the bacterial and protozoal ribosomal decoding sites” 
ChemMedChem, 8, 733-739 (2013).* Selected as a back cover picture

25. Jiro Kondo*, Mai Koganei & Tomoko Kasahara.

“Crystal structure and specific binding mode of sisomicin to the bacterial ribosomal decoding site” 
ACS Med. Chem. Lett., 3, 741-744 (2012).

 

24. Jiro Kondo*.

“A structural basis for the antibiotic resistance conferred by an A1408G mutation in 16S rRNA and for the antiprotozoal activity of aminoglycosides” 
Angew. Chem. Int. Ed., 51, 465-468. (2012).
プレスリリース報道記事こちら)

23. Janek Szychowski, Jiro Kondo, Omar Zahr, Karine Auclair, Eric Westhof, Stephen Hanessian* & Jeffrey W. Keillor*.

“Inhibition of aminoglycoside-deactivating enzymes APH(3')-IIIa and AAC(6')-Ii by amphiphilic paromomycin O2"-ether analogues” 
ChemMedChem, 6, 1961-1966. (2011). * Selected as an inside cover picture

 

22. Jiro Kondo* & Eric Westhof. 
“Classification of pseudo pairs between nucleotide bases and amino acids by analysis of nucleotide–protein complexes” 
Nucleic Acids Res., 39, 8628-8637 (2011). * Selected as a cover picture

 

21. Stephen Hanessian*, Kandasamy Pachamuthu, Janek Szychowski, Alexandre Giguère, Eric E. Swayze, Michael T. Migawa, Boris François, Jiro Kondo & Eric Westhof.

“Structure-based design, synthesis and A-site rRNA co-crystal complexes of novel amphiphilic aminoglycoside antibiotics with new binding modes: a synergistic hydrophobic effect against resistant bacteria”
Bioorg. Med. Chem. Lett., 20, 7097-7101. (2010).

 

20. Jiro Kondo & Eric Westhof*.

“Base pairs and pseudo pairs observed in RNA-ligand complexes” 
J. Mol. Recognit., 23, 241-252. (2010).

 

19. Jiro Kondo, Ludmila Urzhumtseva & Alexandre Urzhumtsev*.
“Patterson-guided ab-initio analysis of structures with helical symmetry” 
Acta Crystallogr., D64, 1078-1091. (2008).

 

18. Jiro Kondo & Eric Westhof*. 
“The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates” 
Nucleic Acids Res., 36, 2654-2666 (2008).

 

17. Jiro Kondo, Pachamuthu Kandasamy, Boris François, Janek Szychowski, Stephen Hanessian* & Eric Westhof*.
“Crystal structure of the bacterial ribosomal decoding site complexed with a synthetic doubly functionalized paromomycin derivative: a new specific binding mode to an A-minor motif enhances in vitro antibacterial activity” 
ChemMedChem, 2, 1631-1638. (2007).

16. Jiro Kondo, Mariana Hainrichson, Igor Nudelman, Dalia Shallom-Shezifi, Christopher M. Barbieri, Daniel S. Pilch, Eric Westhof* & Timor Baasov*. 
“Differential selectivity of natural and synthetic aminoglycosides towards the eukaryotic and prokaryotic decoding A sites” 
ChemBioChem, 8, 1700-1709. (2007). * Selected as a cover picture

 

15. Jiro Kondo, Tomoko Sunami & Akio Takénaka*. 
“The structure of a d(gcGAACgc) duplex containing two consecutive bulged A residues in both strands suggests a molecular switch” 
Acta Crystallogr., D63, 671-681. (2007). * Selected as a cover picture

 

14. Stephen Hanessian, Janek Szychowski, Susanta S. Adhikari, Guillermo Vasquez, Pachamuthu Kandasamy, Eric E. Swayze, Michael T. Migawa, Ray Ranken, Boris François, Julia Wirmer-Bartoschek, Jiro Kondo & Eric Westhof*. 
“Structure-based design, synthesis and A-site rRNA co-crystal complexes of functionally novel aminoglycoside antibiotics: C2'' ether analogues of paromomycin” 
J. Med. Chem., 50, 2352-2369. (2007).

 

13. Ella Czarina Magat Juan, Jiro Kondo, Takeshi Kurihara, Takanori Ito, Yoshihito Ueno, Akira Matsuda & Akio Takénaka*.
“Crystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(N-aminohexyl) carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules” 
Nucleic Acids Res., 35, 1969-1977. (2007).

 

12. Yoshiteru Sato, Mitomi Kenta, Sunami Tomoko, Jiro Kondo & Akio Takénaka.
“DNA octaplex formation with an I-motif of water-mediated A-quartets: reinterpretation of the crystal structure of d(GCGAAAGC)” 
J. Biochem., (Tokyo), 140, 759-762. (2006).

 

11. Jiro Kondo, Boris François, Rupert J. M. Russell, James B. Murray & Eric Westhof*.
“Crystal structure of the bacterial ribosomal decoding site complexed with amikacin containing the γ-amino-α-hydroxybutyryl (haba) group” 
Biochimie, 88, 1027-1031. (2006).

 

10. Jiro Kondo, Ciengshin Tanashaya, Ella Czarina Magat Juan, Yoshiteru Sato, Kenta Mitomi, Satoru Shimizu & Akio Takénaka*. 
“Crystal structure of d(gcGXGAgc) with X=G; a mutation at X is possible to occur in a base-intercalated duplex for multiplex formation” 
Nucleosides, Nucleotides & Nucleic Acids, 25, 693-704. (2006).

 

9. Jiro Kondo, Boris François, Alexandre Urzhumtsev & Eric Westhof*.
“Crystal structure of the Homo sapiens cytoplasmic ribosomal decoding site complexed with apramycin” 
Angew. Chem. Int. Ed. Engl., 45, 3310-3314. (2006).

8. Jiro Kondo, Alexandre Urzhumtsev & Eric Westhof. 
“Two conformational states in the crystal structure of the Homo sapiens cytoplasmic ribosomal decoding A site” 
Nucleic Acids Res., 34, 676-685. (2006).

7. Jiro Kondo, Wataru Adachi, Shun-ichi Umeda, Tomoko Sunami & Akio Takénaka*.
“Crystal structures of a DNA octaplex with I-motif of G-quartets and its splitting into two quadruplexes suggest a folding mechanism of eight tandem repeats” 
Nucleic Acids Res., 32, 2541-2549. (2004). * Selected as a cover picture

6. Tomoko Sunami, Jiro Kondo, Ichiro Hirao, Kimitsuna Watanabe, Kin-ichiro Miura & Akio Takénaka*. 
“Crystal structures of d(GCGAAGC) and d(GCGAAAGC) (tetragonal form); a switching of partners of the sheared G.A pairs to form a functional G:AxA:G crossing” 
Acta Crystallogr., D60, 422-431. (2004).

 

5. Tomoko Sunami, Jiro Kondo, Ichiro Hirao, Kimitsuna Watanabe, Kin-ichiro Miura & Akio Takénaka*. 
“Structure of d(GCGAAAGC) (hexagonal form): a base-intercalated duplex as a stable structure” 
Acta Crystallogr., D60, 90-96. (2004).

 

4. Jiro Kondo, Shun-ichi Umeda, Kazuhiro Fujita, Tomoko Sunami & Akio Takénaka*. 
“X-ray analyses of d(GCGAXAGC) containing G and T at X: the base-intercalated duplex is still stable even in point mutants at the fifth residue” 
J. Synchrotron Rad., 11, 117-120. (2004).

 

3. Tomoko Sunami, Jiro Kondo, Tomonori Kobuna, Ichiro Hirao, Kimitsuna Watanabe, Kin-ichiro Miura & Akio Takénaka*. 
“Crystal structure of d(GCGAAAGCT) containing a parallel-stranded duplex with homo base pairs and an anti-parallel duplex with Watson-Crick base pairs” 
Nucleic Acids Res., 30, 5253-5260. (2002).

 

2. Masaru Tsunoda, Jiro Kondo, Naoko Karino, Yoshihito Ueno, Akira Matsuda & Akio Takénaka*. 
“Water mediated Dickerson-Drew-type crystal of DNA dodecamer containing 2'-deoxy-5- formyluridine” 
Biophys. Chem., 95, 227-233. (2002).

 

1. M. Tofazzal Hossain, Jiro Kondo, Yoshihito Ueno, Akira Matsuda & Akio Takénaka*. 
“X-Ray analysis of d(CGCGAATTXGCG)2 containing 2'-deoxy-N4-methoxycytosine residue at X: A characteristic pattern of sugar puckers in crystalline state of the Dickerson-Drew-type DNA dodecamers” 
Biophys. Chem., 95, 69-77. (2002).