![](paper.jpg)
![](line_01.gif)
![](ncontent[3].gif) ![](bigactaf.gif)
![](line_01.gif)
43. Hiroki Kanazawa, Fumika Baba, Mai Koganei & Jiro Kondo*.
“A structural basis ofr the antibiotic resistance conferred by an N1-methylation
of A1408 in 16S rRNA.”
Nucleic Acids Res., published online (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., published online (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.”
Nature Chemistry, 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 Advances., 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1、2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).
(プレスリリースと報道記事はこちら)
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).
(プレスリリースと報道記事こちら)
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).
|