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Jiro KONDO

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TOP 3
Jiro KONDO; Vu Linh Ly; Juan Pablo Maianti; Mai Koganei; Stephen Hanessian
Crystal structures of a bioactive 6'-hydroxy variant of sisomicin bound to the bacterial and protozoal ribosomal decoding sites.
Jiro KONDO
A structural basis for the antibiotic resistance conferred by an A1408G mutation in 16S rRNA and for the antiprotozoal activity of aminoglycosides.
Janek Szychowski; Eric Westhof; Omar Zahr; Karine Auclair; Stephen Hanessian; Jiro KONDO; Jeffrey W Keillor
Inhibition of aminoglycoside-deactivating enzymes APH(3')-IIIa and AAC(6')-Ii by amphiphilic paromomycin O2''-ether analogues.

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All Publications

2013: Jiro KONDO; Vu Linh Ly; Juan Pablo Maianti; Mai Koganei; Stephen Hanessian
Crystal structures of a bioactive 6'-hydroxy variant of sisomicin bound to the bacterial and protozoal ribosomal decoding sites.
ChemMedChem 2013;8(5):733-9.
2012: Jiro KONDO
A structural basis for the antibiotic resistance conferred by an A1408G mutation in 16S rRNA and for the antiprotozoal activity of aminoglycosides.
Angewandte Chemie (International ed. in English) 2012;51(2):465-8.
2011: Janek Szychowski; Eric Westhof; Omar Zahr; Karine Auclair; Stephen Hanessian; Jiro KONDO; Jeffrey W Keillor
Inhibition of aminoglycoside-deactivating enzymes APH(3')-IIIa and AAC(6')-Ii by amphiphilic paromomycin O2''-ether analogues.
ChemMedChem 2011;6(11):1961-6.
2011: Jiro KONDO; Eric Westhof
Classification of pseudo pairs between nucleotide bases and amino acids by analysis of nucleotide-protein complexes.
Nucleic acids research 2011;39(19):8628-37.
2010: 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.
Bioorganic & medicinal chemistry letters 2010;20(23):7097-101.
2010: Jiro KONDO; Eric Westhof
Base pairs and pseudo pairs observed in RNA-ligand complexes.
Journal of molecular recognition : JMR 2010;23(2):241-52.
2009: Jiro KONDO
[Exploring the "motion" = "function" of the ribosomal A-site molecular switch].
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme 2009;54(11):1356-62.
2008: Jiro KONDO; Ludmila Urzhumtseva; Alexandre Urzhumtsev
Patterson-guided ab initio analysis of structures with helical symmetry.
Acta crystallographica. Section D, Biological crystallography 2008;64(Pt 10):1078-91.
2008: Jiro KONDO; Eric Westhof
The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates.
Nucleic acids research 2008;36(8):2654-66.
2007: Jiro KONDO; Kandasamy Pachamuthu; 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 2007;2(11):1631-8.
2007: 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 : a European journal of chemical biology 2007;8(14):1700-9.
2007: 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 crystallographica. Section D, Biological crystallography 2007;63(Pt 6):673-81.
2007: Stephen Hanessian; Janek Szychowski; Susanta Sekhar 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 cocrystal complexes of functionally novel aminoglycoside antibiotics: C2" ether analogues of paromomycin.
Journal of medicinal chemistry 2007;50(10):2352-69.
2007: 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 research 2007;35(6):1969-77.
2006: Yoshiteru Sato; Kenta Mitomi; Tomoko Sunami; Jiro KONDO; Akio Takénaka
DNA octaplex formation with an I-motif of water-mediated A-quartets: reinterpretation of the crystal structure of d(GCGAAAGC).
Journal of biochemistry 2006;140(6):759-62.
2006: 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 gamma-amino-alpha-hydroxybutyryl (haba) group.
Biochimie 2006;88(8):1027-31.
2006: Jiro KONDO; Boris François; Alexandre Urzhumtsev; Eric Westhof
Crystal structure of the Homo sapiens cytoplasmic ribosomal decoding site complexed with apramycin.
Angewandte Chemie (International ed. in English) 2006;45(20):3310-4.
2006: Yoshiteru Sato; Kenta Mitomi; Hiromu Sugiyama; Satoru Shimizu; Ella Czarina Magat Juan; Jiro KONDO; Akio Takénaka
Multiplex formation of repetitive sequences d([G]nA)m through non-WC pairings: crystal structure of d(gcGAGGGAgc).
Nucleic acids symposium series (2004) 2006;(50):39-40.
2006: Jiro KONDO; Tanashaya Ciengshin; 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 2006;25(4-6):693-704.
2006: Jiro KONDO; Alexandre Urzhumtsev; Eric Westhof
Two conformational states in the crystal structure of the Homo sapiens cytoplasmic ribosomal decoding A site.
Nucleic acids research 2006;34(2):676-85.
2005: Jiro KONDO; Boris François; Alexandre Urzhumtsev; Eric Westhof
Crystallographic studies of Homo sapiens ribosomal decoding A site complexed with aminoglycosides.
Nucleic acids symposium series (2004) 2005;(49):253-4.
2005: Kenta Mitomi; Jiro KONDO; Wataru Adachi; Shun-ichi Umeda; Kazuhiro Fujita; Tomoko Sunami; Akio Takénaka
Octaplex formation of d(GCGAAAGC) with the double A-quartet.
Nucleic acids symposium series (2004) 2005;(49):71-2.
2005: Ella Czarina Magat Juan; Jiro KONDO; Takanori Ito; Yoshihito Ueno; Akira Matsuda; Akio Takénaka
X-ray analyses of hybrid duplexes between antisense oligonucleotides containing 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine and their target RNAs.
Nucleic acids symposium series (2004) 2005;(49):65-6.
2004: Tomoko Sunami; Jiro KONDO; Ichiro Hirao; Kimitsuna Watanabe; Kin-ichiro Miura; Akio Takénaka
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 crystallographica. Section D, Biological crystallography 2004;60(Pt 3):422-31.
2004: Ella Czarina Magat Juan; Takeshi Kurihara; Jiro KONDO; Takanori Ito; Yoshihito Ueno; Akira Matsuda; Akio Takénaka
X-ray analyses of DNA duplexes containing 5-(N-aminohexyl)carbamoyl modifications.
Nucleic acids symposium series (2004) 2004;(48):305-6.
2004: Kenta Mitomi; Tanashaya Ciengshin; Jiro KONDO; Akio Takénaka
Structural stability and length of I-motif of G-quartet in DNA octaplex.
Nucleic acids symposium series (2004) 2004;(48):121-2.
2004: 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 research 2004;32(8):2541-9.
2004: 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 crystallographica. Section D, Biological crystallography 2004;60(Pt 1):90-6.
2004: 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.
Journal of synchrotron radiation 2004;11(Pt 1):117-20.
2003: Jiro KONDO; Shun-ichi Umeda; Tomoko Sunami; Akio Takénaka
The octaplex structure of d(GCGAGAGC) with I-motif of guanine quartet, controlled by potassium concentration.
Nucleic acids research. Supplement (2001) 2003;(3):223-4.
2003: Jiro KONDO; Shun-ichi Umeda; Kazuhiro Fujita; Tomoko Sunami; Akio Takénaka
The base-intercalated duplexes of d(GCGAXAGC) with mutation at X (X=G, T or C).
Nucleic acids research. Supplement (2001) 2003;(3):175-6.
2002: 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 research 2002;30(23):5253-60.
2002: Masaru Tsunoda; Jiro KONDO; Naoko Karino; Yoshihito Ueno; Akira Matsuda; Akio Takenaka
Water mediated Dickerson-Drew-type crystal of DNA dodecamer containing 2'-deoxy-5-formyluridine.
Biophysical chemistry 2002;95(3):227-33.
2002: Md Tofazzal Hossain; Jiro KONDO; Yoshihito Ueno; Akira Matsuda; Akio Takénaka
X-Ray analysis of d(CGCGAATTXGCG)(2) containing a 2' or minute-deoxy-N(4)-methoxycytosine residue at X: a characteristic pattern of sugar puckers in the crystalline state of the Dickerson-Drew type DNA dodecamers.
Biophysical chemistry 2002;95(1):69-77.
2002: Tomoko Sunami; Jiro KONDO; Masaru Tsunoda; Takeshi Sekiguchi; Ichiro Hirao; Kimitsuna Watanabe; Kin-ichiro Miura; Akio Takénaka
X-ray structure of d(GCGAAGC); switching of partner for G:A pair in duplex form.
Nucleic acids research. Supplement (2001) 2002;(2):181-2.
2002: Tomonori Kobuna; Tomoko Sunami; Jiro KONDO; Akio Takénaka
X-ray structure of d(CGAA), parallel-stranded DNA duplex with homo base pairs.
Nucleic acids research. Supplement (2001) 2002;(2):179-80.
2002: Tomoko Sunami; Tomonori Kobuna; Jiro KONDO; Ichiro Hirao; Kimitsuna Watanabe; Kin-ichiro Miura; Akio Takénaka
Crystal structure of d(GCGAAAGCT) containing parallel-stranded duplex with homo base pairs and anti-parallel duplex with Watson-Crick base pairs.
Nucleic acids research. Supplement (2001) 2002;(2):51-2.
2001: Jiro KONDO; Tomoko Sunami; Ichiro Hirao; Kin-ichiro Miura; Akio Takénaka
X-ray analysis of d(GCGAACGC); intra-duplex and inter-duplex hand-in-pocket motifs.
Nucleic acids research. Supplement (2001) 2001;(1):199-200.
2001: Tomoko Sunami; Jiro KONDO; Chatake Toshiyuki; Ichiro Hirao; Kimitsuna Watanabe; Kin-ichiro Miura; Akio Takénaka
X-ray analyses of d(GCGAAAGC) and d(GXGAAAGCT), where X = 2'-deoxy-5-iodocytidine.
Nucleic acids research. Supplement (2001) 2001;(1):191-2.
2000: Jiro KONDO; Akio Takénaka
Crystallization of the most active RNA-cleaving deoxyribozyme.
Nucleic acids symposium series 2000;(44):201-2.