Jiro Kondo

Jiro Kondo
Sophia University · Department of Materials and Life Sciences

Doctor of Science

About

115
Publications
9,673
Reads
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1,686
Citations
Additional affiliations
April 2015 - present
Sophia University
Position
  • Professor (Associate)
April 2010 - March 2015
Sophia University
Position
  • Professor (Assistant)
April 2004 - March 2010
University of Strasbourg
Position
  • PostDoc Position
Education
April 1999 - March 2004
Tokyo Institute of Technology
Field of study
  • Structural Biology

Publications

Publications (115)
Article
DNA/RNA duplexes containing metal‐ion‐mediated base pairs (metallo‐base pairs) have potential applications in developing nucleic acid‐based nanodevices and genetic code expansion. Many metallo‐base pairs are formed within duplexes stabilized by Watson‐Crick base pairs. Recently, the crystal structure of an Ag(I)‐DNA nanowire with an uninterrupted o...
Article
DNA/RNA duplexes containing metal‐ion‐mediated base pairs (metallo‐base pairs) have potential applications in developing nucleic acid‐based nanodevices and genetic code expansion. Many metallo‐base pairs are formed within duplexes stabilized by Watson‐Crick base pairs. Recently, the crystal structure of an Ag(I)‐DNA nanowire with an uninterrupted o...
Article
The effect of replacing guanosines with inosines in the two stabilizing strands (5’-CACCTAGCGA-3’) of the NIR emissive DNA-Ag16NC was investigated. The spectroscopic behavior of the inosine mutants is position-dependent: when...
Article
Ag+-mediated base pairing is valuable for synthesising DNA-based silver nanoparticles (AgNPs) and nanoclusters (AgNCs). Recently, we reported the formation of a [Ag(cytidine)2]+ complex in dimethyl sulfoxide (DMSO), which facilitated the evaluation of the effect of cytosine-Ag+-cytosine (C-Ag+-C) base pairing on the degree of AgNP aggregation in so...
Article
High-speed, fully automated data collection allows us to conduct DNA Monozukuri (manufacturing) based on a large number of 3D structural information. In the process of designing and synthesizing prototype DNAs by mimicking structures deposited in Protein Data Bank (PDB), brushing up their functions, and obtaining the finished products, each of the...
Article
The redox properties of metallo-base pairs remain to be elucidated. Herein, we report the detailed 1H/13C/109Ag NMR spectroscopic and cyclic voltammetric characterisation of the [Ag(cytidine)2]+ complex as isolated cytosine-Ag+-cytosine (C-Ag+-C) base pairs. We also performed comparative studies between cytidine/Ag+ and other nucleoside/Ag+ systems...
Experiment Findings
http://www.rcsb.org/structure/7BSH
Experiment Findings
http://www.rcsb.org/structure/7BSE
Experiment Findings
http://www.rcsb.org/structure/7BSF
Experiment Findings
http://www.rcsb.org/structure/7BSG
Article
Mutation of position 5 in a ten-base DNA sequence allowed us to probe its role in the photophysical and structural properties of a DNA-stabilized silver 16 nanocluster (DNA-Ag16NC). A comparison of the original T5 (thymine at position 5) compound with the new modifications: X5 (abasic site), C5 (cytosine), A5 (adenine) and G5 (guanine), was made. A...
Experiment Findings
https://www.rcsb.org/structure/6M2P
Article
Full-text available
The role of the terminal adenosine (A10) on the spectroscopic and structural properties of a previously described DNA-stabilized Ag16 nanocluster (DNA:Ag16NC) is presented. In the original DNA:Ag16NCs (5′-CACCTAGCGA-3′), the A10 nucleobase was involved in an Ag⁺-mediated interaction with an A10 in a neighboring asymmetric unit, and did not interact...
Article
Full-text available
To understand a structural basis for the fitness cost of the A1408G antibiotic-resistance mutation in the ribosomal A-site RNA, we have determined crystal structures of its A1408C and A1408U lethal mutants, and made comparison with previously solved structures of the wild type and the antibiotic-resistant mutant. The A-site RNA containing an asymme...
Article
The X‐ray crystal structure of the DNA–Ag16 nanocluster, which is a near‐infrared emitter composed of sixteen Ag atoms and two DNA decamer fragments, is presented by T. Vosch, J. Kondo, et al. in their Communication (DOI: 10.1002/anie.201906766). The structural information will aid in the characterization of the photophysical properties of this cla...
Article
Die Röntgenkristallstruktur des DNA‐Ag16‐Nanoclusters, der ein Nahinfrarot‐Emitter aus sechzehn Ag‐Atomen und zwei DNA‐Decamer‐Fragmenten ist, wird von T. Vosch, J. Kondo et al. in ihrer Zuschrift vorgestellt (DOI: 10.1002/ange.201906766). Die Strukturinformationen helfen bei der Charakterisierung der photophysikalischen Eigenschaften dieser Emitte...
Article
Numerous applications of metal ion‐mediated base pairs (metallo‐base pairs) to nucleic acid‐based nanodevices and genetic code expansion have extensively been studied. Many of these metallo‐base pairs are formed in DNA and RNA duplexes containing Watson‐Crick base pairs. Recently, a crystal structure of a metal‐DNA nanowires with uninterrupted one‐...
Article
Ein Energiebündel: Ein Hg-DNA-Kabel aus HgII-vermittelten T:T-und T:G-Basenpaaren, sowie Wasser-vermittelten C:C-Paaren, wurde durch das Mischen des kurzen Oligonukleotids 5′-d(TTTGC)-3′ und HgII-Ionen erhalten. Dieses neuartige DNA-Nanokabel, das keine Watson-Crick-Paare enthält, konnte durch Kristallstrukturanalyse charakterisiert werden. Abstra...
Experiment Findings
https://www.rcsb.org/structure/6JR4
Article
If the A-form helix is the major structural motif found in RNA, the loops that cap them constitute the second most important family of motifs. Among those, two are overrepresented, GNRA and UNCG tetraloops. Recent surveys of RNA structures deposited in the PDB show that GNRA and UNCG tetraloops can adopt tertiary folds that are very different from...
Article
Die Röntgenkristallstruktur eines DNA-verkapselten, Nahinfrarot-emittierenden Ag16-Nanoclusters (Ag16NC) wurde gelöst. Jedes Ag16NC ist durch zwei DNA-Decamere verkapselt und fast vollständig vom umgebenen Lösungsmittel abgeschirmt. Diese strukturelle Erkenntnis wird für die Charakterisierung der photopysikalischen Eigenschaften dieser Klasse von E...
Article
In the last 15 years, scientists have used DNA as a scaffold to stabilize small, atomically monodisperse silver nanoclusters. These DNA‐templated nanoclusters have attracted a lot of attention due to their intriguing photophysical properties. Here, we describe the crystal structure of a DNA‐encapsulated, near‐infrared emitting Ag16 nanocluster (DNA...
Article
Full-text available
The crystal structure of a DNA duplex cross-linked by 6-thioguanine–6-thioguanine disulfides has been solved.
Article
DNA is very attractive as bio-nanomaterials, since it is chemically stable, biocompatible, less toxic, environmentally friendly and easy to synthesize. In addition, the discovery of metal-mediated base pairs, such as T-Hg(II)-T and C-A(gI)-C, has inspired scientists to develop several nanodevices including heavy metal sensor and trapping beads. Rec...
Article
Aminoglycosides (AG) are antibiotics that lower the accuracy of protein synthesis by targeting a highly‐conserved RNA helix of the ribosomal A‐site. The discovery of AGs that selectively target the eukaryotic ribosome, but lack activity in prokaryotes, are promising as antiprotozoals for the treatment of neglected tropical diseases, and as therapie...
Article
Full-text available
The crystal structures of 4-thiothymine–2Ag I –4-thiothymine base pairs in B-form DNA duplexes have been solved.
Article
The aminoglycoside resistance conferred by an N1-methylation of A1408 in 16S rRNA by a novel plasmid-mediated methyltransferase NpmA can be a future health threat. In the present study, we have determined crystal structures of the bacterial ribosomal decoding A site with an A1408m1A antibiotic-resistance mutation both in the presence and absence of...
Article
We have determined a crystal structure of an RNA duplex containing a novel metal-binding motif. The motif is composed of two sheared G○A base pairs, two unpaired A residues and four phosphate groups in close proximity. Four A residues make an A-A-A-A stacking column at the minor groove side and two G bases are highly inclined, thereby forming the p...
Article
The double-helix structure of DNA, in which complementary strands reversibly hybridize to each other, not only explains how genetic information is stored and replicated, but also has proved very attractive for the development of nanomaterials. The discovery of metal-mediated base pairs has prompted the generation of short metal–DNA hybrid duplexes...
Article
Full-text available
The effect of microwave heating (MW) on the activity of a well-known enzyme (catalase) was elucidated by examining the catalase-assisted decomposition of hydrogen peroxide (H2O2 at various heating times (0 to 12 min)). For comparison, conventional water bath heating (WB) was also examined under identical temperature conditions. Microwave radiation...
Article
Full-text available
Recently, metal-mediated base-pairs (metallo-base-pairs) have been studied extensively with the aim of exploring novel base-pairs; their structures, physicochemical properties, and applications have been studied. This trend has become more evident after the discovery of Hg(II)-mediated thymine-thymine (T-Hg(II)-T) and Ag(I)-mediated cytosine-cytosi...
Article
Metallo-base pairs have been extensively studied for applications in nucleic acid-based nanodevices and genetic code expansion. Metallo-base pairs composed of natural nucleobases are attractive because nanodevices containing natural metallo-base pairs can be easily prepared from commercially available sources. Previously, we have reported a crystal...
Article
An RNA molecular switch in the aminoacyl-tRNA decoding site (A site) of the ribosome plays a key role in the decoding process of the protein biosynthesis. The switch discriminates a single cognate-tRNA from near-cognate tRNAs by changing its conformation from "off" to "on" states and recognizing the first two base pairs of codon-anticodon mini-heli...
Article
Full-text available
It has been confirmed by our previous studies that a 2',4'-BNA(NC)[N-Me]-modified antisense gapmer displays high affinity and selectivity to the target RNA strand, promising mRNA inhibitory activity and excellent nuclease resistance. Herein, we have obtained a crystal structure that provides insights into these excellent antisense properties.
Article
Full-text available
This study reports the synthesis, antibacterial evaluation and nature of fluorine–rRNA contacts revealed by an X-ray co-crystal structure of a series of 4′-deoxy-4′-fluoro B-neomycin analogs. 4′-Deoxyfluorination improves the inhibition profile towards resistant enzymes and renders equally potent antibiotics compared to the parent neomycin B. The 4...
Article
Full-text available
The DNA duplex containing mercury-mediated base pairs (T-Hg(II)-T) is an attractive biomacromolecular nanomaterials. In a recent study, it was confirmed that the Hg(II) ion significantly stabilizes a DNA duplex by binding selectively to a T-T mispair [1]. Based on the phenomenon observed, a DNA-based sensing system that selectively and sensitively...
Article
Full-text available
Crystal structures of several functional non-coding RNAs, such as ribozymes, aptamers, ribosomes and tRNAs, have been reported so far. Unusual structural motifs and non-complementary base pairs are important for their functions. In the present study, we have determined a crystal structure of an unusual RNA duplex containing a strontium ion binding...
Article
Full-text available
We have studied structures of metal-mediated base-pairs, HgII-mediated T–T (T–HgII–T) and AgI-mediated C–C (C–AgI–C). We have definitely determined the chemical structure of the T–HgII–T basepair with HgII-mediated 15N–15N J-coupling (2JNN). Based on this chemical structure, we further determined 3-dimensional (3D) structure of a DNA duplex with ta...
Article
Aminoglycoside antibiotics are pseudosaccharides decorated with ammonium groups that are critical for their potent broad-spectrum antibacterial activity. Despite over three decades of speculation whether or not modulation of pKa is a viable strategy to curtail aminoglycoside kidney toxicity, there is a lack of methods to systematically probe amine-...
Article
The metallo DNA duplex containing mercury‐mediated T–T base pairs is an attractive biomacromolecular nanomaterial which can be applied to nanodevices such as ion sensors. Reported herein is the first crystal structure of a B‐form DNA duplex containing two consecutive T–Hg–T base pairs. The Hg ion occupies the center between two T residues. The N3‐H...
Article
The metallo DNA duplex containing mercury-mediated T-T base pairs is an attractive biomacromolecular nanomaterial which can be applied to nanodevices such as ion sensors. Reported herein is the first crystal structure of a B-form DNA duplex containing two consecutive T-Hg(II) -T base pairs. The Hg(II) ion occupies the center between two T residues....
Article
Full-text available
The human bacterial pathogen Listeria monocytogenes is emerging as a model organism to study RNA-mediated regulation in pathogenic bacteria. A class of non-coding RNAs called CRISPRs (clustered regularly interspaced short palindromic repeats) has been described to confer bacterial resistance against invading bacteriophages and conjugative plasmids....
Article
Full-text available
We have determined the three-dimensional (3D) structure of DNA duplex that includes tandem Hg(II)-mediated T-T base pairs (thymine-Hg(II)-thymine, T-Hg(II)-T) with NMR spectroscopy in solution. This is the first 3D structure of metallo-DNA (covalently metallated DNA) composed exclusively of 'NATURAL' bases. The T-Hg(II)-T base pairs whose chemical...
Article
Full-text available
Leishmaniasis, a parasitic disease caused by protozoa of the genus Leishmania, affects millions of people worldwide. Aminoglycosides are mostly known as highly potent, broad-spectrum antibiotics that exert their antibacterial activity by selectively targeting the decoding A site of the bacterial ribosome, leading to aberrant protein synthesis. Rece...
Article
Full-text available
In the course of a crystallographic study of a 132 nt variant of Aquifex aeolicus 6S RNA, a crystal structure of an A-form RNA duplex containing 12 base pairs was solved at a resolution of 2.6 Å. In fact, the RNA duplex is part of the 6S RNA and was obtained by accidental but precise degradation of the 6S RNA in a crystallization droplet. 6S RNA de...
Article
Parasitic infections recognized as neglected tropical diseases are a source of concern for several regions of the world. Aminoglycosides are potent antimicrobial agents that have been extensively studied by biochemical and structural studies in prokaryotes. However, the molecular mechanism of their potential antiprotozoal activity is less well unde...
Article
Sisomicin with an unsaturated sugar ring I displays better antibacterial activity than other structurally related aminoglycosides, such as gentamicin, tobramycin, and amikacin. In the present study, we have confirmed by X-ray analyses that the binding mode of sisomicin is basically similar but not identical to that of the related compounds having s...
Article
Resistance explained: The crystal structures of the ribosomal decoding A site with an A1408G antibiotic-resistance mutation were solved in the presence and absence of the aminoglycoside geneticin (see structure, geneticin carbon framework in yellow). These structures show how bacteria acquire high-level resistance against aminoglycosides by the mut...
Article
The inside cover picture shows a semi-synthetic amphiphilic aminoglycoside, active against S. aureus and E. coli, binding in the bacterial ribosomal decoding A site. Aminoglycoside ring I makes a pseudo pair with universally conserved A1408. The hydrophobic ether chain extends across the deep groove and points into the solvent. For more details, se...
Article
Paromomycin analogue activity: Novel amphiphilic aminoglycosides are shown to inhibit clinically relevant deactivating enzymes, without undergoing significant deactivation themselves.
Article
Full-text available
Nucleotide bases are recognized by amino acid residues in a variety of DNA/RNA binding and nucleotide binding proteins. In this study, a total of 446 crystal structures of nucleotide–protein complexes are analyzed manually and pseudo pairs together with single and bifurcated hydrogen bonds observed between bases and amino acids are classified and a...
Article
Incorporation of an hydrophobic (phenethylamino)ethyl ether at C2″ of N1-(HABA)-3',4'-dideoxyparomomycin led to a novel analog with an excellent antibacterial profile against a host of resistant bacteria.
Article
Full-text available
The aminoacyl-tRNA decoding site (A-site) on the small ribosomal subunit is an RNA molecular switch guaranteeing high translation fidelity. Due to the similarity of the secondary structure of the A-site, it has long been believed that the functional characteristics and tertiary structure of the A-site molecular switch are basically conserved in thr...
Article
Previously, a geometric nomenclature was proposed in which RNA base pairs were classified by their interaction edges (Watson-Crick, Hoogsteen or sugar-edge) and the glycosidic bond orientations relative to the hydrogen bonds formed (cis or trans). Here, base pairs and pseudo pairs observed in RNA-ligand complexes are classified in a similar manner....
Article
Full-text available
Patterson maps, which have a peak for intermolecular vectors between two molecules linked by a pseudo-translation, are widely used for structure solution. However, these maps may contain other peaks that indicate additional important information. In particular, if a molecule has internal symmetry, the Patterson maps may have a peak even when the re...
Article
Full-text available
The A site of the small ribosomal subunit participates in the fidelity of decoding by switching between two states, a resting ‘off’ state and an active decoding ‘on’ state. Eight crystal structures of RNA duplexes containing two minimal decoding A sites of the Homo sapiens mitochondrial wild-type, the A1555G mutant or bacteria have been solved. The...
Article
The crystal structure of the complex between oligonucleotide containing the bacterial ribosomal decoding site (A site) and the synthetic paromomycin analogue 1, which contains the gamma-amino-alpha-hydroxybutyryl (L-haba) group at position N1 of ring II (2-DOS ring), and an ether chain with an O-phenethylaminoethyl group at position C2'' of ring II...
Article
Full-text available
The cover picture shows the X-ray crystal structure of an NB33–rRNA complex along with 3D representations (unoptimized Chem3D models) of NB33 and apramycin. The two A sites of the X-ray structure represent the “on” [A1492(blue)/A1493(red) bulging out and A1491(green) tucked in] and “off” (A1491/A1493 bulging out and A1492 tucked in) conformational...
Article
The lack of absolute prokaryotic selectivity of natural antibiotics is widespread and is a significant clinical problem. The use of this disadvantage of aminoglycoside antibiotics for the possible treatment of human genetic diseases is extremely challenging. Here, we have used a combination of biochemical and structural analysis to compare and cont...
Article
Full-text available
In previous studies, it was reported that DNA fragments with the sequence d(gcGXYAgc) (where X = A or G and Y = A, T or G) form a stable base-intercalated duplex (Bi-duplex) in which the central X and Y residues are not involved in any base-pair interactions but are alternately stacked on each other between the two strands. To investigate the struc...