Papers -
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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
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Thermodynamic stability of Hoogsteen and Watson-Crick base pairs in the presence of histone H3-mimicking peptide Reviewed International coauthorship
Smritimoy Pramanik, Kaori Nakamura, Kenji Usui, Shu-ichi Nakano, Sarika Saxena, Jun Matsui, Daisuke Miyoshi, Naoki Sugimoto
CHEMICAL COMMUNICATIONS 47 ( 10 ) 2790 - 2792 2011
Publisher：ROYAL SOC CHEMISTRY
We found that Hoogsteen base pairs were stabilized by molecular crowding and a histone H3-mimicking peptide, which was not observed for Watson-Crick base pairs. Our findings demonstrate that the type of DNA base pair is critical for the interaction between DNA and histones.
DOI： 10.1039/c0cc05776b
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Use of a designed peptide library to screen for binders to a particular DNA G-quadruplex sequence Reviewed
Keita Kobayashi, Noriko Matsui, Kenji Usui
Journal of Nucleic Acids 2011 572873 2011
We demonstrated a method to screen for binders to a particular G-quadruplex sequence using easily designed short peptides consisting of naturally occurring amino acids and mining of binding data using statistical methods such as hierarchical clustering analysis (HCA). Despite the small size of the library used in this study, candidates of specific binders were identified. In addition, a selected peptide stabilized the G-quadruplex structure of a DNA oligonucleotide derived from the promoter region of the protooncogene c-MYC. This study illustrates how a peptide library can be designed and presents a screening guideline for construction of G-quadruplex binders. Such G-quadruplex peptide binders could be functionally modified to enable switching, cellular penetration, and organelle-targeting for cell and tissue engineering. © 2011 Keita Kobayashi et al.
DOI： 10.4061/2011/572873
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PNA-Peptide Conjugates for Regulation of DNA and RNA G-Quadruplex Structures Depending on a Particular Protease Concentration Reviewed
Kenji Usui, Keita Kobayashi, Naoki Sugimoto
Peptides 2010 2010 608 - 609 2011
Joint Work
Authorship：Lead author
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Nanomolar aggregation of amyloid-beta peptides covalently and site-specifically modified by cholesterol oxidation products Reviewed International coauthorship
Kenji Usui, Evan T. Powers, Johan F. Paulsson, Sarah J. Siegel & Jeffery W. Kelly
Peptides 2008 2008 588 - 589 2011
Joint Work
Authorship：Lead author
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Fluorescent and Luminescent Fusion Proteins for Detection of Amyloid Beta Peptide Localization and Aggregation Reviewed
Kenji Usui, Masayasu Mie, Takashi Andou, Naoki Sugimoto, Hisakazu Mihara, Eiry Kobatake
Peptides 2010 2010 488 - 489 2011
Joint Work
Authorship：Lead author
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Designed Peptide Libraries for Protein and Cell analyses Reviewed
K. Kikuchi, K. Usui, K.-Y. Tomizaki, T. Takahashi, H. Mihara
Peptide Science 2010 2010 21 - 21 2011
Joint Work
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A Novel Nitric Oxide Sensor Using Fluorescent Peptides Attached to Iron Complexes Reviewed
Hiroshi Miyazaki, Kenji Usui, Satoshi Fujii
Peptides 2011 2011 224 - 255 2011
Joint Work
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A PNA Peptide Inducing DNAs to Form G-Quadruplex Structures Depending on a Protease Activity Reviewed
Kenji Usui, Keita Kobayashi, Naoki Sugimoto
Peptides 2011 2011 152 - 153 2011
Joint Work
Authorship：Lead author
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Nanomolar Aggregation and Neurotoxicity of Amyloid beta Peptides with Site-Specific Modification of Oxidized Cholesterol Reviewed International coauthorship
K. Usui, J. D. Hulleman, J. F. Paulsson, S. J. Siegel, E. T. Powers, J. W. Kelly
Peptide Science 2010 2010 169 - 169 2011
Joint Work
Authorship：Lead author
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Synthesis of Au Nanocrystals/Porous Coordination Polymer Compoosites by Perferential Self-Assembly of Frameworks Reviewed
H. Kawasaki, M. Kumano, M. Yamashita, T. Tsuruoka, H. Nawafune, K. Akamatsu
Trans. Mater. Res. Soc. Jpn. 37 181 - 184 2011
Joint Work
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In situ synthesis of comosite nanowires consisting of metal nanoparticles in ion-exchangeable polymer matrix using porous alumina tenplates
Y. Fukumoto, T. Tsuruoka, T.Yanagishita, H. Masuda, H. Nawafune, K. Akamatsu
Trans. Mater. Res. Soc. Jpn. 37 185 - 188 2011
Joint Work
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Molecular Decoding using Luminescence from an Entangled Porous Framework Reviewed
Yohei Takashima, Virginia Mart?nez Mart?nez, Shuhei Furukawa, Mio Kondo, Satoru Shimomura, Hiromitsu Uehara, Masashi Nakahama, Kunihisa Sugimoto, Susumu Kitagawa
Nature Commun 2 168 - 168 2011
Joint Work
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Thermodynamically controlled coordination-engineering of novel 2D cadmium thiolate coordination polymers Reviewed
Nicolas Louvain, Yohei Takashima, Susumu Kitagawa, Shuhei Furukawa
New J. Chem. 35 1265 - 1269 2011
Joint Work
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Control of the Charge-Transfer Interaction between a Flexible Porous Coordination Host and Aromatic Guests by Framework Isomerism Reviewed
Yohei Takashima, Shuhei Furukawa, Susumu Kitagawa
CrystEngComm 13 3360 - 3363 2011
Joint Work
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Ultrasensitive and Selective Detection of a Prognostic Indicator in Early-Stage Cancer Using Graphene Oxide and Carbon Nanotubes Reviewed
Xiaohui Wang, Chunyan Wang, Konggang Qu, Yujun Song, Jinsong Ren, Daisuke Miyoshi, Naoki Sugimoto, and Xiaogang Qu
Advanced Functional Materials 20 3967 - 3971 2010.12
Joint Work
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Comparative thermodynamic analysis of RNA-protein interaction on surface and in solution（共著）
Y. Tanaka, K. Ishidate, K. Kishimoto, N. Sugimoto, and J. Kawakami
Proc. 37th Intl. Symp. Nucleic Acids Chemistry 276 - 277 2010.11
Joint Work
Authorship：Lead author
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A rapid and sensitive "add-mix-measure" assay for multiple proteinases based on one goldnanoparticle-peptide-fluorophore conjugate Reviewed
X.Wang, J.Geng, D.Miyoshi, J.Ren, N.Sugimoto, and X.Qu
Biosens. Bioelectron. 26 743 - 747 2010.11
Joint Work
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Stacking interaction in the middle and at the end of a DNA helix studied with non-natural nucleotides Reviewed
S. Nakano, H. Oka, Y. Uotani, K. Uenishi, M. Fujii, and N. Sugimoto
Mol. BioSyst. 6 2023 - 2029 2010.10
Joint Work
DOI： 10.1039/C0MB00002G
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Sole and stable RNA duplexes of G-rich sequences located in the 5'-untranslated region of protooncogenes Reviewed
Sarika Saxena, Daisuke Miyoshi, Naoki Sugimoto
Biochemistry 49 7190 - 7201 2010.9
Joint Work
Authorship：Lead author