Papers - USUI Kenji
-
Site-Specific Control of Silica Mineralization on DNA Using Designed Peptides Reviewed
K. Usui, K. Nagai, H. Nishiyama, A. yamada, T. Tsuruoka, S. Fujii, K.-y. Tomizaki
Peptide Science 2013 2415 - 2416 2014.3
Joint Work
Authorship：Lead author
-
Peptides targeting G-quadruplex structures Reviewed
Kenji Usui, Arisa Okada
Chemical Biology of Nucleic Acids: Fundamentals and Clinical Applications 459 - 475 2014.1
Publisher：Springer Berlin Heidelberg
Research in recent decades has revealed that some DNA and RNA secondary structures modulate a variety of cellular events. One secondary structure, the Guanine(G)-quadruplex, also regulates various cellular events that are mostly related to serious diseases. Systems capable of controlling DNA and RNA G-quadruplex structures would therefore be useful for the modulation of various cellular events to produce biological effects. Because of their biological importance, many G-quadruplex-targeting compounds have been described. However, the next generation of targeting molecules should exhibit increased G-quadruplex sequence specificity, a higher structure-inducing or -collapsing ability, and a greater degree of functionality, including on–off switches of binding ability and cellular penetration. Peptides might be good candidates for these next-generation Gquadruplex- targeting molecules due to the following advantages: (1) their easy design and synthesis, (2) their ability to mimic protein–G–quadruplex interactions, (3) the possibility of employing artificial amino acids in addition to naturally occurring amino acids, and (4) the ability to combine G-quadruplex-binding sequences with other functional sequences. Accordingly, several peptide-based compounds, such as furan-based cyclic peptides, PNA-conjugated peptides, and small molecule-peptide conjugates, have been developed. In this chapter, we introduce all these peptide ligands and describe most of the approaches for targeting G-quadruplex structures. We then conclude that peptides are among the most promising functional ligands for G-quadruplexes to control various biological events in next-generation approaches.
-
Control of Site-Specific Silica Precipitation Using PNA Peptides and DNAs Reviewed
K. Usui, H. Nishiyama, K. Nagai, T. Tsuruoka, S. Fujii, K.-y. Tomizaki
Peptides 2013 162 - 163 2013.12
Joint Work
Authorship：Lead author
-
Designed Peptide Libraries for Cell Analyzing Microarrays Reviewed
H. Mihara, K. Usui, H. Tsutsumi, K. Nokihara
Peptides 2013 22 - 23 2013.12
Joint Work
-
Peptide-DNA Hybrid G-Quadruplex Structures for Regulation of Protein Expression Depending on Protease Activity Reviewed
A. Okada, M. Taniguchi, K. Usui, N. Sugimoto
Peptides 2013 180 - 181 2013.12
Joint Work
Authorship：Lead author
-
Systematic screening of the cellular uptake of designed alpha-helix peptides Reviewed
Kenji Usui, Takuya Kikuchi, Masayasu Mie, Eiry Kobatake, Hisakazu Mihara
BIOORGANIC & MEDICINAL CHEMISTRY 21 ( 9 ) 2560 - 2567 2013.5
Publisher：PERGAMON-ELSEVIER SCIENCE LTD
The cellular penetration (CP) activity of functional molecules has attracted significant attention as one of the most promising new approaches for drug delivery. In particular, cell-penetrating peptides (CPPs) have been studied extensively in cellular engineering. Because there have been few large-scale systematic studies to identify peptide sequences with optimal CP activity or that are suitable for further applications in cell engineering, such as cell-specific penetration and cell-selective culture, we screened and compared the cellular uptake (CU) activity of 54 systematically designed a-helical peptides in HeLa cells. Furthermore, the CU activity of 24 designed peptides was examined in four cell lines using a cell fingerprinting technique and statistical approaches. The CU activities in various cells depended on amino acid residues of peptide sequences as well as charge, a-helical content and hydrophobicity of the peptides. Notably, the mutation of a single residue significantly altered the CU ability of a peptide, highlighting the variability of cell uptake mechanisms. Moreover, these results demonstrated the feasibility of cell-selective culture by conducting cell-selective permeation and death in cultures containing two cell types. These studies may lead to further peptide library design and screening for new classes of CPPs with useful functions. (C) 2013 Elsevier Ltd. All rights reserved.
-
A peptide release system using a photo-cleavable linker in a cell array format for cell-toxicity analysis Invited Reviewed
Takashi Kakiyama, Kenji Usui, Kin-ya Tomizaki, Masayasu Mie, Eiry Kobatake, Hisakazu Mihara
POLYMER JOURNAL 45 ( 5 ) 525 - 539 2013.5
Joint Work
Authorship：Lead author Publisher：NATURE PUBLISHING GROUP
We constructed a novel peptide-array format system for cellular toxicity analysis. In this system, a peptide was immobilized on a conventional 96-well plate bottom via a photo-cleavable linker. Once UV light irradiated the desired wells, the peptide was released from the bottom. As a result, the cytotoxic behavior of the peptide could be monitored. Immobilization and light-irradiation conditions were optimized. The immobilized peptide showed no cytotoxicity; therefore, the cells could be cultured on the peptide-immobilizing plate from the beginning of the experiment. Cell-toxicity assays with this system for three cell types were performed. All cell types showed similar to 25% lowering of viability with the photo-released 5-(and-6)-carboxytetramethylrhodamine (TMR)-GKLAKLAKKLAKLAKKLAKLAKGC (TMR-KLA-C) peptide compared with the non-coated plate. This relative toxicity nearly corresponded to that of similar to 10 mu M TMR-KLA-C in solution, and we found that the released peptide concentration per well was similar to 10 mu M at 60 min irradiation. Throughout this study, we successfully immobilized peptides via the photo-cleavable linker, released them by UV irradiation spatiotemporally and conducted the cell-toxicity assay. This study implies that the peptide photo-releasing array system will allow the realization of high-throughput cell arrays for cellomics analyses and cell-based phenotypic drug screenings.
DOI： 10.1038/pj.2013.20
-
Construction of Artificial Peptides for Control of DNA G-quadruplex Structures Depending on Protease Activity toward Regulation of Protein Expression Reviewed
Arisa Okada, Kenji Usui, Mai Taniguchi, Keita Kobayashi, Naoki Sugimoto
Peptide Science 2012 285 - 286 2013.3
Joint Work
Authorship：Lead author
-
A PNA Peptide for the Control of Site-Specific Silica Precipitation on DNA Reviewed
Kenji Usui, Kazuma Nagai, Hiroto Nishiyama, Takaaki Tsuruoka, Satoshi Fujii
Peptide Science 2012 375 - 376 2013.3
Joint Work
Authorship：Lead author
-
A novel array format for monitoring cellular uptake using a photo-cleavable linker for peptide release Reviewed
Kenji Usui, Takuya Kikuchi, Kin-ya Tomizaki, Takashi Kakiyama, Hisakazu Mihara
CHEMICAL COMMUNICATIONS 49 ( 57 ) 6394 - 6396 2013
Publisher：ROYAL SOC CHEMISTRY
We developed a novel peptide array format incorporating a photo-cleavable linker for monitoring cellular uptake. Model peptides were successfully immobilised via the photo-cleavable linker onto conventional plates and could be released spatiotemporally using UV irradiation. Incorporation of confocal microscopy allowed for detailed real-time monitoring of cellular internalisation of peptides.
DOI： 10.1039/c3cc41632a
-
Screening of Designed Peptides for Binders to a DNA G-Quadruplex Structure Reviewed
N. Matsui, K. Kobayashi, K. Usui
Peptide Science 2011 2011 315 - 316 2012.3
Joint Work
Authorship：Lead author
-
De Novo Designed Nitric Oxide Sensor Protein consisted of Iron Complex-Peptide Conjugate Reviewed
H. Miyazaki, K. Usui, S. Fujii
Peptide Science 2011 2011 303 - 304 2012.3
Joint Work
-
Development of PNA-Peptides Controlling DNA G-Quadruplex Structures Depending on Protease Activity Reviewed
K. Usui, K. Kobayashi, N. Sugimoto
Peptide Science 2011 2012 315 - 316 2012.3
Joint Work
Authorship：Lead author
-
Cell fingerprint patterns using designed alpha-helical peptides to screen for cell-specific toxicity Reviewed
Kenji Usui, Takashi Kakiyama, Kin-ya Tomizaki, Masayasu Mie, Eiry Kobatake, Hisakazu Mihara
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS 21 ( 21 ) 6281 - 6284 2011.11
Publisher：PERGAMON-ELSEVIER SCIENCE LTD
We conducted cell-based cytotoxicity screening of a 101-membered alpha-helical peptide library using cell fingerprints (CFPs). The CFP data suggested that there is a relationship between cytotoxicity and peptide characteristics, such as hydrophobicity, charge, and amino acid composition. In spite of the small size of the library used in this study, several peptides demonstrated cell-specific toxicity. The strategy of combining a designed peptide library with CFP thus shows real promise for peptide-based screening with cells. (C) 2011 Elsevier Ltd. All rights reserved.
-
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
-
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
-
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
-
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
-
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
-
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