Search

Your search keyword '"Hidaka, Kumi"' showing total 338 results
Start Over Author "Hidaka, Kumi"
338 results on '"Hidaka, Kumi"'

13. Photocontrolled DNA Origami Assembly by Using Two Photoswitches

Author

Hiroshi Sugiyama, Tomoko Emura, Hidaka Kumi, Soyoung Park, Shubham Mishra, and Masayuki Endo

Subjects
chemistry.chemical_classification, Nanostructure, Light, Photoisomerization, Photoswitch, Tandem, 010405 organic chemistry, Biomolecule, Organic Chemistry, Nanotechnology, DNA, General Chemistry, Photochemical Processes, 010402 general chemistry, 01 natural sciences, Catalysis, Nanostructures, 0104 chemical sciences, chemistry.chemical_compound, Azobenzene, chemistry, Nucleic Acid Conformation, Molecule, DNA origami
Abstract

Stimuli-responsive switching molecules have been widely investigated for the purpose of the mechanical control of biomolecules. Recently developed arylazopyrazole (AAP) shows photoisomerization activity, displaying a faster response to light-induced conformational changes and unique absorption spectral properties compared with those of conventionally used azobenzene. Herein, it is demonstrated that AAP can be used as a photoswitching molecule to control photoinduced assembly and disassembly of DNA origami nanostructures. An AAP-modified DNA origami has been designed and constructed. It is observed that the repeated assembly and disassembly of AAP-modified X-shaped DNA origami and hexagonal origami with complementary strands can be achieved by alternating UV and visible-light irradiation. Closed and linear assemblies of AAP-modified X-shaped origami were successfully formed by photoirradiation, and more than 1 μm linear assemblies were formed. Finally, it is shown that the two photoswitches, AAP and azobenzene, can be used in tandem to independently control different assembly configurations by using different irradiation wavelengths. AAP can extend the variety of available wavelengths of photoswitches and stably result in the assembly and disassembly of various DNA origami nanostructures.

Published
2020

15. DNA density-dependent uptake of DNA origami-based two-or three-dimensional nanostructures by immune cells

Author

Maezawa, Tatsuoki, Ohtsuki, Shozo, Hidaka, Kumi, Sugiyama, Hiroshi, Endo, Masayuki, Takahashi, Yuki, Takakura, Yoshinobu, and Nishikawa, Makiya

Abstract

DNA nanostructures are expected to be applied for targeted drug delivery to immune cells. However, the structural properties of DNA nanostructures required for the delivery have not fully been elucidated. In this study, we focused on the DNA density that can be important for the their recognition and uptake by immune cells. To examine this, DNA nanostructures with almost identical molecular weights and structural flexibility, but with different shapes and DNA densities, were designed using DNA origami technology. We compared the following five types of DNA nanostructures, all of which consisted of ten DNA helices using an identical circular, single-stranded scaffold and staples. Rec180 had a rectangular-shaped, almost flat structure. Rec90, Rec50 and Rec0 were bent forms of Rec180 at the center by 90, 50 or 0 degrees, respectively. Rec50/50 has two bends of 50 degrees each so that the both ends stick together to form a triangular prism shape. The fluctuation, or flexibility, of these DNA nanostructures under solution conditions was estimated using CanDo software. The DNA density estimated from the average distance between any two of the ten DNA helices in the DNA nanostructures was different among them; Rec50, Rec0 and Rec50/50 had a higher density than Rec180 and Rec90. Agarose gel electrophoresis and atomic force microscopy showed that all of the nanostructures were prepared with high yield. Flow cytometry analysis revealed that the uptake of DNA nanostructures by murine macrophage-like RAW264.7 cells was higher for those with higher DNA density than those with low density. There was a positive correlation between the density and cellular uptake. These results indicate that DNA nanostructures with high DNA density are suitable for delivery to immune cells.

Published
2020

16. Characterization of a Conformation-Restricted Amyloid β Peptide and Immunoreactivity of Its Antibody in Human AD brain

Author

Kageyama, Yusuke, primary, Irie, Yumi, additional, Matsushima, Yuka, additional, Segawa, Tatsuya, additional, Bellier, Jean-Pierre, additional, Hidaka, Kumi, additional, Sugiyama, Hiroshi, additional, Kaneda, Daita, additional, Hashizume, Yoshio, additional, Akatsu, Hiroyasu, additional, Miki, Kunio, additional, Kita, Akiko, additional, Walker, Douglas G., additional, Irie, Kazuhiro, additional, and Tooyama, Ikuo, additional

Published
2021
Full Text
View/download PDF

23. Triggering nucleic acid nanostructure assembly by conditional kissing interactions

Author

Azéma, Laurent, Bonnet-Salomon, Servane, Endo, Masayuki, Takeuchi, Yosuke, Durand, Guillaume, Emura, Tomoko, Hidaka, Kumi, Dausse, Eric, Sugiyama, Hiroshi, and Toulmé, Jean-Jacques

Subjects
Adenosine, Binding Sites, Nanotubes, Base Sequence, Inverted Repeat Sequences, Oligonucleotides, DNA, Aptamers, Nucleotide, Ligands, Chemical Biology and Nucleic Acid Chemistry, Nanotechnology, Nucleic Acid Conformation, RNA, Base Pairing
Abstract

Nucleic acids are biomolecules of amazing versatility. Beyond their function for information storage they can be used for building nano-objects. We took advantage of loop–loop or kissing interactions between hairpin building blocks displaying complementary loops for driving the assembly of nucleic acid nano-architectures. It is of interest to make the interaction between elementary units dependent on an external trigger, thus allowing the control of the scaffold formation. To this end we exploited the binding properties of structure-switching aptamers (aptaswitch). Aptaswitches are stem–loop structured oligonucleotides that engage a kissing complex with an RNA hairpin in response to ligand-induced aptaswitch folding. We demonstrated the potential of this approach by conditionally assembling oligonucleotide nanorods in response to the addition of adenosine.

Published
2017

27. Single-molecule observations of RNA-RNA kissing interactions in a DNA nanostructure

Author

Takeuchi, Yosuke, Endo, Masayuki, Suzuki, Yuki, Hidaka, Kumi, Durand, Guillaume, Dausse, Eric, Toulmé, Jean Jacques, and Sugiyama, Hiroshi

Abstract

RNA molecules uniquely form a complex through specific hairpin loops, called a kissing complex. The kissing complex is widely investigated and used for the construction of RNA nanostructures. Molecular switches have also been created by combining a kissing loop and a ligand-binding aptamer to control the interactions of RNA molecules. In this study, we incorporated two kinds of RNA molecules into a DNA origami structure and used atomic force microscopy to observe their ligand-responsive interactions at the single-molecule level. We used a designed RNA aptamer called GTPswitch, which has a guanosine triphosphate (GTP) responsive domain and can bind to the target RNA hairpin named Aptakiss in the presence of GTP. We observed shape changes of the DNA/RNA strands in the DNA origami, which are induced by the GTPswitch, into two different shapes in the absence and presence of GTP, respectively. We also found that the switching function in the nanospace could be improved by using a cover strand over the kissing loop of the GTPswitch or by deleting one base from this kissing loop. These newly designed ligand-responsive aptamers can be used for the controlled assembly of the various DNA and RNA nanostructures.

Published
2016

28. Translation-dependent unwinding of stem–loops by UPF1 licenses Regnase-1 to degrade inflammatory mRNAs

Author

Mino, Takashi, primary, Iwai, Noriki, additional, Endo, Masayuki, additional, Inoue, Kentaro, additional, Akaki, Kotaro, additional, Hia, Fabian, additional, Uehata, Takuya, additional, Emura, Tomoko, additional, Hidaka, Kumi, additional, Suzuki, Yutaka, additional, Standley, Daron M, additional, Okada-Hatakeyama, Mariko, additional, Ohno, Shigeo, additional, Sugiyama, Hiroshi, additional, Yamashita, Akio, additional, and Takeuchi, Osamu, additional

Published
2019
Full Text
View/download PDF

30. Programming Rotary Motions with a Hexagonal DNA Nanomachine

Author

Yang, Yangyang, primary, Zhang, Shiwei, additional, Yao, Shengtao, additional, Pan, Rizhao, additional, Hidaka, Kumi, additional, Emura, Tomoko, additional, Fan, Chunhai, additional, Sugiyama, Hiroshi, additional, Xu, Yufang, additional, Endo, Masayuki, additional, and Qian, Xuhong, additional

Published
2019
Full Text
View/download PDF

34. Effects of Physical Damage in the Intermediate Phase on the Progression of Amyloid β Fibrillization.

Author

Tashiro, Ryu, Taguchi, Hiroaki, Hidaka, Kumi, Endo, Masayuki, and Sugiyama, Hiroshi

Subjects
AMYLOID, AMYLOID beta-protein, ATOMIC force microscopy, ALZHEIMER'S disease, CHEMICAL stability
Abstract

Understanding the mechanism responsible for the progression of amyloid deposition is important for developing methods to suppress this process in the treatment of Alzheimer's disease. The effects of physical damage during the transition phase of amyloid β fibril formation are unclear. In this study, we used high‐speed atomic force microscopy to investigate the effects of damage to the intermediates of amyloid β in real time. Physical damage to intermediates did not suppress, but instead promoted fibrillization. This progression was accompanied by morphological changes from globular oligomers to protofibrils. These results suggest that the properties of the intermediates, such as structural fragility and stability, are highly related to the rate of fibrillization. [ABSTRACT FROM AUTHOR]

Published
2019
Full Text
View/download PDF

35. DNA Origami Scaffolds as Templates for Functional Tetrameric Kir3 K+ Channels

Author

Kurokawa, Tatsuki, primary, Kiyonaka, Shigeki, additional, Nakata, Eiji, additional, Endo, Masayuki, additional, Koyama, Shohei, additional, Mori, Emiko, additional, Tran, Nam Ha, additional, Dinh, Huyen, additional, Suzuki, Yuki, additional, Hidaka, Kumi, additional, Kawata, Masaaki, additional, Sato, Chikara, additional, Sugiyama, Hiroshi, additional, Morii, Takashi, additional, and Mori, Yasuo, additional

Published
2018
Full Text
View/download PDF

37. Visualization of dynamic conformational switching of the G-quadruplex in a DNA nanostructure

Author

Sannohe, Yuta, Endo, Masayuki, Katsuda, Yousuke, Hidaka, Kumi, and Sugiyama, Hiroshi

Subjects
Atomic force microscopy -- Usage, DNA -- Structure, DNA -- Chemical properties, Potassium -- Atomic properties, Potassium -- Chemical properties, Chemistry
Abstract

The real-time observation of G-quadruplex formation is presented by monitoring the G-quadruplex-induced global change of two duplexes incorporated in a DNA nanoscaffold. The G-rich strands have formed an interstrand (3+1) G-quadruplex structure in the presence of [K.sup.+] and the conformational changes are visualized in a nanoscaffold in real-time with fast-scanning atomic force microscopy.

Published
2010

38. Regulation of DNA methylation using different tensions of double strands constructed in a defined DNA nanostructure

Author

Endo, Masayuki, Katsuda, Yousuke, Hidaka, Kumi, and Sugiyama, Hiroshi

Subjects
DNA -- Structure, DNA -- Chemical properties, Methylation -- Analysis, Methyltransferases -- Chemical properties, Methyltransferases -- Structure, Chemistry
Abstract

A nanoscale DNA scaffold was designed and utilized to develop a new strategy for regulation of an enzymatic DNA modification reaction. The results indicated that the structurally controlled double-strand DNAs constructed in the DNA frame nanostructure could be used to regulate the DNA methylation.

Published
2010

39. DNA prism structures constructed by folding of multiple rectangular arms

Author

Endo, Masayuki, Hidaka, Kumi, Kato, Takayuki, Namba, Keiichi, and Sugiyama, Hiroshi

Subjects
Atomic force microscopy -- Usage, DNA -- Structure, DNA -- Chemical properties, Chemistry
Abstract

Novel multiarm DNA structures are designed by using two-dimensional DNA origami scaffolds and these structures are folded into hollow three-dimensional (3D) structures by introducing connection strands into the arms. The opening of the prism structures is examined by high-speed AFM imaging, which has showed the dissociation of the connecting arms in the 3D structures.

Published
2009

40. Protein-driven RNA nanostructured devices that function in vitro and control mammalian cell fate

Author

Shibata, Tomonori, primary, Fujita, Yoshihiko, additional, Ohno, Hirohisa, additional, Suzuki, Yuki, additional, Hayashi, Karin, additional, Komatsu, Kaoru R., additional, Kawasaki, Shunsuke, additional, Hidaka, Kumi, additional, Yonehara, Shin, additional, Sugiyama, Hiroshi, additional, Endo, Masayuki, additional, and Saito, Hirohide, additional

Published
2017
Full Text
View/download PDF

44. Direct Observation of the Double‐Stranded DNA Formation through Metal Ion‐Mediated Base Pairing in the Nanoscale Structure.

Author

Xing, Xiwen, Feng, Yihong, Yu, Zutao, Hidaka, Kumi, Liu, Fenyong, Ono, Akira, Sugiyama, Hiroshi, and Endo, Masayuki

Subjects
BASE pairs, DNA nanotechnology, METAL ions, DISSOCIATION (Chemistry), ATOMIC force microscopy
Abstract

This work demonstrates single‐molecule imaging of metal‐ion induced double‐stranded DNA formation in DNA nanostructures. The formation of the metal ion‐mediated base pairing in a DNA origami frame was examined using C‐Ag‐C and T‐Hg‐T metallo‐base pairs. The target DNA strands containing consecutive C or T were incorporated into the DNA frame, and the binding was controlled by the addition of metal ions. Double‐stranded DNA formation was monitored by observing the structural changes in the incorporated DNA strands using high‐speed atomic force microscopy (AFM). Using the T‐Hg‐T base pair, the dynamic formation of unique dsDNA and its dissociation were observed. The formation of an unusual shape of dsDNA with consecutive T‐Hg‐T base pairs was visualized in the designed nanoscale structure. Single‐molecule imaging of the metal‐ion‐mediated formation of dsDNA in a DNA frame was demonstrated. By using two types of metallo‐base pairs C‐Ag‐C and T‐Hg‐T, formation of dsDNA from two consecutive C and T strands in the presence of metal ions was characterized. The dynamic formation of dsDNA using T‐Hg‐T was directly observed using high‐speed atomic force microscopy. [ABSTRACT FROM AUTHOR]

Published
2019
Full Text
View/download PDF

49. Optimal Arrangement of Four Short DNA Strands for Delivery of Immunostimulatory Nucleic Acids to Immune Cells

Author

Ohtsuki, Shozo, primary, Matsuzaki, Noriyuki, additional, Mohri, Kohta, additional, Endo, Masayuki, additional, Emura, Tomoko, additional, Hidaka, Kumi, additional, Sugiyama, Hiroshi, additional, Takahashi, Yuki, additional, Ishiyama, Kenichi, additional, Kadowaki, Norimitsu, additional, Takakura, Yoshinobu, additional, and Nishikawa, Makiya, additional

Published
2015
Full Text
View/download PDF

50. DNA Origami Scaffolds as Templates for Functional Tetrameric Kir3 K+ Channels.

Author

Kurokawa, Tatsuki, Kiyonaka, Shigeki, Nakata, Eiji, Endo, Masayuki, Koyama, Shohei, Mori, Emiko, Tran, Nam Ha, Dinh, Huyen, Suzuki, Yuki, Hidaka, Kumi, Kawata, Masaaki, Sato, Chikara, Sugiyama, Hiroshi, Morii, Takashi, and Mori, Yasuo

Subjects
DNA folding, METAL complexes, TISSUE scaffolds, MEMBRANE proteins, ZINC-finger proteins, ATOMIC force microscopy
Abstract

Abstract: In native systems, scaffolding proteins play important roles in assembling proteins into complexes to transduce signals. This concept is yet to be applied to the assembly of functional transmembrane protein complexes in artificial systems. To address this issue, DNA origami has the potential to serve as scaffolds that arrange proteins at specific positions in complexes. Herein, we report that Kir3 K+ channel proteins are assembled through zinc‐finger protein (ZFP)‐adaptors at specific locations on DNA origami scaffolds. Specific binding of the ZFP‐fused Kir3 channels and ZFP‐based adaptors on DNA origami were confirmed by atomic force microscopy and gel electrophoresis. Furthermore, the DNA origami with ZFP binding sites nearly tripled the K+ channel current activity elicited by heterotetrameric Kir3 channels in HEK293T cells. Thus, our method provides a useful template to control the oligomerization states of membrane protein complexes in vitro and in living cells. [ABSTRACT FROM AUTHOR]

Published
2018
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results