1
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Krishnamurthy K, Rajendran A, Nakata E, Morii T. Near Quantitative Ligation Results in Resistance of DNA Origami Against Nuclease and Cell Lysate. Small Methods 2024; 8:e2300999. [PMID: 37736703 DOI: 10.1002/smtd.202300999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Indexed: 09/23/2023]
Abstract
There have been limited efforts to ligate the staple nicks in DNA origami which is crucial for their stability against thermal and mechanical treatments, and chemical and biological environments. Here, two near quantitative ligation methods are demonstrated for the native backbone linkage at the nicks in origami: i) a cosolvent dimethyl sulfoxide (DMSO)-assisted enzymatic ligation and ii) enzyme-free chemical ligation by CNBr. Both methods achieved over 90% ligation in 2D origami, only CNBr-method resulted in ≈80% ligation in 3D origami, while the enzyme-alone yielded 31-55% (2D) or 22-36% (3D) ligation. Only CNBr-method worked efficiently for 3D origami. The CNBr-mediated reaction is completed within 5 min, while DMSO-method took overnight. Ligation by these methods improved the structural stability up to 30 °C, stability during the electrophoresis and subsequent extraction, and against nuclease and cell lysate. These methods are straightforward, non-tedious, and superior in terms of cost, reaction time, and efficiency.
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Affiliation(s)
| | - Arivazhagan Rajendran
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
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Zhang S, Nakata E, Lin P, Morii T. An Artificial Liposome Compartment with Size Exclusion Molecular Transport. Chemistry 2023; 29:e202302093. [PMID: 37668304 DOI: 10.1002/chem.202302093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/28/2023] [Accepted: 09/04/2023] [Indexed: 09/06/2023]
Abstract
The cellular compartment plays an essential role in organizing the complex and diverse biochemical reactions within the cell. By mimicking the function of such cellular compartments, the challenge of constructing artificial compartments has been taken up to develop new biochemical tools for efficient material production and diagnostics. The important features required for the artificial compartment are that it isolates the interior from the external environment and is further functionalized to control the transport of target chemicals to regulate the interior concentration of both substrate and reaction products. In this study, an artificial compartment with size-selective molecular transport function was constructed by using a DNA origami-guided liposome prepared by modifying the method reported by Perrault et al. This completely isolates the liposome interior, including the DNA origami skeleton, from the external environment and allows the assembly of a defined number of molecules of interest inside and/or outside the compartment. By incorporating a bacterial membrane protein, OmpF, into the liposome, the resulting artificial compartment was shown to transport only the molecule of interest with a molecular weight below 600 Da from the external environment into the interior of the compartment.
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Affiliation(s)
- Shiwei Zhang
- Institute of Advanced Energy, Kyoto University Uji, Kyoto, 6110011, Japan
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University Uji, Kyoto, 6110011, Japan
| | - Peng Lin
- Institute of Advanced Energy, Kyoto University Uji, Kyoto, 6110011, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University Uji, Kyoto, 6110011, Japan
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3
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Hirose H, Nakata E, Zhang Z, Shibano Y, Maekawa M, Morii T, Futaki S. Macropinoscope: Real-Time Simultaneous Tracking of pH and Cathepsin B Activity in Individual Macropinosomes. Anal Chem 2023. [PMID: 37468434 DOI: 10.1021/acs.analchem.3c01645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
A fluorescent sensor that allows simultaneous analysis of environmental factors in a limited cellular space is useful for understanding precise molecular interactions in live cells and their biological responses. Macropinocytosis is a ubiquitous endocytic pathway for massive uptake of extracellular fluids, resulting in the formation of macropinosomes. Although macropinocytosis may impact intracellular delivery and cancer proliferation, information on the intracellular behaviors of macropinosomes is limited. Here, we aimed to develop a macropinoscope, a sensor that simultaneously detects pH and cathepsin B activity in individual macropinosomes. A macropinosome-specific marker, dextran (70 kDa), was employed as a platform, onto which fluorescein, Oregon Green, and tetramethylrhodamine were loaded for ratiometric pH sensing and imaging. A cathepsin-B-cleavable peptide sequence bearing sulfo-Cy5 and the quencher BHQ-3 was also mounted; cleavage of the sequence was detected as an increase in sulfo-Cy5 fluorescence. A steep decrease in pH was observed 5-10 min after macropinosome formation, which was accompanied by an immediate increase in cathepsin B activity. Our design concept will lead to the development of other macropinoscopes for the simultaneous detection of other parameters in individual macropinosomes.
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Affiliation(s)
- Hisaaki Hirose
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Zhengxiao Zhang
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Yuya Shibano
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Masashi Maekawa
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Minato, Tokyo 105-8512, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Shiroh Futaki
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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4
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Konishi H, Nakata E, Komatsubara F, Morii T. Controlled Assembly of Fluorophores inside a Nanoliposome. Molecules 2023; 28:molecules28020911. [PMID: 36677968 PMCID: PMC9864194 DOI: 10.3390/molecules28020911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/13/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023]
Abstract
Cellular compartmentalization plays an essential role in organizing the complex and multiple biochemical reactions in the cell. An artificial compartment would provide powerful strategies to develop new biochemical tools for material production and diagnosis, but it is still a great challenge to synthesize the compartments that encapsulate materials of interest while controlling their accurate locations, numbers, and stoichiometry. In this study, we evaluated chemical characteristics of a liposome-encapsulated compartment, which has great potential to locate various materials of interest with precise control of their locations and numbers in the compartment. A nanoliposome was constructed inside a ring-shaped DNA origami skeleton according to the method of Yang et al., and further equipped with a double-stranded DNA platform to assemble molecules of interest in the nanoliposome. Upon formation of the nanoliposome, a pH-sensitive fluorophore on the bridged platform showed little or no response to the pH change of the outer buffer, ensuring that the molecules assembled on the platform are effectively shielded from the outer environment. The ring-shaped DNA skeleton equipped with a double-stranded DNA platform allows spatial assembly of several functional molecules inside the nanoliposome to isolate them from the outer environment.
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Nakata E, Dinh H, Lin P, Morii T. Enzyme Cascade Reactions on DNA Origami Scaffold. Methods Mol Biol 2023; 2639:275-299. [PMID: 37166723 DOI: 10.1007/978-1-0716-3028-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The protocols for constructing, characterizing, and analyzing enzyme cascade reaction systems on the DNA scaffold are described. Two-step and three-step enzyme cascade reactions were adapted from the xylose metabolic pathway as the example of natural metabolic pathway and were assembled on the DNA scaffold by using the DNA binding adaptors.
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Affiliation(s)
- Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Huyen Dinh
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Peng Lin
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan.
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Nakata E, Gerelbaatar K, Komatsubara F, Morii T. Stimuli-Responsible SNARF Derivatives as a Latent Ratiometric Fluorescent Probe. Molecules 2022; 27:molecules27217181. [PMID: 36364006 PMCID: PMC9658230 DOI: 10.3390/molecules27217181] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/09/2022] [Accepted: 10/17/2022] [Indexed: 11/23/2022] Open
Abstract
Fluorescence imaging is a powerful technique for continuous observation of dynamic intracellular processes of living cells. Fluorescent probes bearing a fluorescence switching property associated with a specific recognition or reaction of target biomolecule, that is, stimuli-responsibility, are important for fluorescence imaging. Thus, fluorescent probes continue to be developed to support approaches with different design strategies. When compared with simple intensity-changing fluorescent probes, ratiometric fluorescent probes typically offer the advantage of less sensitivity to errors associated with probe concentration, photobleaching, and environmental effects. For intracellular usage, ratiometric fluorescent probes based on small molecules must be loaded into the cells. Thus, probes having intrinsic fluorescence may obscure a change in intracellular signal if the background fluorescence of the remaining extracellular probes is high. To overcome such disadvantages, it is necessary to minimize the extracellular background fluorescence of fluorescent probes. Here, the design strategy of the latent ratiometric fluorescent probe for wash-free ratiometric imaging using a xanthene dye seminapthorhodafluor (SNARF) as the scaffold of fluorophore is discussed.
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Lin P, Yang H, Nakata E, Morii T. Mechanistic Aspects for the Modulation of Enzyme Reactions on the DNA Scaffold. Molecules 2022; 27:molecules27196309. [PMID: 36234845 PMCID: PMC9572797 DOI: 10.3390/molecules27196309] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 12/03/2022] Open
Abstract
Cells have developed intelligent systems to implement the complex and efficient enzyme cascade reactions via the strategies of organelles, bacterial microcompartments and enzyme complexes. The scaffolds such as the membrane or protein in the cell are believed to assist the co-localization of enzymes and enhance the enzymatic reactions. Inspired by nature, enzymes have been located on a wide variety of carriers, among which DNA scaffolds attract great interest for their programmability and addressability. Integrating these properties with the versatile DNA–protein conjugation methods enables the spatial arrangement of enzymes on the DNA scaffold with precise control over the interenzyme distance and enzyme stoichiometry. In this review, we survey the reactions of a single type of enzyme on the DNA scaffold and discuss the proposed mechanisms for the catalytic enhancement of DNA-scaffolded enzymes. We also review the current progress of enzyme cascade reactions on the DNA scaffold and discuss the factors enhancing the enzyme cascade reaction efficiency. This review highlights the mechanistic aspects for the modulation of enzymatic reactions on the DNA scaffold.
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Hiraga H, Machida R, Kawai A, Matsumoto Y, Yonemoto T, Nishida Y, Nagano A, Ae K, Yoshida S, Asanuma K, Toguchida J, Huruta D, Nakayama R, Akisue T, Hiruma T, Morii T, Tanaka K, Kataoka T, Fukuda H, Ozaki T. 1482O A phase III study comparing methotrexate (M), adriamycin (A) and cisplatin (P) with MAP + ifosfamide (MAP + IF) for the treatment of osteosarcoma: JCOG0905. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.1585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Zhang Z, Nakata E, Shibano Y, Morii T. FRET-based cathepsin probes for simultaneous detection of cathepsin B and D activities. Chembiochem 2022; 23:e202200319. [PMID: 35929606 DOI: 10.1002/cbic.202200319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/05/2022] [Indexed: 11/09/2022]
Abstract
Fluorescent cathepsin probes were prepared by modification of peptidic substrates for cathepsin B (CTSB) and cathepsin D (CTSD) with FRET pairs. Fluorophores with distinguishable emission characteristics were applied to CTSB and CTSD probes with their appropriate quenchers to simultaneously monitor the activity of CTSB and/or CTSD. Conjugation of both the CTSB and CTSD probes with short single-stranded DNA drastically increased their reactivity to cathepsins over the parent probes possibly by improving their solubility. The activity of CTSB and CTSD were simultaneously detected by using these orthogonal FRET-based cathepsin probes.
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Affiliation(s)
- Zhengxiao Zhang
- Kyoto University: Kyoto Daigaku, Institute of Advanced Energy, Gokasyo, 611-0011, Uji, JAPAN
| | - Eiji Nakata
- Kyoto University: Kyoto Daigaku, Institute of Advanced Energy, Gokasyo, 611-0011, Uji, JAPAN
| | - Yuya Shibano
- Kyoto University - Uji Campus: Kyoto Daigaku - Uji Campus, Institute of Advanced energy, Gokasyo, 6110011, Uji, JAPAN
| | - Takashi Morii
- Kyoto University: Kyoto Daigaku, Institute of Advanced Energy, Gokasyo, 611-0011, Uji, JAPAN
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Tajima S, Nakata E, Sakaguchi R, Saimura M, Mori Y, Morii T. A two-step screening to optimize the signal response of an auto-fluorescent protein-based biosensor. RSC Adv 2022; 12:15407-15419. [PMID: 35693243 PMCID: PMC9121230 DOI: 10.1039/d2ra02226e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/15/2022] [Indexed: 11/21/2022] Open
Abstract
Auto-fluorescent protein (AFP)-based biosensors transduce the structural change in their embedded recognition modules induced by recognition/reaction events to fluorescence signal changes of AFP. The lack of detailed structural information on the recognition module often makes it difficult to optimize AFP-based biosensors. To enhance the signal response derived from detecting the putative structural change in the nitric oxide (NO)-sensing segment of transient receptor potential canonical 5 (TRPC5) fused to enhanced green fluorescent protein (EGFP), EGFP-TRPC5, a facile two-step screening strategy, in silico first and in vitro second, was applied to variants of EGFP-TRPC5 deletion-mutated within the recognition module. In in silico screening, the structural changes of the recognition modules were evaluated as root-mean-square-deviation (RMSD) values, and 10 candidates were efficiently selected from 47 derivatives. Through in vitro screening, four mutants were identified that showed a larger change in signal response than the parent EGFP-TRPC5. One mutant in particular, 551-575, showed four times larger change upon reaction with NO and H2O2. Furthermore, mutant 551-575 also showed a signal response upon reaction with H2O2 in mammalian HEK293 cells, indicating that the mutant has the potential to be applied as a biosensor for cell measurement. Therefore, this two-step screening method effectively allows the selection of AFP-based biosensors with sufficiently enhanced signal responses for application in mammalian cells. A two-step screening procedure allows optimization of the optical response of an auto-fluorescent protein-based biosensor for nitric oxide without structural information.![]()
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Affiliation(s)
- Shunsuke Tajima
- Institute of Advanced Energy, Kyoto University Uji Kyoto 611-0011 Japan
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University Uji Kyoto 611-0011 Japan
| | - Reiko Sakaguchi
- School of Medicine, University of Occupational and Environmental Health 1-1 Iseigaoka, Yahatanishi-ku Kitakyushu Fukuoka 807-8555 Japan
| | - Masayuki Saimura
- Institute of Advanced Energy, Kyoto University Uji Kyoto 611-0011 Japan
| | - Yasuo Mori
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University Kyotodaigakukatsura, Nishikyo-ku Kyoto 615-8510 Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University Uji Kyoto 611-0011 Japan
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Rajendran A, Krishnamurthy K, Park S, Nakata E, Kwon Y, Morii T. Topologically‐Interlocked Minicircles as Probes of DNA Topology and DNA–Protein Interactions. Chemistry 2022; 28:e202200839. [DOI: 10.1002/chem.202200839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | | | - Seojeong Park
- College of Pharmacy Ewha Womans University Seoul 120-750 Republic of Korea
| | - Eiji Nakata
- Institute of Advanced Energy Kyoto University Uji Kyoto 611-0011 Japan
| | - Youngjoo Kwon
- College of Pharmacy Ewha Womans University Seoul 120-750 Republic of Korea
| | - Takashi Morii
- Institute of Advanced Energy Kyoto University Uji Kyoto 611-0011 Japan
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Rajendran A, Krishnamurthy K, Park S, Nakata E, Kwon Y, Morii T. Topologically‐Interlocked Minicircles as Probes of DNA Topology and DNA‐Protein Interactions. Chemistry 2022; 28:e202200108. [DOI: 10.1002/chem.202200108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Indexed: 12/30/2022]
Affiliation(s)
| | | | - Seojeong Park
- College of Pharmacy Ewha Womans University Seoul 120-750 Republic of Korea
| | - Eiji Nakata
- Institute of Advanced Energy Kyoto University Uji Kyoto, 611–0011 Japan
| | - Youngjoo Kwon
- College of Pharmacy Ewha Womans University Seoul 120-750 Republic of Korea
| | - Takashi Morii
- Institute of Advanced Energy Kyoto University Uji Kyoto, 611–0011 Japan
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Rajendran A, Krishnamurthy K, Park S, Nakata E, Kwon Y, Morii T. Front Cover: Topologically‐Interlocked Minicircles as Probes of DNA Topology and DNA‐Protein Interactions (Chem. Eur. J. 22/2022). Chemistry 2022. [DOI: 10.1002/chem.202200838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | | | - Seojeong Park
- College of Pharmacy Ewha Womans University Seoul 120-750 Republic of Korea
| | - Eiji Nakata
- Institute of Advanced Energy Kyoto University Uji Kyoto, 611–0011 Japan
| | - Youngjoo Kwon
- College of Pharmacy Ewha Womans University Seoul 120-750 Republic of Korea
| | - Takashi Morii
- Institute of Advanced Energy Kyoto University Uji Kyoto, 611–0011 Japan
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Zhang Z, Nakata E, Dinh H, Saimura M, Rajendran A, Matsuda K, Morii T. Tuning the Reactivity of a Substrate for SNAP-Tag Expands Its Application for Recognition-Driven DNA-Protein Conjugation. Chemistry 2021; 27:18118-18128. [PMID: 34747070 DOI: 10.1002/chem.202103304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Indexed: 11/09/2022]
Abstract
Recognition-driven modification has been emerging as a novel approach to modifying biomolecular targets of interest site-specifically and efficiently. To this end, protein modular adaptors (MAs) are the ideal reaction model for recognition-driven modification of DNA as they consist of both a sequence-specific DNA-binding domain (DBD) and a self-ligating protein-tag. Coupling DNA recognition by DBD and the chemoselective reaction of the protein tag could provide a highly efficient sequence-specific reaction. However, combining an MA consisting of a reactive protein-tag and its substrate, for example, SNAP-tag and benzyl guanine (BG), revealed rather nonselective reaction with DNA. Therefore new substrates of SNAP-tag have been designed to realize sequence-selective rapid crosslinking reactions of MAs with SNAP-tag. The reactions of substrates with SNAP-tag were verified by kinetic analyses to enable the sequence-selective crosslinking reaction of MA. The new substrate enables the distinctive orthogonality of SNAP-tag against CLIP-tag to achieve orthogonal DNA-protein crosslinking by six unique MAs.
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Affiliation(s)
- Zhengxiao Zhang
- Institute of Advanced Energy, Kyoto University Uji, Kyoto, 6110011, Japan
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University Uji, Kyoto, 6110011, Japan
| | - Huyen Dinh
- Institute of Advanced Energy, Kyoto University Uji, Kyoto, 6110011, Japan
| | - Masayuki Saimura
- Institute of Advanced Energy, Kyoto University Uji, Kyoto, 6110011, Japan
| | | | - Kazunari Matsuda
- Institute of Advanced Energy, Kyoto University Uji, Kyoto, 6110011, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University Uji, Kyoto, 6110011, Japan
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15
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Hara T, Takatsuka Y, Nakata E, Morii T. Augmentation of an Engineered Bacterial Strain Potentially Improves the Cleanup of PCB Water Pollution. Microbiol Spectr 2021; 9:e0192621. [PMID: 34937186 PMCID: PMC8694117 DOI: 10.1128/spectrum.01926-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 11/23/2021] [Indexed: 12/04/2022] Open
Abstract
Polychlorinated biphenyls (PCBs) are recalcitrant organohalide pollutants, consisting of 209 congeners. PCB cleanup in natural landscapes is expected to be achieved by the metabolic activity of microorganisms, but aerobic PCB-degrading bacteria that inhabit sites polluted by PCBs cannot degrade all PCB congeners due to the specificity of their enzymes. In this study, we investigated the degradability of PCBs when a genetically modified PCB-degrading bacterium was compounded with wild-type PCB-degrading bacteria. We used two bacterial strains, Comamonas testosteroni YAZ2 isolated from a PCB-uncontaminated natural landscape and Escherichia coli BL21(DE3) transformed with a biphenyl dioxygenase (BphA) gene from a well-known PCB degrader, Burkholderia xenovorans LB400. The enzymatic specificities of BphA were 2,3-dioxygenation in the YAZ2 and 2,3- and 3,4-dioxygenations in the recombinant E. coli. For the PCB-degrading experiment, a dedicated bioreactor capable of generating oxygen microbubbles was prototyped and used. The combined cells of the recombinant and the wild-type strains with an appropriate composite ratio degraded 40 mg/L of Kaneclor KC-300 to 0.3 ± 0.1 mg/L within 24 h. All of the health-toxic coplanar PCB congeners in KC-300 were degraded. This study suggested that the augmentation of an engineered bacterial strain could improve the cleanup of PCB water pollution. It also revealed the importance of the ratio of the strains with different PCB-degrading profiles to efficient degradation and that the application of oxygen microbubbles could rapidly accelerate the cleanup. IMPORTANCE PCB cleanup technique in a natural environment relies on the use of enzymes from microorganisms, primarily biphenyl dioxygenase and dehalogenase. Herein, we focused on biphenyl dioxygenase and created a recombinant PCB-degrading E. coli strain. Despite the development of environments for the field use of transgenic microbial strains around the world, verification of the applicability of transgenic microbial strains for PCB cleanup in the field has not yet been reported. We tentatively verified the extent to which degradability could be obtained by an augmentation model of a transgenic strain, the enzyme expression of which is easily regulated in rivers and lakes with PCB pollution. Our experiments used a dedicated bioreactor to model the natural landscape and produced results superior to those of bioremediation or biostimulation methods. The application of micro-nano bubbles, which has recently been discussed, to the cleanup of environmental pollution was also found to be useful in this study.
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Affiliation(s)
- Tomijiro Hara
- Environmental Microbiology Research Section, Laboratory for Complex Energy Processes, Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
| | - Yumiko Takatsuka
- Environmental Microbiology Research Section, Laboratory for Complex Energy Processes, Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
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16
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Lin P, Dinh H, Nakata E, Morii T. Conditional dependence of enzyme cascade reaction efficiency on the inter-enzyme distance. Chem Commun (Camb) 2021; 57:11197-11200. [PMID: 34622899 DOI: 10.1039/d1cc04162b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A dual-enzyme cascade, xylitol dehydrogenase and xylulose kinase, derived from the xylose metabolic pathway, was constructed on a three-dimensional DNA scaffold which exhibited a dynamic shape transition from an open state to a closed hexagonal prism. Evaluation of the cascade reaction efficiencies in the open and closed states revealed little to no inter-enzyme distance dependence, presumably due to the far larger catalytic constant of the downstream enzyme. The inter-enzyme distance was not the dominant factor for cascade efficiency when the kinetic parameters of the cascade enzymes were imbalanced with the highly efficient downstream enzyme.
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Affiliation(s)
- Peng Lin
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Huyen Dinh
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
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17
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Rajendran A, Krishnamurthy K, Giridasappa A, Nakata E, Morii T. Stabilization and structural changes of 2D DNA origami by enzymatic ligation. Nucleic Acids Res 2021; 49:7884-7900. [PMID: 34289063 PMCID: PMC8373134 DOI: 10.1093/nar/gkab611] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/16/2021] [Accepted: 07/06/2021] [Indexed: 12/15/2022] Open
Abstract
The low thermal stability of DNA nanostructures is the major drawback in their practical applications. Most of the DNA nanotubes/tiles and the DNA origami structures melt below 60°C due to the presence of discontinuities in the phosphate backbone (i.e., nicks) of the staple strands. In molecular biology, enzymatic ligation is commonly used to seal the nicks in the duplex DNA. However, in DNA nanotechnology, the ligation procedures are neither optimized for the DNA origami nor routinely applied to link the nicks in it. Here, we report a detailed analysis and optimization of the conditions for the enzymatic ligation of the staple strands in four types of 2D square lattice DNA origami. Our results indicated that the ligation takes overnight, efficient at 37°C rather than the usual 16°C or room temperature, and typically requires much higher concentration of T4 DNA ligase. Under the optimized conditions, up to 10 staples ligation with a maximum ligation efficiency of 55% was achieved. Also, the ligation is found to increase the thermal stability of the origami as low as 5°C to as high as 20°C, depending on the structure. Further, our studies indicated that the ligation of the staple strands influences the globular structure/planarity of the DNA origami, and the origami is more compact when the staples are ligated. The globular structure of the native and ligated origami was also found to be altered dynamically and progressively upon ethidium bromide intercalation in a concentration-dependent manner.
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Affiliation(s)
| | | | - Amulya Giridasappa
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
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18
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Lin P, Dinh H, Nakata E, Morii T. Dynamic Shape Transformation of a DNA Scaffold Applied for an Enzyme Nanocarrier. Front Chem 2021; 9:697857. [PMID: 34249866 PMCID: PMC8263910 DOI: 10.3389/fchem.2021.697857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/01/2021] [Indexed: 11/13/2022] Open
Abstract
Structural programmability and accurate addressability of DNA nanostructures are ideal characteristics for the platform of arranging enzymes with the nanoscale precision. In this study, a three-dimensional DNA scaffold was designed to enable a dynamic shape transition from an open plate-like structure to its closed state of a hexagonal prism structure. The two domains in the open state were folded together to transform into the closed state by hybridization of complementary short DNA closing keys at both of the facing edges in over 90% yield. The shape transformation of the DNA scaffold was extensively studied by means of the fluorescence energy transfer measurement, atomic force microscope images, and agarose gel electrophoretic analyses. A dimeric enzyme xylitol dehydrogenase was assembled on the DNA scaffold in its open state in a high-loading yield. The enzyme loaded on the scaffold was subsequently transformed to its closed state by the addition of short DNA closing keys. The enzyme encapsulated in the closed state displayed comparable activity to that in the open state, ensuring that the catalytic activity of the enzyme was well maintained in the DNA nanocarrier. The nanocarrier with efficient encapsulation ability is potentially applicable for drug delivery, biosensing, biocatalytic, and diagnostic tools.
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Affiliation(s)
- Peng Lin
- Institute of Advanced Energy, Kyoto University, Kyoto, Japan
| | - Huyen Dinh
- Institute of Advanced Energy, Kyoto University, Kyoto, Japan
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Kyoto, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Kyoto, Japan
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19
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Nakata E, Hirose H, Gerelbaatar K, Arafiles JVV, Zhang Z, Futaki S, Morii T. A facile combinatorial approach to construct a ratiometric fluorescent sensor: application for the real-time sensing of cellular pH changes. Chem Sci 2021; 12:8231-8240. [PMID: 34194714 PMCID: PMC8208317 DOI: 10.1039/d1sc01575c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/04/2021] [Indexed: 02/02/2023] Open
Abstract
Realtime monitoring of the cellular environment, such as the intracellular pH, in a defined cellular space provides a comprehensive understanding of the dynamics processes in a living cell. Considering the limitation of spatial resolution in conventional microscopy measurements, multiple types of fluorophores assembled within that space would behave as a single fluorescent probe molecule. Such a character of microscopic measurements enables a much more flexible combinatorial design strategy in developing fluorescent probes for given targets. Nanomaterials with sizes smaller than the microscopy spatial resolution provide a scaffold to assemble several types of fluorophores with a variety of optical characteristics, therefore providing a convenient strategy for designing fluorescent pH sensors. In this study, fluorescein (CF) and tetramethylrhodamine (CR) were assembled on a DNA nanostructure with controlling the number of each type of fluorophore. By taking advantage of the different responses of CF and CR emissions to the pH environment, an appropriate assembly of both CF and CR on DNA origami enabled a controlled intensity of fluorescence emission and ratiometric pH monitoring within the space defined by DNA origami. The CF and CR-assembled DNA origami was successfully applied for monitoring the intracellular pH changes.
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Affiliation(s)
- Eiji Nakata
- Institute of Advanced Energy, Kyoto University Kyoto Japan
| | - Hisaaki Hirose
- Institute for Chemical Research, Kyoto University Kyoto Japan
| | | | | | | | - Shiroh Futaki
- Institute for Chemical Research, Kyoto University Kyoto Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University Kyoto Japan
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20
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Marongiu L, Mingozzi F, Cigni C, Marzi R, Di Gioia M, Garrè M, Parazzoli D, Sironi L, Collini M, Sakaguchi R, Morii T, Crosti M, Moro M, Schurmans S, Catelani T, Rotem R, Colombo M, Shears S, Prosperi D, Zanoni I, Granucci F. Inositol 1,4,5-trisphosphate 3-kinase B promotes Ca 2+ mobilization and the inflammatory activity of dendritic cells. Sci Signal 2021; 14:14/676/eaaz2120. [PMID: 33785611 DOI: 10.1126/scisignal.aaz2120] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Innate immune responses to Gram-negative bacteria depend on the recognition of lipopolysaccharide (LPS) by a receptor complex that includes CD14 and TLR4. In dendritic cells (DCs), CD14 enhances the activation not only of TLR4 but also that of the NFAT family of transcription factors, which suppresses cell survival and promotes the production of inflammatory mediators. NFAT activation requires Ca2+ mobilization. In DCs, Ca2+ mobilization in response to LPS depends on phospholipase C γ2 (PLCγ2), which produces inositol 1,4,5-trisphosphate (IP3). Here, we showed that the IP3 receptor 3 (IP3R3) and ITPKB, a kinase that converts IP3 to inositol 1,3,4,5-tetrakisphosphate (IP4), were both necessary for Ca2+ mobilization and NFAT activation in mouse and human DCs. A pool of IP3R3 was located on the plasma membrane of DCs, where it colocalized with CD14 and ITPKB. Upon LPS binding to CD14, ITPKB was required for Ca2+ mobilization through plasma membrane-localized IP3R3 and for NFAT nuclear translocation. Pharmacological inhibition of ITPKB in mice reduced both LPS-induced tissue swelling and the severity of inflammatory arthritis to a similar extent as that induced by the inhibition of NFAT using nanoparticles that delivered an NFAT-inhibiting peptide specifically to phagocytic cells. Our results suggest that ITPKB may represent a promising target for anti-inflammatory therapies that aim to inhibit specific DC functions.
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Affiliation(s)
- Laura Marongiu
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Francesca Mingozzi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Clara Cigni
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Roberta Marzi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Marco Di Gioia
- Harvard Medical School and Division of Immunology, Division of Gastroenterology, Boston Children's Hospital, Boston, MA 02115, USA
| | | | | | - Laura Sironi
- Department of Physics, University of Milano-Bicocca, Piazza della Scienza 3, 20126 Milan, Italy
| | - Maddalena Collini
- Department of Physics, University of Milano-Bicocca, Piazza della Scienza 3, 20126 Milan, Italy
| | - Reiko Sakaguchi
- Institute for Integrated Cell-Material Sciences, Kyoto University Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Mariacristina Crosti
- INGM, Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", 20122 Milan, Italy
| | - Monica Moro
- INGM, Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", 20122 Milan, Italy
| | - Stéphane Schurmans
- Laboratory of Functional Genetics, GIGA-B34, University of Liège, 4000 Liège, Belgium
| | - Tiziano Catelani
- Piattaforma Interdipartimentale di Microscopia, University of Milano-Bicocca, Piazza della Scienza 3, 20126 Milan, Italy
| | - Rany Rotem
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Miriam Colombo
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Stephen Shears
- Signal Transduction Laboratory, NIEHS/NIH, 111 TW Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Davide Prosperi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Ivan Zanoni
- Harvard Medical School and Division of Immunology, Division of Gastroenterology, Boston Children's Hospital, Boston, MA 02115, USA.,Division of Immunology, Harvard Medical School, Boston Children's Hospital, Boston, MA 02115, USA
| | - Francesca Granucci
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy. .,INGM, Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", 20122 Milan, Italy
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21
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Lin P, Dinh H, Morita Y, Zhang Z, Nakata E, Kinoshita M, Morii T. Evaluation of the role of the DNA surface for enhancing the activity of scaffolded enzymes. Chem Commun (Camb) 2021; 57:3925-3928. [PMID: 33871490 DOI: 10.1039/d1cc00276g] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The catalytic enhancements of enzymes loaded on DNA nanostructures have been attributed to the characteristics provided by highly negative charges on the surface of the DNA scaffold, such as the modulation of the local pH near enzymes. In this study, two types of enzymes with optimal activity at pH 6 and 8 equally displayed significant catalytic enhancements on the DNA scaffold surface. By using a ratiometric pH indicator, a lower local pH shift of 0.8 was observed near the DNA scaffold surface. The postulated local pH change near the DNA scaffold surface is unlikely to play a general role in enhancing the activity of the scaffolded enzymes.
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Affiliation(s)
- Peng Lin
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Huyen Dinh
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Yuki Morita
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Zhengxiao Zhang
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Masahiro Kinoshita
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
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Furubayashi T, Ishida K, Nakata E, Morii T, Naruse K, Matsushita M, Fujiyoshi S. Cryogenic Far-Field Fluorescence Nanoscopy: Evaluation with DNA Origami. J Phys Chem B 2020; 124:7525-7536. [PMID: 32790384 DOI: 10.1021/acs.jpcb.0c04721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Far-field fluorescence localization nanoscopy of individual fluorophores at a temperature of 1.8 K was demonstrated using DNA origami as a one-nanometer-accurate scaffold. Red and near-infrared fluorophores were modified to the scaffold, and the fluorophores were 11 or 77 nm apart. We performed the localization nanoscopy of these two fluorophores at 1.8 K with a far-field fluorescence microscope. Under the cryogenic conditions, the fluorophores were perfectly immobilized and their photobleaching was drastically suppressed; consequently, the lateral spatial precision (a measure of reproducibility) was increased to 1 nm. However, the lateral spatial accuracy (a measure of trueness) remained tens of nanometers. We observed that the fluorophore centroids were laterally shifted as a function of the axial position. Because the orientation of the transition dipole of the fluorophores was fixed under cryogenic conditions, the anisotropic emission from the single fixed dipole had led to the lateral shift. This systematic error due to the dipole-orientation effect could be corrected by the three-dimensional localization of the individual fluorophores with spatial precisions of (lateral) 1 nm and (axial) 17 nm. In addition, the xy-error arising from the three-dimensional (3D) orientation of the scaffold with the two fluorophores 11 nm apart was estimated to be 0.3 nm. As a result, the individual fluorophores on the DNA origami were localized at the designed position, and the lateral spatial accuracy was quantified to be 4 nm in the standard error.
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Affiliation(s)
- Taku Furubayashi
- Department of Physics, Tokyo Institute of Technology, Meguro, Tokyo 152-8550, Japan
| | - Keita Ishida
- Department of Physics, Tokyo Institute of Technology, Meguro, Tokyo 152-8550, Japan
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Kanta Naruse
- Department of Physics, Tokyo Institute of Technology, Meguro, Tokyo 152-8550, Japan
| | - Michio Matsushita
- Department of Physics, Tokyo Institute of Technology, Meguro, Tokyo 152-8550, Japan
| | - Satoru Fujiyoshi
- Department of Physics, Tokyo Institute of Technology, Meguro, Tokyo 152-8550, Japan
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23
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Dinh H, Nakata E, Mutsuda-Zapater K, Saimura M, Kinoshita M, Morii T. Enhanced enzymatic activity exerted by a packed assembly of a single type of enzyme. Chem Sci 2020; 11:9088-9100. [PMID: 34094190 PMCID: PMC8161546 DOI: 10.1039/d0sc03498c] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 07/25/2020] [Indexed: 01/07/2023] Open
Abstract
In contrast to the dilute conditions employed for in vitro biochemical studies, enzymes are spatially organized at high density in cellular micro-compartments. In spite of being crucial for cellular functions, enzymatic reactions in such highly packed states have not been fully addressed. Here, we applied a protein adaptor to assemble a single type of monomeric enzyme on a DNA scaffold in the packed or dispersed states for carbonic anhydrase. The enzymatic reactions proceeded faster in the packed than in the dispersed state. Acceleration of the reaction in the packed assembly was more prominent for substrates with higher hydrophobicity. In addition, carbonic anhydrase is more tolerant of inhibitors in the packed assembly. Such an acceleration of the reaction in the packed state over the dispersed state was also observed for xylose reductase. We propose that the entropic force of water increases local substrate or cofactor concentration within the domain confined between enzyme surfaces, thus accelerating the reaction. Our system provides a reasonable model of enzymes in a packed state; this would help in engineering artificial metabolic systems.
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Affiliation(s)
- Huyen Dinh
- Institute of Advanced Energy, Kyoto University Uji Kyoto 611-0011 Japan
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University Uji Kyoto 611-0011 Japan
| | | | - Masayuki Saimura
- Institute of Advanced Energy, Kyoto University Uji Kyoto 611-0011 Japan
| | | | - Takashi Morii
- Institute of Advanced Energy, Kyoto University Uji Kyoto 611-0011 Japan
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24
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Nakano S, Konishi H, Morii T. Receptor-based fluorescent sensors constructed from ribonucleopeptide. Methods Enzymol 2020; 641:183-223. [PMID: 32713523 DOI: 10.1016/bs.mie.2020.04.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Receptor-based fluorescent sensors are the representative tool for quantitative detection of target ligands. The high substrate-selectivity originated from biomacromolecule receptor is one of the advantages of this tool, but a laborious trial and error is usually required to construct sensors showing satisfactory fluorescence intensity changes without diminishing the function of parent receptor. Ribonucleopeptide (RNP) provides a scaffold of fluorescent sensors to improve such issues. RNP receptors for the ligand of interest are constructed by applying in vitro selection for RNA-derived RNP library. Simple modification of the N-terminal of peptide in RNP by an appropriate fluorophore converts the RNP receptor into the fluorescent sensor with retaining the affinity and selectivity for the substrate. In this chapter, we introduce the protocols for construction of fluorescent RNP sensors through selection from a library of fluorophore-modified RNP complex or by a structure-based modular design. Furthermore, we describe the application of covalently linked RNP sensors for simultaneous detection of multiple ligands.
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Affiliation(s)
- Shun Nakano
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
| | - Hiroaki Konishi
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan.
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25
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Adachi I, Ahlburg P, Aihara H, Akopov N, Aloisio A, Anh Ky N, Asner DM, Atmacan H, Aushev T, Aushev V, Aziz T, Babu V, Baehr S, Bambade P, Banerjee S, Bansal V, Barrett M, Baudot J, Becker J, Behera PK, Bennett JV, Bernieri E, Bernlochner FU, Bertemes M, Bessner M, Bettarini S, Bianchi F, Biswas D, Bozek A, Bračko M, Branchini P, Briere RA, Browder TE, Budano A, Burmistrov L, Bussino S, Campajola M, Cao L, Casarosa G, Cecchi C, Červenkov D, Chang MC, Cheaib R, Chekelian V, Chen YQ, Chen YT, Cheon BG, Chilikin K, Cho K, Cho S, Choi SK, Choudhury S, Cinabro D, Corona L, Cremaldi LM, Cunliffe S, Czank T, Dattola F, De La Cruz-Burelo E, De Nardo G, De Nuccio M, De Pietro G, de Sangro R, Destefanis M, Dey S, De Yta-Hernandez A, Di Capua F, Doležal Z, Domínguez Jiménez I, Dong TV, Dort K, Dossett D, Dubey S, Duell S, Dujany G, Eidelman S, Eliachevitch M, Fast JE, Ferber T, Ferlewicz D, Finocchiaro G, Fiore S, Fodor A, Forti F, Fulsom BG, Ganiev E, Garcia-Hernandez M, Garg R, Gaur V, Gaz A, Gellrich A, Gemmler J, Geßler T, Giordano R, Giri A, Gobbo B, Godang R, Goldenzweig P, Golob B, Gomis P, Gradl W, Graziani E, Greenwald D, Guan Y, Hadjivasiliou C, Halder S, Hara T, Hartbrich O, Hayasaka K, Hayashii H, Hearty C, Hedges MT, Heredia de la Cruz I, Hernández Villanueva M, Hershenhorn A, Higuchi T, Hill EC, Hoek M, Hsu CL, Hu Y, Iijima T, Inami K, Inguglia G, Irakkathil Jabbar J, Ishikawa A, Itoh R, Iwasaki Y, Jacobs WW, Jaffe DE, Jang EJ, Jeon HB, Jia S, Jin Y, Joo C, Joo KK, Kahn J, Kakuno H, Kaliyar AB, Kandra J, Karyan G, Kato Y, Kawasaki T, Kim BH, Kim CH, Kim DY, Kim KH, Kim SH, Kim YK, Kim Y, Kimmel TD, Kindo H, Kleinwort C, Kodyš P, Koga T, Kohani S, Komarov I, Korpar S, Kovalchuk N, Kraetzschmar TMG, Križan P, Kroeger R, Krokovny P, Kuhr T, Kumar J, Kumar M, Kumar R, Kumara K, Kurz S, Kuzmin A, Kwon YJ, Lacaprara S, La Licata C, Lanceri L, Lange JS, Lautenbach K, Lee IS, Lee SC, Leitl P, Levit D, Li LK, Li YB, Libby J, Lieret K, Li Gioi L, Liptak Z, Liu QY, Liventsev D, Longo S, Luo T, Maeda Y, Maggiora M, Manoni E, Marcello S, Marinas C, Martini A, Masuda M, Matsuda T, Matsuoka K, Matvienko D, Meggendorfer F, Mei JC, Meier F, Merola M, Metzner F, Milesi M, Miller C, Miyabayashi K, Miyake H, Mizuk R, Azmi K, Mohanty GB, Moon T, Morii T, Moser HG, Mueller F, Müller FJ, Muller T, Muroyama G, Mussa R, Nakano E, Nakao M, Nayak M, Nazaryan G, Neverov D, Niebuhr C, Nisar NK, Nishida S, Nishimura K, Nishimura M, Oberhof B, Ogawa K, Onishchuk Y, Ono H, Onuki Y, Oskin P, Ozaki H, Pakhlov P, Pakhlova G, Paladino A, Panta A, Paoloni E, Park H, Paschen B, Passeri A, Pathak A, Paul S, Pedlar TK, Peruzzi I, Peschke R, Pestotnik R, Piccolo M, Piilonen LE, Popov V, Praz C, Prencipe E, Prim MT, Purohit MV, Rados P, Rasheed R, Reiter S, Remnev M, Resmi PK, Ripp-Baudot I, Ritter M, Rizzo G, Rizzuto LB, Robertson SH, Rodríguez Pérez D, Roney JM, Rosenfeld C, Rostomyan A, Rout N, Russo G, Sahoo D, Sakai Y, Sandilya S, Sangal A, Santelj L, Sartori P, Sato Y, Savinov V, Scavino B, Schueler J, Schwanda C, Seddon RM, Seino Y, Selce A, Senyo K, Sfienti C, Shen CP, Shiu JG, Shwartz B, Sibidanov A, Simon F, Sobie RJ, Soffer A, Sokolov A, Solovieva E, Spataro S, Spruck B, Starič M, Stefkova S, Stottler ZS, Stroili R, Strube J, Sumihama M, Sumiyoshi T, Summers DJ, Suzuki SY, Tabata M, Takizawa M, Tamponi U, Tanaka S, Tanida K, Taniguchi N, Taras P, Tenchini F, Torassa E, Trabelsi K, Tsuboyama T, Uchida M, Unger K, Unno Y, Uno S, Ushiroda Y, Vahsen SE, van Tonder R, Varner GS, Varvell KE, Vinokurova A, Vitale L, Vossen A, Wakai M, Wakeling HM, Wan Abdullah W, Wang CH, Wang MZ, Warburton A, Watanabe M, Webb J, Wehle S, Wessel C, Wiechczynski J, Windel H, Won E, Yabsley B, Yamada S, Yan W, Yang SB, Ye H, Yin JH, Yonenaga M, Yuan CZ, Yusa Y, Zani L, Zhang Z, Zhilich V, Zhou QD, Zhou XY, Zhukova VI. Search for an Invisibly Decaying Z^{'} Boson at Belle II in e^{+}e^{-}→μ^{+}μ^{-}(e^{±}μ^{∓}) Plus Missing Energy Final States. Phys Rev Lett 2020; 124:141801. [PMID: 32338980 DOI: 10.1103/physrevlett.124.141801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 02/24/2020] [Indexed: 06/11/2023]
Abstract
Theories beyond the standard model often predict the existence of an additional neutral boson, the Z^{'}. Using data collected by the Belle II experiment during 2018 at the SuperKEKB collider, we perform the first searches for the invisible decay of a Z^{'} in the process e^{+}e^{-}→μ^{+}μ^{-}Z^{'} and of a lepton-flavor-violating Z^{'} in e^{+}e^{-}→e^{±}μ^{∓}Z^{'}. We do not find any excess of events and set 90% credibility level upper limits on the cross sections of these processes. We translate the former, in the framework of an L_{μ}-L_{τ} theory, into upper limits on the Z^{'} coupling constant at the level of 5×10^{-2}-1 for M_{Z^{'}}≤6 GeV/c^{2}.
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Affiliation(s)
- I Adachi
- The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
| | | | - H Aihara
- Department of Physics, University of Tokyo, Tokyo 113-0033
| | - N Akopov
- Alikhanyan National Science Laboratory, Yerevan 0036
| | - A Aloisio
- INFN Sezione di Napoli, I-80126 Napoli
- Dipartimento di Scienze Fisiche, Università di Napoli Federico II, I-80126 Napoli
| | - N Anh Ky
- Institute of Theoretical and Applied Research (ITAR), Duy Tan University, Hanoi 100000, Vietnam
- Institute of Physics, Hanoi
| | - D M Asner
- Brookhaven National Laboratory, Upton, New York 11973
| | - H Atmacan
- University of Cincinnati, Cincinnati, Ohio 45221
| | - T Aushev
- Moscow Institute of Physics and Technology, Moscow Region 141700
| | - V Aushev
- Taras Shevchenko National Univ. of Kiev, Kiev
| | - T Aziz
- Tata Institute of Fundamental Research, Mumbai 400005
| | - V Babu
- Deutsches Elektronen-Synchrotron, 22607 Hamburg
| | - S Baehr
- Institut für Experimentelle Teilchenphysik, Karlsruher Institut für Technologie, 76131 Karlsruhe
| | - P Bambade
- Laboratoire de l'Accélérateur Linéaire, IN2P3/CNRS et Université Paris-Sud 11, Centre Scientifique d'Orsay, F-91898 Orsay Cedex
| | - Sw Banerjee
- University of Louisville, Louisville, Kentucky 40292
| | - V Bansal
- Pacific Northwest National Laboratory, Richland, Washington 99352
| | - M Barrett
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
| | - J Baudot
- Université de Strasbourg, CNRS, IPHC, UMR 7178, 67037 Strasbourg
| | - J Becker
- Institut für Experimentelle Teilchenphysik, Karlsruher Institut für Technologie, 76131 Karlsruhe
| | - P K Behera
- Indian Institute of Technology Madras, Chennai 600036
| | - J V Bennett
- University of Mississippi, University, Mississippi 38677
| | | | | | - M Bertemes
- Institute of High Energy Physics, Vienna 1050, Austria
| | - M Bessner
- University of Hawaii, Honolulu, Hawaii 96822
| | - S Bettarini
- INFN Sezione di Pisa, I-56127 Pisa
- Dipartimento di Fisica, Università di Pisa, I-56127 Pisa
| | - F Bianchi
- INFN Sezione di Torino, I-10125 Torino
- Dipartimento di Fisica, Università di Torino, I-10125 Torino
| | - D Biswas
- University of Louisville, Louisville, Kentucky 40292
| | - A Bozek
- H. Niewodniczanski Institute of Nuclear Physics, Krakow 31-342
| | - M Bračko
- J. Stefan Institute, 1000 Ljubljana
- University of Maribor, 2000 Maribor
| | | | - R A Briere
- Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - T E Browder
- University of Hawaii, Honolulu, Hawaii 96822
| | - A Budano
- INFN Sezione di Roma Tre, I-00146 Roma
| | - L Burmistrov
- Laboratoire de l'Accélérateur Linéaire, IN2P3/CNRS et Université Paris-Sud 11, Centre Scientifique d'Orsay, F-91898 Orsay Cedex
| | - S Bussino
- INFN Sezione di Roma Tre, I-00146 Roma
- Dipartimento di Matematica e Fisica, Università di Roma Tre, I-00146 Roma
| | - M Campajola
- INFN Sezione di Napoli, I-80126 Napoli
- Dipartimento di Scienze Fisiche, Università di Napoli Federico II, I-80126 Napoli
| | - L Cao
- University of Bonn, 53115 Bonn
| | - G Casarosa
- INFN Sezione di Pisa, I-56127 Pisa
- Dipartimento di Fisica, Università di Pisa, I-56127 Pisa
| | - C Cecchi
- INFN Sezione di Perugia, I-06123 Perugia
- Dipartimento di Fisica, Università di Perugia, I-06123 Perugia
| | - D Červenkov
- Faculty of Mathematics and Physics, Charles University, 121 16 Prague
| | - M-C Chang
- Department of Physics, Fu Jen Catholic University, Taipei 24205
| | - R Cheaib
- University of British Columbia, Vancouver, British Columbia, V6T 1Z1
| | - V Chekelian
- Max-Planck-Institut für Physik, 80805 München
| | - Y Q Chen
- University of Science and Technology of China, Hefei 230026
| | - Y-T Chen
- Department of Physics, National Taiwan University, Taipei 10617
| | - B G Cheon
- Department of Physics and Institute of Natural Sciences, Hanyang University, Seoul 04763
| | - K Chilikin
- P.N. Lebedev Physical Institute of the Russian Academy of Sciences, Moscow 119991
| | - K Cho
- Korea Institute of Science and Technology Information, Daejeon 34141
| | - S Cho
- Yonsei University, Seoul 03722
| | - S-K Choi
- Gyeongsang National University, Jinju 52828
| | - S Choudhury
- Indian Institute of Technology Hyderabad, Telangana 502285
| | - D Cinabro
- Wayne State University, Detroit, Michigan 48202
| | - L Corona
- INFN Sezione di Pisa, I-56127 Pisa
- Dipartimento di Fisica, Università di Pisa, I-56127 Pisa
| | - L M Cremaldi
- University of Mississippi, University, Mississippi 38677
| | - S Cunliffe
- Deutsches Elektronen-Synchrotron, 22607 Hamburg
| | - T Czank
- Kavli Institute for the Physics and Mathematics of the Universe (WPI), University of Tokyo, Kashiwa 277-8583
| | - F Dattola
- Deutsches Elektronen-Synchrotron, 22607 Hamburg
| | - E De La Cruz-Burelo
- Centro de Investigacion y de Estudios Avanzados del Instituto Politecnico Nacional, Mexico City 07360
| | - G De Nardo
- INFN Sezione di Napoli, I-80126 Napoli
- Dipartimento di Scienze Fisiche, Università di Napoli Federico II, I-80126 Napoli
| | - M De Nuccio
- Deutsches Elektronen-Synchrotron, 22607 Hamburg
| | - G De Pietro
- INFN Sezione di Roma Tre, I-00146 Roma
- Dipartimento di Matematica e Fisica, Università di Roma Tre, I-00146 Roma
| | - R de Sangro
- INFN Laboratori Nazionali di Frascati, I-00044 Frascati
| | - M Destefanis
- INFN Sezione di Torino, I-10125 Torino
- Dipartimento di Fisica, Università di Torino, I-10125 Torino
| | - S Dey
- Tel Aviv University, School of Physics and Astronomy, Tel Aviv, 69978
| | - A De Yta-Hernandez
- Centro de Investigacion y de Estudios Avanzados del Instituto Politecnico Nacional, Mexico City 07360
| | - F Di Capua
- INFN Sezione di Napoli, I-80126 Napoli
- Dipartimento di Scienze Fisiche, Università di Napoli Federico II, I-80126 Napoli
| | - Z Doležal
- Faculty of Mathematics and Physics, Charles University, 121 16 Prague
| | | | - T V Dong
- Key Laboratory of Nuclear Physics and Ion-beam Application (MOE) and Institute of Modern Physics, Fudan University, Shanghai 200443
| | - K Dort
- Justus-Liebig-Universität Gießen, 35392 Gießen
| | - D Dossett
- School of Physics, University of Melbourne, Victoria 3010
| | - S Dubey
- University of Hawaii, Honolulu, Hawaii 96822
| | - S Duell
- University of Bonn, 53115 Bonn
| | - G Dujany
- Université de Strasbourg, CNRS, IPHC, UMR 7178, 67037 Strasbourg
| | - S Eidelman
- Budker Institute of Nuclear Physics SB RAS, Novosibirsk 630090
- P.N. Lebedev Physical Institute of the Russian Academy of Sciences, Moscow 119991
- Novosibirsk State University, Novosibirsk 630090
| | | | - J E Fast
- Pacific Northwest National Laboratory, Richland, Washington 99352
| | - T Ferber
- Deutsches Elektronen-Synchrotron, 22607 Hamburg
| | - D Ferlewicz
- School of Physics, University of Melbourne, Victoria 3010
| | - G Finocchiaro
- INFN Laboratori Nazionali di Frascati, I-00044 Frascati
| | - S Fiore
- INFN Sezione di Roma, I-00185 Roma
| | - A Fodor
- McGill University, Montréal, Québec, H3A 2T8
| | - F Forti
- INFN Sezione di Pisa, I-56127 Pisa
- Dipartimento di Fisica, Università di Pisa, I-56127 Pisa
| | - B G Fulsom
- Pacific Northwest National Laboratory, Richland, Washington 99352
| | - E Ganiev
- INFN Sezione di Trieste, I-34127 Trieste
- Dipartimento di Fisica, Università di Trieste, I-34127 Trieste
| | - M Garcia-Hernandez
- Centro de Investigacion y de Estudios Avanzados del Instituto Politecnico Nacional, Mexico City 07360
| | - R Garg
- Panjab University, Chandigarh 160014
| | - V Gaur
- Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061
| | - A Gaz
- Graduate School of Science, Nagoya University, Nagoya 464-8602
- Kobayashi-Maskawa Institute, Nagoya University, Nagoya 464-8602
| | - A Gellrich
- Deutsches Elektronen-Synchrotron, 22607 Hamburg
| | - J Gemmler
- Institut für Experimentelle Teilchenphysik, Karlsruher Institut für Technologie, 76131 Karlsruhe
| | - T Geßler
- Justus-Liebig-Universität Gießen, 35392 Gießen
| | - R Giordano
- INFN Sezione di Napoli, I-80126 Napoli
- Dipartimento di Scienze Fisiche, Università di Napoli Federico II, I-80126 Napoli
| | - A Giri
- Indian Institute of Technology Hyderabad, Telangana 502285
| | - B Gobbo
- INFN Sezione di Trieste, I-34127 Trieste
| | - R Godang
- University of South Alabama, Mobile, Alabama 36688
| | - P Goldenzweig
- Institut für Experimentelle Teilchenphysik, Karlsruher Institut für Technologie, 76131 Karlsruhe
| | - B Golob
- J. Stefan Institute, 1000 Ljubljana
- Faculty of Mathematics and Physics, University of Ljubljana, 1000 Ljubljana
| | - P Gomis
- Instituto de Fisica Corpuscular, Paterna 46980
| | - W Gradl
- Johannes Gutenberg-Universität Mainz, Institut für Kernphysik, D-55099 Mainz
| | | | - D Greenwald
- Department of Physics, Technische Universität München, 85748 Garching
| | - Y Guan
- University of Cincinnati, Cincinnati, Ohio 45221
| | - C Hadjivasiliou
- Pacific Northwest National Laboratory, Richland, Washington 99352
| | - S Halder
- Tata Institute of Fundamental Research, Mumbai 400005
| | - T Hara
- The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
| | - O Hartbrich
- University of Hawaii, Honolulu, Hawaii 96822
| | | | | | - C Hearty
- Institute of Particle Physics (Canada), Victoria, British Columbia V8W 2Y2
- University of British Columbia, Vancouver, British Columbia, V6T 1Z1
| | - M T Hedges
- University of Hawaii, Honolulu, Hawaii 96822
| | - I Heredia de la Cruz
- Centro de Investigacion y de Estudios Avanzados del Instituto Politecnico Nacional, Mexico City 07360
- Consejo Nacional de Ciencia y Tecnología, Mexico City 03940
| | | | - A Hershenhorn
- University of British Columbia, Vancouver, British Columbia, V6T 1Z1
| | - T Higuchi
- Kavli Institute for the Physics and Mathematics of the Universe (WPI), University of Tokyo, Kashiwa 277-8583
| | - E C Hill
- University of British Columbia, Vancouver, British Columbia, V6T 1Z1
| | - M Hoek
- Johannes Gutenberg-Universität Mainz, Institut für Kernphysik, D-55099 Mainz
| | - C-L Hsu
- School of Physics, University of Sydney, New South Wales 2006
| | - Y Hu
- Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049
| | - T Iijima
- Graduate School of Science, Nagoya University, Nagoya 464-8602
- Kobayashi-Maskawa Institute, Nagoya University, Nagoya 464-8602
| | - K Inami
- Graduate School of Science, Nagoya University, Nagoya 464-8602
| | - G Inguglia
- Institute of High Energy Physics, Vienna 1050, Austria
| | - J Irakkathil Jabbar
- Institut für Experimentelle Teilchenphysik, Karlsruher Institut für Technologie, 76131 Karlsruhe
| | - A Ishikawa
- The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
| | - R Itoh
- The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
| | - Y Iwasaki
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
| | - W W Jacobs
- Indiana University, Bloomington, Indiana 47408
| | - D E Jaffe
- Brookhaven National Laboratory, Upton, New York 11973
| | - E-J Jang
- Gyeongsang National University, Jinju 52828
| | - H B Jeon
- Kyungpook National University, Daegu 41566
| | - S Jia
- Beihang University, Beijing 100191
| | - Y Jin
- INFN Sezione di Trieste, I-34127 Trieste
| | - C Joo
- Kavli Institute for the Physics and Mathematics of the Universe (WPI), University of Tokyo, Kashiwa 277-8583
| | - K K Joo
- Chonnam National University, Gwangju 61186
| | - J Kahn
- Institut für Experimentelle Teilchenphysik, Karlsruher Institut für Technologie, 76131 Karlsruhe
| | - H Kakuno
- Tokyo Metropolitan University, Tokyo 192-0397
| | - A B Kaliyar
- Tata Institute of Fundamental Research, Mumbai 400005
| | - J Kandra
- Faculty of Mathematics and Physics, Charles University, 121 16 Prague
| | - G Karyan
- Alikhanyan National Science Laboratory, Yerevan 0036
| | - Y Kato
- Graduate School of Science, Nagoya University, Nagoya 464-8602
- Kobayashi-Maskawa Institute, Nagoya University, Nagoya 464-8602
| | - T Kawasaki
- Kitasato University, Sagamihara 252-0373
| | - B H Kim
- Seoul National University, Seoul 08826
| | - C-H Kim
- Department of Physics and Institute of Natural Sciences, Hanyang University, Seoul 04763
| | - D Y Kim
- Soongsil University, Seoul 06978
| | - K-H Kim
- Yonsei University, Seoul 03722
| | - S-H Kim
- Department of Physics and Institute of Natural Sciences, Hanyang University, Seoul 04763
| | - Y K Kim
- Yonsei University, Seoul 03722
| | - Y Kim
- Korea University, Seoul 02841
| | - T D Kimmel
- Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061
| | - H Kindo
- The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
| | - C Kleinwort
- Deutsches Elektronen-Synchrotron, 22607 Hamburg
| | - P Kodyš
- Faculty of Mathematics and Physics, Charles University, 121 16 Prague
| | - T Koga
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
| | - S Kohani
- University of Hawaii, Honolulu, Hawaii 96822
| | - I Komarov
- Deutsches Elektronen-Synchrotron, 22607 Hamburg
| | - S Korpar
- J. Stefan Institute, 1000 Ljubljana
- University of Maribor, 2000 Maribor
| | - N Kovalchuk
- Deutsches Elektronen-Synchrotron, 22607 Hamburg
| | | | - P Križan
- J. Stefan Institute, 1000 Ljubljana
- Faculty of Mathematics and Physics, University of Ljubljana, 1000 Ljubljana
| | - R Kroeger
- University of Mississippi, University, Mississippi 38677
| | - P Krokovny
- Budker Institute of Nuclear Physics SB RAS, Novosibirsk 630090
- Novosibirsk State University, Novosibirsk 630090
| | - T Kuhr
- Ludwig Maximilians University, 80539 Munich
| | - J Kumar
- Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - M Kumar
- Malaviya National Institute of Technology Jaipur, Jaipur 302017
| | - R Kumar
- Punjab Agricultural University, Ludhiana 141004
| | - K Kumara
- Wayne State University, Detroit, Michigan 48202
| | - S Kurz
- Deutsches Elektronen-Synchrotron, 22607 Hamburg
| | - A Kuzmin
- Budker Institute of Nuclear Physics SB RAS, Novosibirsk 630090
- Novosibirsk State University, Novosibirsk 630090
| | | | | | - C La Licata
- Kavli Institute for the Physics and Mathematics of the Universe (WPI), University of Tokyo, Kashiwa 277-8583
| | - L Lanceri
- INFN Sezione di Trieste, I-34127 Trieste
| | - J S Lange
- Justus-Liebig-Universität Gießen, 35392 Gießen
| | | | - I-S Lee
- Department of Physics and Institute of Natural Sciences, Hanyang University, Seoul 04763
| | - S C Lee
- Kyungpook National University, Daegu 41566
| | - P Leitl
- Max-Planck-Institut für Physik, 80805 München
| | - D Levit
- Department of Physics, Technische Universität München, 85748 Garching
| | - L K Li
- University of Cincinnati, Cincinnati, Ohio 45221
| | - Y B Li
- Peking University, Beijing 100871
| | - J Libby
- Indian Institute of Technology Madras, Chennai 600036
| | - K Lieret
- Ludwig Maximilians University, 80539 Munich
| | - L Li Gioi
- Max-Planck-Institut für Physik, 80805 München
| | - Z Liptak
- University of Hawaii, Honolulu, Hawaii 96822
| | - Q Y Liu
- Key Laboratory of Nuclear Physics and Ion-beam Application (MOE) and Institute of Modern Physics, Fudan University, Shanghai 200443
| | - D Liventsev
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
- Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061
| | - S Longo
- University of Victoria, Victoria, British Columbia, V8W 3P6
| | - T Luo
- Key Laboratory of Nuclear Physics and Ion-beam Application (MOE) and Institute of Modern Physics, Fudan University, Shanghai 200443
| | - Y Maeda
- Graduate School of Science, Nagoya University, Nagoya 464-8602
- Kobayashi-Maskawa Institute, Nagoya University, Nagoya 464-8602
| | - M Maggiora
- INFN Sezione di Torino, I-10125 Torino
- Dipartimento di Fisica, Università di Torino, I-10125 Torino
| | - E Manoni
- INFN Sezione di Perugia, I-06123 Perugia
| | - S Marcello
- INFN Sezione di Torino, I-10125 Torino
- Dipartimento di Fisica, Università di Torino, I-10125 Torino
| | - C Marinas
- Instituto de Fisica Corpuscular, Paterna 46980
| | - A Martini
- INFN Sezione di Roma Tre, I-00146 Roma
- Dipartimento di Matematica e Fisica, Università di Roma Tre, I-00146 Roma
| | - M Masuda
- Earthquake Research Institute, University of Tokyo, Tokyo 113-0032
- Research Center for Nuclear Physics, Osaka University, Osaka 567-0047
| | - T Matsuda
- University of Miyazaki, Miyazaki 889-2192
| | - K Matsuoka
- Graduate School of Science, Nagoya University, Nagoya 464-8602
- Kobayashi-Maskawa Institute, Nagoya University, Nagoya 464-8602
| | - D Matvienko
- Budker Institute of Nuclear Physics SB RAS, Novosibirsk 630090
- P.N. Lebedev Physical Institute of the Russian Academy of Sciences, Moscow 119991
- Novosibirsk State University, Novosibirsk 630090
| | | | - J C Mei
- Key Laboratory of Nuclear Physics and Ion-beam Application (MOE) and Institute of Modern Physics, Fudan University, Shanghai 200443
| | - F Meier
- Duke University, Durham, North Carolina 27708
| | - M Merola
- INFN Sezione di Napoli, I-80126 Napoli
- Dipartimento di Scienze Fisiche, Università di Napoli Federico II, I-80126 Napoli
| | - F Metzner
- Institut für Experimentelle Teilchenphysik, Karlsruher Institut für Technologie, 76131 Karlsruhe
| | - M Milesi
- School of Physics, University of Melbourne, Victoria 3010
| | - C Miller
- University of Victoria, Victoria, British Columbia, V8W 3P6
| | | | - H Miyake
- The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
| | - R Mizuk
- P.N. Lebedev Physical Institute of the Russian Academy of Sciences, Moscow 119991
| | - K Azmi
- National Centre for Particle Physics, University Malaya, 50603 Kuala Lumpur
| | - G B Mohanty
- Tata Institute of Fundamental Research, Mumbai 400005
| | - T Moon
- Seoul National University, Seoul 08826
| | - T Morii
- Kavli Institute for the Physics and Mathematics of the Universe (WPI), University of Tokyo, Kashiwa 277-8583
| | - H-G Moser
- Max-Planck-Institut für Physik, 80805 München
| | - F Mueller
- Max-Planck-Institut für Physik, 80805 München
| | - F J Müller
- Deutsches Elektronen-Synchrotron, 22607 Hamburg
| | - Th Muller
- Institut für Experimentelle Teilchenphysik, Karlsruher Institut für Technologie, 76131 Karlsruhe
| | - G Muroyama
- Graduate School of Science, Nagoya University, Nagoya 464-8602
| | - R Mussa
- INFN Sezione di Torino, I-10125 Torino
| | - E Nakano
- Osaka City University, Osaka 558-8585
| | - M Nakao
- The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
| | - M Nayak
- Tel Aviv University, School of Physics and Astronomy, Tel Aviv, 69978
| | - G Nazaryan
- Alikhanyan National Science Laboratory, Yerevan 0036
| | - D Neverov
- Graduate School of Science, Nagoya University, Nagoya 464-8602
| | - C Niebuhr
- Deutsches Elektronen-Synchrotron, 22607 Hamburg
| | - N K Nisar
- University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - S Nishida
- The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
| | - K Nishimura
- University of Hawaii, Honolulu, Hawaii 96822
| | - M Nishimura
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
| | - B Oberhof
- INFN Laboratori Nazionali di Frascati, I-00044 Frascati
| | - K Ogawa
- Niigata University, Niigata 950-2181
| | - Y Onishchuk
- Taras Shevchenko National Univ. of Kiev, Kiev
| | - H Ono
- Niigata University, Niigata 950-2181
| | - Y Onuki
- Department of Physics, University of Tokyo, Tokyo 113-0033
| | - P Oskin
- P.N. Lebedev Physical Institute of the Russian Academy of Sciences, Moscow 119991
| | - H Ozaki
- The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
| | - P Pakhlov
- P.N. Lebedev Physical Institute of the Russian Academy of Sciences, Moscow 119991
- Moscow Physical Engineering Institute, Moscow 115409
| | - G Pakhlova
- P.N. Lebedev Physical Institute of the Russian Academy of Sciences, Moscow 119991
- Moscow Institute of Physics and Technology, Moscow Region 141700
| | - A Paladino
- INFN Sezione di Pisa, I-56127 Pisa
- Dipartimento di Fisica, Università di Pisa, I-56127 Pisa
| | - A Panta
- University of Mississippi, University, Mississippi 38677
| | - E Paoloni
- INFN Sezione di Pisa, I-56127 Pisa
- Dipartimento di Fisica, Università di Pisa, I-56127 Pisa
| | - H Park
- Kyungpook National University, Daegu 41566
| | | | - A Passeri
- INFN Sezione di Roma Tre, I-00146 Roma
| | - A Pathak
- University of Louisville, Louisville, Kentucky 40292
| | - S Paul
- Department of Physics, Technische Universität München, 85748 Garching
| | | | - I Peruzzi
- INFN Laboratori Nazionali di Frascati, I-00044 Frascati
| | - R Peschke
- University of Hawaii, Honolulu, Hawaii 96822
| | | | - M Piccolo
- INFN Laboratori Nazionali di Frascati, I-00044 Frascati
| | - L E Piilonen
- Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061
| | - V Popov
- P.N. Lebedev Physical Institute of the Russian Academy of Sciences, Moscow 119991
- Moscow Institute of Physics and Technology, Moscow Region 141700
| | - C Praz
- Deutsches Elektronen-Synchrotron, 22607 Hamburg
| | | | - M T Prim
- Institut für Experimentelle Teilchenphysik, Karlsruher Institut für Technologie, 76131 Karlsruhe
| | - M V Purohit
- Okinawa Institute of Science and Technology, Okinawa 904-0495
| | - P Rados
- Deutsches Elektronen-Synchrotron, 22607 Hamburg
| | - R Rasheed
- Université de Strasbourg, CNRS, IPHC, UMR 7178, 67037 Strasbourg
| | - S Reiter
- Justus-Liebig-Universität Gießen, 35392 Gießen
| | - M Remnev
- Budker Institute of Nuclear Physics SB RAS, Novosibirsk 630090
- P.N. Lebedev Physical Institute of the Russian Academy of Sciences, Moscow 119991
| | - P K Resmi
- Indian Institute of Technology Madras, Chennai 600036
| | - I Ripp-Baudot
- Université de Strasbourg, CNRS, IPHC, UMR 7178, 67037 Strasbourg
| | - M Ritter
- Ludwig Maximilians University, 80539 Munich
| | - G Rizzo
- INFN Sezione di Pisa, I-56127 Pisa
- Dipartimento di Fisica, Università di Pisa, I-56127 Pisa
| | | | - S H Robertson
- Institute of Particle Physics (Canada), Victoria, British Columbia V8W 2Y2
- McGill University, Montréal, Québec, H3A 2T8
| | | | - J M Roney
- Institute of Particle Physics (Canada), Victoria, British Columbia V8W 2Y2
- University of Victoria, Victoria, British Columbia, V8W 3P6
| | - C Rosenfeld
- University of South Carolina, Columbia, South Carolina 29208
| | - A Rostomyan
- Deutsches Elektronen-Synchrotron, 22607 Hamburg
| | - N Rout
- Indian Institute of Technology Madras, Chennai 600036
| | - G Russo
- INFN Sezione di Napoli, I-80126 Napoli
- Dipartimento di Scienze Fisiche, Università di Napoli Federico II, I-80126 Napoli
| | - D Sahoo
- Tata Institute of Fundamental Research, Mumbai 400005
| | - Y Sakai
- The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
| | - S Sandilya
- University of Cincinnati, Cincinnati, Ohio 45221
| | - A Sangal
- University of Cincinnati, Cincinnati, Ohio 45221
| | - L Santelj
- J. Stefan Institute, 1000 Ljubljana
- Faculty of Mathematics and Physics, University of Ljubljana, 1000 Ljubljana
| | - P Sartori
- INFN Sezione di Padova, I-35131 Padova
- Dipartimento di Fisica e Astronomia, Università di Padova, I-35131 Padova
| | - Y Sato
- Department of Physics, Tohoku University, Sendai 980-8578
| | - V Savinov
- University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - B Scavino
- Johannes Gutenberg-Universität Mainz, Institut für Kernphysik, D-55099 Mainz
| | - J Schueler
- University of Hawaii, Honolulu, Hawaii 96822
| | - C Schwanda
- Institute of High Energy Physics, Vienna 1050, Austria
| | - R M Seddon
- McGill University, Montréal, Québec, H3A 2T8
| | - Y Seino
- Niigata University, Niigata 950-2181
| | - A Selce
- INFN Sezione di Perugia, I-06123 Perugia
| | - K Senyo
- Yamagata University, Yamagata 990-8560
| | - C Sfienti
- Johannes Gutenberg-Universität Mainz, Institut für Kernphysik, D-55099 Mainz
| | - C P Shen
- Beihang University, Beijing 100191
| | - J-G Shiu
- Department of Physics, National Taiwan University, Taipei 10617
| | - B Shwartz
- Budker Institute of Nuclear Physics SB RAS, Novosibirsk 630090
- P.N. Lebedev Physical Institute of the Russian Academy of Sciences, Moscow 119991
| | - A Sibidanov
- University of Victoria, Victoria, British Columbia, V8W 3P6
| | - F Simon
- Max-Planck-Institut für Physik, 80805 München
| | - R J Sobie
- University of Victoria, Victoria, British Columbia, V8W 3P6
| | - A Soffer
- Tel Aviv University, School of Physics and Astronomy, Tel Aviv, 69978
| | - A Sokolov
- Institute for High Energy Physics, Protvino 142281
| | - E Solovieva
- P.N. Lebedev Physical Institute of the Russian Academy of Sciences, Moscow 119991
| | - S Spataro
- INFN Sezione di Torino, I-10125 Torino
- Dipartimento di Fisica, Università di Torino, I-10125 Torino
| | - B Spruck
- Johannes Gutenberg-Universität Mainz, Institut für Kernphysik, D-55099 Mainz
| | - M Starič
- J. Stefan Institute, 1000 Ljubljana
| | - S Stefkova
- Deutsches Elektronen-Synchrotron, 22607 Hamburg
| | - Z S Stottler
- Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061
| | - R Stroili
- INFN Sezione di Padova, I-35131 Padova
- Dipartimento di Fisica e Astronomia, Università di Padova, I-35131 Padova
| | - J Strube
- Pacific Northwest National Laboratory, Richland, Washington 99352
| | - M Sumihama
- Gifu University, Gifu 501-1193
- Research Center for Nuclear Physics, Osaka University, Osaka 567-0047
| | - T Sumiyoshi
- Tokyo Metropolitan University, Tokyo 192-0397
| | - D J Summers
- University of Mississippi, University, Mississippi 38677
| | - S Y Suzuki
- The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
| | - M Tabata
- Chiba University, Chiba 263-8522
| | - M Takizawa
- J-PARC Branch, KEK Theory Center, High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
- Theoretical Research Division, Nishina Center, RIKEN, Saitama 351-0198
- Showa Pharmaceutical University, Tokyo 194-8543
| | - U Tamponi
- INFN Sezione di Torino, I-10125 Torino
| | - S Tanaka
- The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
| | - K Tanida
- Advanced Science Research Center, Japan Atomic Energy Agency, Naka 319-1195
| | - N Taniguchi
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
| | - P Taras
- Université de Montréal, Physique des Particules, Montréal, Québec, H3C 3J7
| | - F Tenchini
- Deutsches Elektronen-Synchrotron, 22607 Hamburg
| | - E Torassa
- INFN Sezione di Padova, I-35131 Padova
| | - K Trabelsi
- Laboratoire de l'Accélérateur Linéaire, IN2P3/CNRS et Université Paris-Sud 11, Centre Scientifique d'Orsay, F-91898 Orsay Cedex
| | - T Tsuboyama
- The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
| | - M Uchida
- Tokyo Institute of Technology, Tokyo 152-8550
| | - K Unger
- Institut für Experimentelle Teilchenphysik, Karlsruher Institut für Technologie, 76131 Karlsruhe
| | - Y Unno
- Department of Physics and Institute of Natural Sciences, Hanyang University, Seoul 04763
| | - S Uno
- The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
| | - Y Ushiroda
- The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
- Department of Physics, University of Tokyo, Tokyo 113-0033
| | - S E Vahsen
- University of Hawaii, Honolulu, Hawaii 96822
| | | | - G S Varner
- University of Hawaii, Honolulu, Hawaii 96822
| | - K E Varvell
- School of Physics, University of Sydney, New South Wales 2006
| | - A Vinokurova
- Budker Institute of Nuclear Physics SB RAS, Novosibirsk 630090
- Novosibirsk State University, Novosibirsk 630090
| | - L Vitale
- INFN Sezione di Trieste, I-34127 Trieste
- Dipartimento di Fisica, Università di Trieste, I-34127 Trieste
| | - A Vossen
- Duke University, Durham, North Carolina 27708
| | - M Wakai
- University of British Columbia, Vancouver, British Columbia, V6T 1Z1
| | | | - W Wan Abdullah
- National Centre for Particle Physics, University Malaya, 50603 Kuala Lumpur
| | - C H Wang
- National United University, Miao Li 36003
| | - M-Z Wang
- Department of Physics, National Taiwan University, Taipei 10617
| | - A Warburton
- McGill University, Montréal, Québec, H3A 2T8
| | | | - J Webb
- School of Physics, University of Melbourne, Victoria 3010
| | - S Wehle
- Deutsches Elektronen-Synchrotron, 22607 Hamburg
| | | | | | - H Windel
- Max-Planck-Institut für Physik, 80805 München
| | - E Won
- Korea University, Seoul 02841
| | - B Yabsley
- School of Physics, University of Sydney, New South Wales 2006
| | - S Yamada
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
| | - W Yan
- University of Science and Technology of China, Hefei 230026
| | | | - H Ye
- Deutsches Elektronen-Synchrotron, 22607 Hamburg
| | - J H Yin
- Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049
| | - M Yonenaga
- Tokyo Metropolitan University, Tokyo 192-0397
| | - C Z Yuan
- Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049
| | - Y Yusa
- Niigata University, Niigata 950-2181
| | - L Zani
- INFN Sezione di Pisa, I-56127 Pisa
- Dipartimento di Fisica, Università di Pisa, I-56127 Pisa
| | - Z Zhang
- University of Science and Technology of China, Hefei 230026
| | - V Zhilich
- Budker Institute of Nuclear Physics SB RAS, Novosibirsk 630090
- Novosibirsk State University, Novosibirsk 630090
| | - Q D Zhou
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
| | - X Y Zhou
- Beihang University, Beijing 100191
| | - V I Zhukova
- P.N. Lebedev Physical Institute of the Russian Academy of Sciences, Moscow 119991
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26
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Tajima S, Nakata E, Sakaguchi R, Saimura M, Mori Y, Morii T. Fluorescence detection of the nitric oxide-induced structural change at the putative nitric oxide sensing segment of TRPC5. Bioorg Med Chem 2020; 28:115430. [DOI: 10.1016/j.bmc.2020.115430] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/04/2020] [Accepted: 03/06/2020] [Indexed: 12/18/2022]
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Abstract
DNA is an attractive molecular building block to construct nanoscale structures for a variety of applications. In addition to their structure and function, modification the DNA nanostructures by other molecules opens almost unlimited possibilities for producing functional DNA-based architectures. Among the molecules to functionalize DNA nanostructures, proteins are one of the most attractive candidates due to their vast functional variations. DNA nanostructures loaded with various types of proteins hold promise for applications in the life and material sciences. When loading proteins of interest on DNA nanostructures, the nanostructures by themselves act as scaffolds to specifically control the location and number of protein molecules. The methods to arrange proteins of interest on DNA scaffolds at high yields while retaining their activity are still the most demanding task in constructing usable protein-modified DNA nanostructures. Here, we provide an overview of the existing methods applied for assembling proteins of interest on DNA scaffolds. The assembling methods were categorized into two main classes, noncovalent and covalent conjugation, with both showing pros and cons. The recent advance of DNA-binding adaptor mediated assembly of proteins on the DNA scaffolds is highlighted and discussed in connection with the future perspectives of protein assembled DNA nanoarchitectures.
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Affiliation(s)
- Tien Anh Ngo
- Vinmec Biobank, Hi-tech Center, Vinmec Healthcare System, 458 Minh Khai, Ha Noi, Vietnam
| | - Huyen Dinh
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Thang Minh Nguyen
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Fong Fong Liew
- MAHSA University, Faculty of Dentistry, Bandar Saujana Putra, 42610 Jenjarom, Selangor, Malaysia
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
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28
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Nguyen TM, Nakata E, Zhang Z, Saimura M, Dinh H, Morii T. Rational design of a DNA sequence-specific modular protein tag by tuning the alkylation kinetics. Chem Sci 2019; 10:9315-9325. [PMID: 32110294 PMCID: PMC7006624 DOI: 10.1039/c9sc02990g] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 08/19/2019] [Indexed: 01/03/2023] Open
Abstract
Sequence-selective chemical modification of DNA by synthetic ligands has been a long-standing challenge in the field of chemistry. Even when the ligand consists of a sequence-specific DNA binding domain and reactive group, sequence-selective reactions by these ligands are often accompanied by off-target reactions. A basic principle to design DNA modifiers that react at specific sites exclusively governed by DNA sequence recognition remains to be established. We have previously reported selective DNA modification by a self-ligating protein tag conjugated with a DNA-binding domain, termed as a modular adaptor, and orthogonal application of modular adaptors by relying on the chemoselectivity of the protein tag. The sequence-specific crosslinking reaction by the modular adaptor is thought to proceed in two steps: the first step involves the formation of a DNA-protein complex, while in the second step, a proximity-driven intermolecular crosslinking occurs. According to this scheme, the specific crosslinking reaction of a modular adaptor would be driven by the DNA recognition process only when the dissociation rate of the DNA complex is much higher than the rate constant for the alkylation reaction. In this study, as a proof of principle, a set of combinations for modular adaptors and their substrates were utilized to evaluate the reactions. Three types of modular adaptors consisting of a single type of self-ligating tag and three types of DNA binding proteins fulfill the kinetic requirements for the reaction of the self-ligating tag with a substrate and the dissociation of the DNA-protein complex. These modular adaptors actually undergo sequence-specific crosslinking reactions exclusively driven by the recognition of a specific DNA sequence. The design principle of sequence-specific modular adaptors based on the kinetic aspects of complex formation and chemical modification is applicable for developing recognition-driven selective modifiers for proteins and other biological macromolecules.
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Affiliation(s)
- Thang Minh Nguyen
- Institute of Advanced Energy , Kyoto University , Uji , Kyoto 611-0011 , Japan .
| | - Eiji Nakata
- Institute of Advanced Energy , Kyoto University , Uji , Kyoto 611-0011 , Japan .
| | - Zhengxiao Zhang
- Institute of Advanced Energy , Kyoto University , Uji , Kyoto 611-0011 , Japan .
| | - Masayuki Saimura
- Institute of Advanced Energy , Kyoto University , Uji , Kyoto 611-0011 , Japan .
| | - Huyen Dinh
- Institute of Advanced Energy , Kyoto University , Uji , Kyoto 611-0011 , Japan .
| | - Takashi Morii
- Institute of Advanced Energy , Kyoto University , Uji , Kyoto 611-0011 , Japan .
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29
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Furubayashi T, Ishida K, Kashida H, Nakata E, Morii T, Matsushita M, Fujiyoshi S. Nanometer Accuracy in Cryogenic Far-Field Localization Microscopy of Individual Molecules. J Phys Chem Lett 2019; 10:5841-5846. [PMID: 31525978 DOI: 10.1021/acs.jpclett.9b02184] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We demonstrate the nanometer accuracy of far-field fluorescence localization microscopy at a temperature of 1.8 K using near-infrared and red fluorophores bonded to double-stranded DNA molecules (10.2 nm length). Although each fluorophore was localized with a 1 nm lateral precision by acquiring an image at one axial position within the focal depth of ±0.7 μm, the distance between the two fluorophores on the lateral plane (Dxy) was distributed from 0 to 50 nm. This systematic error was mainly due to detecting with the large focal depth the dipole emission from orientationally fixed fluorophores. Each fluorophore was localized with precisions of ±1 nm (lateral) and simultaneously ±11 nm (axial) by acquiring images every 100 nm in the axial direction from -900 to 900 nm. By correcting the dipole orientation effects, the distribution of Dxy was centered around the DNA length. The average and standard deviation of Dxy were 10 and 5 nm.
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Affiliation(s)
- Taku Furubayashi
- Department of Physics , Tokyo Institute of Technology , Meguro , Tokyo 152-8550 , Japan
| | - Keita Ishida
- Department of Physics , Tokyo Institute of Technology , Meguro , Tokyo 152-8550 , Japan
| | - Hiromu Kashida
- Graduate School of Engineering , Nagoya University , Chikusa, Nagoya 464-8603 , Japan
| | - Eiji Nakata
- Institute of Advanced Energy , Kyoto University , Uji , Kyoto 611-0011 , Japan
| | - Takashi Morii
- Institute of Advanced Energy , Kyoto University , Uji , Kyoto 611-0011 , Japan
| | - Michio Matsushita
- Department of Physics , Tokyo Institute of Technology , Meguro , Tokyo 152-8550 , Japan
| | - Satoru Fujiyoshi
- Department of Physics , Tokyo Institute of Technology , Meguro , Tokyo 152-8550 , Japan
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30
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Polat OK, Uno M, Maruyama T, Tran HN, Imamura K, Wong CF, Sakaguchi R, Ariyoshi M, Itsuki K, Ichikawa J, Morii T, Shirakawa M, Inoue R, Asanuma K, Reiser J, Tochio H, Mori Y, Mori MX. Contribution of Coiled-Coil Assembly to Ca 2+/Calmodulin-Dependent Inactivation of TRPC6 Channel and its Impacts on FSGS-Associated Phenotypes. J Am Soc Nephrol 2019; 30:1587-1603. [PMID: 31266820 DOI: 10.1681/asn.2018070756] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 04/23/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND TRPC6 is a nonselective cation channel, and mutations of this gene are associated with FSGS. These mutations are associated with TRPC6 current amplitude amplification and/or delay of the channel inactivation (gain-of-function phenotype). However, the mechanism of the gain-of-function in TRPC6 activity has not yet been clearly solved. METHODS We performed electrophysiologic, biochemical, and biophysical experiments to elucidate the molecular mechanism underlying calmodulin (CaM)-mediated Ca2+-dependent inactivation (CDI) of TRPC6. To address the pathophysiologic contribution of CDI, we assessed the actin filament organization in cultured mouse podocytes. RESULTS Both lobes of CaM helped induce CDI. Moreover, CaM binding to the TRPC6 CaM-binding domain (CBD) was Ca2+-dependent and exhibited a 1:2 (CaM/CBD) stoichiometry. The TRPC6 coiled-coil assembly, which brought two CBDs into adequate proximity, was essential for CDI. Deletion of the coiled-coil slowed CDI of TRPC6, indicating that the coiled-coil assembly configures both lobes of CaM binding on two CBDs to induce normal CDI. The FSGS-associated TRPC6 mutations within the coiled-coil severely delayed CDI and often increased TRPC6 current amplitudes. In cultured mouse podocytes, FSGS-associated channels and CaM mutations led to sustained Ca2+ elevations and a disorganized cytoskeleton. CONCLUSIONS The gain-of-function mechanism found in FSGS-causing mutations in TRPC6 can be explained by impairments of the CDI, caused by disruptions of TRPC's coiled-coil assembly which is essential for CaM binding. The resulting excess Ca2+ may contribute to structural damage in the podocytes.
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Affiliation(s)
- Onur K Polat
- Laboratory of Molecular Biology, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering
| | - Masatoshi Uno
- Department of Biophysics, Graduate School of Science.,Department of Molecular Engineering, Graduate School of Engineering
| | - Terukazu Maruyama
- Laboratory of Molecular Biology, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering
| | - Ha Nam Tran
- Laboratory of Molecular Biology, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering.,Department of Technology and Ecology, Laboratory of Environmental Systems Biology, Graduate School of Global Environmental Studies
| | - Kayo Imamura
- Department of Biophysics, Graduate School of Science
| | - Chee Fah Wong
- Laboratory of Molecular Biology, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering.,Department of Biology, Faculty of Science and Mathematics, Universiti Pendidikan Sultan Idris, Perak, Malaysia
| | - Reiko Sakaguchi
- Laboratory of Molecular Biology, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering.,Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, Japan
| | - Mariko Ariyoshi
- Department of Molecular Engineering, Graduate School of Engineering
| | - Kyohei Itsuki
- Department of Physiology, Fukuoka University School of Medicine, Fukuoka, Japan
| | - Jun Ichikawa
- Department of Physiology, Fukuoka University School of Medicine, Fukuoka, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Kyoto, Japan
| | | | - Ryuji Inoue
- Department of Physiology, Fukuoka University School of Medicine, Fukuoka, Japan
| | - Katsuhiko Asanuma
- Department of Nephrology, School of Medicine, Chiba University, Chiba, Japan
| | - Jochen Reiser
- Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois
| | | | - Yasuo Mori
- Laboratory of Molecular Biology, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering
| | - Masayuki X Mori
- Laboratory of Molecular Biology, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering,
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31
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Nakano S, Shimizu M, Dinh H, Morii T. Highly selective dual sensing of ATP and ADP using fluorescent ribonucleopeptide sensors. Chem Commun (Camb) 2019; 55:1611-1614. [PMID: 30657140 DOI: 10.1039/c8cc09934k] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Highly selective fluorescent sensors for ATP and ADP were constructed from RNA aptamers by applying a modular design of a ribonucleopeptide scaffold. These sensors allow facile and quantitative detection of ATP and ADP simultaneously in a solution and enable monitoring of the time-course changes of ATP and ADP concentrations in an enzymatic reaction.
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Affiliation(s)
- Shun Nakano
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
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32
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Abstract
DNA nanostructures serve as the ideal scaffolds to assemble materials of interest. Among these, proteins are of particularly interesting class of molecules to assemble because of their huge functional variability. Sequence-specific DNA binding proteins have been applied as adaptors to stably locate the fused proteins at defined positions of DNA scaffold in high loading yields. The strategy allows to control the number of enzyme molecules and to maintain the catalytic activity. By fusing a chemoselective self-ligating protein tag to the DNA binding protein, the modular adaptors formed covalent bonds at respective sequences on DNA scaffold with fast reaction kinetics. Application of a set of orthogonal modular adaptors enables spatial organization of multiple types of enzymes.
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Affiliation(s)
- Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
| | - Huyen Dinh
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
| | | | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan.
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33
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Kawamoto-Ozaki Y, Kotani N, Nakatsuka R, Morii T, Okada T. 1pB_MT4What is High-speed AFM? ~Visualize nano-world!!~. Microscopy (Oxf) 2018. [DOI: 10.1093/jmicro/dfy051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - Norito Kotani
- Research Institute of Biomolecule Metrology Co., Ltd., Tsukuba
| | - Ryo Nakatsuka
- Research Institute of Biomolecule Metrology Co., Ltd., Tsukuba
| | - Takashi Morii
- Research Institute of Biomolecule Metrology Co., Ltd., Tsukuba
| | - Takao Okada
- Research Institute of Biomolecule Metrology Co., Ltd., Tsukuba
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34
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Kurokawa T, Kiyonaka S, Nakata E, Endo M, Koyama S, Mori E, Tran NH, Dinh H, Suzuki Y, Hidaka K, Kawata M, Sato C, Sugiyama H, Morii T, Mori Y. DNA Origami Scaffolds as Templates for Functional Tetrameric Kir3 K +
Channels. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201709982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Tatsuki Kurokawa
- Department of Synthetic Chemistry and Biological Chemistry; Graduate School of Engineering; Kyoto University, Kyotodaigakukatsura, Nishikyo-ku; Kyoto 615-8510 Japan
- Core Research for Evolutional Science and Technology (Japan); Science and Technology Agency; 4-1-8 Hon-cho, Kawaguchi Saitama 332-0012 Japan
| | - Shigeki Kiyonaka
- Department of Synthetic Chemistry and Biological Chemistry; Graduate School of Engineering; Kyoto University, Kyotodaigakukatsura, Nishikyo-ku; Kyoto 615-8510 Japan
- Core Research for Evolutional Science and Technology (Japan); Science and Technology Agency; 4-1-8 Hon-cho, Kawaguchi Saitama 332-0012 Japan
- Department of Technology and Ecology, Hall of Global Environmental Studies; Kyoto University, Kyotodaigakukatsura, Nishikyo-ku; Kyoto 615-8510 Japan
| | - Eiji Nakata
- Core Research for Evolutional Science and Technology (Japan); Science and Technology Agency; 4-1-8 Hon-cho, Kawaguchi Saitama 332-0012 Japan
- Institute of Advanced Energy; Kyoto University, Gokasho, Uji; Kyoto 611-0011 Japan
| | - Masayuki Endo
- Core Research for Evolutional Science and Technology (Japan); Science and Technology Agency; 4-1-8 Hon-cho, Kawaguchi Saitama 332-0012 Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS); Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku; Kyoto 606-8501 Japan
| | - Shohei Koyama
- Department of Synthetic Chemistry and Biological Chemistry; Graduate School of Engineering; Kyoto University, Kyotodaigakukatsura, Nishikyo-ku; Kyoto 615-8510 Japan
| | - Emiko Mori
- Department of Synthetic Chemistry and Biological Chemistry; Graduate School of Engineering; Kyoto University, Kyotodaigakukatsura, Nishikyo-ku; Kyoto 615-8510 Japan
- Core Research for Evolutional Science and Technology (Japan); Science and Technology Agency; 4-1-8 Hon-cho, Kawaguchi Saitama 332-0012 Japan
| | - Nam Ha Tran
- Department of Technology and Ecology, Hall of Global Environmental Studies; Kyoto University, Kyotodaigakukatsura, Nishikyo-ku; Kyoto 615-8510 Japan
| | - Huyen Dinh
- Institute of Advanced Energy; Kyoto University, Gokasho, Uji; Kyoto 611-0011 Japan
| | - Yuki Suzuki
- Core Research for Evolutional Science and Technology (Japan); Science and Technology Agency; 4-1-8 Hon-cho, Kawaguchi Saitama 332-0012 Japan
- Department of Chemistry; Graduate School of Science; Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku; Kyoto 606-8502 Japan
| | - Kumi Hidaka
- Department of Chemistry; Graduate School of Science; Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku; Kyoto 606-8502 Japan
| | - Masaaki Kawata
- Biomedical Research Institute; National Institute of Advanced Industrial Science and Technology; 1-1-1 Higashi, Tsukuba Ibaraki 305-8566 Japan
| | - Chikara Sato
- Biomedical Research Institute; National Institute of Advanced Industrial Science and Technology; 1-1-1 Higashi, Tsukuba Ibaraki 305-8566 Japan
| | - Hiroshi Sugiyama
- Core Research for Evolutional Science and Technology (Japan); Science and Technology Agency; 4-1-8 Hon-cho, Kawaguchi Saitama 332-0012 Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS); Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku; Kyoto 606-8501 Japan
- Department of Chemistry; Graduate School of Science; Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku; Kyoto 606-8502 Japan
| | - Takashi Morii
- Core Research for Evolutional Science and Technology (Japan); Science and Technology Agency; 4-1-8 Hon-cho, Kawaguchi Saitama 332-0012 Japan
- Institute of Advanced Energy; Kyoto University, Gokasho, Uji; Kyoto 611-0011 Japan
| | - Yasuo Mori
- Department of Synthetic Chemistry and Biological Chemistry; Graduate School of Engineering; Kyoto University, Kyotodaigakukatsura, Nishikyo-ku; Kyoto 615-8510 Japan
- Core Research for Evolutional Science and Technology (Japan); Science and Technology Agency; 4-1-8 Hon-cho, Kawaguchi Saitama 332-0012 Japan
- Department of Technology and Ecology, Hall of Global Environmental Studies; Kyoto University, Kyotodaigakukatsura, Nishikyo-ku; Kyoto 615-8510 Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS); Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku; Kyoto 606-8501 Japan
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35
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Kurokawa T, Kiyonaka S, Nakata E, Endo M, Koyama S, Mori E, Tran NH, Dinh H, Suzuki Y, Hidaka K, Kawata M, Sato C, Sugiyama H, Morii T, Mori Y. DNA Origami Scaffolds as Templates for Functional Tetrameric Kir3 K + Channels. Angew Chem Int Ed Engl 2018; 57:2586-2591. [PMID: 29341462 DOI: 10.1002/anie.201709982] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/15/2017] [Indexed: 01/17/2023]
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.
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Affiliation(s)
- Tatsuki Kurokawa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyotodaigakukatsura, Nishikyo-ku, Kyoto, 615-8510, Japan.,Core Research for Evolutional Science and Technology (Japan), Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi, Saitama, 332-0012, Japan
| | - Shigeki Kiyonaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyotodaigakukatsura, Nishikyo-ku, Kyoto, 615-8510, Japan.,Core Research for Evolutional Science and Technology (Japan), Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi, Saitama, 332-0012, Japan.,Department of Technology and Ecology, Hall of Global Environmental Studies, Kyoto University, Kyotodaigakukatsura, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Eiji Nakata
- Core Research for Evolutional Science and Technology (Japan), Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi, Saitama, 332-0012, Japan.,Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Masayuki Endo
- Core Research for Evolutional Science and Technology (Japan), Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi, Saitama, 332-0012, Japan.,Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Shohei Koyama
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyotodaigakukatsura, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Emiko Mori
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyotodaigakukatsura, Nishikyo-ku, Kyoto, 615-8510, Japan.,Core Research for Evolutional Science and Technology (Japan), Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi, Saitama, 332-0012, Japan
| | - Nam Ha Tran
- Department of Technology and Ecology, Hall of Global Environmental Studies, Kyoto University, Kyotodaigakukatsura, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Huyen Dinh
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Yuki Suzuki
- Core Research for Evolutional Science and Technology (Japan), Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi, Saitama, 332-0012, Japan.,Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Masaaki Kawata
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Chikara Sato
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Hiroshi Sugiyama
- Core Research for Evolutional Science and Technology (Japan), Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi, Saitama, 332-0012, Japan.,Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto, 606-8501, Japan.,Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Takashi Morii
- Core Research for Evolutional Science and Technology (Japan), Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi, Saitama, 332-0012, Japan.,Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Yasuo Mori
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyotodaigakukatsura, Nishikyo-ku, Kyoto, 615-8510, Japan.,Core Research for Evolutional Science and Technology (Japan), Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi, Saitama, 332-0012, Japan.,Department of Technology and Ecology, Hall of Global Environmental Studies, Kyoto University, Kyotodaigakukatsura, Nishikyo-ku, Kyoto, 615-8510, Japan.,Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto, 606-8501, Japan
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36
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Affiliation(s)
- Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011
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37
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Park Y, Nim-Anussornkul D, Vilaivan T, Morii T, Kim BH. Facile conversion of ATP-binding RNA aptamer to quencher-free molecular aptamer beacon. Bioorg Med Chem Lett 2017; 28:77-80. [PMID: 29248297 DOI: 10.1016/j.bmcl.2017.12.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 11/23/2017] [Accepted: 12/05/2017] [Indexed: 01/02/2023]
Abstract
We have developed RNA-based quencher-free molecular aptamer beacons (RNA-based QF-MABs) for the detection of ATP, taking advantage of the conformational changes associated with ATP binding to the ATP-binding RNA aptamer. The RNA aptamer, with its well-defined structure, was readily converted to the fluorescence sensors by incorporating a fluorophore into the loop region of the hairpin structure. These RNA-based QF-MABs exhibited fluorescence signals in the presence of ATP relative to their low background signals in the absence of ATP. The fluorescence emission intensity increased upon formation of a RNA-based QF-MAB·ATP complex.
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Affiliation(s)
- Yoojin Park
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | | | - Tirayut Vilaivan
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Byeang Hyean Kim
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea.
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38
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Nakano S, Tamura T, Das RK, Nakata E, Chang YT, Morii T. A Diversity-Oriented Library of Fluorophore-Modified Receptors Constructed from a Chemical Library of Synthetic Fluorophores. Chembiochem 2017; 18:2212-2216. [PMID: 28879678 DOI: 10.1002/cbic.201700403] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Indexed: 12/16/2022]
Abstract
The practical application of biosensors can be determined by evaluating the sensing ability of fluorophore-modified derivatives of a receptor with appropriate recognition characteristics for target molecules. One of the key determinants for successfully obtaining a useful biosensor is wide variation in the fluorophores attached to a given receptor. Thus, using a larger fluorophore-modified receptor library provides a higher probability of obtaining a practically useful biosensor. However, no effective method has yet been developed for constructing such a diverse library of fluorophore-modified receptors. Herein, we report a method for constructing fluorophore-modified receptors by using a chemical library of synthetic fluorophores with a thiol-reactive group. This library was converted into a library of fluorophore-modified adenosine-binding ribonucleopeptide (RNP) receptors by introducing the fluorophores to the Rev peptide of the RNP complex by alkylation of the thiol group. This method enabled the construction of 263 fluorophore-modified ATP-binding RNP receptors and allowed the selection of suitable receptor-based fluorescent sensors that target ATP.
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Affiliation(s)
- Shun Nakano
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Tomoki Tamura
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Raj Kumar Das
- Bharat Petroleum Corporation Ltd., Corporate R&D Centre, Plot No. 2 A, Udyog Kendra, Surajpur Industrial Area, Greater Noida, 201 306, India
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Young-Tae Chang
- Department of Chemistry and MedChem Program of Life Sciences, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore.,Department of Chemistry, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Korea
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan
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39
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Nguyen TM, Nakata E, Saimura M, Dinh H, Morii T. Design of Modular Protein Tags for Orthogonal Covalent Bond Formation at Specific DNA Sequences. J Am Chem Soc 2017; 139:8487-8496. [PMID: 28521084 DOI: 10.1021/jacs.7b01640] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Simultaneous formation of specific covalent linkages at nucleotides in given DNA sequences demand distinct orthogonal reactivity of DNA modification agents. Such highly specific reactions require well-balanced reactivity and affinity of the DNA modification agents. Conjugation of a sequence-specific DNA binding zinc finger protein and a self-ligating protein tag provides a modular adaptor that expedites formation of a covalent bond between the protein tag and a substrate-modified nucleotide at a specific DNA sequence. The modular adaptor stably locates a protein of interest fused to it at the target position on DNA scaffold in its functional form. Modular adaptors with orthogonal selectivity and fast reaction kinetics to specific DNA sequences enable site-specific location of different protein molecules simultaneously. Three different modular adaptors consisting of zinc finger proteins with distinct DNA sequence specificities and self-ligating protein tags with different substrate specificities achieved orthogonal covalent bond formation at respective sequences on the same DNA scaffold with an overall coassembly yield over 90%. Application of this unique set of orthogonal modular adaptors enabled construction of a cascade reaction of three enzymes from xylose metabolic pathway on DNA scaffold.
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Affiliation(s)
- Thang Minh Nguyen
- Institute of Advanced Energy, Kyoto University , Uji, Kyoto 611-0011, Japan
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University , Uji, Kyoto 611-0011, Japan
| | - Masayuki Saimura
- Institute of Advanced Energy, Kyoto University , Uji, Kyoto 611-0011, Japan
| | - Huyen Dinh
- Institute of Advanced Energy, Kyoto University , Uji, Kyoto 611-0011, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University , Uji, Kyoto 611-0011, Japan
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40
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Affiliation(s)
| | - Eiji Nakata
- Institute of Advanced Energy; Kyoto University; Uji Kyoto 611-0011 Japan
| | - Shun Nakano
- Institute of Advanced Energy; Kyoto University; Uji Kyoto 611-0011 Japan
| | - Takashi Morii
- Institute of Advanced Energy; Kyoto University; Uji Kyoto 611-0011 Japan
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41
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Tamura T, Nakano S, Nakata E, Morii T. Construction of a library of structurally diverse ribonucleopeptides with catalytic groups. Bioorg Med Chem 2017; 25:1881-1888. [PMID: 28223024 DOI: 10.1016/j.bmc.2017.02.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 01/31/2017] [Accepted: 02/03/2017] [Indexed: 01/20/2023]
Abstract
Functional screening of structurally diverse libraries consisting of proteins or nucleic acids is an effective method to obtain receptors or aptamers with unique molecular recognition characteristics. However, further modification of these selected receptors to exert a newly desired function is still a challenging task. We have constructed a library of structurally diverse ribonucleopeptides (RNPs) that are modified with a catalytic group, in which the catalytic group aligns with various orientations against the ATP binding pocket of RNA subunit. As a proof-of-principle, the screening of the constructed RNP library for the catalytic reaction of ester hydrolysis was successfully carried out. The size of both the substrate-binding RNA library and the catalytic group modified peptide library are independently expandable, and thus, the size of RNPs library could be enlarged by a combination of these two subunits. We anticipate that the library of functionalized and structurally diverse RNPs would be expanded for various other catalytic reactions.
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Affiliation(s)
- Tomoki Tamura
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Shun Nakano
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
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42
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Kotani N, Kumaresan R, Kawamoto-Ozaki Y, Morii T, Okada T. High-Speed AFM Reveals Advanced Details on Dynamic Behavior of Antibody. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.3159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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43
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Nakata E, Yukimachi Y, Uto Y, Hori H, Morii T. Latent pH-responsive ratiometric fluorescent cluster based on self-assembled photoactivated SNARF derivatives. Sci Technol Adv Mater 2016; 17:431-436. [PMID: 27877893 PMCID: PMC5101900 DOI: 10.1080/14686996.2016.1204888] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 06/16/2016] [Accepted: 06/19/2016] [Indexed: 05/23/2023]
Abstract
We have developed a self-assembled fluorescent cluster comprising a seminaphthorhodafluor (SNARF) derivative protected by a photoremovable o-nitrobenzyl group. Prior to UV irradiation, a colorless and nonfluorescent cluster was spontaneously assembled in aqueous solution. After UV irradiation, the self-assembled cluster remained intact and showed a large enhancement in pH-responsive fluorescence. The unique pH responsive fluorescent cluster could be used as a dual-emissive ratiometric fluorescent pH probe not only in the test tube but also in HeLa cell cultures.
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Affiliation(s)
- Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
| | - Yoshihiro Yukimachi
- Department of Life System, Institute of Technology and Science, Graduate School, The University of Tokushima, Tokushima, Japan
| | - Yoshihiro Uto
- Department of Life System, Institute of Technology and Science, Graduate School, The University of Tokushima, Tokushima, Japan
| | - Hitoshi Hori
- Department of Life System, Institute of Technology and Science, Graduate School, The University of Tokushima, Tokushima, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
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Abstract
We report the construction of an artificial enzyme cascade based on the xylose metabolic pathway. Two enzymes, xylose reductase and xylitol dehydrogenase, were assembled at specific locations on DNA origami by using DNA-binding protein adaptors with systematic variations in the interenzyme distances and defined numbers of enzyme molecules. The reaction system, which localized the two enzymes in close proximity to facilitate transport of reaction intermediates, resulted in significantly higher yields of the conversion of xylose into xylulose through the intermediate xylitol with recycling of the cofactor NADH. Analysis of the initial reaction rate, regenerated amount of NADH, and simulation of the intermediates' diffusion indicated that the intermediates diffused to the second enzyme by Brownian motion. The efficiency of the cascade reaction with the bimolecular transport of xylitol and NAD(+) likely depends more on the interenzyme distance than that of the cascade reaction with unimolecular transport between two enzymes.
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Affiliation(s)
- Tien Anh Ngo
- Institute of Advanced Energy, Kyoto University , Uji, Kyoto 611-0011, Japan
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University , Uji, Kyoto 611-0011, Japan
| | - Masayuki Saimura
- Institute of Advanced Energy, Kyoto University , Uji, Kyoto 611-0011, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University , Uji, Kyoto 611-0011, Japan
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45
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Himuro Y, Miyagawa F, Fukumoto T, Morii T, Hasegawa M, Kobayashi N, Asada H. Hypersensitivity to influenza vaccine in a case of Epstein-Barr virus-associated T-lymphoproliferative disorder. Br J Dermatol 2015; 172:1686-1688. [DOI: 10.1111/bjd.13713] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Y. Himuro
- Department of Dermatology; Nara Medical University School of Medicine; 840 Shijo-cho Kashihara Nara 634-8522 Japan
| | - F. Miyagawa
- Department of Dermatology; Nara Medical University School of Medicine; 840 Shijo-cho Kashihara Nara 634-8522 Japan
| | - T. Fukumoto
- Department of Dermatology; Nara Medical University School of Medicine; 840 Shijo-cho Kashihara Nara 634-8522 Japan
| | - T. Morii
- Department of Hematology; Nara Medical University School of Medicine; 840 Shijo-cho Kashihara Nara 634-8522 Japan
| | - M. Hasegawa
- Department of Radiation Oncology; Nara Medical University School of Medicine; 840 Shijo-cho Kashihara Nara 634-8522 Japan
| | - N. Kobayashi
- Department of Dermatology; Nara Medical University School of Medicine; 840 Shijo-cho Kashihara Nara 634-8522 Japan
| | - H. Asada
- Department of Dermatology; Nara Medical University School of Medicine; 840 Shijo-cho Kashihara Nara 634-8522 Japan
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Nakata E, Nazumi Y, Yukimachi Y, Uto Y, Hori H, Morii T. Self-Assembled Fluorescent Nanoprobe for the Detection of Fluoride Ions in Aqueous Solutions. BCSJ 2015. [DOI: 10.1246/bcsj.20140303] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Eiji Nakata
- Institute of Advanced Energy, Kyoto University
| | - Yoshijiro Nazumi
- Department of Life Systems, Institute of Technology and Science, The University of Tokushima
| | - Yoshihiro Yukimachi
- Department of Life Systems, Institute of Technology and Science, The University of Tokushima
| | - Yoshihiro Uto
- Department of Life Systems, Institute of Technology and Science, The University of Tokushima
| | - Hitoshi Hori
- Department of Life Systems, Institute of Technology and Science, The University of Tokushima
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47
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Kotani N, Hirano T, Morii T, Okada T. High-Speed AFM Observation of Antibody IGG Characteristic of Swinging Arms. Biophys J 2015. [DOI: 10.1016/j.bpj.2014.11.2071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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48
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Nakata E, Dinh H, Ngo TA, Saimura M, Morii T. A modular zinc finger adaptor accelerates the covalent linkage of proteins at specific locations on DNA nanoscaffolds. Chem Commun (Camb) 2015; 51:1016-9. [DOI: 10.1039/c4cc08167f] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A modular adaptor assists efficient occupation of specific addresses on DNA nanostructures by proteins of interest through a covalent linkage.
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Affiliation(s)
- Eiji Nakata
- Institute of Advanced Energy
- Kyoto University
- Uji
- Japan
| | - Huyen Dinh
- Institute of Advanced Energy
- Kyoto University
- Uji
- Japan
| | - Tien Anh Ngo
- Institute of Advanced Energy
- Kyoto University
- Uji
- Japan
| | | | - Takashi Morii
- Institute of Advanced Energy
- Kyoto University
- Uji
- Japan
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49
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Inoue M, Kaida S, Nakano S, Annoni C, Nakata E, Konno T, Morii T. Phosphorylation regulates fibrillation of an aggregation core peptide in the second repeat of microtubule-binding domain of human tau. Bioorg Med Chem 2014; 22:6471-80. [DOI: 10.1016/j.bmc.2014.09.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 09/12/2014] [Accepted: 09/12/2014] [Indexed: 12/26/2022]
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Hori H, Tada R, Uto Y, Nakata E, Morii T, Masuda K. A neutron dynamic therapy with a boron tracedrug UTX-51 using a compact neutron generator. Anticancer Res 2014; 34:4557-4560. [PMID: 25075099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
BACKGROUND/AIM We are developing a neutron dynamic therapy (NDT) with boron tracedrugs for a new mechanical-clearance treatment of pathotoxic misfolded, aggregated, and self-propagating prion-associated disease proteins. We present a compact neutron generator-based NDT using a boron tracedrug UTX-51. Our NDT is based on the weak thermal neutron-bombarded destructive action of UTX-51 on bovine serum albumin (BSA) using the neutron beams produced from a compact inertial electrostatic confinement fusion (IECF) neutron generator. RESULTS BSA as an NDT molecular target was subjected to thermal neutron irradiation for eight hours using a compact neutron generator. The sodium dodecyl sulfate-polyacrylamide gel electrophoresis pattern showed no protein band when 2 nmoles of BSA were irradiated with more than 100 nmoles of UTX-51, while BSA was not affected when irradiated without UTX-51. CONCLUSION For the first time, we have succeeded in the molecular destruction of a prion-disease model protein, BSA, by NDT with a boron tracedrug, UTX-51, using a compact neutron generator.
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Affiliation(s)
- Hitoshi Hori
- Department of Life System, Institute of Technology and Science, Graduate School, The University of Tokushima, Tokushima, Japan
| | - Ryu Tada
- Department of Life System, Institute of Technology and Science, Graduate School, The University of Tokushima, Tokushima, Japan
| | - Yoshihiro Uto
- Department of Life System, Institute of Technology and Science, Graduate School, The University of Tokushima, Tokushima, Japan
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
| | - Kai Masuda
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
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