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Behnam MAM, Basché T, Klein CDP. 2,2'-Bithiophene as sensor tag for ligand-protein binding assays based on Förster resonance energy transfer. Anal Biochem 2023; 682:115335. [PMID: 37777080 DOI: 10.1016/j.ab.2023.115335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/15/2023] [Accepted: 09/27/2023] [Indexed: 10/02/2023]
Abstract
Ligand-protein binding assays based on intrinsic protein fluorescence are straightforward, inexpensive methods to study ligand-protein interactions. However, their applicability is limited to ligands that can interfere with protein emission. In this Note, we describe the applicability of 2,2'-bithiophene as a FRET-based sensor tag, that can be incorporated into high-affinity ligands to generate target-specific compounds able to quench protein fluorescence upon binding. The generated ligands were assessed in different assay designs. Considerations to account for possible sources of interference with the assay readout are addressed, besides interpretation of the obtained results.
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Affiliation(s)
- Mira A M Behnam
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Thomas Basché
- Department of Chemistry, Johannes Gutenberg-University, Mainz, Germany
| | - Christian D P Klein
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany.
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2
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Kamiya K, Kayama K, Nobuoka M, Sakaguchi S, Sakurai T, Kawata M, Tsutsui Y, Suda M, Idesaki A, Koshikawa H, Sugimoto M, Lakshmi GBVS, Avasthi DK, Seki S. Ubiquitous organic molecule-based free-standing nanowires with ultra-high aspect ratios. Nat Commun 2021; 12:4025. [PMID: 34188041 PMCID: PMC8241875 DOI: 10.1038/s41467-021-24335-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/08/2021] [Indexed: 11/08/2022] Open
Abstract
The critical dimension of semiconductor devices is approaching the single-nm regime, and a variety of practical devices of this scale are targeted for production. Planar structures of nano-devices are still the center of fabrication techniques, which limit further integration of devices into a chip. Extension into 3D space is a promising strategy for future; however, the surface interaction in 3D nanospace make it hard to integrate nanostructures with ultrahigh aspect ratios. Here we report a unique technique using high-energy charged particles to produce free-standing 1D organic nanostructures with high aspect ratios over 100 and controlled number density. Along the straight trajectory of particles penetrating the films of various sublimable organic molecules, 1D nanowires were formed with approximately 10~15 nm thickness and controlled length. An all-dry process was developed to isolate the nanowires, and planar or coaxial heterojunction structures were built into the nanowires. Electrical and structural functions of the developed standing nanowire arrays were investigated, demonstrating the potential of the present ultrathin organic nanowire systems.
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Affiliation(s)
- Koshi Kamiya
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Kazuto Kayama
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Masaki Nobuoka
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Shugo Sakaguchi
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Tsuneaki Sakurai
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan.
| | - Minori Kawata
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Yusuke Tsutsui
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Masayuki Suda
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Akira Idesaki
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology, Takasaki, Gunma, Japan
| | - Hiroshi Koshikawa
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology, Takasaki, Gunma, Japan
| | - Masaki Sugimoto
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology, Takasaki, Gunma, Japan
| | - G B V S Lakshmi
- Special Center for Nanoscience, Jawaharlal Nehru University, New Delhi, India
| | - D K Avasthi
- Department of Physics, School of Engineering, University of Petroleum and Energy Studies, Dehradun, India
| | - Shu Seki
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan.
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3
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Interactions of Single Particle with Organic Matters: A Facile Bottom-Up Approach to Low Dimensional Nanostructures. QUANTUM BEAM SCIENCE 2020. [DOI: 10.3390/qubs4010007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A particle induces a pack of chemical reactions in nanospace: chemical reactions confined into extremely small space provide an ultimate technique for the nanofabrication of organic matter with a variety of functions. Since the discovery of particle accelerators, an extremely high energy density can be deposited, even by a single isolated particle with MeV-ordered kinetic energy. However, this was considered to cause severe damages to organic molecules due to its relatively small bond energies, and lack of ability to control the reactions precisely to form the structures while retaining physico-chemical molecular functionalities. Practically, the severely damaged area along a particle trajectory: a core of a particle track has been simply visualized for the detection/dosimetry of an incident particle to the matters, or been removed to lead nanopores and functionalized by refilling/grafting of fresh organic/inorganic materials. The use of intra-track reactions in the so-called “penumbra” or “halo” area of functional organic materials has been realized and provided us with novel and facile protocols to provide low dimensional nano-materials with perfect size controllability in the 21st century. These protocols are now referred to as single particle nanofabrication technique (SPNT) and/or single particle triggered linear polymerization technique (STLiP), paving the way towards a new approach for nanomaterials with desired functionalities from original molecules. Herein, we report on the extremely wide applicability of SPNT/STLiP protocols for the future development of materials for opto-electronic, catalytic, and biological applications among others.
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Anantha-Iyengar G, Shanmugasundaram K, Nallal M, Lee KP, Whitcombe MJ, Lakshmi D, Sai-Anand G. Functionalized conjugated polymers for sensing and molecular imprinting applications. Prog Polym Sci 2019. [DOI: 10.1016/j.progpolymsci.2018.08.001] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Sakaguchi S, Sakurai T, Ma J, Sugimoto M, Yamaki T, Chiba A, Saito Y, Seki S. Conjugated Nanowire Sensors via High-Energy Single-Particle-Induced Linear Polymerization of 9,9'-Spirobi[9 H-fluorene] Derivatives. J Phys Chem B 2018; 122:8614-8623. [PMID: 30134093 DOI: 10.1021/acs.jpcb.8b06310] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nanostructures composed of conjugated polymers or π-conjugated molecules provide sensing platforms with large specific surface areas. One of the feasible approaches to accessing such nanostructured miniaturized sensors with ultrahigh sensitivity is to develop a network of organic nanowires with optical/electronic properties that can measure signals upon interacting with the analytes at their surfaces. In this work, organic nanowires with controlled number density and uniform length were fabricated by one-dimensional solid-state polymerization of 9,9'-spirobi[9 H-fluorene] (SBF) derivatives triggered by high-energy single particles. SBF was chosen as a conjugated molecular motif with the interplay of high density of π-electrons, high solubility, and uniform solid-state structures, allowing us to fabricate sensing platforms via solution processing. The as-deposited energy density in linear polymerization nanospace was theoretically analyzed by a collision model, interpreting nanowire sizes at subnanometer levels. The substitution of bromine atoms was confirmed to be effective not only for the higher collision probability of the incident particles but also for the remarkable increase in radiolytic neutral radical yield via C-Br cleavages or electron-dissociative attachments onto the bromine atoms. The fluorescence spectra of SBF-based nanowires were different from those of SBF derivatives due to extended bond formation as a result of polymerization reactions. Fluorescence was quenched by the addition of nitrobenzene, indicating the potential use of our nanowires for fluorometric sensing applications. Microwave-based conductivity measurements revealed that the SBF-based nanowires exhibited charge carrier transport property upon photoexcitation, and that the conductivity was changed upon treatment with nitrobenzene vapors. The presented strategy of bromination of aromatic rings for efficient fabrication of controlled nanowire networks with favorable fluorescent and charge transport properties of nanowires advances the development of nanostructured sensing systems.
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Affiliation(s)
- Shugo Sakaguchi
- Department of Molecular Engineering, Graduate School of Engineering , Kyoto University , Nishikyo-ku, Kyoto 615-8510 , Japan
| | - Tsuneaki Sakurai
- Department of Molecular Engineering, Graduate School of Engineering , Kyoto University , Nishikyo-ku, Kyoto 615-8510 , Japan
| | - Jun Ma
- Department of Molecular Engineering, Graduate School of Engineering , Kyoto University , Nishikyo-ku, Kyoto 615-8510 , Japan
| | - Masaki Sugimoto
- Takasaki Advanced Radiation Research Institute , National Institutes for Quantum and Radiological Science and Technology , Takasaki , Gunma 370-1292 , Japan
| | - Tetsuya Yamaki
- Takasaki Advanced Radiation Research Institute , National Institutes for Quantum and Radiological Science and Technology , Takasaki , Gunma 370-1292 , Japan
| | - Atsuya Chiba
- Takasaki Advanced Radiation Research Institute , National Institutes for Quantum and Radiological Science and Technology , Takasaki , Gunma 370-1292 , Japan
| | - Yuichi Saito
- Takasaki Advanced Radiation Research Institute , National Institutes for Quantum and Radiological Science and Technology , Takasaki , Gunma 370-1292 , Japan
| | - Shu Seki
- Department of Molecular Engineering, Graduate School of Engineering , Kyoto University , Nishikyo-ku, Kyoto 615-8510 , Japan
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Kulkarni B, Jayakannan M. Fluorescent-Tagged Biodegradable Polycaprolactone Block Copolymer FRET Probe for Intracellular Bioimaging in Cancer Cells. ACS Biomater Sci Eng 2017; 3:2185-2197. [DOI: 10.1021/acsbiomaterials.7b00426] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Bhagyashree Kulkarni
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
| | - Manickam Jayakannan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
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7
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Horio A, Sakurai T, Lakshmi GBVS, Kumar Avasthi D, Sugimoto M, Yamaki T, Seki S. Formation of nanowires via single particle-triggered linear polymerization of solid-state aromatic molecules. NANOSCALE 2016; 8:14925-14931. [PMID: 27355341 DOI: 10.1039/c6nr03297d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Nanowires occupy a prestigious place in nanoelectronics, nanomechanics, and biomimetics. Although there are notable methods to grow nanowires via self-assembly, there is a key drawback in the need to find out the specific conditions appropriate for each system. In this sense, universal techniques to fabricate such nanowires from various organic materials have been sought for the continued progress of the related research field. Here we report one of the promising and facile methodologies to quantitatively produce nanowires with controlled geometrical parameters. In this method, referred to as "Single Particle-Triggered Linear Polymerization (STLiP)", organic thin films on a supporting substrate were irradiated with high-energy charged particles, accelerated by particle accelerators. Each particle penetrates from the top of the films to the substrate while gradually releasing kinetic energy along its trajectory (ion track), generating reactive intermediates such as radical species that eventually induce propagation reactions. The resulting polymerized products were integrated into nanowires with uniform diameter and length that can be isolated via development with appropriate organic solvents. Considering the widely applicable nature of STLiP to organic materials, the present technique opens a new door for access to a number of functional nanowires and their assembly.
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Affiliation(s)
- Akifumi Horio
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan.
| | - Tsuneaki Sakurai
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan.
| | - G B V S Lakshmi
- Inter University Accelerator Centre, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Devesh Kumar Avasthi
- Inter University Accelerator Centre, Aruna Asaf Ali Marg, New Delhi 110067, India and Amity Institute of Nanotechnology, Amity University, Noida 201313, India
| | - Masaki Sugimoto
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology, 1233 Watanuki-machi, Takasaki, Gunma 370-1292, Japan
| | - Tetsuya Yamaki
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology, 1233 Watanuki-machi, Takasaki, Gunma 370-1292, Japan
| | - Shu Seki
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan.
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