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Kamei R, Hosomi T, Kanai M, Kanao E, Liu J, Takahashi T, Li W, Tanaka W, Nagashima K, Nakano K, Otsuka K, Kubo T, Yanagida T. Rational Strategy for Space-Confined Atomic Layer Deposition. ACS APPLIED MATERIALS & INTERFACES 2023; 15:23931-23937. [PMID: 37155349 DOI: 10.1021/acsami.3c01443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Atomic layer deposition (ALD) offers excellent controllability of spatial uniformity, film thickness at the Angstrom level, and film composition even for high-aspect-ratio nanostructured surfaces, which are rarely attainable by other conventional deposition methodologies. Although ALD has been successfully applied to various substrates under open-top circumstances, the applicability of ALD to confined spaces has been limited because of the inherent difficulty of supplying precursors into confined spaces. Here, we propose a rational methodology to apply ALD growths to confined spaces (meter-long microtubes with an aspect ratio of up to 10 000). The ALD system, which can generate differential pressures to confined spaces, was newly developed. By using this ALD system, it is possible to deposit TiOx layers onto the inner surface of capillary tubes with a length of 1000 mm and an inner diameter of 100 μm with spatial deposition uniformity. Furthermore, we show the superior thermal and chemical robustness of TiOx-coated capillary microtubes for molecular separations when compared to conventional molecule-coated capillary microtubes. Thus, the present rational strategy of space-confined ALD offers a useful approach to design the chemical and physical properties of the inner surfaces of various confined spaces.
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Affiliation(s)
- Ryoma Kamei
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
- Institute for Materials Chemistry and Engineering, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka, 816-8580, Japan
| | - Takuro Hosomi
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
- JST-PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Masaki Kanai
- Institute for Materials Chemistry and Engineering, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka, 816-8580, Japan
| | - Eisuke Kanao
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
- National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
| | - Jiangyang Liu
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Tsunaki Takahashi
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
- JST-PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Wenjun Li
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Wataru Tanaka
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Kazuki Nagashima
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
- JST-PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Katsuya Nakano
- Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Koji Otsuka
- Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Takuya Kubo
- Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Takeshi Yanagida
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
- Institute for Materials Chemistry and Engineering, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka, 816-8580, Japan
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Takahashi H, Baba Y, Yasui T. Oxide nanowire microfluidics addressing previously-unattainable analytical methods for biomolecules towards liquid biopsy. Chem Commun (Camb) 2021; 57:13234-13245. [PMID: 34825908 DOI: 10.1039/d1cc05096f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nanowire microfluidics using a combination of self-assembly and nanofabrication technologies is expected to be applied to various fields due to its unique properties. We have been working on the fabrication of nanowire microfluidic devices and the development of analytical methods for biomolecules using the unique phenomena generated by the devices. The results of our research are not just limited to the development of nanospace control with "targeted dimensions" in "targeted arrangements" with "targeted materials/surfaces" in "targeted spatial locations/structures" in microfluidic channels, but also cover a wide range of analytical methods for biomolecules (extraction, separation/isolation, and detection) that are impossible to achieve with conventional technologies. Specifically, we are working on the extraction technology "the cancer-related microRNA extraction method in urine," the separation technology "the ultrafast and non-equilibrium separation method for biomolecules," and the detection technology "the highly sensitive electrical measurement method." These research studies are not just limited to the development of biomolecule analysis technology using nanotechnology, but are also opening up a new academic field in analytical chemistry that may lead to the discovery of new pretreatment, separation, and detection principles.
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Affiliation(s)
- Hiromi Takahashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Yoshinobu Baba
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.,Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.,Institute of Quantum Life Science, National Institutes for Quantum Science and Technology, Anagawa 4-9-1, Inage-ku, Chiba 263-8555, Japan
| | - Takao Yasui
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.,Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.,Japan Science and Technology Agency (JST), PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
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Marchal N, da Câmara Santa Clara Gomes T, Abreu Araujo F, Piraux L. Giant Magnetoresistance and Magneto-Thermopower in 3D Interconnected Ni xFe 1-x/Cu Multilayered Nanowire Networks. NANOMATERIALS 2021; 11:nano11051133. [PMID: 33925733 PMCID: PMC8146549 DOI: 10.3390/nano11051133] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/21/2021] [Accepted: 04/24/2021] [Indexed: 11/16/2022]
Abstract
The versatility of the template-assisted electrodeposition technique to fabricate complex three-dimensional networks made of interconnected nanowires allows one to easily stack ferromagnetic and non-magnetic metallic layers along the nanowire axis. This leads to the fabrication of unique multilayered nanowire network films showing giant magnetoresistance effect in the current-perpendicular-to-plane configuration that can be reliably measured along the macroscopic in-plane direction of the films. Moreover, the system also enables reliable measurements of the analogous magneto-thermoelectric properties of the multilayered nanowire networks. Here, three-dimensional interconnected NixFe1−x/Cu multilayered nanowire networks (with 0.60≤x≤0.97) are fabricated and characterized, leading to large magnetoresistance and magneto-thermopower ratios up to 17% and −25% in Ni80Fe20/Cu, respectively. A strong contrast is observed between the amplitudes of magnetoresistance and magneto-thermoelectric effects depending on the Ni content of the NiFe alloys. In particular, for the highest Ni concentrations, a strong increase in the magneto-thermoelectric effect is observed, more than a factor of 7 larger than the magnetoresistive effect for Ni97Fe3/Cu multilayers. This sharp increase is mainly due to an increase in the spin-dependent Seebeck coefficient from −7 µV/K for the Ni60Fe40/Cu and Ni70Fe30/Cu nanowire arrays to −21 µV/K for the Ni97Fe3/Cu nanowire array. The enhancement of the magneto-thermoelectric effect for multilayered nanowire networks based on dilute Ni alloys is promising for obtaining a flexible magnetic switch for thermoelectric generation for potential applications in heat management or logic devices using thermal energy.
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Kamei R, Hosomi T, Kanao E, Kanai M, Nagashima K, Takahashi T, Zhang G, Yasui T, Terao J, Otsuka K, Baba Y, Kubo T, Yanagida T. Rational Strategy for Space-Confined Seeded Growth of ZnO Nanowires in Meter-Long Microtubes. ACS APPLIED MATERIALS & INTERFACES 2021; 13:16812-16819. [PMID: 33784465 DOI: 10.1021/acsami.0c22709] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Seeded crystal growths of nanostructures within confined spaces offer an interesting approach to design chemical reaction spaces with tailored inner surface properties. However, such crystal growth within confined spaces tends to be inherently difficult as the length increases as a result of confinement effects. Here, we demonstrate a space-confined seeded growth of ZnO nanowires within meter-long microtubes of 100 μm inner diameter with the aspect ratio of up to 10 000, which had been unattainable to previous methods of seeded crystal growths. ZnO nanowires could be grown via seeded hydrothermal crystal growth for relatively short microtubes below the length of 40 mm, while any ZnO nanostructures were not observable at all for longer microtubes above 60 mm with the aspect ratio of 600. Microstructural and mass spectrometric analysis revealed that a conventional seed layer formation using zinc acetate is unfeasible within the confined space of long microtubes as a result of the formation of detrimental residual Zn complex compounds. To overcome this space-confined issue, a flow-assisted seed layer formation is proposed. This flow-assisted method enables growth of spatially uniform ZnO nanowires via removing residual compounds even for 1 m long microtubes with the aspect ratio of up to 10 000. Finally, the applicably of ZnO-nanowire-decorated long microtubes for liquid-phase separations was demonstrated.
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Affiliation(s)
- Ryoma Kamei
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
- Institute for Materials Chemistry and Engineering, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka 816-8580, Japan
| | - Takuro Hosomi
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Eisuke Kanao
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
- National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
| | - Masaki Kanai
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
- Institute for Materials Chemistry and Engineering, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka 816-8580, Japan
| | - Kazuki Nagashima
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Tsunaki Takahashi
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Guozhu Zhang
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Takao Yasui
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Jun Terao
- Department of Basic Science, Graduate School of Art and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Koji Otsuka
- Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Yoshinobu Baba
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Takuya Kubo
- Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Takeshi Yanagida
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
- Institute for Materials Chemistry and Engineering, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka 816-8580, Japan
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Suwatthanarak T, Thiodorus IA, Tanaka M, Shimada T, Takeshita D, Yasui T, Baba Y, Okochi M. Microfluidic-based capture and release of cancer-derived exosomes via peptide-nanowire hybrid interface. LAB ON A CHIP 2021; 21:597-607. [PMID: 33367429 DOI: 10.1039/d0lc00899k] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Cancer-derived circulating exosomes or nanoscale extracellular vesicles are emerging biomarkers for disease detection and treatment because of their cell-specific constituents and unique intercellular pathways. For efficient exosome isolation from bio-fluids, the design of high-affinity nanointerfaces is of great importance in the development of miniaturized systems for the collection of exosomes. Herein, we report peptide-functionalized nanowires as a biorecognition interface for the capture and release of cancer-derived exosomes within a microfluidic channel. Based on the amino-acid sequence of EWI-2 protein, a partial peptide that bound to the CD9 exosome marker and thus targeted cancer exosomes was screened. Linkage of the exosome-targeting peptide with a ZnO-binding sequence allowed one-step and reagent-free peptide modification of the ZnO nanowire array. As a result of peptide functionalization, the exosome-capturing ability of ZnO nanowires was significantly improved. Furthermore, the captured exosomes could be subsequently released from the nanowires under a neutral salt condition for downstream applications. This engineered surface that enhances the nanowires' efficiency in selective and controllable collection of cancer-derived exosomes provides an alternative foundation for developing microfluidic platforms for exosome-based diagnostics and therapeutics.
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Affiliation(s)
- Thanawat Suwatthanarak
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8552, Japan.
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Musa M, Yasui T, Nagashima K, Horiuchi M, Zhu Z, Liu Q, Shimada T, Arima A, Yanagida T, Baba Y. ZnO/SiO 2 core/shell nanowires for capturing CpG rich single-stranded DNAs. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:337-344. [PMID: 33393567 DOI: 10.1039/d0ay02138e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Atomic layer deposition (ALD) is capable of providing an ultrathin layer on high-aspect ratio structures with good conformality and tunable film properties. In this research, we modified the surface of ZnO nanowires through ALD for the fabrication of a ZnO/SiO2 (core/shell) nanowire microfluidic device which we utilized for the capture of CpG-rich single-stranded DNAs (ssDNA). Structural changes of the nanowires while varying the number of ALD cycles were evaluated by statistical analysis and their relationship with the capture efficiency was investigated. We hypothesized that finding the optimum number of ALD cycles would be crucial to ensure adequate coating for successful tuning to the desired surface properties, besides promoting a sufficient trapping region with optimal spacing size for capturing the ssDNAs as the biomolecules traverse through the dispersed nanowires. Using the optimal condition, we achieved high capture efficiency of ssDNAs (86.7%) which showed good potential to be further extended for the analysis of CpG sites in cancer-related genes. This finding is beneficial to the future design of core/shell nanowires for capturing ssDNAs in biomedical applications.
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Affiliation(s)
- Marina Musa
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.
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7
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Magneto-Transport in Flexible 3D Networks Made of Interconnected Magnetic Nanowires and Nanotubes. NANOMATERIALS 2021; 11:nano11010221. [PMID: 33467036 PMCID: PMC7830720 DOI: 10.3390/nano11010221] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/07/2021] [Accepted: 01/12/2021] [Indexed: 11/17/2022]
Abstract
Electrochemical deposition of interconnected nanowires and nanotubes made of ferromagnetic metals into track-etched polycarbonate templates with crossed nanochannels has been revealed suitable for the fabrication of mechanically stable three-dimensional magnetic nanostructures with large surface area. These 3D networks embedded into flexible polymer membranes are also planar and lightweight. This fabrication technique allows for the control of the geometric characteristics and material composition of interconnected magnetic nanowire or nanotube networks, which can be used to fine-tune their magnetic and magneto-transport properties. The magnetostatic contribution to the magnetic anisotropy of crossed nanowire networks can be easily controlled using the diameter, packing density, or angle distribution characteristics. Furthermore, the fabrication of Co and Co-rich NiCo alloy crossed nanowires with textured hcp phases leads to an additional significant magnetocrystalline contribution to the magnetic anisotropy that can either compete or add to the magnetostatic contribution. The fabrication of an interconnected nanotube network has also been demonstrated, where the hollow core and the control over the tube wall thickness add another degree of freedom to control the magnetic properties and magnetization reversal mechanisms. Finally, three-dimensional networks made of interconnected multilayered nanowire with a succession of ferromagnetic and non-magnetic layers have been successfully fabricated, leading to giant magnetoresistance responses measured in the current-perpendicular-to-plane configuration. These interconnected nanowire networks have high potential as integrated, reliable, and stable magnetic field sensors; magnetic devices for memory and logic operations; or neuromorphic computing.
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8
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Chami B, Milon N, Fuentes Rojas JL, Charlot S, Marrot JC, Bancaud A. Single-step electrohydrodynamic separation of 1-150 kbp in less than 5 min using homogeneous glass/adhesive/glass microchips. Talanta 2020; 217:121013. [PMID: 32498826 DOI: 10.1016/j.talanta.2020.121013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/02/2020] [Accepted: 04/06/2020] [Indexed: 11/18/2022]
Abstract
Electrohydrodynamic migration, which is based on hydrodynamic actuation with an opposing electrophoretic force, enables the separation of DNA molecules of 3-100 kbp in glass capillary within 1 h. Here, we wish to enhance these performances using microchip technologies. This study starts with the fabrication of microchips with uniform surfaces, as motivated by our observation that band splitting occurs in microchannels made out of heterogeneous materials such as glass and silicon. The resulting glass-adhesive-glass microchips feature the highest reported bonding strength of 11 MPa for such materials (115 kgf/cm2), a high lateral resolution of critical dimension 5 μm, and minimal auto-fluorescence. These devices enable us to report the separation of 13 DNA bands in the size range of 1-150 kbp in one experiment of 5 min, i.e. 13 times faster than with capillary. In turn, we observe that bands split during electrohydrodynamic migration in heterogeneous glass-silicon but not in homogeneous glass-adhesive-glass microchips. We suggest that this effect arises from differential Electro-Osmotic Flow (EOF) in between the upper and lower walls of heterogeneous channels, and provide evidence that this phenomenon of differential EOF causes band broadening in electrophoresis during microchip electrophoresis. We finally prove that our electrohydrodynamic separation compares very favorably to microchip technologies in terms of resolution length and features the broadest analytical range reported so far.
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Affiliation(s)
- Bayan Chami
- CNRS, LAAS, 7 Avenue Du Colonel Roche, F-31400, Toulouse, France
| | - Nicolas Milon
- CNRS, LAAS, 7 Avenue Du Colonel Roche, F-31400, Toulouse, France; Adelis Technologies, 478 Rue de La Découverte, 31670, Labège, France
| | | | - Samuel Charlot
- CNRS, LAAS, 7 Avenue Du Colonel Roche, F-31400, Toulouse, France
| | | | - Aurélien Bancaud
- CNRS, LAAS, 7 Avenue Du Colonel Roche, F-31400, Toulouse, France.
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Li X, Mo J, Fang J, Xu D, Yang C, Zhang M, Li H, Xie X, Hu N, Liu F. Vertical nanowire array-based biosensors: device design strategies and biomedical applications. J Mater Chem B 2020; 8:7609-7632. [PMID: 32744274 DOI: 10.1039/d0tb00990c] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Biosensors have been extensively studied in the areas of biology, electronics, chemistry, biotechnology, medicine, and various engineering fields. The interdisciplinarity creates an ideal platform for scientists to analyze biological species and chemical materials in a direct, efficient, and sensitive manner; this is expected to revolutionize the life sciences, basic medicine, and the healthcare industry. To carry out high-performance biosensing, nanoprobes - with specific nanoscale properties - have been proposed for ultrasensitive and in situ monitoring/detection of tracer biomolecules, cellular behavior, cellular microenvironments, and electrophysiological activity. Here, we review the development of vertical nanowire (VNW) array-based devices for the effective collection of biomedical information at the molecular level, extracellular level, and intracellular level. In particular, we summarize VNW-based technologies in the aspects of detecting biochemical information, cellular information, and bioelectrical information, all of which facilitate the understanding of fundamental biology and development of therapeutic techniques. Finally, we present a conclusion and prospects for the development of VNW platforms in practical biomedical applications, and we identify the challenges and opportunities for VNW-based biosensor systems in future biological research.
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Affiliation(s)
- Xiangling Li
- The First Affiliated Hospital of Sun Yat-Sen University, School of Biomedical Engineering, Guangdong Province Key Laboratory of Display Material and Technology, School of Electronics and Information Technology, Sun Yat-Sen University, Guangzhou, 510006, China.
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10
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Matsuda T, Takada K, Yano K, Tsutsumi R, Yoshikawa K, Shimomura S, Shimizu Y, Nagashima K, Yanagida T, Ishikawa F. Controlling Bi-Provoked Nanostructure Formation in GaAs/GaAsBi Core-Shell Nanowires. NANO LETTERS 2019; 19:8510-8518. [PMID: 31525986 DOI: 10.1021/acs.nanolett.9b02932] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We control the formation of Bi-induced nanostructures on the growth of GaAs/GaAsBi core-shell nanowires (NWs). Bi serves as not only a constituent but also a surfactant and nanowire growth catalyst. Thus, we paved a way to achieve unexplored III-V nanostructures employing the characteristic supersaturation of catalyst droplets, structural modifications induced by strain, and incorporation into the host GaAs matrix correlated with crystalline defects and orientations. When Ga is deficient during growth, Bi accumulates on the vertex of core GaAs NWs and serves as a nanowire growth catalyst for the branched structures to azimuthal <112>. We find a strong correlation between Bi accumulation and stacking faults. Furthermore, Bi is preferentially incorporated on the GaAs (112)B surface, leading to spatially selective Bi incorporation into a confined area that has a Bi concentration of over 7%. The obtained GaAs/GaAsBi/GaAs heterostructure with an interface defined by the crystalline twin defects in a zinc-blende structure can be potentially applied to a quantum confined structure. Our finding provides a rational design concept for the creation of GaAsBi based nanostructures and the control of Bi incorporation beyond the fundamental limit.
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Affiliation(s)
- Teruyoshi Matsuda
- Graduate School of Science and Engineering , Ehime University , 3 Bunkyo-cho , Matsuyama , Ehime 790-8577 , Japan
| | - Kyohei Takada
- Graduate School of Science and Engineering , Ehime University , 3 Bunkyo-cho , Matsuyama , Ehime 790-8577 , Japan
| | - Kohsuke Yano
- Graduate School of Science and Engineering , Ehime University , 3 Bunkyo-cho , Matsuyama , Ehime 790-8577 , Japan
| | - Rikuo Tsutsumi
- Graduate School of Science and Engineering , Ehime University , 3 Bunkyo-cho , Matsuyama , Ehime 790-8577 , Japan
| | - Kohei Yoshikawa
- Graduate School of Science and Engineering , Ehime University , 3 Bunkyo-cho , Matsuyama , Ehime 790-8577 , Japan
| | - Satoshi Shimomura
- Graduate School of Science and Engineering , Ehime University , 3 Bunkyo-cho , Matsuyama , Ehime 790-8577 , Japan
| | - Yumiko Shimizu
- Toray Research Center , 3-3-7 Sonoyama , Otsu , Shiga 520-8567 , Japan
| | - Kazuki Nagashima
- Institute for Materials Chemistry and Engineering , Kyushu University , Fukuoka 816-8580 , Japan
| | - Takeshi Yanagida
- Institute for Materials Chemistry and Engineering , Kyushu University , Fukuoka 816-8580 , Japan
| | - Fumitaro Ishikawa
- Graduate School of Science and Engineering , Ehime University , 3 Bunkyo-cho , Matsuyama , Ehime 790-8577 , Japan
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11
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Wunsch BH, Kim SC, Gifford SM, Astier Y, Wang C, Bruce RL, Patel JV, Duch EA, Dawes S, Stolovitzky G, Smith JT. Gel-on-a-chip: continuous, velocity-dependent DNA separation using nanoscale lateral displacement. LAB ON A CHIP 2019; 19:1567-1578. [PMID: 30920559 DOI: 10.1039/c8lc01408f] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
We studied the trajectories of polymers being advected while diffusing in a pressure driven flow along a periodic pillar nanostructure known as nanoscale deterministic lateral displacement (nanoDLD) array. We found that polymers follow different trajectories depending on their length, flow velocity and pillar array geometry, demonstrating that nanoDLD devices can be used as a continuous polymer fractionation tool. As a model system, we used double-stranded DNA (dsDNA) with various contour lengths and demonstrated that dsDNA in the range of 100-10 000 base pairs (bp) can be separated with a size-selective resolution of 200 bp. In contrast to spherical colloids, a polymer elongates by shear flow and the angle of polymer trajectories with respect to the mean flow direction decreases as the mean flow velocity increases. We developed a phenomenological model that explains the qualitative dependence of the polymer trajectories on the gap size and on the flow velocity. Using this model, we found the optimal separation conditions for dsDNA of different sizes and demonstrated the separation and extraction of dsDNA fragments with over 75% recovery and 3-fold concentration. Importantly, this velocity dependence provides a means of fine-tuning the separation efficiency and resolution, independent of the nanoDLD pillar geometry.
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Affiliation(s)
- Benjamin H Wunsch
- IBM T. J. Watson Research Center, Yorktown Heights, New York 10598, USA.
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12
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Yasui T, Yanagida T, Shimada T, Otsuka K, Takeuchi M, Nagashima K, Rahong S, Naito T, Takeshita D, Yonese A, Magofuku R, Zhu Z, Kaji N, Kanai M, Kawai T, Baba Y. Engineering Nanowire-Mediated Cell Lysis for Microbial Cell Identification. ACS NANO 2019; 13:2262-2273. [PMID: 30758938 DOI: 10.1021/acsnano.8b08959] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Researchers have demonstrated great promise for inorganic nanowire use in analyzing cells or intracellular components. Although a stealth effect of nanowires toward cell surfaces allows preservation of the living intact cells when analyzing cells, as a completely opposite approach, the applicability to analyze intracellular components through disrupting cells is also central to understanding cellular information. However, the reported lysis strategy is insufficient for microbial cell lysis due to the cell robustness and wrong approach taken so far ( i. e., nanowire penetration into a cell membrane). Here we propose a nanowire-mediated lysis method for microbial cells by introducing the rupture approach initiated by cell membrane stretching; in other words, the nanowires do not penetrate the membrane, but rather they break the membrane between the nanowires. Entangling cells with the bacteria-compatible and flexible nanowires and membrane stretching of the entangled cells, induced by the shear force, play important roles for the nanowire-mediated lysis to Gram-positive and Gram-negative bacteria and yeast cells. Additionally, the nanowire-mediated lysis is readily compatible with the loop-mediated isothermal amplification (LAMP) method because the lysis is triggered by simply introducing the microbial cells. We show that an integration of the nanowire-mediated lysis with LAMP provides a means for a simple, rapid, one-step identification assay (just introducing a premixed solution into a device), resulting in visual chromatic identification of microbial cells. This approach allows researchers to develop a microfluidic analytical platform not only for microbial cell identification including drug- and heat-resistance cells but also for on-site detection without any contamination.
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Affiliation(s)
- Takao Yasui
- Japan Science and Technology Agency (JST), Precursory Research for Embryonic Science and Technology (PRESTO) , 4-1-8 Honcho , Kawaguchi , Saitama 332-0012 , Japan
| | - Takeshi Yanagida
- Institute of Materials Chemistry and Engineering , Kyushu University , 6-1 Kasuga-Koen , Kasuga, Fukuoka 816-8580 , Japan
- Institute of Scientific and Industrial Research , Osaka University , 8-1 Mihogaoka-cho , Ibaraki, Osaka 567-0047 , Japan
| | | | | | | | - Kazuki Nagashima
- Institute of Materials Chemistry and Engineering , Kyushu University , 6-1 Kasuga-Koen , Kasuga, Fukuoka 816-8580 , Japan
| | - Sakon Rahong
- College of Nanotechnology , King Mongkut's Institute of Technology Ladkrabang , Chalongkrung Rd. , Ladkrabang, Bangkok 10520 , Thailand
| | - Toyohiro Naito
- Department of Material Chemistry, Graduate School of Engineering , Kyoto University , Katsura, Nishikyo-ku, Kyoto 615-8510 , Japan
| | | | | | | | - Zetao Zhu
- Institute of Materials Chemistry and Engineering , Kyushu University , 6-1 Kasuga-Koen , Kasuga, Fukuoka 816-8580 , Japan
| | - Noritada Kaji
- Japan Science and Technology Agency (JST), Precursory Research for Embryonic Science and Technology (PRESTO) , 4-1-8 Honcho , Kawaguchi , Saitama 332-0012 , Japan
- Department of Chemistry and Biochemistry, Graduate School of Engineering , Kyushu University , Moto-oka 744 , Nishi-ku, Fukuoka 819-0395 , Japan
| | - Masaki Kanai
- Institute of Materials Chemistry and Engineering , Kyushu University , 6-1 Kasuga-Koen , Kasuga, Fukuoka 816-8580 , Japan
| | - Tomoji Kawai
- Institute of Scientific and Industrial Research , Osaka University , 8-1 Mihogaoka-cho , Ibaraki, Osaka 567-0047 , Japan
| | - Yoshinobu Baba
- Health Research Institute , National Institute of Advanced Industrial Science and Technology (AIST) , Takamatsu 761-0395 , Japan
- College of Pharmacy , Kaohsiung Medical University , Kaohsiung 807 , 80708 Kaohsiung City , Taiwan , R.O.C
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13
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Iubini S, Orlandini E, Michieletto D, Baiesi M. Topological Sieving of Rings According to Their Rigidity. ACS Macro Lett 2018; 7:1408-1412. [PMID: 35651235 DOI: 10.1021/acsmacrolett.8b00719] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We present a novel mechanism for resolving the mechanical rigidity of nanoscopic circular polymers that flow in a complex environment. The emergence of a regime of negative differential mobility induced by topological interactions between the rings and the substrate is the key mechanism for selective sieving of circular polymers with distinct flexibilities. A simple model accurately describes the sieving process observed in molecular dynamics simulations and yields experimentally verifiable analytical predictions, which can be used as a reference guide for improving filtration procedures of circular filaments. The topological sieving mechanism we propose ought to be relevant also in probing the microscopic details of complex substrates.
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Affiliation(s)
- Stefano Iubini
- Department of Physics and Astronomy, University of Padova, Via Marzolo 8, I-35131 Padova, Italy
| | - Enzo Orlandini
- Department of Physics and Astronomy, University of Padova, Via Marzolo 8, I-35131 Padova, Italy
- INFN, Sezione di Padova, Via Marzolo 8, I-35131 Padova, Italy
| | - Davide Michieletto
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, U.K
| | - Marco Baiesi
- Department of Physics and Astronomy, University of Padova, Via Marzolo 8, I-35131 Padova, Italy
- INFN, Sezione di Padova, Via Marzolo 8, I-35131 Padova, Italy
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14
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Wongkaew N, Simsek M, Griesche C, Baeumner AJ. Functional Nanomaterials and Nanostructures Enhancing Electrochemical Biosensors and Lab-on-a-Chip Performances: Recent Progress, Applications, and Future Perspective. Chem Rev 2018; 119:120-194. [DOI: 10.1021/acs.chemrev.8b00172] [Citation(s) in RCA: 303] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Nongnoot Wongkaew
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, 93053 Regensburg, Germany
| | - Marcel Simsek
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, 93053 Regensburg, Germany
| | - Christian Griesche
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, 93053 Regensburg, Germany
| | - Antje J. Baeumner
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, 93053 Regensburg, Germany
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15
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Abstract
Long-read genomic applications, such as genome mapping in nanochannels, require long DNA that is free of small-DNA impurities. We have developed a chip-based system based on entropic trapping that can simultaneously concentrate and purify a long DNA sample under the alternating application of an applied pressure (for sample injection) and an electric field (for filtration and concentration). In contrast, short DNA tends to pass through the filter owing to its comparatively weak entropic penalty for entering the nanoslit. The single-stage prototype developed here, which operates in a continuous pulsatile manner, achieves selectivities of up to 3.5 for λ-phage DNA (48.5 kilobase pairs) compared to a 2 kilobase pair standard based on experimental data for the fraction filtered using pure samples of each species. The device is fabricated in fused silica using standard clean-room methods, making it compatible for integration with long-read genomics technologies.
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Affiliation(s)
- Pranav Agrawal
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, USA.
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16
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Contreras-Naranjo JC, Wu HJ, Ugaz VM. Microfluidics for exosome isolation and analysis: enabling liquid biopsy for personalized medicine. LAB ON A CHIP 2017; 17:3558-3577. [PMID: 28832692 PMCID: PMC5656537 DOI: 10.1039/c7lc00592j] [Citation(s) in RCA: 394] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Exosomes, the smallest sized extracellular vesicles (∽30-150 nm) packaged with lipids, proteins, functional messenger RNAs and microRNAs, and double-stranded DNA from their cells of origin, have emerged as key players in intercellular communication. Their presence in bodily fluids, where they protect their cargo from degradation, makes them attractive candidates for clinical application as innovative diagnostic and therapeutic tools. But routine isolation and analysis of high purity exosomes in clinical settings is challenging, with conventional methods facing a number of drawbacks including low yield and/or purity, long processing times, high cost, and difficulties in standardization. Here we review a promising solution, microfluidic-based technologies that have incorporated a host of separation and sensing capabilities for exosome isolation, detection, and analysis, with emphasis on point-of-care and clinical applications. These new capabilities promise to advance fundamental research while paving the way toward routine exosome-based liquid biopsy for personalized medicine.
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Affiliation(s)
- Jose C Contreras-Naranjo
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, USA.
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17
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Duan L, Cao Z, Yobas L. Continuous-Flow Electrophoresis of DNA and Proteins in a Two-Dimensional Capillary-Well Sieve. Anal Chem 2017; 89:10022-10028. [DOI: 10.1021/acs.analchem.7b02484] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lian Duan
- Department
of Electronic and Computer Engineering, and ‡Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China
| | - Zhen Cao
- Department
of Electronic and Computer Engineering, and ‡Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China
| | - Levent Yobas
- Department
of Electronic and Computer Engineering, and ‡Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China
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18
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Michieletto D, Marenduzzo D, Orlandini E, Turner MS. Ring Polymers: Threadings, Knot Electrophoresis and Topological Glasses. Polymers (Basel) 2017; 9:E349. [PMID: 30971026 PMCID: PMC6418951 DOI: 10.3390/polym9080349] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 08/04/2017] [Accepted: 08/05/2017] [Indexed: 01/12/2023] Open
Abstract
Elucidating the physics of a concentrated suspension of ring polymers, or of an ensemble of ring polymers in a complex environment, is an important outstanding question in polymer physics. Many of the characteristic features of these systems arise due to topological interactions between polymers, or between the polymers and the environment, and it is often challenging to describe this quantitatively. Here we review recent research which suggests that a key role is played by inter-ring threadings (or penetrations), which become more abundant as the ring size increases. As we discuss, the physical consequences of such threadings are far-reaching: for instance, they lead to a topologically-driven glassy behaviour of ring polymer melts under pinning perturbations, while they can also account for the shape of experimentally observed patterns in two-dimensional gel electrophoresis of DNA knots.
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Affiliation(s)
- Davide Michieletto
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
| | - Davide Marenduzzo
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
| | - Enzo Orlandini
- Dipartimento di Fisica e Astronomia, Sezione INFN, Università di Padova, Via Marzolo 8, 35131 Padova, Italy.
| | - Matthew S Turner
- Department of Physics and Centre for Complexity Science, University of Warwick, Coventry CV4 7AL, UK.
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19
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Qian W, Doi K, Kawano S. Effects of Polymer Length and Salt Concentration on the Transport of ssDNA in Nanofluidic Channels. Biophys J 2017; 112:838-849. [PMID: 28297643 PMCID: PMC5355498 DOI: 10.1016/j.bpj.2017.01.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 01/23/2017] [Accepted: 01/24/2017] [Indexed: 11/25/2022] Open
Abstract
Electrokinetic phenomena in micro/nanofluidic channels have attracted considerable attention because precise control of molecular transport in liquids is required to optically and electrically capture the behavior of single molecules. However, the detailed mechanisms of polymer transport influenced by electroosmotic flows and electric fields in micro/nanofluidic channels have not yet been elucidated. In this study, a Langevin dynamics simulation was used to investigate the electrokinetic transport of single-stranded DNA (ssDNA) in a cylindrical nanochannel, employing a coarse-grained bead-spring model that quantitatively reproduced the radius of gyration, diffusion coefficient, and electrophoretic mobility of the polymer. Using this practical scale model, transport regimes of ssDNA with respect to the ζ-potential of the channel wall, the ion concentration, and the polymer length were successfully characterized. It was found that the relationship between the radius of gyration of ssDNA and the channel radius is critical to the formation of deformation regimes in a narrow channel. We conclude that a combination of electroosmotic flow velocity gradients and electric fields due to electrically polarized channel surfaces affects the alignment of molecular conformations, such that the ssDNA is stretched/compressed at negative/positive ζ-potentials in comparatively low-concentration solutions. Furthermore, this work suggests the possibility of controlling the center-of-mass position by tuning the salt concentration. These results should be applicable to the design of molecular manipulation techniques based on liquid flows in micro/nanofluidic devices.
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Affiliation(s)
- Weixin Qian
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, Japan
| | - Kentaro Doi
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, Japan.
| | - Satoyuki Kawano
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, Japan.
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20
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da Câmara Santa Clara Gomes T, De La Torre Medina J, Lemaitre M, Piraux L. Magnetic and Magnetoresistive Properties of 3D Interconnected NiCo Nanowire Networks. NANOSCALE RESEARCH LETTERS 2016; 11:466. [PMID: 27757947 PMCID: PMC5069242 DOI: 10.1186/s11671-016-1679-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 10/07/2016] [Indexed: 05/12/2023]
Abstract
Track-etched polymer membranes with crossed nanochannels have been revealed to be most suitable as templates to produce large surface area and mechanically stable 3D interconnected nanowire (NW) networks by electrodeposition. Geometrically controlled NW superstructures made of NiCo ferromagnetic alloys exhibit appealing magnetoresistive properties. The combination of exact alloy compositions with the spatial arrangement of NWs in the 3D network is decisive to obtain specific magnetic and magneto-transport behavior. A proposed simple model based on topological aspects of the 3D NW networks is used to accurately determine the anisotropic magnetoresistance ratios. Despite of their complex topology, the microstructure of Co-rich NiCo NW networks display mixed fcc-hcp phases with the c-axis of the hcp phase oriented perpendicular to their axis. These interconnected NW networks have high potential as reliable and stable magnetic field sensors.
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Affiliation(s)
| | - Joaquín De La Torre Medina
- Instituto de Investigaciones en Materiales - Unidad Morelia, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro No. 8701 Col. Ex Hacienda de San José de la Huerta, Morelia, 58190, Mexico.
| | - Matthieu Lemaitre
- Institute of Condensed Matter and Nanosciences, Université catholique de Louvain, Place Croix du Sud 1, Louvain-la-Neuve, B-1348, Belgium
| | - Luc Piraux
- Institute of Condensed Matter and Nanosciences, Université catholique de Louvain, Place Croix du Sud 1, Louvain-la-Neuve, B-1348, Belgium
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21
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Rahong S, Yasui T, Kaji N, Baba Y. Recent developments in nanowires for bio-applications from molecular to cellular levels. LAB ON A CHIP 2016; 16:1126-38. [PMID: 26928289 DOI: 10.1039/c5lc01306b] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
This review highlights the most promising applications of nanowires for bioanalytical chemistry and medical diagnostics. The materials discussed here are metal oxide and Si semiconductors, which are integrated with various microfluidic systems. Nanowire structures offer desirable advantages such as a very small diameter size with a high aspect ratio and a high surface-to-volume ratio without grain boundaries; consequently, nanowires are promising tools to study biological systems. This review starts with the integration of nanowire structures into microfluidic systems, followed by the discussion of the advantages of nanowire structures in the separation, manipulation and purification of biomolecules (DNA, RNA and proteins). Next, some representative nanowire devices are introduced for biosensors from molecular to cellular levels based on electrical and optical approaches. Finally, we conclude the review by highlighting some bio-applications for nanowires and presenting the next challenges that must be overcome to improve the capabilities of nanowire structures for biological and medical systems.
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Affiliation(s)
- Sakon Rahong
- Department of Applied Chemistry, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan. and ImPACT Research Center for Advanced Nanobiodevices, Nagoya University, Japan
| | - Takao Yasui
- Department of Applied Chemistry, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan. and ImPACT Research Center for Advanced Nanobiodevices, Nagoya University, Japan and JST, PRESTO, Graduate School of Engineering, Nagoya University, Japan
| | - Noritada Kaji
- Department of Applied Chemistry, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan. and ImPACT Research Center for Advanced Nanobiodevices, Nagoya University, Japan and ERATO Higashiyama Live-Holonics Project, Graduate School of Science, Nagoya University, Japan
| | - Yoshinobu Baba
- Department of Applied Chemistry, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan. and ImPACT Research Center for Advanced Nanobiodevices, Nagoya University, Japan and Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Takamatsu 761-0395, Japan
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22
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Michieletto D, Marenduzzo D, Orlandini E. Topological patterns in two-dimensional gel electrophoresis of DNA knots. Proc Natl Acad Sci U S A 2015; 112:E5471-7. [PMID: 26351668 PMCID: PMC4603474 DOI: 10.1073/pnas.1506907112] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gel electrophoresis is a powerful experimental method to probe the topology of DNA and other biopolymers. Although there is a large body of experimental work that allows us to accurately separate different topoisomers of a molecule, a full theoretical understanding of these experiments has not yet been achieved. Here we show that the mobility of DNA knots depends crucially and subtly on the physical properties of the gel and, in particular, on the presence of dangling ends. The topological interactions between these and DNA molecules can be described in terms of an "entanglement number" and yield a nonmonotonic mobility at moderate fields. Consequently, in 2D electrophoresis, gel bands display a characteristic arc pattern; this turns into a straight line when the density of dangling ends vanishes. We also provide a novel framework to accurately predict the shape of such arcs as a function of molecule length and topological complexity, which may be used to inform future experiments.
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Affiliation(s)
- Davide Michieletto
- Department of Physics and Complexity Science, University of Warwick, Coventry CV4 7AL, United Kingdom;
| | - Davide Marenduzzo
- School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
| | - Enzo Orlandini
- Dipartimento di Fisica e Astronomia and Sezione, Istituto Nazionale di Fisica Nucleare, Universitá di Padova, 35131 Padova, Italy
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23
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Rahong S, Yasui T, Yanagida T, Nagashima K, Kanai M, Meng G, He Y, Zhuge F, Kaji N, Kawai T, Baba Y. Three-dimensional Nanowire Structures for Ultra-Fast Separation of DNA, Protein and RNA Molecules. Sci Rep 2015; 5:10584. [PMID: 26073192 PMCID: PMC4466590 DOI: 10.1038/srep10584] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 04/17/2015] [Indexed: 11/09/2022] Open
Abstract
Separation and analysis of biomolecules represent crucial processes for biological and biomedical engineering development; however, separation resolution and speed for biomolecules analysis still require improvements. To achieve separation and analysis of biomolecules in a short time, the use of highly-ordered nanostructures fabricated by top-down or bottom-up approaches have been proposed. Here, we reported on the use of three-dimensional (3D) nanowire structures embedded in microchannels fabricated by a bottom-up approach for ultrafast separation of small biomolecules, such as DNA, protein, and RNA molecules. The 3D nanowire structures could analyze a mixture of DNA molecules (50-1000 bp) within 50 s, a mixture of protein molecules (20-340 kDa) within 5 s, and a mixture of RNA molecules (100-1000 bases) within 25 s. And, we could observe the electrophoretic mobility difference of biomolecules as a function of molecular size in the 3D nanowire structures. Since the present methodology allows users to control the pore size of sieving materials by varying the number of cycles for nanowire growth, the 3D nanowire structures have a good potential for use as alternatives for other sieving materials.
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Affiliation(s)
- Sakon Rahong
- Institute of Innovation for Future Society, Nagoya University, JAPAN
- FIRST Research Center for Innovative Nanobiodevices, Nagoya University, JAPAN
| | - Takao Yasui
- FIRST Research Center for Innovative Nanobiodevices, Nagoya University, JAPAN
- Department of Applied Chemistry, Graduate School of Engineering, Nagoya University, JAPAN
| | - Takeshi Yanagida
- The Institute of Scientific and Industrial Research, Osaka University, JAPAN
| | - Kazuki Nagashima
- The Institute of Scientific and Industrial Research, Osaka University, JAPAN
| | - Masaki Kanai
- The Institute of Scientific and Industrial Research, Osaka University, JAPAN
| | - Gang Meng
- The Institute of Scientific and Industrial Research, Osaka University, JAPAN
| | - Yong He
- The Institute of Scientific and Industrial Research, Osaka University, JAPAN
| | - Fuwei Zhuge
- The Institute of Scientific and Industrial Research, Osaka University, JAPAN
| | - Noritada Kaji
- FIRST Research Center for Innovative Nanobiodevices, Nagoya University, JAPAN
- Department of Applied Chemistry, Graduate School of Engineering, Nagoya University, JAPAN
| | - Tomoji Kawai
- The Institute of Scientific and Industrial Research, Osaka University, JAPAN
| | - Yoshinobu Baba
- Institute of Innovation for Future Society, Nagoya University, JAPAN
- FIRST Research Center for Innovative Nanobiodevices, Nagoya University, JAPAN
- Department of Applied Chemistry, Graduate School of Engineering, Nagoya University, JAPAN
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), JAPAN
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24
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Yasui T, Kaji N, Ogawa R, Hashioka S, Tokeshi M, Horiike Y, Baba Y. Arrangement of a nanostructure array to control equilibrium and nonequilibrium transports of macromolecules. NANO LETTERS 2015; 15:3445-3451. [PMID: 25879141 DOI: 10.1021/acs.nanolett.5b00783] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Exploiting the nonequilibrium transport of macromolecules makes it possible to increase the separation speed without any loss of separation resolution. Here we report the arrangement of a nanostructure array in microchannels to control equilibrium and nonequilibrium transports of macromolecules. The direct observation and separation of macromolecules in the nanopillar array reported here are the first to reveal the nonequilibrium transport, which has a potential to overcome the intrinsic trade-off between the separation speed and resolution.
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Affiliation(s)
| | - Noritada Kaji
- △ERATO Higashiyama Live-Holonics Project, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Ryo Ogawa
- §National Institute for Materials Science, Tsukuba 305-0044, Japan
| | - Shingi Hashioka
- §National Institute for Materials Science, Tsukuba 305-0044, Japan
| | - Manabu Tokeshi
- ∥Division of Biotechnology and Macromolecular Chemistry, Faculty of Engineering, Hokkaido University, Kita 13 Nishi 8, Kita-ku, Sapporo 060-8628, Japan
| | - Yasuhiro Horiike
- §National Institute for Materials Science, Tsukuba 305-0044, Japan
| | - Yoshinobu Baba
- ⊥Institute of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
- #Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Takamatsu 761-0395, Japan
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25
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Liu L, Veerappan V, Bian Y, Guo G, Wang X. Influence of elution conditions on DNA transport behavior in free solution by hydrodynamic chromatography. Sci China Chem 2015. [DOI: 10.1007/s11426-015-5384-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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26
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Michieletto D, Baiesi M, Orlandini E, Turner MS. Rings in random environments: sensing disorder through topology. SOFT MATTER 2015; 11:1100-1106. [PMID: 25523275 DOI: 10.1039/c4sm02324b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In this paper we study the role of topology in DNA gel electrophoresis experiments via molecular dynamics simulations. The gel is modelled as a 3D array of obstacles from which half edges are removed at random with probability p, thereby generating a disordered environment. Changes in the microscopic structure of the gel are captured by measuring the electrophoretic mobility of ring polymers moving through the medium, while their linear counterparts provide a control system as we show they are insensitive to these changes. We show that ring polymers provide a novel, non-invasive way of exploiting topology to sense microscopic disorder. Finally, we compare the results from the simulations with an analytical model for the non-equilibrium differential mobility, and find a striking agreement between simulation and theory.
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Affiliation(s)
- Davide Michieletto
- Department of Physics and Centre for Complexity Science, University of Warwick, Coventry CV4 7AL, UK.
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27
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BABA Y. Nano- and Microbiodevices for High-Performance Separation of Biomolecules. CHROMATOGRAPHY 2015. [DOI: 10.15583/jpchrom.2015.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Yoshinobu BABA
- Department of Applied Chemistry, Graduate School of Engineering, ImPACT Research Center for Advanced Nanobiodevices, Department of Advanced Medical Science, Graduate School of Medicine, Nagoya University, Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
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RAHONG S, YASUI T, YANAGIDA T, NAGASHIMA K, KANAI M, MENG G, HE Y, ZHUGE F, KAJI N, KAWAI T, BABA Y. Self-assembled Nanowire Arrays as Three-dimensional Nanopores for Filtration of DNA Molecules. ANAL SCI 2015; 31:153-7. [DOI: 10.2116/analsci.31.153] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Sakon RAHONG
- FIRST Research Center for Innovative Nanobiodevices, Nagoya University
- Institute of Innovation for Future Society, Nagoya University
| | - Takao YASUI
- Department of Applied Chemistry, Graduate School of Engineering, Nagoya University
- FIRST Research Center for Innovative Nanobiodevices, Nagoya University
| | - Takeshi YANAGIDA
- The Institute of Scientific and Industrial Research, Osaka University
| | - Kazuki NAGASHIMA
- The Institute of Scientific and Industrial Research, Osaka University
| | - Masaki KANAI
- The Institute of Scientific and Industrial Research, Osaka University
| | - Gang MENG
- The Institute of Scientific and Industrial Research, Osaka University
| | - Yong HE
- The Institute of Scientific and Industrial Research, Osaka University
| | - Fuwei ZHUGE
- The Institute of Scientific and Industrial Research, Osaka University
| | - Noritada KAJI
- Department of Applied Chemistry, Graduate School of Engineering, Nagoya University
- FIRST Research Center for Innovative Nanobiodevices, Nagoya University
| | - Tomoji KAWAI
- The Institute of Scientific and Industrial Research, Osaka University
| | - Yoshinobu BABA
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
- Department of Applied Chemistry, Graduate School of Engineering, Nagoya University
- FIRST Research Center for Innovative Nanobiodevices, Nagoya University
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Yasui T, Rahong S, Kaji N, Baba Y. Nanopillar, Nanowall, and Nanowire Devices for Fast Separation of Biomolecules. Isr J Chem 2014. [DOI: 10.1002/ijch.201400102] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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