1
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Mao Z, Zheng W, Hu S, Peng X, Luo Y, Lee J, Chen H. Multifunctional DNA scaffold mediated gap plasmon resonance: Application to sensitive PD-L1 sensor. Biosens Bioelectron 2024; 247:115938. [PMID: 38141442 DOI: 10.1016/j.bios.2023.115938] [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: 06/13/2023] [Revised: 12/12/2023] [Accepted: 12/16/2023] [Indexed: 12/25/2023]
Abstract
The introduction of noble metal nanoparticles with good LSPR characteristics can greatly improve the sensitivity of SPR through resonance coupling effect. The plasma resonance response and optical properties of film coupling nanoparticle systems largely depends on the ingenious design of gap structures. Nucleic acid nanostructures have good stability, flexibility, and high biocompatibility, making them ideal materials for gap construction. 2D MOF (Cu-Tcpp) has a large conjugated surface similar to graphene, which can provide a stable substrate for the directional fixation of nucleic acid nanostructures. However, research on gap coupling plasmon based on nucleic acid nanostructures and 2D MOF is still rarely reported. By integrating the advantages of Cu-Tcpp assembled film and DNA tetrahedron immobilization, a nano gap with porous scaffold structure between the gold film and gold nanorod was build. The rigidity of DNA tetrahedron can precisely control the gap size, and its unique programmability allows us to give the coupling structure greater flexibility through the design of nucleic acid chain. The experimental results and FDTD simulation show that the film coupling nanoparticle systems constructed with DNA tetrahedrons greatly enhance the electric field strength near the chip surface and effectively improve the sensitivity of SPR. This research shows the huge potential of nucleic acid nanomaterials in the construction of SPR chip surface microstructures.
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Affiliation(s)
- Zhihui Mao
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China; School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wenjia Zheng
- School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Shiqi Hu
- College of Science and Engineering, Jinan University, Guangzhou, 510632, China
| | - Xinsheng Peng
- School of Medicine, Shanghai University, Shanghai, 200444, China
| | - Yunhan Luo
- College of Science and Engineering, Jinan University, Guangzhou, 510632, China
| | - Jaebeom Lee
- Department of Chemistry, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Hongxia Chen
- School of Life Sciences, Shanghai University, Shanghai, 200444, China.
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2
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Ariga K, Song J, Kawakami K. Layer-by-layer designer nanoarchitectonics for physical and chemical communications in functional materials. Chem Commun (Camb) 2024; 60:2152-2167. [PMID: 38291864 DOI: 10.1039/d3cc04952c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Nanoarchitectonics, as a post-nanotechnology concept, constructs functional materials and structures using nanounits of atoms, molecules, and nanomaterials as materials. With the concept of nanoarchitectonics, asymmetric structures, and hierarchical organization, rather than mere assembly and organization of structures, can be produced, where rational physical and chemical communications will lead to the development of more advanced functional materials. Layer-by-layer assembly can be a powerful tool for this purpose, as exemplified in this feature paper. This feature article explores the possibility of constructing advanced functional systems based on recent examples of layer-by-layer assembly. We will illustrate both the development of more basic methods and more advanced nanoarchitectonics systems aiming towards practical applications. Specifically, the following sections will provide examples of (i) advancement in basics and methods, (ii) physico-chemical aspects and applications, (iii) bio-chemical aspects and applications, and (iv) bio-medical applications. It can be concluded that materials nanoarchitectonics based on layer-by-layer assembly is a useful method for assembling asymmetric structures and hierarchical organization, and is a powerful technique for developing functions through physical and chemical communication.
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Affiliation(s)
- Katsuhiko Ariga
- Research Center for Materials Nanoarchitectonics, National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba 305-0044, Japan.
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwa-no-ha, Kashiwa 277-8561, Japan
| | - Jingwen Song
- Research Center for Functional Materials, National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba 305-0044, Ibaraki, Japan
| | - Kohsaku Kawakami
- Research Center for Functional Materials, National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba 305-0044, Ibaraki, Japan
- Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Ibaraki, Japan
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3
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Ariga K. 2D Materials Nanoarchitectonics for 3D Structures/Functions. MATERIALS (BASEL, SWITZERLAND) 2024; 17:936. [PMID: 38399187 PMCID: PMC10890396 DOI: 10.3390/ma17040936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 02/09/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024]
Abstract
It has become clear that superior material functions are derived from precisely controlled nanostructures. This has been greatly accelerated by the development of nanotechnology. The next step is to assemble materials with knowledge of their nano-level structures. This task is assigned to the post-nanotechnology concept of nanoarchitectonics. However, nanoarchitectonics, which creates intricate three-dimensional functional structures, is not always easy. Two-dimensional nanoarchitectonics based on reactions and arrangements at the surface may be an easier target to tackle. A better methodology would be to define a two-dimensional structure and then develop it into a three-dimensional structure and function. According to these backgrounds, this review paper is organized as follows. The introduction is followed by a summary of the three issues; (i) 2D to 3D dynamic structure control: liquid crystal commanded by the surface, (ii) 2D to 3D rational construction: a metal-organic framework (MOF) and a covalent organic framework (COF); (iii) 2D to 3D functional amplification: cells regulated by the surface. In addition, this review summarizes the important aspects of the ultimate three-dimensional nanoarchitectonics as a perspective. The goal of this paper is to establish an integrated concept of functional material creation by reconsidering various reported cases from the viewpoint of nanoarchitectonics, where nanoarchitectonics can be regarded as a method for everything in materials science.
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Affiliation(s)
- Katsuhiko Ariga
- Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba 305-0044, Ibaraki, Japan;
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8561, Chiba, Japan
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4
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Ariga K. Materials Nanoarchitectonics at Dynamic Interfaces: Structure Formation and Functional Manipulation. MATERIALS (BASEL, SWITZERLAND) 2024; 17:271. [PMID: 38204123 PMCID: PMC10780059 DOI: 10.3390/ma17010271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 12/25/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024]
Abstract
The next step in nanotechnology is to establish a methodology to assemble new functional materials based on the knowledge of nanotechnology. This task is undertaken by nanoarchitectonics. In nanoarchitectonics, we architect functional material systems from nanounits such as atoms, molecules, and nanomaterials. In terms of the hierarchy of the structure and the harmonization of the function, the material created by nanoarchitectonics has similar characteristics to the organization of the functional structure in biosystems. Looking at actual biofunctional systems, dynamic properties and interfacial environments are key. In other words, nanoarchitectonics at dynamic interfaces is important for the production of bio-like highly functional materials systems. In this review paper, nanoarchitectonics at dynamic interfaces will be discussed, looking at recent typical examples. In particular, the basic topics of "molecular manipulation, arrangement, and assembly" and "material production" will be discussed in the first two sections. Then, in the following section, "fullerene assembly: from zero-dimensional unit to advanced materials", we will discuss how various functional structures can be created from the very basic nanounit, the fullerene. The above examples demonstrate the versatile possibilities of architectonics at dynamic interfaces. In the last section, these tendencies will be summarized, and future directions will be discussed.
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Affiliation(s)
- Katsuhiko Ariga
- Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba 305-0044, Ibaraki, Japan;
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8561, Chiba, Japan
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5
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Ariga K. Molecular Machines and Microrobots: Nanoarchitectonics Developments and On-Water Performances. MICROMACHINES 2022; 14:mi14010025. [PMID: 36677086 PMCID: PMC9860627 DOI: 10.3390/mi14010025] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/16/2022] [Accepted: 12/21/2022] [Indexed: 05/14/2023]
Abstract
This review will focus on micromachines and microrobots, which are objects at the micro-level with similar machine functions, as well as nano-level objects such as molecular machines and nanomachines. The paper will initially review recent examples of molecular machines and microrobots that are not limited to interfaces, noting the diversity of their functions. Next, examples of molecular machines and micromachines/micro-robots functioning at the air-water interface will be discussed. The behaviors of molecular machines are influenced significantly by the specific characteristics of the air-water interface. By placing molecular machines at the air-water interface, the scientific horizon and depth of molecular machine research will increase dramatically. On the other hand, for microrobotics, more practical and advanced systems have been reported, such as the development of microrobots and microswimmers for environmental remediations and biomedical applications. The research currently being conducted on the surface of water may provide significant basic knowledge for future practical uses of molecular machines and microrobots.
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Affiliation(s)
- Katsuhiko Ariga
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan;
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
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6
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Handrea-Dragan IM, Botiz I, Tatar AS, Boca S. Patterning at the micro/nano-scale: Polymeric scaffolds for medical diagnostic and cell-surface interaction applications. Colloids Surf B Biointerfaces 2022; 218:112730. [DOI: 10.1016/j.colsurfb.2022.112730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/15/2022] [Accepted: 07/25/2022] [Indexed: 11/27/2022]
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Abstract
Hierarchical assembly of programmable DNA frameworks─such as DNA origami─paves the way for versatile nanometer-precise parallel nanopatterning up to macroscopic scales. As of now, the rapid evolution of the DNA nanostructure design techniques and the accessibility of these methods provide a feasible platform for building highly ordered DNA-based assemblies for various purposes. So far, a plethora of different building blocks based on DNA tiles and DNA origami have been introduced, but the dynamics of the large-scale lattice assembly of such modules is still poorly understood. Here, we focus on the dynamics of two-dimensional surface-assisted DNA origami lattice assembly at mica and lipid substrates and the techniques for prospective three-dimensional assemblies, and finally, we summarize the potential applications of such systems.
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Affiliation(s)
- Sofia Julin
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Adrian Keller
- Paderborn
University, Technical and Macromolecular
Chemistry, Warburger
Str. 100, 33098 Paderborn, Germany,
| | - Veikko Linko
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland,LIBER
Center of Excellence, Aalto University, 00076 Aalto, Finland,
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8
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Shen X, Song J, Kawakami K, Ariga K. Molecule-to-Material-to-Bio Nanoarchitectonics with Biomedical Fullerene Nanoparticles. MATERIALS (BASEL, SWITZERLAND) 2022; 15:5404. [PMID: 35955337 PMCID: PMC9369991 DOI: 10.3390/ma15155404] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/28/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
Nanoarchitectonics integrates nanotechnology with various other fields, with the goal of creating functional material systems from nanoscale units such as atoms, molecules, and nanomaterials. The concept bears strong similarities to the processes and functions seen in biological systems. Therefore, it is natural for materials designed through nanoarchitectonics to truly shine in bio-related applications. In this review, we present an overview of recent work exemplifying how nanoarchitectonics relates to biology and how it is being applied in biomedical research. First, we present nanoscale interactions being studied in basic biology and how they parallel nanoarchitectonics concepts. Then, we overview the state-of-the-art in biomedical applications pursuant to the nanoarchitectonics framework. On this basis, we take a deep dive into a particular building-block material frequently seen in nanoarchitectonics approaches: fullerene. We take a closer look at recent research on fullerene nanoparticles, paying special attention to biomedical applications in biosensing, gene delivery, and radical scavenging. With these subjects, we aim to illustrate the power of nanomaterials and biomimetic nanoarchitectonics when applied to bio-related applications, and we offer some considerations for future perspectives.
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Affiliation(s)
- Xuechen Shen
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8561, Chiba, Japan
| | - Jingwen Song
- Research Center for Functional Materials, National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba 305-0044, Ibaraki, Japan
| | - Kohsaku Kawakami
- Research Center for Functional Materials, National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba 305-0044, Ibaraki, Japan
- Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Ibaraki, Japan
| | - Katsuhiko Ariga
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8561, Chiba, Japan
- WPI Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba 305-0044, Ibaraki, Japan
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9
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Tudureanu R, Handrea-Dragan IM, Boca S, Botiz I. Insight and Recent Advances into the Role of Topography on the Cell Differentiation and Proliferation on Biopolymeric Surfaces. Int J Mol Sci 2022; 23:ijms23147731. [PMID: 35887079 PMCID: PMC9315624 DOI: 10.3390/ijms23147731] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/11/2022] [Accepted: 07/11/2022] [Indexed: 01/27/2023] Open
Abstract
It is well known that surface topography plays an important role in cell behavior, including adhesion, migration, orientation, elongation, proliferation and differentiation. Studying these cell functions is essential in order to better understand and control specific characteristics of the cells and thus to enhance their potential in various biomedical applications. This review proposes to investigate the extent to which various surface relief patterns, imprinted in biopolymer films or in polymeric films coated with biopolymers, by utilizing specific lithographic techniques, influence cell behavior and development. We aim to understand how characteristics such as shape, dimension or chemical functionality of surface relief patterns alter the orientation and elongation of cells, and thus, finally make their mark on the cell proliferation and differentiation. We infer that such an insight is a prerequisite for pushing forward the comprehension of the methodologies and technologies used in tissue engineering applications and products, including skin or bone implants and wound or fracture healing.
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Affiliation(s)
- Raluca Tudureanu
- Interdisciplinary Research Institute in Bio-Nano-Sciences, Babeș-Bolyai University, 400271 Cluj-Napoca, Romania; (R.T.); (I.M.H.-D.); (S.B.)
- Faculty of Physics, Babeș-Bolyai University, 400084 Cluj-Napoca, Romania
| | - Iuliana M. Handrea-Dragan
- Interdisciplinary Research Institute in Bio-Nano-Sciences, Babeș-Bolyai University, 400271 Cluj-Napoca, Romania; (R.T.); (I.M.H.-D.); (S.B.)
- Faculty of Physics, Babeș-Bolyai University, 400084 Cluj-Napoca, Romania
| | - Sanda Boca
- Interdisciplinary Research Institute in Bio-Nano-Sciences, Babeș-Bolyai University, 400271 Cluj-Napoca, Romania; (R.T.); (I.M.H.-D.); (S.B.)
| | - Ioan Botiz
- Interdisciplinary Research Institute in Bio-Nano-Sciences, Babeș-Bolyai University, 400271 Cluj-Napoca, Romania; (R.T.); (I.M.H.-D.); (S.B.)
- Correspondence:
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10
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Cervantes-Salguero K, Biaggne A, Youngsman JM, Ward BM, Kim YC, Li L, Hall JA, Knowlton WB, Graugnard E, Kuang W. Strategies for Controlling the Spatial Orientation of Single Molecules Tethered on DNA Origami Templates Physisorbed on Glass Substrates: Intercalation and Stretching. Int J Mol Sci 2022; 23:ijms23147690. [PMID: 35887059 PMCID: PMC9323263 DOI: 10.3390/ijms23147690] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/08/2022] [Accepted: 07/10/2022] [Indexed: 11/18/2022] Open
Abstract
Nanoarchitectural control of matter is crucial for next-generation technologies. DNA origami templates are harnessed to accurately position single molecules; however, direct single molecule evidence is lacking regarding how well DNA origami can control the orientation of such molecules in three-dimensional space, as well as the factors affecting control. Here, we present two strategies for controlling the polar (θ) and in-plane azimuthal (ϕ) angular orientations of cyanine Cy5 single molecules tethered on rationally-designed DNA origami templates that are physically adsorbed (physisorbed) on glass substrates. By using dipolar imaging to evaluate Cy5′s orientation and super-resolution microscopy, the absolute spatial orientation of Cy5 is calculated relative to the DNA template. The sequence-dependent partial intercalation of Cy5 is discovered and supported theoretically using density functional theory and molecular dynamics simulations, and it is harnessed as our first strategy to achieve θ control for a full revolution with dispersion as small as ±4.5°. In our second strategy, ϕ control is achieved by mechanically stretching the Cy5 from its two tethers, being the dispersion ±10.3° for full stretching. These results can in principle be applied to any single molecule, expanding in this way the capabilities of DNA as a functional templating material for single-molecule orientation control. The experimental and modeling insights provided herein will help engineer similar self-assembling molecular systems based on polymers, such as RNA and proteins.
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Affiliation(s)
- Keitel Cervantes-Salguero
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
- Correspondence: (K.C.-S.); (W.K.)
| | - Austin Biaggne
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
| | - John M. Youngsman
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
| | - Brett M. Ward
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
| | - Young C. Kim
- Materials Science and Technology Division, U.S. Naval Research Laboratory, Code 6300, Washington, DC 20375, USA;
| | - Lan Li
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
- Center for Advanced Energy Studies, Idaho Falls, ID 83401, USA
| | - John A. Hall
- Division of Research and Economic Development, Boise State University, Boise, ID 83725, USA;
| | - William B. Knowlton
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
- Department of Electrical and Computer Engineering, Boise State University, Boise, ID 83725, USA
| | - Elton Graugnard
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
- Center for Advanced Energy Studies, Idaho Falls, ID 83401, USA
| | - Wan Kuang
- Department of Electrical and Computer Engineering, Boise State University, Boise, ID 83725, USA
- Correspondence: (K.C.-S.); (W.K.)
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11
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Yang Y, Liang S, Wu H, Shi G, Fang H. Revisit the Hydrated Cation-π Interaction at the Interface: A New View of Dynamics and Statistics. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:2401-2408. [PMID: 35171618 DOI: 10.1021/acs.langmuir.1c03106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Carbon-based matter, such as biomolecules and graphitic structures, often form a liquid-solid/soft matter interface in salt solution and continuously affect the surrounding cations through hydrated cation-π interactions. In this Perspective, we revisit the effect of the hydrated cation-π interactions at the interface using statistical physics, which reveals how hydrated cation-π interactions affect every component dynamically and cause a time-dependent statistical effect at the liquid-solid/soft interface. We also highlight several pieces of experimental evidence from a statistical perspective and discuss the remarkable applications related to environmental protection, industrial manufacturing, and biological sciences.
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Affiliation(s)
- Yizhou Yang
- School of Physics, East China University of Science and Technology, Shanghai, 200237, China
| | - Shanshan Liang
- School of Physics, East China University of Science and Technology, Shanghai, 200237, China
| | - Hao Wu
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang 325001, China
| | - Guosheng Shi
- State Key Laboratory Advanced Special Steel, Shanghai Applied Radiation Institute, Shanghai University, Shanghai 200444, China
| | - Haiping Fang
- School of Physics, East China University of Science and Technology, Shanghai, 200237, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
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12
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Mishra E, Majumder S, Varma S, Dowben PA. X-ray photoemission studies of the interaction of metals and metal ions with DNA. Z PHYS CHEM 2021. [DOI: 10.1515/zpch-2021-3037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Abstract
X-ray Photoelectron Spectroscopy (XPS) has been used to study the interactions of heavy metal ions with DNA with some success. Surface sensitivity and selectivity of XPS are advantageous for identifying and characterizing the chemical and elemental structure of the DNA to metal interaction. This review summarizes the status of what amounts to a large part of the photoemission investigations of biomolecule interactions with metals and offers insight into the mechanism for heavy metal-bio interface interactions. Specifically, it is seen that metal interaction with DNA results in conformational changes in the DNA structure.
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Affiliation(s)
- Esha Mishra
- Department of Physics and Astronomy , University of Nebraska–Lincoln , Jorgenson Hall, 855 North 16th Street , Lincoln , NE 68588-0299 , USA
| | - Subrata Majumder
- Department of Physics , National Institute of Technology , Patna , Bihar 800005 , India
| | - Shikha Varma
- Institute of Physics , Sachivalaya Marg , Bhubaneswar 751005 , India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar , Mumbai 400085 , India
| | - Peter A. Dowben
- Department of Physics and Astronomy , University of Nebraska–Lincoln , Jorgenson Hall, 855 North 16th Street , Lincoln , NE 68588-0299 , USA
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13
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Podder A, Lee HJ, Kim BH. Fluorescent Nucleic Acid Systems for Biosensors. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200351] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Arup Podder
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Ha Jung Lee
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Byeang Hyean Kim
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
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14
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Handrea-Dragan M, Botiz I. Multifunctional Structured Platforms: From Patterning of Polymer-Based Films to Their Subsequent Filling with Various Nanomaterials. Polymers (Basel) 2021; 13:445. [PMID: 33573248 PMCID: PMC7866561 DOI: 10.3390/polym13030445] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/20/2022] Open
Abstract
There is an astonishing number of optoelectronic, photonic, biological, sensing, or storage media devices, just to name a few, that rely on a variety of extraordinary periodic surface relief miniaturized patterns fabricated on polymer-covered rigid or flexible substrates. Even more extraordinary is that these surface relief patterns can be further filled, in a more or less ordered fashion, with various functional nanomaterials and thus can lead to the realization of more complex structured architectures. These architectures can serve as multifunctional platforms for the design and the development of a multitude of novel, better performing nanotechnological applications. In this work, we aim to provide an extensive overview on how multifunctional structured platforms can be fabricated by outlining not only the main polymer patterning methodologies but also by emphasizing various deposition methods that can guide different structures of functional nanomaterials into periodic surface relief patterns. Our aim is to provide the readers with a toolbox of the most suitable patterning and deposition methodologies that could be easily identified and further combined when the fabrication of novel structured platforms exhibiting interesting properties is targeted.
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Affiliation(s)
- Madalina Handrea-Dragan
- Interdisciplinary Research Institute in Bio-Nano-Sciences, Babes-Bolyai University, 42 Treboniu Laurian Str. 400271 Cluj-Napoca, Romania;
- Faculty of Physics, Babes-Bolyai University, 1 M. Kogalniceanu Str. 400084 Cluj-Napoca, Romania
| | - Ioan Botiz
- Interdisciplinary Research Institute in Bio-Nano-Sciences, Babes-Bolyai University, 42 Treboniu Laurian Str. 400271 Cluj-Napoca, Romania;
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15
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Ariga K, Mori T, Kitao T, Uemura T. Supramolecular Chiral Nanoarchitectonics. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1905657. [PMID: 32191374 DOI: 10.1002/adma.201905657] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 12/26/2019] [Indexed: 05/06/2023]
Abstract
Exploration of molecular functions and material properties based on the control of chirality would be a scientifically elegant approach. Here, the fabrication and function of chiral-featured materials from both chiral and achiral components using a supramolecular nanoarchitectonics concept are discussed. The contents are classified in to three topics: i) chiral nanoarchitectonics of rather general molecular assemblies; ii) chiral nanoarchitectonics of metal-organic frameworks (MOFs); iii) chiral nanoarchitectonics in liquid crystals. MOF structures are based on nanoscopically well-defined coordinations, while mesoscopic orientations of liquid-crystalline phases are often flexibly altered. Discussion on the effects and features in these representative materials systems with totally different natures reveals the universal importance of supramolecular chiral nanoarchitectonics. Amplification of chiral molecular information from molecules to materials-level structures and the creation of chirality from achiral components upon temporal statistic fluctuations are universal, regardless of the nature of the assemblies. These features are thus surely advantageous characteristics for a wide range of applications.
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Affiliation(s)
- Katsuhiko Ariga
- WPI-MANA, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Taizo Mori
- WPI-MANA, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Takashi Kitao
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Takashi Uemura
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
- CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
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Abstract
Chirality is a fundamental property of a molecule, and the significant progress in chirality detection and quantification of a molecule has inspired major advances in various fields ranging from chemistry, biology, to biotechnology and pharmacology. Chiral molecules have identical molecular formulas, atom-to-atom linkages, and bonding distances, and as such they are difficult to distinguish both sensitively and selectively. Today, most new drugs and those under development are chiral, which requires technological developments in the separation and detection of chiral molecules. Therefore, rapid and facile methods to detect and discriminate chiral compounds are necessary to accelerate advances in many research fields. The challenges in analysis stem from the obvious fact that chiral molecules have the same physical properties. Although significant progress on the detection of enantiomeric composition has been achieved in the past decade, in order to fully realize the capacity of chiral molecular interrogation, highly sensitive and selective, portable, and easy-to-use detection remains challenging because of the limitation of conventional techniques.Soft nanoarchitectonics is a new concept for the fabrication of functional soft material systems through harmonization of various actions including atomic/molecular-level manipulation, chemical reactions, self-assembly and self-organization, and their modulation by external fields/stimuli. Soft nanoarchitectonics has been widely used as a key enabling technology for integrating predefined molecular functionalities including electrochemical, optical, catalytic, or biological properties into biosensing devices, which provides exciting opportunities to design, assemble, and fabricate tailored nanosystems to enable new sensing strategies for chiral molecules.In this Account, we aim to concisely discuss how these molecule-inspired soft nanoarchitectonics work for enantioselective sensing. We will first outline the basic principle and mechanistic insights of the soft nanoarchitectonics approach for enantioselective sensing, and then we will describe the new breakthroughs and trends in the area that have been most recently reported by our groups and others. There will also be a discussion on the merits of soft nanoarchitectonics based sensing in comparison to conventional analytical methods. Finally, with this Account, we hope to spark new chiral molecule sensing strategies by fundamentally understanding chiral recognition and engineering soft nanoarchitectonics with programmable structures and predictable sensing properties.
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Affiliation(s)
- Jing Liu
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria 3216, Australia
| | - Hong Zhou
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria 3216, Australia
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Wenrong Yang
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria 3216, Australia
| | - Katsuhiko Ariga
- World Premier International (WPI) Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
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Ariga K, Nishikawa M, Mori T, Takeya J, Shrestha LK, Hill JP. Self-assembly as a key player for materials nanoarchitectonics. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2019; 20:51-95. [PMID: 30787960 PMCID: PMC6374972 DOI: 10.1080/14686996.2018.1553108] [Citation(s) in RCA: 215] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/23/2018] [Accepted: 11/25/2018] [Indexed: 05/07/2023]
Abstract
The development of science and technology of advanced materials using nanoscale units can be conducted by a novel concept involving combination of nanotechnology methodology with various research disciplines, especially supramolecular chemistry. The novel concept is called 'nanoarchitectonics' where self-assembly processes are crucial in many cases involving a wide range of component materials. This review of self-assembly processes re-examines recent progress in materials nanoarchitectonics. It is composed of three main sections: (1) the first short section describes typical examples of self-assembly research to outline the matters discussed in this review; (2) the second section summarizes self-assemblies at interfaces from general viewpoints; and (3) the final section is focused on self-assembly processes at interfaces. The examples presented demonstrate the strikingly wide range of possibilities and future potential of self-assembly processes and their important contribution to materials nanoarchitectonics. The research examples described in this review cover variously structured objects including molecular machines, molecular receptors, molecular pliers, molecular rotors, nanoparticles, nanosheets, nanotubes, nanowires, nanoflakes, nanocubes, nanodisks, nanoring, block copolymers, hyperbranched polymers, supramolecular polymers, supramolecular gels, liquid crystals, Langmuir monolayers, Langmuir-Blodgett films, self-assembled monolayers, thin films, layer-by-layer structures, breath figure motif structures, two-dimensional molecular patterns, fullerene crystals, metal-organic frameworks, coordination polymers, coordination capsules, porous carbon spheres, mesoporous materials, polynuclear catalysts, DNA origamis, transmembrane channels, peptide conjugates, and vesicles, as well as functional materials for sensing, surface-enhanced Raman spectroscopy, photovoltaics, charge transport, excitation energy transfer, light-harvesting, photocatalysts, field effect transistors, logic gates, organic semiconductors, thin-film-based devices, drug delivery, cell culture, supramolecular differentiation, molecular recognition, molecular tuning, and hand-operating (hand-operated) nanotechnology.
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Affiliation(s)
- Katsuhiko Ariga
- WPI-MANA, National Institute for Materials Science (NIMS), Ibaraki, Japan
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | | | - Taizo Mori
- WPI-MANA, National Institute for Materials Science (NIMS), Ibaraki, Japan
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Jun Takeya
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Lok Kumar Shrestha
- WPI-MANA, National Institute for Materials Science (NIMS), Ibaraki, Japan
| | - Jonathan P. Hill
- WPI-MANA, National Institute for Materials Science (NIMS), Ibaraki, Japan
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Ariga K, Mori T, Shrestha LK. Nanoarchitectonics from Molecular Units to Living-Creature-Like Motifs. CHEM REC 2017; 18:676-695. [PMID: 29205796 DOI: 10.1002/tcr.201700070] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 11/14/2017] [Indexed: 01/20/2023]
Abstract
Important points for the fabrication of functional materials are the creation of nanoscale/molecular-scale units and architecting them into functional materials and systems. Recently, a new conceptual paradigm, nanoarchitectonics, has been proposed to combine nanotechnology and other methodologies including supramolecular chemistry, self-assembly and self-organization to satisfy major features of nanoscience and promote the creation of functional materials and systems. In this account article, our recent research results in materials development based on the nanoarchitectonics concept are summarized in two stories, (i) nanoarchitectonics from fullerenes as the simplest nano-units and (ii) dimension-dependent nanoarchitectonics from various structural units. The former demonstrates creativity of the nanoarchitectonics concept only with simple construction stuffs on materials fabrications, and a wide range of material applicability for the nanoarchitectonics strategy is realized in the latter ones.
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Affiliation(s)
- Katsuhiko Ariga
- World Premier International (WPI) Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS) 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan.,Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-0827, Japan
| | - Taizo Mori
- World Premier International (WPI) Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS) 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan
| | - Lok Kumar Shrestha
- World Premier International (WPI) Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS) 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan
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19
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Volkov IL, Smirnova A, Makarova AA, Reveguk ZV, Ramazanov RR, Usachov DY, Adamchuk VK, Kononov AI. DNA with Ionic, Atomic, and Clustered Silver: An XPS Study. J Phys Chem B 2017; 121:2400-2406. [DOI: 10.1021/acs.jpcb.6b11218] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ivan L. Volkov
- Saint-Petersburg State University, 199034 St. Petersburg, Russia
| | | | - Anna A. Makarova
- Institut
für Festkörperphysik, Technische Universität Dresden, 01062 Dresden, Germany
| | | | | | | | - Vera K. Adamchuk
- Saint-Petersburg State University, 199034 St. Petersburg, Russia
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20
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Komiyama M. Design of Highly Active Ce(IV) Catalysts for DNA Hydrolysis and Their Applications. CHEM LETT 2016. [DOI: 10.1246/cl.160786] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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21
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Yonamine Y, Cervantes-Salguero K, Nakanishi W, Kawamata I, Minami K, Komatsu H, Murata S, Hill JP, Ariga K. In situ 2D-extraction of DNA wheels by 3D through-solution transport. Phys Chem Chem Phys 2016; 17:32122-5. [PMID: 26583486 DOI: 10.1039/c5cp05765e] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Controlled transfer of DNA nanowheels from a hydrophilic to a hydrophobic surface was achieved by complexation of the nanowheels with a cationic lipid (2C12N(+)). 2D surface-assisted extraction, '2D-extraction', enabled structure-persistent transfer of DNA wheels, which could not be achieved by simple drop-casting.
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Affiliation(s)
- Yusuke Yonamine
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS) 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan. and CREST, JST, Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Keitel Cervantes-Salguero
- Department of Bioengineering and Robotics, Tohoku University, 6-6-1 Aobayama, Sendai, 980-8579, Japan.
| | - Waka Nakanishi
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS) 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan.
| | - Ibuki Kawamata
- Department of Bioengineering and Robotics, Tohoku University, 6-6-1 Aobayama, Sendai, 980-8579, Japan.
| | - Kosuke Minami
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS) 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan.
| | - Hirokazu Komatsu
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS) 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan.
| | - Satoshi Murata
- Department of Bioengineering and Robotics, Tohoku University, 6-6-1 Aobayama, Sendai, 980-8579, Japan.
| | - Jonathan P Hill
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS) 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan. and CREST, JST, Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Katsuhiko Ariga
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS) 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan. and CREST, JST, Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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22
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Ariga K, Malgras V, Ji Q, Zakaria MB, Yamauchi Y. Coordination nanoarchitectonics at interfaces between supramolecular and materials chemistry. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.01.015] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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23
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Hager R, Burns JR, Grydlik MJ, Halilovic A, Haselgrübler T, Schäffler F, Howorka S. Co-Immobilization of Proteins and DNA Origami Nanoplates to Produce High-Contrast Biomolecular Nanoarrays. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:2877-2884. [PMID: 27062557 DOI: 10.1002/smll.201600311] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 02/18/2016] [Indexed: 06/05/2023]
Abstract
The biofunctionalization of nanopatterned surfaces with DNA origami nanostructures is an important topic in nanobiotechnology. An unexplored challenge is, however, to co-immobilize proteins with DNA origami at pre-determined substrate sites in high contrast relative to the nontarget areas. The immobilization should, in addition, preferably be achieved on a transparent substrate to allow ultrasensitive optical detection. If successful, specific co-binding would be a step towards stoichiometrically defined arrays with few to individual protein molecules per site. Here, we successfully immobilize with high specificity positively charged avidin proteins and negatively charged DNA origami nanoplates on 100 nm-wide carbon nanoislands while suppressing undesired adsorption to surrounding nontarget areas. The arrays on glass slides achieve unprecedented selectivity factors of up to 4000 and allow ultrasensitive fluorescence read-out. The co-immobilization onto the nanoislands leads to layered biomolecular architectures, which are functional because bound DNA origami influences the number of capturing sites on the nanopatches for other proteins. The novel hybrid DNA origami-protein nanoarrays allow the fabrication of versatile research platforms for applications in biosensing, biophysics, and cell biology, and, in addition, represent an important step towards single-molecule protein arrays.
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Affiliation(s)
- Roland Hager
- Center for Advanced Bioanalysis GmbH, 4020, Linz, Austria
| | - Jonathan R Burns
- Department of Chemistry, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Martyna J Grydlik
- Institute for Semiconductor and Solid State Physics, Johannes Kepler University, 4040, Linz, Austria
| | - Alma Halilovic
- Institute for Semiconductor and Solid State Physics, Johannes Kepler University, 4040, Linz, Austria
| | | | - Friedrich Schäffler
- Institute for Semiconductor and Solid State Physics, Johannes Kepler University, 4040, Linz, Austria
| | - Stefan Howorka
- Center for Advanced Bioanalysis GmbH, 4020, Linz, Austria
- Department of Chemistry, Institute of Structural and Molecular Biology, University College London, London, UK
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Ariga K, Li J, Fei J, Ji Q, Hill JP. Nanoarchitectonics for Dynamic Functional Materials from Atomic-/Molecular-Level Manipulation to Macroscopic Action. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:1251-86. [PMID: 26436552 DOI: 10.1002/adma.201502545] [Citation(s) in RCA: 291] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 07/27/2015] [Indexed: 05/21/2023]
Abstract
Objects in all dimensions are subject to translational dynamism and dynamic mutual interactions, and the ability to exert control over these events is one of the keys to the synthesis of functional materials. For the development of materials with truly dynamic functionalities, a paradigm shift from "nanotechnology" to "nanoarchitectonics" is proposed, with the aim of design and preparation of functional materials through dynamic harmonization of atomic-/molecular-level manipulation and control, chemical nanofabrication, self-organization, and field-controlled organization. Here, various examples of dynamic functional materials are presented from the atom/molecular-level to macroscopic dimensions. These systems, including atomic switches, molecular machines, molecular shuttles, motional crystals, metal-organic frameworks, layered assemblies, gels, supramolecular assemblies of biomaterials, DNA origami, hollow silica capsules, and mesoporous materials, are described according to their various dynamic functions, which include short-term plasticity, long-term potentiation, molecular manipulation, switchable catalysis, self-healing properties, supramolecular chirality, morphological control, drug storage and release, light-harvesting, mechanochemical transduction, molecular tuning molecular recognition, hand-operated nanotechnology.
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Affiliation(s)
- Katsuhiko Ariga
- World Premier International (WPI) Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, 305-0044, Japan
| | - Junbai Li
- Beijing National Laboratory for Molecular Science, CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Science, Beijing, 100190, P. R. China
| | - Jinbo Fei
- Beijing National Laboratory for Molecular Science, CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Science, Beijing, 100190, P. R. China
| | - Qingmin Ji
- World Premier International (WPI) Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, 305-0044, Japan
| | - Jonathan P Hill
- World Premier International (WPI) Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, 305-0044, Japan
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Ariga K, Minami K, Shrestha LK. Nanoarchitectonics for carbon-material-based sensors. Analyst 2016; 141:2629-38. [DOI: 10.1039/c6an00057f] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Recently, the nanoarchitectonics concept has been proposed to fabricate functional materials on the basis of concerted harmonization actions to control materials organization.
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Affiliation(s)
- Katsuhiko Ariga
- World Premier International Center for Materials Nanoarchitectonics (WPI-MANA)
- National Institute for Materials Science (NIMS)
- Tsukuba 305-0044
- Japan
| | - Kosuke Minami
- World Premier International Center for Materials Nanoarchitectonics (WPI-MANA)
- National Institute for Materials Science (NIMS)
- Tsukuba 305-0044
- Japan
| | - Lok Kumar Shrestha
- World Premier International Center for Materials Nanoarchitectonics (WPI-MANA)
- National Institute for Materials Science (NIMS)
- Tsukuba 305-0044
- Japan
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26
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Ariga K, Naito M, Ji Q, Payra D. Molecular cavity nanoarchitectonics for biomedical application and mechanical cavity manipulation. CrystEngComm 2016. [DOI: 10.1039/c6ce00432f] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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27
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Lee DS, Qian H, Tay CY, Leong DT. Cellular processing and destinies of artificial DNA nanostructures. Chem Soc Rev 2016; 45:4199-225. [DOI: 10.1039/c5cs00700c] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This review gives a panoramic view of the many DNA nanotechnology applications in cells, mechanistic understanding of how and where their interactions occur and their subsequent outcomes.
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Affiliation(s)
- Di Sheng Lee
- Department of Chemical and Biomolecular Engineering
- National University of Singapore
- Singapore 117585
- Singapore
- Department of Materials Science and Engineering
| | - Hang Qian
- Department of Chemical and Biomolecular Engineering
- National University of Singapore
- Singapore 117585
- Singapore
| | - Chor Yong Tay
- Department of Chemical and Biomolecular Engineering
- National University of Singapore
- Singapore 117585
- Singapore
- School of Materials Science and Engineering
| | - David Tai Leong
- Department of Chemical and Biomolecular Engineering
- National University of Singapore
- Singapore 117585
- Singapore
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28
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Fornaro T, Burini D, Biczysko M, Barone V. Hydrogen-Bonding Effects on Infrared Spectra from Anharmonic Computations: Uracil–Water Complexes and Uracil Dimers. J Phys Chem A 2015; 119:4224-36. [DOI: 10.1021/acs.jpca.5b01561] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Teresa Fornaro
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
| | - Diletta Burini
- Dipartimento
di Matematica e Informatica, Università di Perugia, INFN Sezione
Perugia Via Vanvitelli, I-106123 Perugia, Italy
| | - Malgorzata Biczysko
- Physics
Department, and International Centre for Quantum and Molecular Structures, Shanghai University, 99 Shangda Road, Shanghai, 200444 China
- Consiglio
Nazionale delle Ricerche, Istituto di Chimica dei Composti OrganoMetallici
(ICCOM-CNR), UOS di Pisa, Area della Ricerca CNR, Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
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29
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30
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Fornaro T, Carnimeo I, Biczysko M. Toward Feasible and Comprehensive Computational Protocol for Simulation of the Spectroscopic Properties of Large Molecular Systems: The Anharmonic Infrared Spectrum of Uracil in the Solid State by the Reduced Dimensionality/Hybrid VPT2 Approach. J Phys Chem A 2014; 119:5313-26. [DOI: 10.1021/jp510101y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Teresa Fornaro
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
| | - Ivan Carnimeo
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
- Compunet, Istituto Italiano di Tecnologia (IIT), Via Morego 30, I-16163 Genova, Italy
| | - Malgorzata Biczysko
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
- Istituto di Chimica
dei Composti OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area della
Ricerca CNR, Consiglio Nazionale delle Ricerche, Via G. Moruzzi 1, I-56124 Pisa, Italy
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31
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Avinash MB, Govindaraju T. Nanoarchitectonics of biomolecular assemblies for functional applications. NANOSCALE 2014; 6:13348-69. [PMID: 25287110 DOI: 10.1039/c4nr04340e] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The stringent processes of natural selection and evolution have enabled extraordinary structure-function properties of biomolecules. Specifically, the archetypal designs of biomolecules, such as amino acids, nucleobases, carbohydrates and lipids amongst others, encode unparalleled information, selectivity and specificity. The integration of biomolecules either with functional molecules or with an embodied functionality ensures an eclectic approach for novel and advanced nanotechnological applications ranging from electronics to biomedicine, besides bright prospects in systems chemistry and synthetic biology. Given this intriguing scenario, our feature article intends to shed light on the emerging field of functional biomolecular engineering.
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Affiliation(s)
- M B Avinash
- Bioorganic Chemistry Laboratory, New Chemistry Unit (NCU), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur P. O., Bangalore 560064, India.
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32
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Conway JW, Madwar C, Edwardson TG, McLaughlin CK, Fahkoury J, Lennox RB, Sleiman HF. Dynamic Behavior of DNA Cages Anchored on Spherically Supported Lipid Bilayers. J Am Chem Soc 2014; 136:12987-97. [PMID: 25140890 DOI: 10.1021/ja506095n] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- J. W. Conway
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - C. Madwar
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - T. G. Edwardson
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - C. K. McLaughlin
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - J. Fahkoury
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - R. B. Lennox
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - H. F. Sleiman
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
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33
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Taguchi T, Endo Y. Crosslinking liposomes/cells using cholesteryl group-modified tilapia gelatin. Int J Mol Sci 2014; 15:13123-34. [PMID: 25056548 PMCID: PMC4139895 DOI: 10.3390/ijms150713123] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 07/14/2014] [Accepted: 07/15/2014] [Indexed: 11/17/2022] Open
Abstract
Cholesteryl group-modified tilapia gelatins (Chol-T-Gltns) with various Chol contents from 3 to 69 mol % per amino group of Gltn were prepared for the assembly of liposomes and cells. Liposomes were physically crosslinked by anchoring Chol groups of Chol-T-Gltns into lipid membranes. The resulting liposome gels were enzymatically degraded by addition of collagenase. Liposome gels prepared using Chol-T-Gltn with high Chol content (69Chol-T-Gltn) showed slower enzymatic degradation when compared with gels prepared using Chol-T-Gltn with low Chol content (3Chol-T-Gltn). The hepatocyte cell line HepG2 showed good assembly properties and no cytotoxic effects after addition of 69Chol-T-Gltns. In addition, the number of HepG2 cells increased with concentration of 69Chol-T-Gltns. Therefore, Chol-T-Gltn, particularly, 69Chol-T-Gltn, can be used as an assembling material for liposomes and various cell types. The resulting organization can be applied to various biomedical fields, such as drug delivery systems, tissue engineering and regenerative medicine.
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Affiliation(s)
- Tetsushi Taguchi
- Biomaterials Unit, Nano-Life Field, International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan.
| | - Yoshiaki Endo
- Biomaterials Unit, Nano-Life Field, International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan.
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34
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Fornaro T, Biczysko M, Monti S, Barone V. Dispersion corrected DFT approaches for anharmonic vibrational frequency calculations: nucleobases and their dimers. Phys Chem Chem Phys 2014; 16:10112-28. [PMID: 24531740 PMCID: PMC4612423 DOI: 10.1039/c3cp54724h] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Computational spectroscopy techniques have become in the last few years an effective means to analyze and assign infrared (IR) spectra of molecular systems of increasing dimensions and in different environments. However, transition from compilation of harmonic data to fully anharmonic simulations of spectra is still underway. The most promising results for large systems have been obtained, in our opinion, by perturbative vibrational approaches based on potential energy surfaces computed by hybrid (especially B3LYP) density functionals and medium size (e.g. SNSD) basis sets. In this framework, we are actively developing a comprehensive and robust computational protocol aimed at quantitative reproduction of the spectra of nucleic acid base complexes and their adsorption on solid supports (organic/inorganic). In this contribution we report the essential results of the first step devoted to isolated monomers and dimers. It is well known that in order to model the vibrational spectra of weakly bound molecular complexes dispersion interactions should be taken into proper account. In this work we have chosen two popular and inexpensive approaches to model dispersion interactions, namely the semi-empirical dispersion correction (D3) and pseudopotential based (DCP) methodologies both in conjunction with the B3LYP functional. These have been used for simulating fully anharmonic IR spectra of nucleobases and their dimers through generalized second order vibrational perturbation theory (GVPT2). We have studied, in particular, isolated adenine, hypoxanthine, uracil, thymine and cytosine, the hydrogen-bonded and stacked adenine and uracil dimers, and the stacked adenine-naphthalene heterodimer. Anharmonic frequencies are compared with standard B3LYP results and experimental findings, while the computed interaction energies and structures of complexes are compared to the best available theoretical estimates.
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Affiliation(s)
- Teresa Fornaro
- Scuola Normale Superiore, piazza dei Cavalieri 7, I-56126 Pisa, Italy.
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35
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Schade M, Berti D, Huster D, Herrmann A, Arbuzova A. Lipophilic nucleic acids--a flexible construction kit for organization and functionalization of surfaces. Adv Colloid Interface Sci 2014; 208:235-51. [PMID: 24650567 DOI: 10.1016/j.cis.2014.02.019] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 02/26/2014] [Accepted: 02/26/2014] [Indexed: 11/19/2022]
Abstract
Lipophilic nucleic acids have become a versatile tool for structuring and functionalization of lipid bilayers and biological membranes as well as cargo vehicles to transport and deliver bioactive compounds, like interference RNA, into cells by taking advantage of reversible hybridization with complementary strands. This contribution reviews the different types of conjugates of lipophilic nucleic acids, and their physicochemical and self-assembly properties. Strategies for choosing a nucleic acid, lipophilic modification, and linker are discussed. Interaction with lipid membranes and its stability, dynamic structure and assembly of lipophilic nucleic acids upon embedding into biological membranes are specific points of the review. A large diversity of conjugates including lipophilic peptide nucleic acid and siRNA provides tailored solutions for specific applications in bio- and nanotechnology as well as in cell biology and medicine, as illustrated through some selected examples.
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Affiliation(s)
- Matthias Schade
- Humboldt-Universität zu Berlin, Institut für Biologie, Invalidenstr. 42, 10115 Berlin, Germany
| | - Debora Berti
- Dipartimento di Chimica, Universita' di Firenze & CSGI, Via della Lastruccia 3, 50019 Sesto Fiorentino, Firenze, Italy
| | - Daniel Huster
- Universität Leipzig, Institut für Medizinische Physik und Biophysik, Härtelstr. 16-18, 04107 Leipzig, Germany
| | - Andreas Herrmann
- Humboldt-Universität zu Berlin, Institut für Biologie, Invalidenstr. 42, 10115 Berlin, Germany
| | - Anna Arbuzova
- Humboldt-Universität zu Berlin, Institut für Biologie, Invalidenstr. 42, 10115 Berlin, Germany.
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36
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Howorka S, Hesse J. Microarrays and single molecules: an exciting combination. SOFT MATTER 2014; 10:931-41. [PMID: 24651891 DOI: 10.1039/c3sm52561a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Biomolecules positioned at interfaces have spawned many applications in bioanalysis, biophysics, and cell biology. This Highlight describes recent developments in the research areas of protein and DNA arrays, and single-molecule sensing. We cover the ultrasensitive scanning of conventional microarrays as well as the generation of arrays composed of individual molecules. The combination of these tools has improved the detection limits and the dynamic range of microarray analysis, helped develop powerful single-molecule sequencing approaches, and offered biophysical examination with high throughput and molecular detail. The topic of this Highlight integrates several disciplines and is written for interested chemists, biophysicists and nanotechnologists.
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Affiliation(s)
- Stefan Howorka
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London WC1H 0AJ, UK.
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37
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Tanabe K, Ando Y, Hara D, Ito T, Nishimoto SI. Oligonucleotides with consecutive alkylated phosphate units: aggregation characteristics and drug transport into living cells. RSC Adv 2014. [DOI: 10.1039/c3ra47662f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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38
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Sikora JR, Rauzan B, Stegemann R, Deckert A. Modeling stopped-flow data for nucleic acid duplex formation reactions: the importance of off-path intermediates. J Phys Chem B 2013; 117:8966-76. [PMID: 23902467 DOI: 10.1021/jp404550a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Evidence for unexpected off-path intermediates to DNA duplex formation is presented. These off-path intermediates are shown to involve unimolecular and, in one case, bimolecular structure in one of the single strands of complementary DNA. Three models are developed to account for the observed single-stranded structures that are formed in parallel with duplex formation. These models are applied to the analysis of stopped-flow data for eight different nonself-complementary duplex formation reactions in order to extract the elementary rate constant for formation of the duplex from the complementary random coil single-stranded DNA. The free energy of activation (at 25 °C) for the denaturation of each duplex is calculated from these data and is shown to have a linear correlation to the overall standard free energy for duplex formation (also at 25 °C). Duplexes that contain mismatches obey a parallel linear free-energy (LFE) relationship with a y-intercept that is greater than that of duplexes without mismatches. Slopes near unity for the LFE relationships indicate that all duplexes go through an early, unstructured transition state.
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Affiliation(s)
- Jacqueline R Sikora
- Department of Chemistry, Allegheny College, 520 North Main Street, Meadville, Pennsylvania 16335, USA
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39
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Mendez MA, Szalai VA. Synapsable quadruplex-mediated fibers. NANOSCALE RESEARCH LETTERS 2013; 8:210. [PMID: 23641903 PMCID: PMC3655031 DOI: 10.1186/1556-276x-8-210] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 04/20/2013] [Indexed: 06/02/2023]
Abstract
We have fabricated a DNA-based nanofiber created by self-assembly of guanine quadruplex (Hoogsteen base pairing) and double-stranded DNA (Watson-Crick base pairing). When duplexes containing a long stretch of contiguous guanines and single-stranded overhangs are incubated in potassium-containing buffer, the preformed duplexes create high molecular weight species that contain quadruplexes. In addition to observation of these larger species by gel electrophoresis, solutions were analyzed by atomic force microscopy to reveal nanofibers. Analysis of the atomic force microscopy images indicates that fibers form with lengths ranging from 250 to 2,000 nm and heights from 0.45 to 4.0 nm. This work is a first step toward the creation of new structurally heterogeneous (quadruplex/duplex), yet controllable, DNA-based materials exhibiting novel properties suitable for a diverse array of nanotechnology applications.
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Affiliation(s)
- Miguel Angel Mendez
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Drive, Baltimore, MD, 21250, USA
- Universidad San Francisco de Quito, Vía Interoceánica Km 2 1/2, Cumbayá, Quito, 17-1200-84, Ecuador
| | - Veronika A Szalai
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Drive, Baltimore, MD, 21250, USA
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899-6204, USA
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