1
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Jiang C, Tan R, Li W, Zhang Y, Liu H. Subtraction-based DNA Origami Cryptography by using Structural Defects for Information Encryption. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2406470. [PMID: 39396380 DOI: 10.1002/smll.202406470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 09/19/2024] [Indexed: 10/15/2024]
Abstract
Conventional cryptographic methods rely on increased computational complexity to counteract the threat posed by growing computing power for sustainable protection. DNA cryptography circumvents this threat by leveraging complex DNA recognition to maintain information security. Specifically, DNA origami has been repurposed for cryptography, using programmable folding of the long scaffold strand carrying additional tagged strands for information encryption. Herein, a subtraction-based cryptographic strategy is presented that uses structural defects on DNA origami to contain encrypted information. Designated staple strands are removed from the staple pool with "hook" strands to create active defect sites on DNA origami for information encryption. These defects can be filled by incubating the structures with the intact pool of biotinylated staple strands, resulting in biotin patterns that can be used for protein-binding steganography. The yields of individual protein pixels reached over 91%, and self-correction codes are implemented to aid the information recovery. Furthermore, the encrypted organization of defective DNA origami structures is investigated to explore the potential of this method for scalable information storage. This method uses DNA origami to encrypt information in hidden structural features, utilizing subtraction for robust cryptography while ensuring the safety and recovery of data.
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Affiliation(s)
- Chu Jiang
- School of Chemical Science and Engineering, Shanghai Research Institute for Intelligent Autonomous Systems, Key Laboratory of Advanced Civil Engineering Materials of Ministry of Education, Tongji University, Shanghai, 200092, China
| | - Ruihao Tan
- School of Chemical Science and Engineering, Shanghai Research Institute for Intelligent Autonomous Systems, Key Laboratory of Advanced Civil Engineering Materials of Ministry of Education, Tongji University, Shanghai, 200092, China
| | - Weiying Li
- College of Environmental Science and Engineering, Shanghai Institute of Pollution Control and Ecological Security, State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai, 200092, China
| | - Yinan Zhang
- School of Chemical Science and Engineering, Shanghai Research Institute for Intelligent Autonomous Systems, Key Laboratory of Advanced Civil Engineering Materials of Ministry of Education, Tongji University, Shanghai, 200092, China
| | - Huajie Liu
- School of Chemical Science and Engineering, Shanghai Research Institute for Intelligent Autonomous Systems, Key Laboratory of Advanced Civil Engineering Materials of Ministry of Education, Tongji University, Shanghai, 200092, China
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2
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Kalra S, Donnelly A, Singh N, Matthews D, Del Villar-Guerra R, Bemmer V, Dominguez C, Allcock N, Cherny D, Revyakin A, Rusling DA. Functionalizing DNA Origami by Triplex-Directed Site-Specific Photo-Cross-Linking. J Am Chem Soc 2024; 146:13617-13628. [PMID: 38695163 PMCID: PMC11100008 DOI: 10.1021/jacs.4c03413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024]
Abstract
Here, we present a cross-linking approach to covalently functionalize and stabilize DNA origami structures in a one-pot reaction. Our strategy involves adding nucleotide sequences to adjacent staple strands, so that, upon assembly of the origami structure, the extensions form short hairpin duplexes targetable by psoralen-labeled triplex-forming oligonucleotides bearing other functional groups (pso-TFOs). Subsequent irradiation with UVA light generates psoralen adducts with one or both hairpin staples leading to site-specific attachment of the pso-TFO (and attached group) to the origami with ca. 80% efficiency. Bis-adduct formation between strands in proximal hairpins further tethers the TFO to the structure and generates "superstaples" that improve the structural integrity of the functionalized complex. We show that directing cross-linking to regions outside of the origami core dramatically reduces sensitivity of the structures to thermal denaturation and disassembly by T7 RNA polymerase. We also show that the underlying duplex regions of the origami core are digested by DNase I and thus remain accessible to read-out by DNA-binding proteins. Our strategy is scalable and cost-effective, as it works with existing DNA origami structures, does not require scaffold redesign, and can be achieved with just one psoralen-modified oligonucleotide.
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Affiliation(s)
- Shantam Kalra
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Amber Donnelly
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Nishtha Singh
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Daniel Matthews
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Rafael Del Villar-Guerra
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Victoria Bemmer
- Centre
for Enzyme Innovation, School of Biological Sciences, University of Portsmouth, Portsmouth, Hampshire PO1 2DY, U.K.
| | - Cyril Dominguez
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Natalie Allcock
- Core
Biotechnology Services Electron Microscopy Facility, University of Leicester, Leicester LE1 7RH, U.K.
| | - Dmitry Cherny
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Andrey Revyakin
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - David A. Rusling
- School
of Medicine, Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DT, U.K.
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3
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Kominami H, Hirata Y, Yamada H, Kobayashi K. Protein nanoarrays using the annexin A5 two-dimensional crystal on supported lipid bilayers. NANOSCALE ADVANCES 2023; 5:3862-3870. [PMID: 37496624 PMCID: PMC10368004 DOI: 10.1039/d3na00335c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 06/16/2023] [Indexed: 07/28/2023]
Abstract
Protein nanoarrays are regularly ordered patterns of proteins fixed on a solid surface with a periodicity on the order of nanometers. They have significant potential applications as highly sensitive bioassays and biosensors. While several researchers have demonstrated the fabrication of protein nanoarrays with lithographic techniques and programmed DNA nanostructures, it has been difficult to fabricate a protein nanoarray containing a massive number of proteins on the surface. We now report the fabrication of nanoarrays of streptavidin molecules using a two-dimensional (2D) crystal of annexin A5 as a template on supported lipid bilayers that are widely used as cell membranes. The 2D crystal of annexin A5 has a six-fold symmetry with a period of about 18 nm. There is a hollow of a diameter of about 10 nm in the unit cell, surrounded by six trimers of annexin A5. We found that a hollow accommodates up to three streptavidin molecules with their orientation controlled, and confirmed that the molecules in the hollow maintain their specific binding capability to biotinylated molecules, which demonstrates that the fabricated nanoarray serves as an effective biosensing platform. This methodology can be directly applied to the fabrication of nanoarrays containing a massive number of any other protein molecules.
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Affiliation(s)
- Hiroaki Kominami
- Department of Electronic Science and Engineering, Kyoto University, Kyoto University Katsura Nishikyo Kyoto 615-8510 Japan
| | - Yoshiki Hirata
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology 1-1-1 Higashi Tsukuba 305-8566 Japan
| | - Hirofumi Yamada
- Department of Electronic Science and Engineering, Kyoto University, Kyoto University Katsura Nishikyo Kyoto 615-8510 Japan
| | - Kei Kobayashi
- Department of Electronic Science and Engineering, Kyoto University, Kyoto University Katsura Nishikyo Kyoto 615-8510 Japan
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4
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Knappe GA, Wamhoff EC, Bathe M. Functionalizing DNA origami to investigate and interact with biological systems. NATURE REVIEWS. MATERIALS 2023; 8:123-138. [PMID: 37206669 PMCID: PMC10191391 DOI: 10.1038/s41578-022-00517-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/11/2022] [Indexed: 05/21/2023]
Abstract
DNA origami has emerged as a powerful method to generate DNA nanostructures with dynamic properties and nanoscale control. These nanostructures enable complex biophysical studies and the fabrication of next-generation therapeutic devices. For these applications, DNA origami typically needs to be functionalized with bioactive ligands and biomacromolecular cargos. Here, we review methods developed to functionalize, purify, and characterize DNA origami nanostructures. We identify remaining challenges, such as limitations in functionalization efficiency and characterization. We then discuss where researchers can contribute to further advance the fabrication of functionalized DNA origami.
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Affiliation(s)
- Grant A. Knappe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Address correspondence to or
| | - Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Address correspondence to or
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5
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Domínguez CM, García-Chamé M, Müller U, Kraus A, Gordiyenko K, Itani A, Haschke H, Lanzerstorfer P, Rabe KS, Niemeyer CM. Linker Engineering of Ligand-Decorated DNA Origami Nanostructures Affects Biological Activity. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2202704. [PMID: 35934828 DOI: 10.1002/smll.202202704] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 07/11/2022] [Indexed: 06/15/2023]
Abstract
News from an old acquaintance: The streptavidin (STV)-biotin binding system is frequently used for the decoration of DNA origami nanostructures (DON) to study biological systems. Here, a surprisingly high dynamic of the STV/DON interaction is reported, which is affected by the structure of the DNA linker system. Analysis of different mono- or bi-dentate linker architectures on DON with a novel high-speed atomic force microscope (HS-AFM) enabling acquisition times as short as 50 ms per frame gave detailed insights into the dynamics of the DON/STV interaction, revealing dwell times in the sub-100 millisecond range. The linker systems are also used to present biotinylated epidermal growth factor on DON to study the activation of the epidermal growth factor receptor signaling cascade in HeLa cells. The studies confirm that cellular activation correlated with the binding properties of linker-specific STV/DON interactions observed by HS-AFM. This work sheds more light on the commonly used STV/DON system and will help to further standardize the use of DNA nanostructures for the study of biological processes.
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Affiliation(s)
- Carmen M Domínguez
- Institute for Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany
| | - Miguel García-Chamé
- Institute for Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany
| | - Ulrike Müller
- School of Engineering, University of Applied Sciences Upper Austria, Wels, 4600, Austria
| | - Andreas Kraus
- Bruker Nano GmbH, JPK BioAFM, Am Studio 2D, 12489, Berlin, Germany
| | - Klavdiya Gordiyenko
- Institute for Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany
| | - Ahmad Itani
- Institute for Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany
| | - Heiko Haschke
- Bruker Nano GmbH, JPK BioAFM, Am Studio 2D, 12489, Berlin, Germany
| | - Peter Lanzerstorfer
- School of Engineering, University of Applied Sciences Upper Austria, Wels, 4600, Austria
| | - Kersten S Rabe
- Institute for Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany
| | - Christof M Niemeyer
- Institute for Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany
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6
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Kong G, Xiong M, Liu L, Hu L, Meng HM, Ke G, Zhang XB, Tan W. DNA origami-based protein networks: from basic construction to emerging applications. Chem Soc Rev 2021; 50:1846-1873. [PMID: 33306073 DOI: 10.1039/d0cs00255k] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Natural living systems are driven by delicate protein networks whose functions are precisely controlled by many parameters, such as number, distance, orientation, and position. Focusing on regulation rather than just imitation, the construction of artificial protein networks is important in many research areas, including biomedicine, synthetic biology and chemical biology. DNA origami, sophisticated nanostructures with rational design, can offer predictable, programmable, and addressable scaffolds for protein assembly with nanometer precision. Recently, many interdisciplinary efforts have achieved the precise construction of DNA origami-based protein networks, and their emerging application in many areas. To inspire more fantastic research and applications, herein we highlight the applicability and potentiality of DNA origami-based protein networks. After a brief introduction to the development and features of DNA origami, some important factors for the precise construction of DNA origami-based protein networks are discussed, including protein-DNA conjugation methods, networks with different patterns and the controllable parameters in the networks. The discussion then focuses on the emerging application of DNA origami-based protein networks in several areas, including enzymatic reaction regulation, sensing, bionics, biophysics, and biomedicine. Finally, current challenges and opportunities in this research field are discussed.
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Affiliation(s)
- Gezhi Kong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Mengyi Xiong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Lu Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Ling Hu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Hong-Min Meng
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou 450001, China
| | - Guoliang Ke
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Xiao-Bing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
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7
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Weinhold E, Chakraborty B. DNA modification and visualization on an origami-based enzyme nano-factory. NANOSCALE 2021; 13:2465-2471. [PMID: 33471009 DOI: 10.1039/d0nr07618j] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The past decade has seen enormous progress in DNA nanotechnology through the advent of DNA origami. Functionalizing the DNA origami for multiple applications is the recent focus of this field. Here we have constructed a novel DNA enzyme nano-factory, which modifies target DNA embedded on a DNA origami platform. The enzyme is programmed to reside in close proximity to the target DNA which enhances significantly the local concentration compared to solution-based DNA modification. To demonstrate this we have immobilized DNA methyltransferase M·TaqI next to the target DNA on the DNA origami and used this enzyme to sequence-specifically modify the target DNA with biotin using a cofactor analogue. Streptavidin binding to biotin is applied as a topographic marker to follow the machine cycle of this enzyme nano-factory using atomic force microscopy imaging. The nano-factory is demonstrated to be recyclable and holds the potential to be expanded to a multi-enzyme, multi-substrate operating system controlled by simple to complex molecules made of DNA, RNA or proteins.
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Affiliation(s)
- Elmar Weinhold
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
| | - Banani Chakraborty
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, India.
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8
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Gerrits L, Hammink R, Kouwer PHJ. Semiflexible polymer scaffolds: an overview of conjugation strategies. Polym Chem 2021. [DOI: 10.1039/d0py01662d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Semiflexible polymers are excellent scaffolds for the presentation of a wide variety of (bio)molecules. This manuscript reviews advantages and challenges of the most common conjugation strategies for the major classes of semiflexible polymers.
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Affiliation(s)
- Lotte Gerrits
- Institute for Molecules and Materials
- Radboud University
- 6525 AJ Nijmegen
- The Netherlands
| | - Roel Hammink
- Department of Tumor Immunology
- Radboud Institute for Molecular Life Sciences
- Radboud University Medical Center
- 6525 GA Nijmegen
- The Netherlands
| | - Paul H. J. Kouwer
- Institute for Molecules and Materials
- Radboud University
- 6525 AJ Nijmegen
- The Netherlands
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9
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Flores Bueso Y, Walker S, Quinn J, Tangney M. A novel cell permeability assay for macromolecules. BMC Mol Cell Biol 2020; 21:75. [PMID: 33126861 PMCID: PMC7602297 DOI: 10.1186/s12860-020-00321-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/20/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Many cell permeabilisation methods to mediate internalisation of various molecules to mammalian or bacterial cells have been developed. However, no size-specific permeability assay suitable for both cell types exists. RESULTS We report the use of intrinsically biotinylated cell components as the target for reporter molecules for assessing permeabilisation. Due to its well-described biotin binding activity, we developed an assay using Streptavidin (SAv) as a molecular weight marker for assessing eukaryotic and prokaryotic cell internalisation, using flow cytometry as a readout. This concept was tested here as part of the development of host DNA depletion strategies for microbiome analysis of formalin-fixed (FF) samples. Host depletion (HD) strategies require differential cell permeabilisation, where mammalian cells but not bacterial cells are permeabilised, and are subsequently treated with a nuclease. Here, the internalisation of a SAv-conjugate was used as a reference for nucleases of similar dimensions. With this assay, it was possible to demonstrate that formalin fixation does not generate pores which allow the introduction of 60 KDa molecules in mammalian or bacterial membranes/envelopes. Among surfactants tested, Saponin derived from Quillaja bark showed the best selectivity for mammalian cell permeabilisation, which, when coupled with Benzonase nuclease, provided the best results for host DNA depletion, representing a new HD strategy for formalin fixed samples. CONCLUSION The assay presented provides researchers with a sensitive and accessible tool for discerning membrane/cell envelop permeability for different size macromolecules.
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Affiliation(s)
- Yensi Flores Bueso
- CancerResearch@UCC, University College Cork, Cork, Ireland.,SynBioCentre, University College Cork, Cork, Ireland.,APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Sidney Walker
- CancerResearch@UCC, University College Cork, Cork, Ireland.,SynBioCentre, University College Cork, Cork, Ireland.,APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jennifer Quinn
- CancerResearch@UCC, University College Cork, Cork, Ireland
| | - Mark Tangney
- CancerResearch@UCC, University College Cork, Cork, Ireland. .,SynBioCentre, University College Cork, Cork, Ireland. .,APC Microbiome Ireland, University College Cork, Cork, Ireland.
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10
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Ngo TA, Dinh H, Nguyen TM, Liew FF, Nakata E, Morii T. Protein adaptors assemble functional proteins on DNA scaffolds. Chem Commun (Camb) 2019; 55:12428-12446. [PMID: 31576822 DOI: 10.1039/c9cc04661e] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
DNA is an attractive molecular building block to construct nanoscale structures for a variety of applications. In addition to their structure and function, modification the DNA nanostructures by other molecules opens almost unlimited possibilities for producing functional DNA-based architectures. Among the molecules to functionalize DNA nanostructures, proteins are one of the most attractive candidates due to their vast functional variations. DNA nanostructures loaded with various types of proteins hold promise for applications in the life and material sciences. When loading proteins of interest on DNA nanostructures, the nanostructures by themselves act as scaffolds to specifically control the location and number of protein molecules. The methods to arrange proteins of interest on DNA scaffolds at high yields while retaining their activity are still the most demanding task in constructing usable protein-modified DNA nanostructures. Here, we provide an overview of the existing methods applied for assembling proteins of interest on DNA scaffolds. The assembling methods were categorized into two main classes, noncovalent and covalent conjugation, with both showing pros and cons. The recent advance of DNA-binding adaptor mediated assembly of proteins on the DNA scaffolds is highlighted and discussed in connection with the future perspectives of protein assembled DNA nanoarchitectures.
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Affiliation(s)
- Tien Anh Ngo
- Vinmec Biobank, Hi-tech Center, Vinmec Healthcare System, 458 Minh Khai, Ha Noi, Vietnam
| | - Huyen Dinh
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Thang Minh Nguyen
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Fong Fong Liew
- MAHSA University, Faculty of Dentistry, Bandar Saujana Putra, 42610 Jenjarom, Selangor, Malaysia
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
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11
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Jahanban-Esfahlan R, Seidi K, Jahanban-Esfahlan A, Jaymand M, Alizadeh E, Majdi H, Najjar R, Javaheri T, Zare P. Static DNA Nanostructures For Cancer Theranostics: Recent Progress In Design And Applications. Nanotechnol Sci Appl 2019; 12:25-46. [PMID: 31686793 PMCID: PMC6800557 DOI: 10.2147/nsa.s227193] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 09/13/2019] [Indexed: 12/13/2022] Open
Abstract
Among the various nano/biomaterials used in cancer treatment, the beauty and benefits of DNA nanocomposites are outstanding. The specificity and programmability of the base pairing of DNA strands, together with their ability to conjugate with different types of functionalities have realized unsurpassed potential for the production of two- and three-dimensional nano-sized structures in any shape, size, surface chemistry and functionality. This review aims to provide an insight into the diversity of static DNA nanodevices, including DNA origami, DNA polyhedra, DNA origami arrays and bioreactors, DNA nanoswitch, DNA nanoflower, hydrogel and dendrimer as young but promising platforms for cancer theranostics. The utility and potential of the individual formats in biomedical science and especially in cancer therapy will be discussed.
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Affiliation(s)
- Rana Jahanban-Esfahlan
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz9841, Iran
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz9841, Iran
| | - Khaled Seidi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz9841, Iran
| | | | - Mehdi Jaymand
- Nano Drug Delivery Research Center (NDDRC), Kermanshah University of Medical Sciences, Kermanshah9883, Iran
| | - Effat Alizadeh
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz9841, Iran
| | - Hasan Majdi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz9841, Iran
| | - Reza Najjar
- Polymer Research Laboratory, Faculty of Chemistry, University of Tabriz, Tabriz9841, Iran
| | - Tahereh Javaheri
- Ludwig Boltzmann Institute for Cancer Research, Vienna1090, Austria
| | - Peyman Zare
- Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw01-938, Poland
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12
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Mathur D, Medintz IL. The Growing Development of DNA Nanostructures for Potential Healthcare-Related Applications. Adv Healthc Mater 2019; 8:e1801546. [PMID: 30843670 PMCID: PMC9285959 DOI: 10.1002/adhm.201801546] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/17/2019] [Indexed: 12/21/2022]
Abstract
DNA self-assembly has proven to be a highly versatile tool for engineering complex and dynamic biocompatible nanostructures from the bottom up with a wide range of potential bioapplications currently being pursued. Primary among these is healthcare, with the goal of developing diagnostic, imaging, and drug delivery devices along with combinatorial theranostic devices. The path to understanding a role for DNA nanotechnology in biomedical sciences is being approached carefully and systematically, starting from analyzing the stability and immune-stimulatory properties of DNA nanostructures in physiological conditions, to estimating their accessibility and application inside cellular and model animal systems. Much remains to be uncovered but the field continues to show promising results toward developing useful biomedical devices. This review discusses some aspects of DNA nanotechnology that makes it a favorable ingredient for creating nanoscale research and biomedical devices and looks at experiments undertaken to determine its stability in vivo. This is presented in conjugation with examples of state-of-the-art developments in biomolecular sensing, imaging, and drug delivery. Finally, some of the major challenges that warrant the attention of the scientific community are highlighted, in order to advance the field into clinically relevant applications.
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Affiliation(s)
- Divita Mathur
- Center for Bio/Molecular Science and EngineeringU.S. Naval Research Laboratory Code 6910WashingtonDC20375USA
- College of ScienceGeorge Mason UniversityFairfaxVA22030USA
| | - Igor L. Medintz
- Center for Bio/Molecular Science and EngineeringU.S. Naval Research Laboratory Code 6907WashingtonDC20375USA
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13
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Yoo S, Dugasani SR, Chopade P, Kesama MR, Gnapareddy B, Park SH. Metal and Lanthanide Ion-Co-doped Synthetic and Salmon DNA Thin Films. ACS OMEGA 2019; 4:6530-6537. [PMID: 31459784 PMCID: PMC6648499 DOI: 10.1021/acsomega.9b00319] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 03/28/2019] [Indexed: 05/27/2023]
Abstract
Researchers have begun to use DNA molecules as an efficient template for arrangement of multiple functionalized nanomaterials for specific target applications. In this research, we demonstrated a simple process to co-dope synthetic DNA nanostructures (by a substrate-assisted growth method) and natural salmon DNA thin films (by a drop-casting method) with divalent metal ions (M2+, e.g., Co2+ and Cu2+) and trivalent lanthanide ions (Ln3+, e.g., Tb3+ and Eu3+). To identify the relationship among the DNA and dopant ions, DNA nanostructures were constructed while varying the Ln3+ concentration ([Ln3+]) at a fixed [M2+] with ion combinations of Co2+-Tb3+, Co2+-Eu3+, Cu2+-Tb3+, and Cu2+-Eu3+. Accordingly, we were able to estimate the critical [Ln3+] (named the optimum [Ln3+], [Ln3+]O) at a given [M2+] in the DNA nanostructures that corresponds to the phase change of the DNA nanostructures from crystalline to amorphous. The phase of the DNA nanostructures stayed crystalline up to [Tb3+]O ≡ 0.4 mM and [Eu3+]O ≡ 0.4 mM for Co2+ ([Tb3+]O ≡ 0.6 mM and [Eu3+]O ≡ 0.6 mM for Cu2+) and then changed to amorphous above 0.4 mM (0.6 mM). Consequently, phase diagrams of the four combinations of dopant ion pairs were created by analyzing the DNA lattice phases at given [M2+] and [Ln3+]. Interestingly, we observed extrema values of the measured physical quantities of DNA thin films near [Ln3+]O, where the maximum current, photoluminescence peak intensity, and minimum absorbance were obtained. M2+- and Ln3+-multidoped DNA nanostructures and DNA thin films may be utilized in the development of useful optoelectronic devices or sensors because of enhancement and contribution of multiple functionalities provided by M2+ and Ln3+.
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Affiliation(s)
- Sanghyun Yoo
- Department
of Physics and SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Republic
of Korea
| | - Sreekantha Reddy Dugasani
- Department
of Physics and SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Republic
of Korea
| | - Prathamesh Chopade
- Department
of Physics and SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Republic
of Korea
| | - Mallikarjuna Reddy Kesama
- Department
of Physics and SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Republic
of Korea
| | - Bramaramba Gnapareddy
- Department
of Physics and SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Republic
of Korea
| | - Sung Ha Park
- Department
of Physics and SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Republic
of Korea
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14
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Huang J, Park JH, Back SH, Feng Y, Cui C, Jin LY, Ahn DJ. Mercury ion-DNA specificity triggers a distinctive photoluminescence depression in organic semiconductor probes guided with a thymine-rich oligonucleotide sequence. NANOSCALE 2018; 10:17540-17545. [PMID: 30215088 DOI: 10.1039/c8nr03879a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
DNA strands have been recently found to play a role in crystallizing organic semiconductors as a substitute for conventional surfactants. Such DNA-guided organic semiconductor particles possessed the recognition ability to complementary target DNAs, resulting in "enhanced luminescence" due to the lesser degree of non-radiative dissipation. Apart from this, in this study we developed selective recognition of mercury ions by utilizing DNA probes having ion-specific thymine-rich motifs. Strikingly, the specific ion-DNA interaction triggered rather distinctive "depressed luminescence" emitting from the particles. The mercury ions were found to be present both at the surface and the inner regions, which were discovered to relate to the drastic morphological distortion of the particles as evidenced by elemental, electron microscopy, and confocal fluorescence microscopy analyses. This novel phenomenon discovered would expand the technological values of organic semiconductors conjugated with oligonucleotides toward a wider range of target-specific applications.
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Affiliation(s)
- Jietao Huang
- Department of Chemistry, College of Science, and Key Laboratory for Organism Resources of the Changbai Mountain and Functional Molecules, Ministry of Education, Yanbian University, Yanji 133002, China.
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15
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Choi Y, Kotthoff L, Olejko L, Resch-Genger U, Bald I. DNA Origami-Based Förster Resonance Energy-Transfer Nanoarrays and Their Application as Ratiometric Sensors. ACS APPLIED MATERIALS & INTERFACES 2018; 10:23295-23302. [PMID: 29916243 DOI: 10.1021/acsami.8b03585] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
DNA origami nanostructures provide a platform where dye molecules can be arranged with nanoscale accuracy allowing to assemble multiple fluorophores without dye-dye aggregation. Aiming to develop a bright and sensitive ratiometric sensor system, we systematically studied the optical properties of nanoarrays of dyes built on DNA origami platforms using a DNA template that provides a high versatility of label choice at minimum cost. The dyes are arranged at distances, at which they efficiently interact by Förster resonance energy transfer (FRET). To optimize array brightness, the FRET efficiencies between the donor fluorescein (FAM) and the acceptor cyanine 3 were determined for different sizes of the array and for different arrangements of the dye molecules within the array. By utilizing nanoarrays providing optimum FRET efficiency and brightness, we subsequently designed a ratiometric pH nanosensor using coumarin 343 as a pH-inert FRET donor and FAM as a pH-responsive acceptor. Our results indicate that the sensitivity of a ratiometric sensor can be improved simply by arranging the dyes into a well-defined array. The dyes used here can be easily replaced by other analyte-responsive dyes, demonstrating the huge potential of DNA nanotechnology for light harvesting, signal enhancement, and sensing schemes in life sciences.
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Affiliation(s)
- Youngeun Choi
- Department of Chemistry, Physical Chemistry , University of Potsdam , 14476 Potsdam , Germany
- BAM Federal Institute for Materials Research and Testing , 12489 Berlin , Germany
- School of Analytical Sciences Adlershof , Humboldt-Universität zu Berlin , 10099 Berlin , Germany
| | - Lisa Kotthoff
- Department of Chemistry, Physical Chemistry , University of Potsdam , 14476 Potsdam , Germany
- BAM Federal Institute for Materials Research and Testing , 12489 Berlin , Germany
| | - Lydia Olejko
- Department of Chemistry, Physical Chemistry , University of Potsdam , 14476 Potsdam , Germany
| | - Ute Resch-Genger
- BAM Federal Institute for Materials Research and Testing , 12489 Berlin , Germany
- School of Analytical Sciences Adlershof , Humboldt-Universität zu Berlin , 10099 Berlin , Germany
| | - Ilko Bald
- Department of Chemistry, Physical Chemistry , University of Potsdam , 14476 Potsdam , Germany
- BAM Federal Institute for Materials Research and Testing , 12489 Berlin , Germany
- School of Analytical Sciences Adlershof , Humboldt-Universität zu Berlin , 10099 Berlin , Germany
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16
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Liu Y, Kumar S, Taylor RE. Mix-and-match nanobiosensor design: Logical and spatial programming of biosensors using self-assembled DNA nanostructures. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2018; 10:e1518. [PMID: 29633568 DOI: 10.1002/wnan.1518] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 01/23/2018] [Accepted: 02/14/2018] [Indexed: 01/04/2023]
Abstract
The evergrowing need to understand and engineer biological and biochemical mechanisms has led to the emergence of the field of nanobiosensing. Structural DNA nanotechnology, encompassing methods such as DNA origami and single-stranded tiles, involves the base pairing-driven knitting of DNA into discrete one-, two-, and three-dimensional shapes at nanoscale. Such nanostructures enable a versatile design and fabrication of nanobiosensors. These systems benefit from DNA's programmability, inherent biocompatibility, and the ability to incorporate and organize functional materials such as proteins and metallic nanoparticles. In this review, we present a mix-and-match taxonomy and approach to designing nanobiosensors in which the choices of bioanalyte and transduction mechanism are fully independent of each other. We also highlight opportunities for greater complexity and programmability of these systems that are built using structural DNA nanotechnology. This article is categorized under: Implantable Materials and Surgical Technologies > Nanomaterials and Implants Diagnostic Tools > Biosensing Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.
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Affiliation(s)
- Ying Liu
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Sriram Kumar
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Rebecca E Taylor
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania.,Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania
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17
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Xavier PL, Chandrasekaran AR. DNA-based construction at the nanoscale: emerging trends and applications. NANOTECHNOLOGY 2018; 29:062001. [PMID: 29232197 DOI: 10.1088/1361-6528/aaa120] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The field of structural DNA nanotechnology has evolved remarkably-from the creation of artificial immobile junctions to the recent DNA-protein hybrid nanoscale shapes-in a span of about 35 years. It is now possible to create complex DNA-based nanoscale shapes and large hierarchical assemblies with greater stability and predictability, thanks to the development of computational tools and advances in experimental techniques. Although it started with the original goal of DNA-assisted structure determination of difficult-to-crystallize molecules, DNA nanotechnology has found its applications in a myriad of fields. In this review, we cover some of the basic and emerging assembly principles: hybridization, base stacking/shape complementarity, and protein-mediated formation of nanoscale structures. We also review various applications of DNA nanostructures, with special emphasis on some of the biophysical applications that have been reported in recent years. In the outlook, we discuss further improvements in the assembly of such structures, and explore possible future applications involving super-resolved fluorescence, single-particle cryo-electron (cryo-EM) and x-ray free electron laser (XFEL) nanoscopic imaging techniques, and in creating new synergistic designer materials.
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Affiliation(s)
- P Lourdu Xavier
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY) and Department of Physics, University of Hamburg, D-22607 Hamburg, Germany. Max-Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, D-22761 Hamburg, Germany
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18
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Ouyang X, De Stefano M, Krissanaprasit A, Bank Kodal AL, Bech Rosen C, Liu T, Helmig S, Fan C, Gothelf KV. Docking of Antibodies into the Cavities of DNA Origami Structures. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706765] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Xiangyuan Ouyang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education of China; Key Laboratory of Modern Separation Science in Shaanxi Province; College of Chemistry & Material Science; Northwest University; Xi'an 710127 China
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
- Division of Physical Biology, Bioimaging Center; Shanghai Synchrotron Radiation Facility (SSRF); Shanghai Institute of Applied Physics, Chinese Academy of Sciences; Shanghai 201800 China
| | - Mattia De Stefano
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
| | - Abhichart Krissanaprasit
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
- Present address: Department of Materials Science and Engineering; North Carolina State University; Raleigh NC 27606 USA
| | - Anne Louise Bank Kodal
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
| | - Christian Bech Rosen
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
| | - Tianqiang Liu
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
| | - Sarah Helmig
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
| | - Chunhai Fan
- Division of Physical Biology, Bioimaging Center; Shanghai Synchrotron Radiation Facility (SSRF); Shanghai Institute of Applied Physics, Chinese Academy of Sciences; Shanghai 201800 China
| | - Kurt V. Gothelf
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
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19
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Ouyang X, De Stefano M, Krissanaprasit A, Bank Kodal AL, Bech Rosen C, Liu T, Helmig S, Fan C, Gothelf KV. Docking of Antibodies into the Cavities of DNA Origami Structures. Angew Chem Int Ed Engl 2017; 56:14423-14427. [DOI: 10.1002/anie.201706765] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/18/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Xiangyuan Ouyang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education of China; Key Laboratory of Modern Separation Science in Shaanxi Province; College of Chemistry & Material Science; Northwest University; Xi'an 710127 China
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
- Division of Physical Biology, Bioimaging Center; Shanghai Synchrotron Radiation Facility (SSRF); Shanghai Institute of Applied Physics, Chinese Academy of Sciences; Shanghai 201800 China
| | - Mattia De Stefano
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
| | - Abhichart Krissanaprasit
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
- Present address: Department of Materials Science and Engineering; North Carolina State University; Raleigh NC 27606 USA
| | - Anne Louise Bank Kodal
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
| | - Christian Bech Rosen
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
| | - Tianqiang Liu
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
| | - Sarah Helmig
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
| | - Chunhai Fan
- Division of Physical Biology, Bioimaging Center; Shanghai Synchrotron Radiation Facility (SSRF); Shanghai Institute of Applied Physics, Chinese Academy of Sciences; Shanghai 201800 China
| | - Kurt V. Gothelf
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
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20
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Hong F, Zhang F, Liu Y, Yan H. DNA Origami: Scaffolds for Creating Higher Order Structures. Chem Rev 2017; 117:12584-12640. [DOI: 10.1021/acs.chemrev.6b00825] [Citation(s) in RCA: 645] [Impact Index Per Article: 92.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Fan Hong
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Fei Zhang
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Yan Liu
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Hao Yan
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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21
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Rajendran A, Nakata E, Nakano S, Morii T. Nucleic-Acid-Templated Enzyme Cascades. Chembiochem 2017; 18:696-716. [DOI: 10.1002/cbic.201600703] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Indexed: 11/08/2022]
Affiliation(s)
| | - Eiji Nakata
- Institute of Advanced Energy; Kyoto University; Uji Kyoto 611-0011 Japan
| | - Shun Nakano
- Institute of Advanced Energy; Kyoto University; Uji Kyoto 611-0011 Japan
| | - Takashi Morii
- Institute of Advanced Energy; Kyoto University; Uji Kyoto 611-0011 Japan
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22
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Mathur D, Medintz IL. Analyzing DNA Nanotechnology: A Call to Arms For The Analytical Chemistry Community. Anal Chem 2017; 89:2646-2663. [DOI: 10.1021/acs.analchem.6b04033] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Divita Mathur
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
- Center
for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Code 6900, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center
for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Code 6900, Washington, D.C. 20375, United States
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23
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Kuzuya A, Sakai Y, Yamazaki T, Xu Y, Yamanaka Y, Ohya Y, Komiyama M. Allosteric control of nanomechanical DNA origami pinching devices for enhanced target binding. Chem Commun (Camb) 2017; 53:8276-8279. [DOI: 10.1039/c7cc03991c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Significant enhancement of single-molecular binding of specific targets was achieved by allosterically controlling nanomechanical DNA origami pinching devices.
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Affiliation(s)
- Akinori Kuzuya
- Department of Chemistry and Materials Engineering
- Kansai University
- Suita
- Japan
| | - Yusuke Sakai
- Research Center for Advanced Science and Technology
- The University of Tokyo
- Tokyo 153-8904
- Japan
| | - Takahiro Yamazaki
- Research Center for Advanced Science and Technology
- The University of Tokyo
- Tokyo 153-8904
- Japan
| | - Yan Xu
- Department of Medical Sciences
- University of Miyazaki
- Miyazaki 889-1692
- Japan
| | - Yusei Yamanaka
- Department of Chemistry and Materials Engineering
- Kansai University
- Suita
- Japan
| | - Yuichi Ohya
- Department of Chemistry and Materials Engineering
- Kansai University
- Suita
- Japan
| | - Makoto Komiyama
- International Center for Materials Nanoarchitectonics
- National Institute for Materials Science
- Tsukuba
- Japan
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24
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Chandrasekaran AR, Anderson N, Kizer M, Halvorsen K, Wang X. Beyond the Fold: Emerging Biological Applications of DNA Origami. Chembiochem 2016; 17:1081-9. [PMID: 26928725 DOI: 10.1002/cbic.201600038] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Indexed: 01/22/2023]
Abstract
The use of DNA as a material for nanoscale construction has blossomed in the past decade. This is largely attributable to the DNA origami technique, which has enabled construction of nanostructures ranging from simple two-dimensional sheets to complex three-dimensional objects with defined curves and edges. These structures are amenable to site-specific functionalization with nanometer precision, and have been shown to exhibit cellular biocompatibility and permeability. The DNA origami technique has already found widespread use in a variety of emerging biological applications such as biosensing, enzyme cascades, biomolecular analysis, biomimetics, and drug delivery. We highlight a few of these applications and comments on the prospects for this rapidly expanding field of research.
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Affiliation(s)
| | - Nate Anderson
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.,Center for Biotechnology and Interdisciplinary Studies (CBIS), Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Megan Kizer
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.,Center for Biotechnology and Interdisciplinary Studies (CBIS), Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Xing Wang
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA. , .,Center for Biotechnology and Interdisciplinary Studies (CBIS), Rensselaer Polytechnic Institute, Troy, NY, 12180, USA. ,
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25
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Chandrasekaran AR. Programmable DNA scaffolds for spatially-ordered protein assembly. NANOSCALE 2016; 8:4436-4446. [PMID: 26852879 DOI: 10.1039/c5nr08685j] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Ever since the notion of using DNA as a material was realized, it has been employed in the construction of complex structures that facilitate the assembly of nanoparticles or macromolecules with nanometer-scale precision. Specifically, tiles fashioned from DNA strands and DNA origami sheets have been shown to be suitable as scaffolds for immobilizing proteins with excellent control over their spatial positioning. Supramolecular assembly of proteins into periodic arrays in one or more dimensions is one of the most challenging aspects in the design of scaffolds for biomolecular investigations and macromolecular crystallization. This review provides a brief overview of how various biomolecular interactions with high degree of specificity such as streptavidin-biotin, antigen-antibody, and aptamer-protein interactions have been used to fabricate linear and multidimensional assemblies of structurally intact and functional proteins. The use of DNA-binding proteins as adaptors, polyamide recognition on DNA scaffolds and oligonucleotide linkers for protein assembly are also discussed.
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26
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Affiliation(s)
- Yuhe R. Yang
- Center for Molecular Design
and Biomimetics, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Yan Liu
- Center for Molecular Design
and Biomimetics, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Hao Yan
- Center for Molecular Design
and Biomimetics, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
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27
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Chao J, Ouyang X, Peng H, Su S, Wang L. Self-assembly of Micrometer-long DNA Nanoribbons with Four Oligonucleotides. CHINESE J CHEM 2015. [DOI: 10.1002/cjoc.201500211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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28
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Kopielski A, Schneider A, Csáki A, Fritzsche W. Isothermal DNA origami folding: avoiding denaturing conditions for one-pot, hybrid-component annealing. NANOSCALE 2015; 7:2102-2106. [PMID: 25558850 DOI: 10.1039/c4nr04176c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The DNA origami technique offers great potential for nanotechnology. Using biomolecular self-assembly, defined 2D and 3D nanoscale DNA structures can be realized. DNA origami allows the positioning of proteins, fluorophores or nanoparticles with an accuracy of a few nanometers and enables thereby novel nanoscale devices. Origami assembly usually includes a thermal denaturation step at 90 °C. Additional components used for nanoscale assembly (such as proteins) are often thermosensitive, and possibly damaged by such harsh conditions. They have therefore to be attached in an extra second step to avoid defects. To enable a streamlined one-step nanoscale synthesis - a so called one-pot folding - an adaptation of the folding procedures is required. Here we present a thermal optimization of this process for a 2D DNA rectangle-shaped origami resulting in an isothermal assembly protocol below 60 °C without thermal denaturation. Moreover, a room temperature protocol is presented using the chemical additive betaine, which is biocompatible in contrast to chemical denaturing approaches reported previously.
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Affiliation(s)
- Andreas Kopielski
- Leibniz Institute of Photonic Technology (IPHT), Jena 07745, Germany
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29
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Yao G, Li J, Chao J, Pei H, Liu H, Zhao Y, Shi J, Huang Q, Wang L, Huang W, Fan C. Gold-Nanoparticle-Mediated Jigsaw-Puzzle-like Assembly of Supersized Plasmonic DNA Origami. Angew Chem Int Ed Engl 2015; 54:2966-9. [DOI: 10.1002/anie.201410895] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 12/31/2014] [Indexed: 11/09/2022]
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30
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Yao G, Li J, Chao J, Pei H, Liu H, Zhao Y, Shi J, Huang Q, Wang L, Huang W, Fan C. Gold-Nanoparticle-Mediated Jigsaw-Puzzle-like Assembly of Supersized Plasmonic DNA Origami. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201410895] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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31
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Gates EP, Jensen JK, Harb JN, Woolley AT. Optimizing gold nanoparticle seeding density on DNA origami. RSC Adv 2015. [DOI: 10.1039/c4ra15451g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Characterization of various experimental parameters leads to optimized conditions for depositing linear strings of gold nanoparticle seeds on DNA origami.
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Affiliation(s)
- E. P. Gates
- Department of Chemistry and Biochemistry
- Brigham Young University
- Provo
- USA
| | - J. K. Jensen
- Department of Chemistry and Biochemistry
- Brigham Young University
- Provo
- USA
| | - J. N. Harb
- Department of Chemical Engineering
- Brigham Young University
- Provo
- USA
| | - A. T. Woolley
- Department of Chemistry and Biochemistry
- Brigham Young University
- Provo
- USA
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Agostinelli E, Vianello F, Magliulo G, Thomas T, Thomas TJ. Nanoparticle strategies for cancer therapeutics: Nucleic acids, polyamines, bovine serum amine oxidase and iron oxide nanoparticles (Review). Int J Oncol 2015; 46:5-16. [PMID: 25333509 DOI: 10.3892/ijo.2014.2706] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 09/01/2014] [Indexed: 11/06/2022] Open
Abstract
Nanotechnology for cancer gene therapy is an emerging field. Nucleic acids, polyamine analogues and cytotoxic products of polyamine oxidation, generated in situ by an enzyme-catalyzed reaction, can be developed for nanotechnology-based cancer therapeutics with reduced systemic toxicity and improved therapeutic efficacy. Nucleic acid-based gene therapy approaches depend on the compaction of DNA/RNA to nanoparticles and polyamine analogues are excellent agents for the condensation of nucleic acids to nanoparticles. Polyamines and amine oxidases are found in higher levels in tumours compared to that of normal tissues. Therefore, the metabolism of polyamines spermidine and spermine, and their diamine precursor, putrescine, can be targets for antineoplastic therapy since these naturally occurring alkylamines are essential for normal mammalian cell growth. Intracellular polyamine concentrations are maintained at a cell type-specific set point through the coordinated and highly regulated interplay between biosynthesis, transport, and catabolism. In particular, polyamine catabolism involves copper-containing amine oxidases. Several studies showed an important role of these enzymes in developmental and disease-related processes in animals through the control of polyamine homeostasis in response to normal cellular signals, drug treatment, and environmental and/or cellular stress. The production of toxic aldehydes and reactive oxygen species (ROS), H2O2 in particular, by these oxidases suggests a mechanism by which amine oxidases can be exploited as antineoplastic drug targets. The combination of bovine serum amine oxidase (BSAO) and polyamines prevents tumour growth, particularly well if the enzyme has been conjugated with a biocompatible hydrogel polymer. The findings described herein suggest that enzymatically formed cytotoxic agents activate stress signal transduction pathways, leading to apoptotic cell death. Consequently, superparamagnetic nanoparticles or other advanced nanosystem based on directed nucleic acid assemblies, polyamine-induced DNA condensation, and bovine serum amine oxidase may be proposed for futuristic anticancer therapy utilizing nucleic acids, polyamines and BSAO. BSAO based nanoparticles can be employed for the generation of cytotoxic polyamine metabolites.
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Affiliation(s)
- Enzo Agostinelli
- Istituto Pasteur-Fondazione Cenci Bolognetti Department of Biochemical Sciences 'A. Rossi Fanelli', Sapienza University of Rome and CNR, Institute of Biology and Molecular Pathology, 00185 Rome, Italy
| | - Fabio Vianello
- Department of Comparative Biomedicine and Food Science, University of Padua, 35020 Legnaro, Italy and Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University in Olomouc, Olomouc 77146, Czech Republic
| | - Giuseppe Magliulo
- Department Organi di Senso, Sapienza University of Rome, 00185 Rome, Italy
| | - Thresia Thomas
- Formerly Department of Environmental and Occupational Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers the State University of New Jersey, Piscataway, NJ 08854, USA
| | - T J Thomas
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers the State University of New Jersey, New Brunswick, NJ 08901, USA
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Wu P, Yu Y, McGhee CE, Tan LH, Lu Y. Applications of synchrotron-based spectroscopic techniques in studying nucleic acids and nucleic acid-functionalized nanomaterials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2014; 26:7849-72. [PMID: 25205057 PMCID: PMC4275547 DOI: 10.1002/adma.201304891] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 06/02/2014] [Indexed: 05/22/2023]
Abstract
In this review, we summarize recent progress in the application of synchrotron-based spectroscopic techniques for nucleic acid research that takes advantage of high-flux and high-brilliance electromagnetic radiation from synchrotron sources. The first section of the review focuses on the characterization of the structure and folding processes of nucleic acids using different types of synchrotron-based spectroscopies, such as X-ray absorption spectroscopy, X-ray emission spectroscopy, X-ray photoelectron spectroscopy, synchrotron radiation circular dichroism, X-ray footprinting and small-angle X-ray scattering. In the second section, the characterization of nucleic acid-based nanostructures, nucleic acid-functionalized nanomaterials and nucleic acid-lipid interactions using these spectroscopic techniques is summarized. Insights gained from these studies are described and future directions of this field are also discussed.
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Affiliation(s)
- Peiwen Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yang Yu
- Center of Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Claire E. McGhee
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Li Huey Tan
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yi Lu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Center of Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Yamazaki T, Heddle JG, Kuzuya A, Komiyama M. Orthogonal enzyme arrays on a DNA origami scaffold bearing size-tunable wells. NANOSCALE 2014; 6:9122-6. [PMID: 24974892 DOI: 10.1039/c4nr01598c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A new waffle-like DNA origami assembly (DNA waffle) with nine nanometer-scale wells in a 3 × 3 matrix pattern has been successfully constructed and used as a scaffold for selective nano-patterning of individual protein molecules. The folding pattern of the scaffold was specially designed so that the dimensions of each well could be independently tuned according to the dimensions of the guest nanoparticles. We demonstrated that two distinct proteins, streptavidin (SA) tetramer (d = 5 nm) and anti-fluorescein antibody (IgG) (inter-paratope distance ∼ 14.0 nm), could be selectively captured in size-variable wells of dimensions 6.8 × 12 × 2.0 nm for SA and 6.8 × 12 × 2.0 nm or 10.2 × 12 × 2.0 nm for IgG, respectively, through the attachment of two biotins or two fluoresceins at the two edges of each well. This allowed the formation of a heterogeneous protein nanoarray of individual molecules. The position of SA or IgG capture can be fully controlled by placement of biotins or fluoresceins in the nanoarray well. Moreover, a hetero-nanoarray consisting of two kinds of enzyme: horseradish peroxidase-labeled streptavidin (HRP-SA) and alkaline phosphatase-labeled anti-FITC antibody (AP-IgG) was successfully constructed through selective attachment of biotin or fluorescein in any desired wells. Successful enzyme-heteroarray formation was confirmed by enzymatic activity analyses after purification of mixtures of enzymes and DNA waffles.
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Affiliation(s)
- Takahiro Yamazaki
- RCAST, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
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35
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Tintoré M, Eritja R, Fábrega C. DNA Nanoarchitectures: Steps towards Biological Applications. Chembiochem 2014; 15:1374-90. [DOI: 10.1002/cbic.201402014] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Indexed: 12/26/2022]
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Abstract
CONSPECTUS: Eight years have passed since the striking debut of the DNA origami technique ( Rothemund, P. W. K. Nature 2006 , 440 , 297 - 302 ), in which long single-stranded DNA is folded into a designed nanostructure, in either 2D or 3D, with the aid of many short staple strands. The number of proposals for new design principles for DNA origami structures seems to have already reached a peak. It is apparent that DNA origami study is now entering the second phase of creating practical applications. The development of functional nanomechanical molecular devices using the DNA origami technique is one such application attracting significant interest from researchers in the field. Nanomechanical DNA origami devices, which maintain the characteristics of DNA origami structures, have various advantages over conventional DNA nanomachines. Comparatively high assembly yield, relatively large size visible via atomic force microscopy (AFM) or transmission electron microscopy (TEM), and the capability to assemble multiple functional groups with precision using multiple staple strands are some of the advantages of the DNA origami technique for constructing sophisticated molecular devices. This Account describes the recent developments of such nanomechanical DNA origami devices and reviews the emerging target of DNA origami studies. First, simple "dynamic" DNA origami structures with transformation capability, such as DNA origami boxes and a DNA origami hatch with structure control, are briefly summarized. More elaborate nanomechanical DNA origami devices are then reviewed. The first example describes DNA origami pinching devices that can be used as "single-molecule" beacons to detect a variety of biorelated molecules, from metal ions at the size of a few tens of atomic mass number units to relatively gigantic proteins with a molecular mass greater than a hundred kilodaltons, all on a single platform. Clamshell-like DNA nanorobots equipped with logic gates can discriminate different cell lines, open their shell, and bind to their target. An intelligent DNA origami "sheath" can mimic the function of suppressors in a transcription regulation system to control the expression of a loaded gene. DNA origami "rolls" are created to construct precisely arranged plasmonic devices with metal nanoparticles. All of their functions are derived from their nanomechanical movement, which is programmable by designing the DNA sequence or by using the significant repository of technical achievements in nucleic acid chemistry. Finally, some studies on detailed structural parameters of DNA origami or their mechanical properties in nanoscale are discussed, which may be useful and inspiring for readers who intend to design new nanomechanical DNA origami devices.
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Affiliation(s)
- Akinori Kuzuya
- Department
of Chemistry and Materials Engineering, Kansai University, 3-3-35
Yamate, Suita, Osaka 564-8680, Japan
- PRESTO, Japan
Science and Technology Agency, 4-1-8
Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Yuichi Ohya
- Department
of Chemistry and Materials Engineering, Kansai University, 3-3-35
Yamate, Suita, Osaka 564-8680, Japan
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37
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Gates EP, Dearden AM, Woolley AT. DNA‐templated lithography and nanofabrication for the fabrication of nanoscale electronic circuitry. Crit Rev Anal Chem 2014; 44:354-70. [DOI: 10.1080/10408347.2014.910636] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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38
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A protein adaptor to locate a functional protein dimer on molecular switchboard. Methods 2014; 67:142-50. [DOI: 10.1016/j.ymeth.2013.10.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 10/09/2013] [Accepted: 10/16/2013] [Indexed: 01/25/2023] Open
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39
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DNA from natural sources in design of functional devices. Methods 2014; 67:105-15. [DOI: 10.1016/j.ymeth.2014.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 02/20/2014] [Accepted: 03/02/2014] [Indexed: 01/01/2023] Open
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40
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Wang ZG, Ding B. DNA-based self-assembly for functional nanomaterials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2013; 25:3905-3914. [PMID: 24048977 DOI: 10.1002/adma.201301450] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2013] [Revised: 04/15/2013] [Indexed: 06/02/2023]
Abstract
The unprecedented development of DNA nanotechnology has caused DNA self-assembly to attract close attention in many disciplines. In this research news article, the employment of DNA self-assembly in the fields of materials science and nanotechnology is described. DNA self-assembly can be used to prepare bulk-scale hydrogels and 3D macroscopic crystals with nanoscale internal structures, to induce the crystallization of nanoparticles, to template the fabrication of organic conductive nanomaterials, and to act as drug delivery vehicles for therapeutic agents. The properties and functions are fully tunable because of the designability and specificity of DNA assembly. Moreover, because of the intrinsic dynamics, DNA self-assembly can act as a program switch and can efficiently control stimuli responsiveness. We highlight the power of DNA self-assembly in the preparation and function regulation of materials, aiming to motivate future multidisciplinary and interdisciplinary research. Finally, we describe some of the challenges currently faced by DNA assembly that may affect the functional evolution of such materials, and we provide our insights into the future directions of several DNA self-assembly-based nanomaterials.
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Affiliation(s)
- Zhen-Gang Wang
- National Center for Nanoscience and Technology, Beijing, 100190, PR China
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41
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Hernández-Ainsa S, Bell NAW, Thacker VV, Göpfrich K, Misiunas K, Fuentes-Perez ME, Moreno-Herrero F, Keyser UF. DNA origami nanopores for controlling DNA translocation. ACS NANO 2013; 7:6024-30. [PMID: 23734828 DOI: 10.1021/nn401759r] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We combine DNA origami structures with glass nanocapillaries to reversibly form hybrid DNA origami nanopores. Trapping of the DNA origami onto the nanocapillary is proven by imaging fluorescently labeled DNA origami structures and simultaneous ionic current measurements of the trapping events. We then show two applications highlighting the versatility of these DNA origami nanopores. First, by tuning the pore size we can control the folding of dsDNA molecules ("physical control"). Second, we show that the specific introduction of binding sites in the DNA origami nanopore allows selective detection of ssDNA as a function of the DNA sequence ("chemical control").
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Affiliation(s)
- Silvia Hernández-Ainsa
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
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42
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Wang ZG, Song C, Ding B. Functional DNA nanostructures for photonic and biomedical applications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:2210-2222. [PMID: 23733711 DOI: 10.1002/smll.201300141] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Indexed: 06/02/2023]
Abstract
DNA nanostructures, especially DNA origami, receive close interest because of the programmable control over their shape and size, precise spatial addressability, easy and high-yield preparation, mechanical flexibility, and biocompatibility. They have been used to organize a variety of nanoscale elements for specific functions, resulting in unprecedented improvements in the field of nanophotonics and nanomedical research. In this review, the discussion focuses on the employment of DNA nanostructures for the precise organization of noble metal nanoparticles to build interesting plasmonic nanoarchitectures, for the fabrication of visualized sensors and for targeted drug delivery. The effects offered by DNA nanostructures are highlighted in the areas of nanoantennas, collective plasmonic behaviors, single-molecule analysis, and cancer-cell targeting or killing. Finally, the challenges in the field of DNA nanotechnology for realistic application are discussed and insights for future directions are provided.
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Affiliation(s)
- Zhen-Gang Wang
- National Center for Nanoscience and Technology, Beijing 100190, PR China
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43
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Smith D, Schüller V, Engst C, Rädler J, Liedl T. Nucleic acid nanostructures for biomedical applications. Nanomedicine (Lond) 2013; 8:105-21. [PMID: 23256495 DOI: 10.2217/nnm.12.184] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
We review the current developments of DNA-based nanostructures for drug delivery, immunotherapy, diagnostics and molecular biology. DNA is a powerful building block, which by the nature of predictable base pairing, allows the creation of molecular scaffolds, cages and multifunctional carriers with nanoscale dimensions. These engineered constructs have unsurpassed structural qualities such as full control over size, shape and dispersity. Site-specific surface modification enables the presentation of biomolecules at defined distances and stochiometries, which allows tailored cell targeting and substance delivery on demand. As the first successful in vivo applications of DNA nanostructures have recently been demonstrated, we now expect a burst of biomedical studies involving this rapidly progressing technology.
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Affiliation(s)
- David Smith
- Physics & Center for NanoScience, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
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44
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Mathur D, Henderson ER. Complex DNA nanostructures from oligonucleotide ensembles. ACS Synth Biol 2013; 2:180-5. [PMID: 23656476 DOI: 10.1021/sb3000518] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The first synthetic DNA nanostructures were created by self-assembly of a small number of oligonucleotides. Introduction of the DNA origami method provided a new paradigm for designing and creating two- and three-dimensional DNA nanostructures by folding a large single-stranded DNA and 'stapling' it together with a library of oligonucleotides. Despite its power and wide-ranging implementation, the DNA origami technique suffers from some limitations. Foremost among these is the limited number of useful single-stranded scaffolds of biological origin. This report describes a new approach to creating large DNA nanostructures exclusively from synthetic oligonucleotides. The essence of this approach is to replace the single-stranded scaffold in DNA origami with a library of oligonucleotides termed "scaples" (scaffold staples). Scaples eliminate the need for scaffolds of biological origin and create new opportunities for producing larger and more diverse DNA nanostructures as well as simultaneous assembly of distinct structures in a "single-pot" reaction.
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Affiliation(s)
- Divita Mathur
- Bioinformatics & Computational Biology Program, Department of Genetics, Development & Cell Biology, Iowa State University, Ames, Iowa, United States
| | - Eric R. Henderson
- Bioinformatics & Computational Biology Program, Department of Genetics, Development & Cell Biology, Iowa State University, Ames, Iowa, United States
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45
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Wong NY, Xing H, Tan LH, Lu Y. Nano-encrypted Morse code: a versatile approach to programmable and reversible nanoscale assembly and disassembly. J Am Chem Soc 2013; 135:2931-4. [PMID: 23373425 PMCID: PMC3612397 DOI: 10.1021/ja3122284] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While much work has been devoted to nanoscale assembly of functional materials, selective reversible assembly of components in the nanoscale pattern at selective sites has received much less attention. Exerting such a reversible control of the assembly process will make it possible to fine-tune the functional properties of the assembly and to realize more complex designs. Herein, by taking advantage of different binding affinities of biotin and desthiobiotin toward streptavidin, we demonstrate selective and reversible decoration of DNA origami tiles with streptavidin, including revealing an encrypted Morse code "NANO" and reversible exchange of uppercase letter "I" with lowercase "i". The yields of the conjugations are high (>90%), and the process is reversible. We expect this versatile conjugation technique to be widely applicable with different nanomaterials and templates.
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Affiliation(s)
- Ngo Yin Wong
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Hang Xing
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Li Huey Tan
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Yi Lu
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
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46
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Saaem I, LaBean TH. Overview of DNA origami for molecular self-assembly. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2013; 5:150-62. [DOI: 10.1002/wnan.1204] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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47
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Endo M, Yang Y, Sugiyama H. DNA origami technology for biomaterials applications. Biomater Sci 2013; 1:347-360. [DOI: 10.1039/c2bm00154c] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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48
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Nakagawa H, Toda M, Atsumi H, Hagihara M, Hayashi-Nishino M, Dohno C, Nakatani K. Assembly of a Small DNA Rectangular Parallelepiped Block into Higher Order Nanostructures. CHEM LETT 2012. [DOI: 10.1246/cl.2012.1550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Hiroyuki Nakagawa
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University
| | - Mariko Toda
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University
| | - Hiroshi Atsumi
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University
| | - Masaki Hagihara
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University
| | - Mitsuko Hayashi-Nishino
- Comprehensive Analysis Center, The Institute of Scientific and Industrial Research, Osaka University
| | - Chikara Dohno
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University
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49
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Structural DNA nanotechnology: from design to applications. Int J Mol Sci 2012; 13:7149-7162. [PMID: 22837684 PMCID: PMC3397516 DOI: 10.3390/ijms13067149] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 05/29/2012] [Accepted: 06/04/2012] [Indexed: 11/16/2022] Open
Abstract
The exploitation of DNA for the production of nanoscale architectures presents a young yet paradigm breaking approach, which addresses many of the barriers to the self-assembly of small molecules into highly-ordered nanostructures via construct addressability. There are two major methods to construct DNA nanostructures, and in the current review we will discuss the principles and some examples of applications of both the tile-based and DNA origami methods. The tile-based approach is an older method that provides a good tool to construct small and simple structures, usually with multiply repeated domains. In contrast, the origami method, at this time, would appear to be more appropriate for the construction of bigger, more sophisticated and exactly defined structures.
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50
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Zhang H, Chao J, Pan D, Liu H, Huang Q, Fan C. Folding super-sized DNA origami with scaffold strands from long-range PCR. Chem Commun (Camb) 2012; 48:6405. [PMID: 22618197 DOI: 10.1039/c2cc32204h] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
A 26 kilobase single strand DNA fragment was obtained from long-range PCR amplification and subsequent enzymatic digestion, which we folded into a super-sized DNA origami nanostructure by using ∼800 staple strands.
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Affiliation(s)
- Honglu Zhang
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.
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