1
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DeLuca M, Duke D, Ye T, Poirier M, Ke Y, Castro C, Arya G. Mechanism of DNA origami folding elucidated by mesoscopic simulations. Nat Commun 2024; 15:3015. [PMID: 38589344 PMCID: PMC11001925 DOI: 10.1038/s41467-024-46998-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 03/18/2024] [Indexed: 04/10/2024] Open
Abstract
Many experimental and computational efforts have sought to understand DNA origami folding, but the time and length scales of this process pose significant challenges. Here, we present a mesoscopic model that uses a switchable force field to capture the behavior of single- and double-stranded DNA motifs and transitions between them, allowing us to simulate the folding of DNA origami up to several kilobases in size. Brownian dynamics simulations of small structures reveal a hierarchical folding process involving zipping into a partially folded precursor followed by crystallization into the final structure. We elucidate the effects of various design choices on folding order and kinetics. Larger structures are found to exhibit heterogeneous staple incorporation kinetics and frequent trapping in metastable states, as opposed to more accessible structures which exhibit first-order kinetics and virtually defect-free folding. This model opens an avenue to better understand and design DNA nanostructures for improved yield and folding performance.
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Affiliation(s)
- Marcello DeLuca
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, 27705, USA
| | - Daniel Duke
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, 27705, USA
| | - Tao Ye
- Department of Chemistry & Biochemistry, University of California, Merced, CA, 95343, USA
- Department of Materials and Biomaterials Science & Engineering, University of California, Merced, CA, 95343, USA
| | - Michael Poirier
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
| | - Yonggang Ke
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30322, USA
| | - Carlos Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Gaurav Arya
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, 27705, USA.
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2
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Gale CD, Levinger NE. Predicting the Geometry of Core-Shell Structures: How a Shape Changes with Constant Added Thickness. J Phys Chem B 2024; 128:1317-1324. [PMID: 38288994 DOI: 10.1021/acs.jpcb.3c07652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The core-shell assembly motif is ubiquitous in chemistry. While the most obvious examples are core/shell-type nanoparticles, many other examples exist. The shape of the core/shell constructs is poorly understood, making it impossible to separate chemical effects from geometric effects. Here, we create a model for the core/shell construct and develop proof for how the eccentricity is expected to change as a function of the shell. We find that the addition of a constant thickness shell always creates a relatively more spherical shape for all shapes covered by our model unless the shape is already spherical or has some underlying radial symmetry. We apply this work to simulated AOT reverse micelles and demonstrate that it is remarkably successful at explaining the observed shapes of the chemical systems. We identify the three specific cases where the model breaks down and how this impacts eccentricity.
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Affiliation(s)
- Christopher D Gale
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Nancy E Levinger
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
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3
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Gao M, Hu J, Wang J, Liu M, Zhu X, Saeed S, Hu C, Song Z, Xu H, Wang Z. Self-Assembly of DNA molecules in magnetic Fields. NANOTECHNOLOGY 2021; 33:065603. [PMID: 34087806 DOI: 10.1088/1361-6528/ac084f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/03/2021] [Indexed: 06/12/2023]
Abstract
In this work, a rich variety of self-assembled DNA patterns were obtained in the magnetic field. Herein, atomic force microscopy (AFM) was utilized to investigate the effects of the concentration of DNA solution, intensity and direction of magnetic field and modification of mica surface by different cations on the self-assembly of DNA molecules. It was found that owning to the change of the DNA concentration, even under the same magnetic field, the DNA self-assembly results were different. Thein situtest results showed that the DNA self-assembly in an magnetic field was more likely to occur in liquid phase than in gas phase. In addition, whether in a horizontal or vertical magnetic field, a single stretched dsDNA was obtained in a certain DNA concentration and magnetic field intensity. Besides, the modification of cations on the mica surface significantly increased the force between the DNA molecules and mica surface, and further changed the self-assembly of DNA molecules under the action of magnetic field.
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Affiliation(s)
- Mingyan Gao
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
| | - Jing Hu
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
| | - Jianfei Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
| | - Mengnan Liu
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
| | - Xiaona Zhu
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
| | - Sadaf Saeed
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
| | - Cuihua Hu
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
| | - Zhengxun Song
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
| | - Hongmei Xu
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
| | - Zuobin Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
- JR3CN & IRAC, University of Bedfordshire, Luton LU1 3JU, United Kingdom
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4
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Green CM, Hughes WL, Graugnard E, Kuang W. Correlative Super-Resolution and Atomic Force Microscopy of DNA Nanostructures and Characterization of Addressable Site Defects. ACS NANO 2021; 15:11597-11606. [PMID: 34137595 DOI: 10.1021/acsnano.1c01976] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
To bring real-world applications of DNA nanostructures to fruition, advanced microscopy techniques are needed to shed light on factors limiting the availability of addressable sites. Correlative microscopy, where two or more microscopies are combined to characterize the same sample, is an approach to overcome the limitations of individual techniques, yet it has seen limited use for DNA nanotechnology. We have developed an accessible strategy for high resolution, correlative DNA-based points accumulation for imaging in nanoscale topography (DNA-PAINT) super-resolution and atomic force microscopy (AFM) of DNA nanostructures, enabled by a simple and robust method to selectively bind DNA origami to cover glass. Using this technique, we examined addressable "docking" sites on DNA origami to distinguish between two defect scenarios-structurally incorporated but inactive docking sites, and unincorporated docking sites. We found that over 75% of defective docking sites were incorporated but inactive, suggesting unincorporated strands played a minor role in limiting the availability of addressable sites. We further explored the effects of strand purification, UV irradiation, and photooxidation on availability, providing insight on potential sources of defects and pathways toward improving the fidelity of DNA nanostructures.
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Affiliation(s)
- Christopher M Green
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory Code 6900, Washington, D.C. 20375, United States
- National Research Council, 500 fifth St NW, Washington, D.C. 20001, United States
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5
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Berengut JF, Berengut JC, Doye JPK, Prešern D, Kawamoto A, Ruan J, Wainwright MJ, Lee LK. Design and synthesis of pleated DNA origami nanotubes with adjustable diameters. Nucleic Acids Res 2020; 47:11963-11975. [PMID: 31728524 PMCID: PMC7145641 DOI: 10.1093/nar/gkz1056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 10/22/2019] [Accepted: 10/25/2019] [Indexed: 12/31/2022] Open
Abstract
DNA origami allows for the synthesis of nanoscale structures and machines with nanometre precision and high yields. Tubular DNA origami nanostructures are particularly useful because their geometry facilitates a variety of applications including nanoparticle encapsulation, the construction of artificial membrane pores and as structural scaffolds that can uniquely spatially arrange nanoparticles in circular, linear and helical arrays. Here we report a system of parametrization for the design of radially symmetric DNA origami nanotubes with adjustable diameter, length, crossover density, pleat angle and chirality. The system is implemented into a computational algorithm that provides a practical means to navigate the complex geometry of DNA origami nanotube design. We apply this in the design, synthesis and characterization of novel DNA origami nanotubes. These include structures with pleated walls where the same number of duplexes can form nanotubes with different diameters, and to vary the diameter within the same structure. We also construct nanotubes that can be reconfigured into different chiral shapes. Finally, we explore the effect of strain on the local and global geometry of DNA origami nanotubes and demonstrate how pleated walls can provide a strategy to rigidify nanotubes and to construct closely packed parallel duplexes.
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Affiliation(s)
- Jonathan F Berengut
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, UNSW Sydney, Kensington, NSW 2052, Australia.,Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | | | - Jonathan P K Doye
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Domen Prešern
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Akihiro Kawamoto
- Institute for Protein Research, Osaka University, Osaka, Kansai, 565-0871, Japan
| | - Juanfang Ruan
- Electron Microscopy Unit, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Madeleine J Wainwright
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Lawrence K Lee
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, UNSW Sydney, Kensington, NSW 2052, Australia.,Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
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6
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Winterwerber P, Harvey S, Ng DYW, Weil T. Photocontrolled Dopamine Polymerization on DNA Origami with Nanometer Resolution. Angew Chem Int Ed Engl 2020; 59:6144-6149. [PMID: 31750608 PMCID: PMC7186833 DOI: 10.1002/anie.201911249] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Indexed: 12/27/2022]
Abstract
Temporal and spatial control over polydopamine formation on the nanoscale can be achieved by installing an irradiation-sensitive polymerization system on DNA origami. Precisely distributed G-quadruplex structures on the DNA template serve as anchors for embedding the photosensitizer protoporphyrin IX, which-upon irradiation with visible light-induces the multistep oxidation of dopamine to polydopamine, producing polymeric structures on designated areas within the origami framework. The photochemical polymerization process allows exclusive control over polydopamine layer formation through the simple on/off switching of the light source. The obtained polymer-DNA hybrid material shows significantly enhanced stability, paving the way for biomedical and chemical applications that are typically not possible owing to the sensitivity of DNA.
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Affiliation(s)
- Pia Winterwerber
- Max Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
| | - Sean Harvey
- Max Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
- Institute of Inorganic Chemistry IUlm UniversityAlbert-Einstein-Allee 189081UlmGermany
| | - David Y. W. Ng
- Max Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
| | - Tanja Weil
- Max Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
- Institute of Inorganic Chemistry IUlm UniversityAlbert-Einstein-Allee 189081UlmGermany
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7
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Peng T, Li X, Li K, Nie Z, Tan W. DNA-Modulated Plasmon Resonance: Methods and Optical Applications. ACS APPLIED MATERIALS & INTERFACES 2020; 12:14741-14760. [PMID: 32154704 DOI: 10.1021/acsami.9b23608] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The near-field effects in the vicinity of metallic nanoparticle surfaces, as induced by electromagnetic radiation with specific wavelength, give rise to a variety of novel optical properties and attractive applications because of surface plasmons, which are the coherent oscillations of conduction electrons on a metal surface. The interdisciplinary field of plasmonics has witnessed vigorous growth, promoting research on the modulation of plasmon resonance by constructing advanced plasmonic nanoarchitectures with controllable size, morphology, or interparticle coupling. Among diversified tools, deoxyribonucleic nucleic acid (DNA) possesses prominent superiority as a result of its designability, programmability, addressability, and ease of nanomaterial modification. In this review, we focus on the methods and optical applications of plasmon resonance modulation accomplished by DNA nanotechnology. Recent developments in the construction of DNA-mediated plasmonic nanoarchitecture and key ongoing research directions utilizing unique optical features are highlighted. Obstacles and challenges in this field are pointed out, followed by preliminary suggestions on some areas of opportunity that deserve attention.
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Affiliation(s)
- Tianhuan Peng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, P. R. China
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
- Molecular Science and Biomedicine Laboratory, Hunan University, Changsha 410082, P. R. China
| | - Xu Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, P. R. China
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
- Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Kun Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, P. R. China
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
- Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, P. R. China
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
- Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Weihong Tan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, P. R. China
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
- Molecular Science and Biomedicine Laboratory, Hunan University, Changsha 410082, P. R. China
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8
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Winterwerber P, Harvey S, Ng DYW, Weil T. Lichtgesteuerte Polymerisation von Dopamin auf DNA‐Origami im Nanometer‐Regime. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201911249] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Pia Winterwerber
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - Sean Harvey
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
- Institut für Anorganische Chemie IUniversität Ulm Albert-Einstein-Allee 1 89081 Ulm Deutschland
| | - David Y. W. Ng
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - Tanja Weil
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
- Institut für Anorganische Chemie IUniversität Ulm Albert-Einstein-Allee 1 89081 Ulm Deutschland
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9
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Klein WP, Thomsen RP, Turner KB, Walper SA, Vranish J, Kjems J, Ancona MG, Medintz IL. Enhanced Catalysis from Multienzyme Cascades Assembled on a DNA Origami Triangle. ACS NANO 2019; 13:13677-13689. [PMID: 31751123 DOI: 10.1021/acsnano.9b05746] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Developing reliable methods of constructing cell-free multienzyme biocatalytic systems is a milestone goal of synthetic biology. It would enable overcoming the limitations of current cell-based systems, which suffer from the presence of competing pathways, toxicity, and inefficient access to extracellular reactants and removal of products. DNA nanostructures have been suggested as ideal scaffolds for assembling sequential enzymatic cascades in close enough proximity to potentially allow for exploiting of channeling effects; however, initial demonstrations have provided somewhat contradictory results toward confirming this phenomenon. In this work, a three-enzyme sequential cascade was realized by site-specifically immobilizing DNA-conjugated amylase, maltase, and glucokinase on a self-assembled DNA origami triangle. The kinetics of seven different enzyme configurations were evaluated experimentally and compared to simulations of optimized activity. A 30-fold increase in the pathway's kinetic activity was observed for enzymes assembled to the DNA. Detailed kinetic analysis suggests that this catalytic enhancement originated from increased enzyme stability and a localized DNA surface affinity or hydration layer effect and not from a directed enzyme-to-enzyme channeling mechanism. Nevertheless, the approach used to construct this pathway still shows promise toward improving other more elaborate multienzymatic cascades and could potentially allow for the custom synthesis of complex (bio)molecules that cannot be realized with conventional organic chemistry approaches.
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Affiliation(s)
- William P Klein
- National Research Council , Washington , D.C. 20001 , United States
| | - Rasmus P Thomsen
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics , Aarhus University , 8000 Aarhus , Denmark
| | | | - Scott A Walper
- National Research Council , Washington , D.C. 20001 , United States
| | - James Vranish
- Ave Maria University , Ave Maria , Florida 34142 , United States
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics , Aarhus University , 8000 Aarhus , Denmark
| | | | - Igor L Medintz
- National Research Council , Washington , D.C. 20001 , United States
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10
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Gao M, Hu J, Wang Y, Liu M, Wang J, Song Z, Xu H, Hu C, Wang Z. Controlled Self-Assembly of λ-DNA Networks with the Synergistic Effect of a DC Electric Field. J Phys Chem B 2019; 123:9809-9818. [PMID: 31682443 DOI: 10.1021/acs.jpcb.9b08891] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Large-scale and morphologically controlled self-assembled λ-DNA networks were successfully constructed by the synergistic effect of a DC electric field. The effect of DNA concentration, direction, and intensity of the electric field, even the modification of the mica surface using Mg2+ on the characteristics of the as-prepared DNA networks, were investigated in detail by atomic force microscopy (AFM). It was found that the horizontal electric field was more advantageous to the formation of DNA networks with more regular structures. At the same concentration, the height of DNA network was not affected significantly by the intensity change of the horizontal electric field. The modification of Mg2+ on mica surface increased the aggregation of DNA molecules, which contributed to the morphological change of the DNA networks. Furthermore, DNA molecules were obviously stretched in both horizontal and vertical electric fields at low DNA concentrations.
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Affiliation(s)
- Mingyan Gao
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing , Changchun University of Science and Technology , Changchun 130022 , China.,International Research Centre for Nano Handling and Manufacturing of China , Changchun University of Science and Technology , Changchun 130022 , China
| | - Jing Hu
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing , Changchun University of Science and Technology , Changchun 130022 , China.,International Research Centre for Nano Handling and Manufacturing of China , Changchun University of Science and Technology , Changchun 130022 , China
| | - Ying Wang
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing , Changchun University of Science and Technology , Changchun 130022 , China.,International Research Centre for Nano Handling and Manufacturing of China , Changchun University of Science and Technology , Changchun 130022 , China
| | - Mengnan Liu
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing , Changchun University of Science and Technology , Changchun 130022 , China.,International Research Centre for Nano Handling and Manufacturing of China , Changchun University of Science and Technology , Changchun 130022 , China
| | - Jianfei Wang
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing , Changchun University of Science and Technology , Changchun 130022 , China.,International Research Centre for Nano Handling and Manufacturing of China , Changchun University of Science and Technology , Changchun 130022 , China
| | - Zhengxun Song
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing , Changchun University of Science and Technology , Changchun 130022 , China.,International Research Centre for Nano Handling and Manufacturing of China , Changchun University of Science and Technology , Changchun 130022 , China
| | - Hongmei Xu
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing , Changchun University of Science and Technology , Changchun 130022 , China.,International Research Centre for Nano Handling and Manufacturing of China , Changchun University of Science and Technology , Changchun 130022 , China
| | - Cuihua Hu
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing , Changchun University of Science and Technology , Changchun 130022 , China.,International Research Centre for Nano Handling and Manufacturing of China , Changchun University of Science and Technology , Changchun 130022 , China
| | - Zuobin Wang
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing , Changchun University of Science and Technology , Changchun 130022 , China.,International Research Centre for Nano Handling and Manufacturing of China , Changchun University of Science and Technology , Changchun 130022 , China.,JR3CN & IRAC , University of Bedfordshire , Luton LU1 3JU , U.K
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11
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Mathur D, Klein WP, Chiriboga M, Bui H, Oh E, Nita R, Naciri J, Johns P, Fontana J, Díaz SA, Medintz IL. Analyzing fidelity and reproducibility of DNA templated plasmonic nanostructures. NANOSCALE 2019; 11:20693-20706. [PMID: 31642466 DOI: 10.1039/c9nr03711j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Synthetic DNA templated nanostructures offer an excellent platform for the precise spatial and orientational positioning of organic and inorganic nanomaterials. Previous reports have shown its applicability in the organization of plasmonic nanoparticles in a number of geometries for the purpose of realizing tunable nanoscale optical devices. However, translation of nanoparticle-DNA constructs to application requires additional efforts to increase scalability, reproducibility, and formation yields. Understanding all these factors is, in turn, predicated on in-depth analysis of each structure and comparing how formation changes with complexity. Towards the latter goal, we assemble seven unique plasmonic nanostructure symmetries of increasing complexity based on assembly of gold nanorods and nanoparticles on two different DNA origami templates, a DNA triangle and rhombus, and characterize them using gel electrophoresis, atomic force- and transmission electron microscopy, as well as optical spectroscopy. In particular, we focus on how much control can be elicited over yield, reproducibility, shape, size, inter-particle angles, gaps, and plasmon shifts as compared to expectations from computer simulations as structural complexity increases. We discuss how these results can contribute to establishing process principles for creating DNA templated plasmonic nanostructures.
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Affiliation(s)
- Divita Mathur
- Center for Bio/Molecular Science and Engineering Code 6900 and U.S. Naval Research Laboratory, 4555 Overlook AV SW, Washington, DC 20375, USA. and College of Science and Institute for Advanced Biomedical Research, George Mason University, Fairfax, VA 22030, USA
| | - William P Klein
- Center for Bio/Molecular Science and Engineering Code 6900 and U.S. Naval Research Laboratory, 4555 Overlook AV SW, Washington, DC 20375, USA. and National Research Council, 500 5th St NW, Washington, DC 20001, USA
| | - Matthew Chiriboga
- Center for Bio/Molecular Science and Engineering Code 6900 and U.S. Naval Research Laboratory, 4555 Overlook AV SW, Washington, DC 20375, USA. and Department of Bioengineering, Institute for Advanced Biomedical Research, George Mason University, Fairfax, VA 22030, USA
| | - Hieu Bui
- Center for Bio/Molecular Science and Engineering Code 6900 and U.S. Naval Research Laboratory, 4555 Overlook AV SW, Washington, DC 20375, USA. and National Research Council, 500 5th St NW, Washington, DC 20001, USA
| | - Eunkeu Oh
- Optical Sciences Division Code 5600, U.S. Naval Research Laboratory, 4555 Overlook AV SW, Washington, DC 20375, USA and KeyW Corporation, Hanover, MD 21076, USA
| | - Rafaela Nita
- Center for Bio/Molecular Science and Engineering Code 6900 and U.S. Naval Research Laboratory, 4555 Overlook AV SW, Washington, DC 20375, USA. and National Research Council, 500 5th St NW, Washington, DC 20001, USA
| | - Jawad Naciri
- Center for Bio/Molecular Science and Engineering Code 6900 and U.S. Naval Research Laboratory, 4555 Overlook AV SW, Washington, DC 20375, USA.
| | - Paul Johns
- Center for Bio/Molecular Science and Engineering Code 6900 and U.S. Naval Research Laboratory, 4555 Overlook AV SW, Washington, DC 20375, USA. and American Society for Engineering Education, 1818 N Street NW, Suite 600, Washington, DC 20036, USA
| | - Jake Fontana
- Center for Bio/Molecular Science and Engineering Code 6900 and U.S. Naval Research Laboratory, 4555 Overlook AV SW, Washington, DC 20375, USA.
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering Code 6900 and U.S. Naval Research Laboratory, 4555 Overlook AV SW, Washington, DC 20375, USA.
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering Code 6900 and U.S. Naval Research Laboratory, 4555 Overlook AV SW, Washington, DC 20375, USA.
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12
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Lee AJ, Wälti C. DNA nanostructures: A versatile lab-bench for interrogating biological reactions. Comput Struct Biotechnol J 2019; 17:832-842. [PMID: 31316727 PMCID: PMC6611922 DOI: 10.1016/j.csbj.2019.06.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/05/2019] [Accepted: 06/11/2019] [Indexed: 01/10/2023] Open
Abstract
At its inception DNA nanotechnology was conceived as a tool for spatially arranging biological molecules in a programmable and deterministic way to improve their interrogation. To date, DNA nanotechnology has provided a versatile toolset of nanostructures and functional devices to augment traditional single molecule investigation approaches - including atomic force microscopy - by isolating, arranging and contextualising biological systems at the single molecule level. This review explores the state-of-the-art of DNA-based nanoscale tools employed to enhance and tune the interrogation of biological reactions, the study of spatially distributed pathways, the visualisation of enzyme interactions, the application and detection of forces to biological systems, and biosensing platforms.
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Affiliation(s)
- Andrew J. Lee
- Bioelectronics, The Pollard Institute, School of Electronic & Electrical Engineering, University of Leeds, LS2 9JT, United Kingdom
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13
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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] [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 Engineering U.S. Naval Research Laboratory Code 6910 Washington DC 20375 USA
- College of Science George Mason University Fairfax VA 22030 USA
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering U.S. Naval Research Laboratory Code 6907 Washington DC 20375 USA
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14
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Brassat K, Ramakrishnan S, Bürger J, Hanke M, Doostdar M, Lindner JKN, Grundmeier G, Keller A. On the Adsorption of DNA Origami Nanostructures in Nanohole Arrays. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14757-14765. [PMID: 29754490 DOI: 10.1021/acs.langmuir.8b00793] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
DNA origami nanostructures are versatile substrates for the controlled arrangement of molecular capture sites with nanometer precision and thus have many promising applications in single-molecule bioanalysis. Here, we investigate the adsorption of DNA origami nanostructures in nanohole arrays which represent an important class of biosensors and may benefit from the incorporation of DNA origami-based molecular probes. Nanoholes with well-defined diameter that enable the adsorption of single DNA origami triangles are fabricated in Au films on Si wafers by nanosphere lithography. The efficiency of directed DNA origami adsorption on the exposed SiO2 areas at the bottoms of the nanoholes is evaluated in dependence of various parameters, i.e., Mg2+ and DNA origami concentrations, buffer strength, adsorption time, and nanohole diameter. We observe that the buffer strength has a surprisingly strong effect on DNA origami adsorption in the nanoholes and that multiple DNA origami triangles with 120 nm edge length can adsorb in nanoholes as small as 120 nm in diameter. We attribute the latter observation to the low lateral mobility of once adsorbed DNA origami on the SiO2 surface, in combination with parasitic adsorption to the Au film. Although parasitic adsorption can be suppressed by modifying the Au film with a hydrophobic self-assembled monolayer, the limited surface mobility of the adsorbed DNA origami still leads to poor localization accuracy in the nanoholes and results in many DNA origami crossing the boundary to the Au film even under optimized conditions. We discuss possible ways to minimize this effect by varying the composition of the adsorption buffer, employing different fabrication conditions, or using other substrate materials for nanohole array fabrication.
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15
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Zhu C, Wang M, Dong J, Zhou C, Wang Q. Modular Assembly of Plasmonic Nanoparticles Assisted by DNA Origami. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14963-14968. [PMID: 30001143 DOI: 10.1021/acs.langmuir.8b01933] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Arraying noble metal nanoparticles with nanoscale features is an important way to develop plasmonic devices with novel optical properties such as plasmonic chiral metamolecules, optical waveguides, and so forth. Along with top-down methods of fabricating plasmonic nanostructures, solution-based self-assembly provides an alternative approach. There are mainly two routes to organizing metal nanoparticles via self-assembly. One is directly linking nanoparticles through linker molecules, and the other is using nanoparticles to decorate a preformed template. We combine these two routes and herein report a strategy for the DNA origami-assisted modular assembly of gold nanoparticles into homogeneous and heterogeneous plasmonic nanostructures. For each module, we designed W-shaped DNA origami with two troughs as two domains. One domain is used to host a gold nanoparticle, and the other domain is designed to capture another gold nanoparticle hosted on a different module. By simply tuning the sequences of capture DNA strands on each module, gold nanoparticles including spherical and rod-shaped gold nanoparticles (denoted as AuNPs and AuNRs) could be well organized in a predefined manner to form versatile plasmonic nanostructures. Since the interparticle distances could be precisely controlled at the nanoscale, we also studied the plasma coupling among the assembled plasmonic nanostructures. This modular assembly strategy represents a simple yet general and effective design principle for DNA-assembled plasmonic nanostructures.
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Affiliation(s)
- Chenggan Zhu
- CAS Key Laboratory of Nano-Bio Interfaces, Division of Nanobiomedicine and i-Lab , Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences , Suzhou 215123 , P. R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 201210 , P. R. China
- Shanghai Institute of Ceramics, Chinese Academy of Sciences , 1295 Dingxi Road , Shanghai 200050 , P. R. China
| | - Meng Wang
- CAS Key Laboratory of Nano-Bio Interfaces, Division of Nanobiomedicine and i-Lab , Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences , Suzhou 215123 , P. R. China
| | - Jinyi Dong
- CAS Key Laboratory of Nano-Bio Interfaces, Division of Nanobiomedicine and i-Lab , Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences , Suzhou 215123 , P. R. China
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 201210 , P. R. China
| | - Chao Zhou
- CAS Key Laboratory of Nano-Bio Interfaces, Division of Nanobiomedicine and i-Lab , Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences , Suzhou 215123 , P. R. China
| | - Qiangbin Wang
- CAS Key Laboratory of Nano-Bio Interfaces, Division of Nanobiomedicine and i-Lab , Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences , Suzhou 215123 , P. R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
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16
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Gür FN, McPolin CPT, Raza S, Mayer M, Roth DJ, Steiner AM, Löffler M, Fery A, Brongersma ML, Zayats AV, König TAF, Schmidt TL. DNA-Assembled Plasmonic Waveguides for Nanoscale Light Propagation to a Fluorescent Nanodiamond. NANO LETTERS 2018; 18:7323-7329. [PMID: 30339400 DOI: 10.1021/acs.nanolett.8b03524] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Plasmonic waveguides consisting of metal nanoparticle chains can localize and guide light well below the diffraction limit, but high propagation losses due to lithography-limited large interparticle spacing have impeded practical applications. Here, we demonstrate that DNA-origami-based self-assembly of monocrystalline gold nanoparticles allows the interparticle spacing to be decreased to ∼2 nm, thus reducing propagation losses to 0.8 dB per 50 nm at a deep subwavelength confinement of 62 nm (∼λ/10). We characterize the individual waveguides with nanometer-scale resolution by electron energy-loss spectroscopy. Light propagation toward a fluorescent nanodiamond is directly visualized by cathodoluminescence imaging spectroscopy on a single-device level, thereby realizing nanoscale light manipulation and energy conversion. Simulations suggest that longitudinal plasmon modes arising from the narrow gaps are responsible for the efficient waveguiding. With this scalable DNA origami approach, micrometer-long propagation lengths could be achieved, enabling applications in information technology, sensing, and quantum optics.
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Affiliation(s)
- Fatih N Gür
- Center for Advancing Electronics Dresden (cfaed) , Technische Universität Dresden , 01062 Dresden , Germany
| | - Cillian P T McPolin
- Department of Physics , King's College London , Strand, London , WC2R 2LS , U.K
| | - Søren Raza
- Geballe Laboratory for Advanced Materials , Stanford University , Stanford , California 94305-4045 , United States
| | - Martin Mayer
- Center for Advancing Electronics Dresden (cfaed) , Technische Universität Dresden , 01062 Dresden , Germany
- Leibniz-Institut für Polymerforschung Dresden e.V. , Institute of Physical Chemistry and Polymer Physics , Hohe Str. 6 , 01069 Dresden , Germany
| | - Diane J Roth
- Department of Physics , King's College London , Strand, London , WC2R 2LS , U.K
| | - Anja Maria Steiner
- Center for Advancing Electronics Dresden (cfaed) , Technische Universität Dresden , 01062 Dresden , Germany
- Leibniz-Institut für Polymerforschung Dresden e.V. , Institute of Physical Chemistry and Polymer Physics , Hohe Str. 6 , 01069 Dresden , Germany
| | - Markus Löffler
- Center for Advancing Electronics Dresden (cfaed) , Technische Universität Dresden , 01062 Dresden , Germany
| | - Andreas Fery
- Center for Advancing Electronics Dresden (cfaed) , Technische Universität Dresden , 01062 Dresden , Germany
- Leibniz-Institut für Polymerforschung Dresden e.V. , Institute of Physical Chemistry and Polymer Physics , Hohe Str. 6 , 01069 Dresden , Germany
- Department of Physical Chemistry of Polymeric Materials , Technische Universität Dresden , Hohe Str. 6 , 01069 Dresden , Germany
| | - Mark L Brongersma
- Geballe Laboratory for Advanced Materials , Stanford University , Stanford , California 94305-4045 , United States
| | - Anatoly V Zayats
- Department of Physics , King's College London , Strand, London , WC2R 2LS , U.K
| | - Tobias A F König
- Center for Advancing Electronics Dresden (cfaed) , Technische Universität Dresden , 01062 Dresden , Germany
- Leibniz-Institut für Polymerforschung Dresden e.V. , Institute of Physical Chemistry and Polymer Physics , Hohe Str. 6 , 01069 Dresden , Germany
| | - Thorsten L Schmidt
- Center for Advancing Electronics Dresden (cfaed) , Technische Universität Dresden , 01062 Dresden , Germany
- B CUBE-Center for Molecular Bioengineering , Technische Universität Dresden , 01062 Dresden , Germany
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17
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Liu Y, Liu Y, Shen Y. Nano-assembly and welding of gold nanorods based on DNA origami and plasmon-induced laser irradiation. INTERNATIONAL JOURNAL OF INTELLIGENT ROBOTICS AND APPLICATIONS 2018. [DOI: 10.1007/s41315-018-0074-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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18
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Kogikoski S, Paschoalino WJ, Kubota LT. Supramolecular DNA origami nanostructures for use in bioanalytical applications. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2018.08.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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19
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Shahbazi MA, Bauleth-Ramos T, Santos HA. DNA Hydrogel Assemblies: Bridging Synthesis Principles to Biomedical Applications. ADVANCED THERAPEUTICS 2018. [DOI: 10.1002/adtp.201800042] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Mohammad-Ali Shahbazi
- Drug Research Program; Division of Pharmaceutical Chemistry and Technology; Faculty of Pharmacy; FI-00014 University of Helsinki; Helsinki Finland
- Department of Micro- and Nanotechnology; Technical University of Denmark; Ørsteds Plads DK-2800 Kgs Lyngby Denmark
- Department of Pharmaceutical Nanotechnology; School of Pharmacy; Zanjan University of Medical Sciences; 56184-45139 Zanjan Iran
| | - Tomás Bauleth-Ramos
- Drug Research Program; Division of Pharmaceutical Chemistry and Technology; Faculty of Pharmacy; FI-00014 University of Helsinki; Helsinki Finland
- Instituto de Investigação e Inovação em Saúde; University of Porto; Rua Alfredo Allen 208 4200-135 Porto Portugal
- Instituto de Engenharia Biomédica; University of Porto; Rua Alfredo Allen 208 4200-135 Porto Portugal
- Instituto Ciências Biomédicas Abel Salazar; University of Porto; Rua Jorge Viterbo 228 4150-180 Porto Portugal
| | - Hélder A. Santos
- Drug Research Program; Division of Pharmaceutical Chemistry and Technology; Faculty of Pharmacy; FI-00014 University of Helsinki; Helsinki Finland
- Helsinki Institute of Life Science; FI-00014 University of Helsinki; Helsinki Finland
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20
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Kuzyk A, Jungmann R, Acuna GP, Liu N. DNA Origami Route for Nanophotonics. ACS PHOTONICS 2018; 5:1151-1163. [PMID: 30271812 PMCID: PMC6156112 DOI: 10.1021/acsphotonics.7b01580] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 02/06/2018] [Accepted: 02/11/2018] [Indexed: 05/21/2023]
Abstract
The specificity and simplicity of the Watson-Crick base pair interactions make DNA one of the most versatile construction materials for creating nanoscale structures and devices. Among several DNA-based approaches, the DNA origami technique excels in programmable self-assembly of complex, arbitrary shaped structures with dimensions of hundreds of nanometers. Importantly, DNA origami can be used as templates for assembly of functional nanoscale components into three-dimensional structures with high precision and controlled stoichiometry. This is often beyond the reach of other nanofabrication techniques. In this Perspective, we highlight the capability of the DNA origami technique for realization of novel nanophotonic systems. First, we introduce the basic principles of designing and fabrication of DNA origami structures. Subsequently, we review recent advances of the DNA origami applications in nanoplasmonics, single-molecule and super-resolution fluorescent imaging, as well as hybrid photonic systems. We conclude by outlining the future prospects of the DNA origami technique for advanced nanophotonic systems with tailored functionalities.
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Affiliation(s)
- Anton Kuzyk
- Max
Planck Institute for Intelligent Systems, Heisenbergstrasse 3, D-70569 Stuttgart, Germany
- Department
of Neuroscience and Biomedical Engineering, Aalto University School of Science, P.O. Box 12200, FI-00076 Aalto, Finland
| | - Ralf Jungmann
- Department
of Physics and Center for Nanoscience, Ludwig
Maximilian University, 80539 Munich, Germany
- Max
Planck Institute of Biochemistry, 82152 Martinsried near Munich, Germany
| | - Guillermo P. Acuna
- Institute
for Physical & Theoretical Chemistry, and Braunschweig Integrated
Centre of Systems Biology (BRICS), and Laboratory for Emerging Nanometrology
(LENA), Braunschweig University of Technology, Rebenring 56, 38106 Braunschweig, Germany
| | - Na Liu
- Max
Planck Institute for Intelligent Systems, Heisenbergstrasse 3, D-70569 Stuttgart, Germany
- Kirchhoff
Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, D-69120 Heidelberg, Germany
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21
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Abstract
Self-assembled nucleic acids perform biological, chemical, and mechanical work at the nanoscale. DNA-based molecular machines have been designed here to perform work by reacting with cancer-specific miRNA mimics and then regulating gene expression in vitro by tuning RNA polymerase activity. Because RNA production is topologically restrained, the machines demonstrate chromatin analogous gene expression (CAGE). With modular and tunable design features, CAGE has potential for molecular biology, synthetic biology, and personalized medicine applications.
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Affiliation(s)
| | - William L. Hughes
- Micron School of Materials Science & Engineering
- College of Innovation + Design, Boise State University, Boise, Idaho 83725, United States
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22
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Liu Q, Liu G, Wang T, Fu J, Li R, Song L, Wang ZG, Ding B, Chen F. Enhanced Stability of DNA Nanostructures by Incorporation of Unnatural Base Pairs. Chemphyschem 2017; 18:2977-2980. [DOI: 10.1002/cphc.201700809] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 08/25/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Qing Liu
- CAS Center for Excellence in Nanoscience; National Center for Nanoscience and Technology; Beijing 100190 P. R. China
- University of Chinese Academy of Sciences; Beijing 100049 P. R. China
| | - Guocheng Liu
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics; Chinese Academy of Sciences; Beijing 100101 P. R. China
| | - Ting Wang
- CAS Center for Excellence in Nanoscience; National Center for Nanoscience and Technology; Beijing 100190 P. R. China
| | - Jing Fu
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics; Chinese Academy of Sciences; Beijing 100101 P. R. China
- University of Chinese Academy of Sciences; Beijing 100049 P. R. China
| | - Rujiao Li
- Big Data Center, Beijing Institute of Genomics; Chinese Academy of Sciences; Beijing 100101 P. R. China
| | - Linlin Song
- CAS Center for Excellence in Nanoscience; National Center for Nanoscience and Technology; Beijing 100190 P. R. China
- University of Chinese Academy of Sciences; Beijing 100049 P. R. China
| | - Zhen-Gang Wang
- CAS Center for Excellence in Nanoscience; National Center for Nanoscience and Technology; Beijing 100190 P. R. China
| | - Baoquan Ding
- CAS Center for Excellence in Nanoscience; National Center for Nanoscience and Technology; Beijing 100190 P. R. China
- University of Chinese Academy of Sciences; Beijing 100049 P. R. China
| | - Fei Chen
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics; Chinese Academy of Sciences; Beijing 100101 P. R. China
- University of Chinese Academy of Sciences; Beijing 100049 P. R. China
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23
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Zessin J, Fischer F, Heerwig A, Kick A, Boye S, Stamm M, Kiriy A, Mertig M. Tunable Fluorescence of a Semiconducting Polythiophene Positioned on DNA Origami. NANO LETTERS 2017; 17:5163-5170. [PMID: 28745060 DOI: 10.1021/acs.nanolett.7b02623] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
A novel approach for the integration of π-conjugated polymers (CPs) into DNA-based nanostructures is presented. Using the controlled Kumada catalyst-transfer polycondensation, well-defined thiophene-based polymers with controllable molecular weight, specific end groups, and water-soluble oligoethylene glycol-based side chains were synthesized. The end groups were used for the easy but highly efficient click chemistry-based attachment of end-functionalized oligodeoxynucleotides (ODNs) with predesigned sequences. As demonstrated by surface plasmon resonance spectroscopy, the prepared block copolymers (BCPs), P3(EO)3T-b-ODN, comprising different ODN lengths and specific or repetitive sequences, undergo specific hybridization with complementary, thiol-functionalized ODNs immobilized on a gold surface. Furthermore, the site-specific attachment of the BCPs to DNA origami structures is studied. We demonstrate that a nanoscale object, that is, a single BCP with a single ODN handle, can be directed and bound to the DNA origami with reasonable yield, site-specificity, and high spatial density. On the basis of these results, we are able to demonstrate for the first time that optical properties of CP molecules densely immobilized on DNA origami can be locally fine-tuned by controlling the attractive π-π-stacking interactions between the CPs. In particular, we show that the fluorescence of the immobilized CP molecules can be significantly enhanced by surfactant-induced breakup of π-π-stacking interactions between the CP's backbones. Such molecular control over the emission intensity of the CPs can be valuable for the construction of sophisticated switchable nanophotonic devices and nanoscale biosensors.
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Affiliation(s)
- Johanna Zessin
- Leibniz-Institut für Polymerforschung Dresden e.V. , 01069 Dresden, Germany
- Physikalische Chemie, Mess- und Sensortechnik, Technische Universität Dresden , 01062 Dresden, Germany
| | - Franziska Fischer
- Leibniz-Institut für Polymerforschung Dresden e.V. , 01069 Dresden, Germany
- Physikalische Chemie, Mess- und Sensortechnik, Technische Universität Dresden , 01062 Dresden, Germany
| | - Andreas Heerwig
- Physikalische Chemie, Mess- und Sensortechnik, Technische Universität Dresden , 01062 Dresden, Germany
- Kurt-Schwabe Institut für Mess- und Sensortechnik e.V. Meinsberg , 04736 Waldheim, Germany
| | - Alfred Kick
- Kurt-Schwabe Institut für Mess- und Sensortechnik e.V. Meinsberg , 04736 Waldheim, Germany
| | - Susanne Boye
- Leibniz-Institut für Polymerforschung Dresden e.V. , 01069 Dresden, Germany
| | - Manfred Stamm
- Leibniz-Institut für Polymerforschung Dresden e.V. , 01069 Dresden, Germany
| | - Anton Kiriy
- Leibniz-Institut für Polymerforschung Dresden e.V. , 01069 Dresden, Germany
| | - Michael Mertig
- Physikalische Chemie, Mess- und Sensortechnik, Technische Universität Dresden , 01062 Dresden, Germany
- Kurt-Schwabe Institut für Mess- und Sensortechnik e.V. Meinsberg , 04736 Waldheim, Germany
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24
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Zadegan RM, Lindau EG, Klein WP, Green C, Graugnard E, Yurke B, Kuang W, Hughes WL. Twisting of DNA Origami from Intercalators. Sci Rep 2017; 7:7382. [PMID: 28785065 PMCID: PMC5547094 DOI: 10.1038/s41598-017-07796-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 07/10/2017] [Indexed: 02/07/2023] Open
Abstract
DNA nanostructures represent the confluence of materials science, computer science, biology, and engineering. As functional assemblies, they are capable of performing mechanical and chemical work. In this study, we demonstrate global twisting of DNA nanorails made from two DNA origami six-helix bundles. Twisting was controlled using ethidium bromide or SYBR Green I as model intercalators. Our findings demonstrate that DNA nanorails: (i) twist when subjected to intercalators and the amount of twisting is concentration dependent, and (ii) twisting saturates at elevated concentrations. This study provides insight into how complex DNA structures undergo conformational changes when exposed to intercalators and may be of relevance when exploring how intercalating drugs interact with condensed biological structures such as chromatin and chromosomes, as well as chromatin analogous gene expression devices.
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Affiliation(s)
- Reza M Zadegan
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho, 83725, United States
| | - Elias G Lindau
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho, 83725, United States
| | - William P Klein
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho, 83725, United States
| | - Christopher Green
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho, 83725, United States
| | - Elton Graugnard
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho, 83725, United States
| | - Bernard Yurke
- Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho, 83725, United States
| | - Wan Kuang
- Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho, 83725, United States
| | - William L Hughes
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho, 83725, United States.
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25
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Roller EM, Besteiro LV, Pupp C, Khorashad LK, Govorov AO, Liedl T. Hot spot-mediated non-dissipative and ultrafast plasmon passage. NATURE PHYSICS 2017; 13:761-765. [PMID: 28781603 PMCID: PMC5540180 DOI: 10.1038/nphys4120] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 03/30/2017] [Indexed: 05/18/2023]
Abstract
Plasmonic nanoparticles hold great promise as photon handling elements and as channels for coherent transfer of energy and information in future all-optical computing devices.1-5 Coherent energy oscillations between two spatially separated plasmonic entities via a virtual middle state exemplify electron-based population transfer, but their realization requires precise nanoscale positioning of heterogeneous particles.6-10 Here, we show the assembly and optical analysis of a triple particle system consisting of two gold nanoparticles with an inter-spaced silver island. We observe strong plasmonic coupling between the spatially separated gold particles mediated by the connecting silver particle with almost no dissipation of energy. As the excitation energy of the silver island exceeds that of the gold particles, only quasi-occupation of the silver transfer channel is possible. We describe this effect both with exact classical electrodynamic modeling and qualitative quantum-mechanical calculations. We identify the formation of strong hot spots between all particles as the main mechanism for the loss-less coupling and thus coherent ultra-fast energy transfer between the remote partners. Our findings could prove useful for quantum gate operations, but also for classical charge and information transfer processes.
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Affiliation(s)
- Eva-Maria Roller
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80539 Munich, Germany
| | - Lucas V. Besteiro
- Department of Physics and Astronomy, Ohio University, Athens, Ohio 45701, USA
| | - Claudia Pupp
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80539 Munich, Germany
| | | | | | - Tim Liedl
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80539 Munich, Germany
- ;
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26
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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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27
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Vogele K, List J, Pardatscher G, Holland NB, Simmel FC, Pirzer T. Self-Assembled Active Plasmonic Waveguide with a Peptide-Based Thermomechanical Switch. ACS NANO 2016; 10:11377-11384. [PMID: 28024323 DOI: 10.1021/acsnano.6b06635] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Nanoscale plasmonic waveguides composed of metallic nanoparticles are capable of guiding electromagnetic energy below the optical diffraction limit. Signal feed-in and readout typically require the utilization of electronic effects or near-field optical techniques, whereas for their fabrication mainly lithographic methods are employed. Here we developed a switchable plasmonic waveguide assembled from gold nanoparticles (AuNPs) on a DNA origami structure that facilitates a simple spectroscopic excitation and readout. The waveguide is specifically excited at one end by a fluorescent dye, and energy transfer is detected at the other end via the fluorescence of a second dye. The transfer distance is beyond the multicolor FRET range and below the Abbé limit. The transmittance of the waveguide can also be reversibly switched by changing the position of a AuNP within the waveguide, which is tethered to the origami platform by a thermoresponsive peptide. High-yield fabrication of the plasmonic waveguides in bulk was achieved using silica particles as solid supports. Our findings enable bulk solution applications for plasmonic waveguides as light-focusing and light-polarizing elements below the diffraction limit.
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Affiliation(s)
- Kilian Vogele
- Systems Biophysics and Bionanotechnology-E14, Physics-Department and ZNN, Technische Universität München , 85748 Garching, Germany
| | - Jonathan List
- Systems Biophysics and Bionanotechnology-E14, Physics-Department and ZNN, Technische Universität München , 85748 Garching, Germany
| | - Günther Pardatscher
- Systems Biophysics and Bionanotechnology-E14, Physics-Department and ZNN, Technische Universität München , 85748 Garching, Germany
| | - Nolan B Holland
- Department of Chemical and Biomedical Engineering, Cleveland State University , 2121 Euclid Avenue, Cleveland, Ohio 44115, United States
| | - Friedrich C Simmel
- Systems Biophysics and Bionanotechnology-E14, Physics-Department and ZNN, Technische Universität München , 85748 Garching, Germany
- Nanosystems Initiative Munich , 80539 Munich, Germany
| | - Tobias Pirzer
- Systems Biophysics and Bionanotechnology-E14, Physics-Department and ZNN, Technische Universität München , 85748 Garching, Germany
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28
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Teschome B, Facsko S, Schönherr T, Kerbusch J, Keller A, Erbe A. Temperature-Dependent Charge Transport through Individually Contacted DNA Origami-Based Au Nanowires. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:10159-10165. [PMID: 27626925 DOI: 10.1021/acs.langmuir.6b01961] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
DNA origami nanostructures have been used extensively as scaffolds for numerous applications such as for organizing both organic and inorganic nanomaterials, studying single molecule reactions, and fabricating photonic devices. Yet, little has been done toward the integration of DNA origami nanostructures into nanoelectronic devices. Among other challenges, the technical difficulties in producing well-defined electrical contacts between macroscopic electrodes and individual DNA origami-based nanodevices represent a serious bottleneck that hinders the thorough characterization of such devices. Therefore, in this work, we have developed a method to electrically contact individual DNA origami-based metallic nanowires using electron beam lithography. We then characterize the charge transport of such nanowires in the temperature range from room temperature down to 4.2 K. The room temperature charge transport measurements exhibit ohmic behavior, whereas at lower temperatures, multiple charge transport mechanisms such as tunneling and thermally assisted transport start to dominate. Our results confirm that charge transport along metallized DNA origami nanostructures may deviate from pure metallic behavior due to several factors including partial metallization, seed inhomogeneities, impurities, and weak electronic coupling among AuNPs. Besides, this study further elucidates the importance of variable temperature measurements for determining the dominant charge transport mechanisms for conductive nanostructures made by self-assembly approaches.
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Affiliation(s)
- Bezu Teschome
- Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf , 01328 Dresden, Germany
- Technische Universität Dresden, Mommsenstraße 13, 01069 Dresden, Germany
| | - Stefan Facsko
- Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf , 01328 Dresden, Germany
| | - Tommy Schönherr
- Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf , 01328 Dresden, Germany
| | - Jochen Kerbusch
- Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf , 01328 Dresden, Germany
| | - Adrian Keller
- Technical and Macromolecular Chemistry, University of Paderborn , Warburger Str. 100, 33098 Paderborn, Germany
| | - Artur Erbe
- Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf , 01328 Dresden, Germany
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29
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Henning-Knechtel A, Wiens M, Lakatos M, Heerwig A, Ostermaier F, Haufe N, Mertig M. Dielectrophoresis of gold nanoparticles conjugated to DNA origami structures. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2016; 7:948-956. [PMID: 27547612 PMCID: PMC4979641 DOI: 10.3762/bjnano.7.87] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/13/2016] [Indexed: 06/06/2023]
Abstract
DNA nanostructures are promising construction materials to bridge the gap between self-assembly of functional molecules and conventional top-down fabrication methods in nanotechnology. Their positioning onto specific locations of a microstructured substrate is an important task towards this aim. Here we study manipulation and positioning of pristine and of gold nanoparticle-conjugated tubular DNA origami structures using ac dielectrophoresis. The dielectrophoretic behavior was investigated employing fluorescence microscopy. For the pristine origami, a significant dielectrophoretic response was found to take place in the megahertz range, whereas, due to the higher polarizability of the metallic nanoparticles, the nanoparticle/DNA hybrid structures required a lower electrical field strength and frequency for a comparable trapping at the edges of the electrode structure. The nanoparticle conjugation additionally resulted in a remarkable alteration of the DNA structure arrangement. The growth of linear, chain-like structures in between electrodes at applied frequencies in the megahertz range was observed. The long-range chain formation is caused by a local, gold nanoparticle-induced field concentration along the DNA nanostructures, which in turn, creates dielectrophoretic forces that enable the observed self-alignment of the hybrid structures.
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Affiliation(s)
- Anja Henning-Knechtel
- Physikalische Chemie, Mess- und Sensortechnik, Technische Universität Dresden, 01062 Dresden, Germany
- Department of Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Matthew Wiens
- Physikalische Chemie, Mess- und Sensortechnik, Technische Universität Dresden, 01062 Dresden, Germany
- Department of Chemistry, University of Alberta, Edmonton, T6G2G2, Canada
| | - Mathias Lakatos
- Physikalische Chemie, Mess- und Sensortechnik, Technische Universität Dresden, 01062 Dresden, Germany
| | - Andreas Heerwig
- Physikalische Chemie, Mess- und Sensortechnik, Technische Universität Dresden, 01062 Dresden, Germany
- Kurt-Schwabe-Institut für Mess- und Sensortechnik Meinsberg e.V., 04736 Waldheim, Germany
| | - Frieder Ostermaier
- Physikalische Chemie, Mess- und Sensortechnik, Technische Universität Dresden, 01062 Dresden, Germany
| | - Nora Haufe
- Physikalische Chemie, Mess- und Sensortechnik, Technische Universität Dresden, 01062 Dresden, Germany
- Kurt-Schwabe-Institut für Mess- und Sensortechnik Meinsberg e.V., 04736 Waldheim, Germany
| | - Michael Mertig
- Physikalische Chemie, Mess- und Sensortechnik, Technische Universität Dresden, 01062 Dresden, Germany
- Kurt-Schwabe-Institut für Mess- und Sensortechnik Meinsberg e.V., 04736 Waldheim, Germany
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30
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Gür FN, Schwarz FW, Ye J, Diez S, Schmidt TL. Toward Self-Assembled Plasmonic Devices: High-Yield Arrangement of Gold Nanoparticles on DNA Origami Templates. ACS NANO 2016; 10:5374-82. [PMID: 27159647 DOI: 10.1021/acsnano.6b01537] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Plasmonic structures allow the manipulation of light with materials that are smaller than the optical wavelength. Such structures can consist of plasmonically active metal nanoparticles and can be fabricated through scalable bottom-up self-assembly on DNA origami templates. To produce functional devices, the precise and high-yield arrangement of each of the nanoparticles on a structure is of vital importance as the absence of a single particle can destroy the functionality of the entire device. Nevertheless, the parameters influencing the yield of the multistep assembly process are still poorly understood. To overcome this deficiency, we employed a test system consisting of a tubular six-helix bundle DNA origami with binding sites for eight oligonucleotide-functionalized gold nanoparticles. We systematically studied the assembly yield as a function of a wide range of parameters such as ionic strength, stoichiometric ratio, oligonucleotide linker chemistry, and assembly kinetics by an automated high-throughput analysis of electron micrographs of the formed heterocomplexes. Our optimized protocols enable particle placement yields up to 98.7% and promise the reliable production of sophisticated DNA-based multiparticle plasmonic devices for applications in photonics, optoelectronics, and nanomedicine.
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Affiliation(s)
- Fatih N Gür
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden , 01062 Dresden, Germany
| | - Friedrich W Schwarz
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden , 01062 Dresden, Germany
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden , 01307 Dresden, Germany
| | - Jingjing Ye
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden , 01062 Dresden, Germany
| | - Stefan Diez
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden , 01062 Dresden, Germany
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden , 01307 Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics , 01307 Dresden, Germany
| | - Thorsten L Schmidt
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden , 01062 Dresden, Germany
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31
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Teschome B, Facsko S, Gothelf KV, Keller A. Alignment of Gold Nanoparticle-Decorated DNA Origami Nanotubes: Substrate Prepatterning versus Molecular Combing. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:12823-12829. [PMID: 26522180 DOI: 10.1021/acs.langmuir.5b02569] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
DNA origami has become an established technique for designing well-defined nanostructures with any desired shape and for the controlled arrangement of functional nanostructures with few nanometer resolution. These unique features make DNA origami nanostructures promising candidates for use as scaffolds in nanoelectronics and nanophotonics device fabrication. Consequently, a number of studies have shown the precise organization of metallic nanoparticles on various DNA origami shapes. In this work, we fabricated large arrays of aligned DNA origami decorated with a high density of gold nanoparticles (AuNPs). To this end, we first demonstrate the high-yield assembly of high-density AuNP arrangements on DNA origami adsorbed to Si surfaces with few unbound background nanoparticles by carefully controlling the concentrations of MgCl2 and AuNPs in the hybridization buffer and the hybridization time. Then, we evaluate two methods, i.e., hybridization to prealigned DNA origami and molecular combing in a receding meniscus, with respect to their potential to yield large arrays of aligned AuNP-decorated DNA origami nanotubes. Because of the comparatively low MgCl2 concentration required for the efficient immobilization of the AuNPs, the prealigned DNA origami become mobile and displaced from their original positions, thereby decreasing the alignment yield. This increased mobility, on the other hand, makes the adsorbed origami susceptible to molecular combing, and a total alignment yield of 86% is obtained in this way.
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Affiliation(s)
- Bezu Teschome
- Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf , 01328 Dresden, Germany
- Technische Universität Dresden, Mommsenstraße 13, 01069 Dresden, Germany
| | - Stefan Facsko
- Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf , 01328 Dresden, Germany
| | - Kurt V Gothelf
- Danish National Research Foundation: Centre for DNA Nanotechnology (CDNA) at Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University , 8000 Aarhus C, Denmark
| | - Adrian Keller
- Technical and Macromolecular Chemistry, University of Paderborn , Warburger Str. 100, 33098 Paderborn, Germany
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32
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Samanta A, Banerjee S, Liu Y. DNA nanotechnology for nanophotonic applications. NANOSCALE 2015; 7:2210-20. [PMID: 25592639 DOI: 10.1039/c4nr06283c] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
DNA nanotechnology has touched the epitome of miniaturization by integrating various nanometer size particles with nanometer precision. This enticing bottom-up approach has employed small DNA tiles, large multi-dimensional polymeric structures or more recently DNA origami to organize nanoparticles of different inorganic materials, small organic molecules or macro-biomolecules like proteins, and RNAs into fascinating patterns that are difficult to achieve by other conventional methods. Here, we are especially interested in the self-assembly of nanomaterials that are potentially attractive elements in the burgeoning field of nanophotonics. These materials include plasmonic nanoparticles, quantum dots, fluorescent organic dyes, etc. DNA based self-assembly allows excellent control over distance, orientation and stoichiometry of these nano-elements that helps to engineer intelligent systems that can potentially pave the path for future technology. Many outstanding structures have been fabricated that are capable of fine tuning optical properties, such as fluorescence intensity and lifetime modulation, enhancement of Raman scattering and emergence of circular dichroism responses. Within the limited scope of this review we have tried to give a glimpse of the development of this still nascent but highly promising field to its current status as well as the existing challenges before us.
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Affiliation(s)
- Anirban Samanta
- Department of Chemistry and Biochemistry & Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.
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33
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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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34
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Takabayashi S, Klein WP, Onodera C, Rapp B, Flores-Estrada J, Lindau E, Snowball L, Sam JT, Padilla JE, Lee J, Knowlton WB, Graugnard E, Yurke B, Kuang W, Hughes WL. High precision and high yield fabrication of dense nanoparticle arrays onto DNA origami at statistically independent binding sites. NANOSCALE 2014; 6:13928-38. [PMID: 25311051 PMCID: PMC4547787 DOI: 10.1039/c4nr03069a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
High precision, high yield, and high density self-assembly of nanoparticles into arrays is essential for nanophotonics. Spatial deviations as small as a few nanometers can alter the properties of near-field coupled optical nanostructures. Several studies have reported assemblies of few nanoparticle structures with controlled spacing using DNA nanostructures with variable yield. Here, we report multi-tether design strategies and attachment yields for homo- and hetero-nanoparticle arrays templated by DNA origami nanotubes. Nanoparticle attachment yield via DNA hybridization is comparable with streptavidin-biotin binding. Independent of the number of binding sites, >97% site-occupation was achieved with four tethers and 99.2% site-occupation is theoretically possible with five tethers. The interparticle distance was within 2 nm of all design specifications and the nanoparticle spatial deviations decreased with interparticle spacing. Modified geometric, binomial, and trinomial distributions indicate that site-bridging, steric hindrance, and electrostatic repulsion were not dominant barriers to self-assembly and both tethers and binding sites were statistically independent at high particle densities.
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Affiliation(s)
- Sadao Takabayashi
- Department of Materials Science & Engineering, Boise, ID 83725, USA.
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35
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Liu H, Shen X, Wang ZG, Kuzyk A, Ding B. Helical nanostructures based on DNA self-assembly. NANOSCALE 2014; 6:9331-9338. [PMID: 24740255 DOI: 10.1039/c3nr06913c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Recent advances in design and fabrication of helical nanostructures based on DNA self-assembly are reviewed. These helical nanostructures are either constructed entirely by DNA or based on DNA guided metal nanoparticles self-assembly. Biophysical properties and optical responses of corresponding helical nanostructures are also discussed.
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Affiliation(s)
- Huan Liu
- National Center for NanoScience and Technology, 11 BeiYiTiao, ZhongGuanCun, Beijing, 100190, China.
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36
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Abstract
Over the past three decades DNA has emerged as an exceptional molecular building block for nanoconstruction due to its predictable conformation and programmable intra- and intermolecular Watson-Crick base-pairing interactions. A variety of convenient design rules and reliable assembly methods have been developed to engineer DNA nanostructures of increasing complexity. The ability to create designer DNA architectures with accurate spatial control has allowed researchers to explore novel applications in many directions, such as directed material assembly, structural biology, biocatalysis, DNA computing, nanorobotics, disease diagnosis, and drug delivery. This Perspective discusses the state of the art in the field of structural DNA nanotechnology and presents some of the challenges and opportunities that exist in DNA-based molecular design and programming.
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Affiliation(s)
- Fei Zhang
- Center for Molecular Design and Biomimicry, Biodesign Institute, and ‡Department of Chemistry and Biochemistry, Arizona State University , Tempe, Arizona 85287, United States
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37
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Zhang F, Nangreave J, Liu Y, Yan H. Structural DNA nanotechnology: state of the art and future perspective. J Am Chem Soc 2014; 136:11198-211. [PMID: 25029570 PMCID: PMC4140475 DOI: 10.1021/ja505101a] [Citation(s) in RCA: 393] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Indexed: 12/12/2022]
Abstract
Over the past three decades DNA has emerged as an exceptional molecular building block for nanoconstruction due to its predictable conformation and programmable intra- and intermolecular Watson-Crick base-pairing interactions. A variety of convenient design rules and reliable assembly methods have been developed to engineer DNA nanostructures of increasing complexity. The ability to create designer DNA architectures with accurate spatial control has allowed researchers to explore novel applications in many directions, such as directed material assembly, structural biology, biocatalysis, DNA computing, nanorobotics, disease diagnosis, and drug delivery. This Perspective discusses the state of the art in the field of structural DNA nanotechnology and presents some of the challenges and opportunities that exist in DNA-based molecular design and programming.
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Affiliation(s)
- Fei Zhang
- Center
for Molecular Design and Biomimicry, Biodesign Institute, and Department of
Chemistry and Biochemistry, Arizona State
University, Tempe, Arizona 85287, United
States
| | - Jeanette Nangreave
- Center
for Molecular Design and Biomimicry, Biodesign Institute, and Department of
Chemistry and Biochemistry, Arizona State
University, Tempe, Arizona 85287, United
States
| | - Yan Liu
- Center
for Molecular Design and Biomimicry, Biodesign Institute, and Department of
Chemistry and Biochemistry, Arizona State
University, Tempe, Arizona 85287, United
States
| | - Hao Yan
- Center
for Molecular Design and Biomimicry, Biodesign Institute, and Department of
Chemistry and Biochemistry, Arizona State
University, Tempe, Arizona 85287, United
States
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38
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Schreiber R, Luong N, Fan Z, Kuzyk A, Nickels PC, Zhang T, Smith DM, Yurke B, Kuang W, Govorov AO, Liedl T. Chiral plasmonic DNA nanostructures with switchable circular dichroism. Nat Commun 2014; 4:2948. [PMID: 24336125 PMCID: PMC3905713 DOI: 10.1038/ncomms3948] [Citation(s) in RCA: 187] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 11/15/2013] [Indexed: 02/06/2023] Open
Abstract
Circular dichroism spectra of naturally occurring molecules and also of synthetic chiral arrangements of plasmonic particles often exhibit characteristic bisignate shapes. Such spectra consist of peaks next to dips (or vice versa) and result from the superposition of signals originating from many individual chiral objects oriented randomly in solution. Here we show that by first aligning and then toggling the orientation of DNA-origami-scaffolded nanoparticle helices attached to a substrate, we are able to reversibly switch the optical response between two distinct circular dichroism spectra corresponding to either perpendicular or parallel helix orientation with respect to the light beam. The observed directional circular dichroism of our switchable plasmonic material is in good agreement with predictions based on dipole approximation theory. Such dynamic metamaterials introduce functionality into soft matter-based optical devices and may enable novel data storage schemes or signal modulators. Plasmonic resonances in nanoparticle helices arranged by the DNA origami method can give rise to strong circular dichroism at visible wavelengths. Schreiber et al. show that aligning and then toggling the orientation of such nanoparticle helices enables reversible switching of the dichroic response.
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Affiliation(s)
- Robert Schreiber
- Fakultät für Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80539 München, Germany
| | - Ngoc Luong
- Department of Electrical and Computer Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Zhiyuan Fan
- Department of Physics and Astronomy, Ohio University, Athens, Ohio 45701, USA
| | - Anton Kuzyk
- Max-Planck-Institute for Intelligent Systems, 70569 Stuttgart, Germany
| | - Philipp C Nickels
- Fakultät für Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80539 München, Germany
| | - Tao Zhang
- Fakultät für Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80539 München, Germany
| | - David M Smith
- Fakultät für Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80539 München, Germany
| | - Bernard Yurke
- Department of Electrical and Computer Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Wan Kuang
- Department of Electrical and Computer Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Alexander O Govorov
- Department of Physics and Astronomy, Ohio University, Athens, Ohio 45701, USA
| | - Tim Liedl
- Fakultät für Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80539 München, Germany
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39
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Wang ZG, Ding B. Engineering DNA self-assemblies as templates for functional nanostructures. Acc Chem Res 2014; 47:1654-62. [PMID: 24588320 DOI: 10.1021/ar400305g] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
CONSPECTUS: DNA is a well-known natural molecule that carries genetic information. In recent decades, DNA has been used beyond its genetic role as a building block for the construction of engineering materials. Many strategies, such as tile assembly, scaffolded origami and DNA bricks, have been developed to design and produce 1D, 2D, and 3D architectures with sophisticated morphologies. Moreover, the spatial addressability of DNA nanostructures and sequence-dependent recognition enable functional elements to be precisely positioned and allow for the control of chemical and biochemical processes. The spatial arrangement of heterogeneous components using DNA nanostructures as the templates will aid in the fabrication of functional materials that are difficult to produce using other methods and can address scientific and technical challenges in interdisciplinary research. For example, plasmonic nanoparticles can be assembled into well-defined configurations with high resolution limit while exhibiting desirable collective behaviors, such as near-field enhancement. Conducting metallic or polymer patterns can be synthesized site-specifically on DNA nanostructures to form various controllable geometries, which could be used for electronic nanodevices. Biomolecules can be arranged into organized networks to perform programmable biological functionalities, such as distance-dependent enzyme-cascade activities. DNA nanostructures can carry multiple cytoactive molecules and cell-targeting groups simultaneously to address medical issues such as targeted therapy and combined administration. In this Account, we describe recent advances in the functionalization of DNA nanostructures in different fashions based on our research efforts in nanophotonics, nanoelectronics, and nanomedicine. We show that DNA origami nanostructures can guide the assembly of achiral, spherical, metallic nanoparticles into nature-mimicking chiral geometries through hybridization between complementary DNA strands on the surface of nanoparticles and DNA scaffolds, to generate circular dichroism (CD) response in the visible light region. We also show that DNA nanostructures, on which a HRP-mimicking DNAzyme acts as the catalyst, can direct the site-selective growth of conductive polymer nanomaterials with template configuration-dependent doping behaviors. We demonstrate that DNA origami nanostructures can act as an anticancer-drug carrier, loading drug through intercalation, and can effectively circumvent the drug resistance of cultured cancer cells. Finally, we show a label-free strategy for probing the location and stability of DNA origami nanocarriers in cellular environments by docking turn-off fluorescence dyes in DNA double helices. These functionalizations require further improvement and expansion for realistic applications. We discuss the future opportunities and challenges of DNA based assemblies. We expect that DNA nanostructures as engineering materials will stimulate the development of multidisciplinary and interdisciplinary research.
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Affiliation(s)
- Zhen-Gang Wang
- National Center for NanoScience and Technology, No. 11
BeiYiTiao, ZhongGuanCun, Beijing, 100190 China
| | - Baoquan Ding
- National Center for NanoScience and Technology, No. 11
BeiYiTiao, ZhongGuanCun, Beijing, 100190 China
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40
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DNA origami based assembly of gold nanoparticle dimers for surface-enhanced Raman scattering. Nat Commun 2014; 5:3448. [DOI: 10.1038/ncomms4448] [Citation(s) in RCA: 340] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 02/13/2014] [Indexed: 12/17/2022] Open
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41
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Noh H, Goodman SM, Mohan P, Goodwin AP, Nagpal P, Cha JN. Direct conjugation of DNA to quantum dots for scalable assembly of photoactive thin films. RSC Adv 2014. [DOI: 10.1039/c3ra47689h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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