1
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Parikka JM, Järvinen H, Sokołowska K, Ruokolainen V, Markešević N, Natarajan AK, Vihinen-Ranta M, Kuzyk A, Tapio K, Toppari JJ. Creation of ordered 3D tubes out of DNA origami lattices. Nanoscale 2023; 15:7772-7780. [PMID: 37057647 DOI: 10.1039/d2nr06001a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Hierarchical self-assembly of nanostructures with addressable complexity has been a promising route for realizing novel functional materials. Traditionally, the fabrication of such structures on a large scale has been achievable using top-down methods but with the cost of complexity of the fabrication equipment versus resolution and limitation mainly to 2D structures. More recently bottom-up methods using molecules like DNA have gained attention due to the advantages of low fabrication costs, high resolution and simplicity in an extension of the methods to the third dimension. One of the more promising bottom-up techniques is DNA origami due to the robust self-assembly of arbitrarily shaped nanostructures with feature sizes down to a few nanometers. Here, we show that under specific ionic conditions of the buffer, the employed plus-shaped, blunt-ended Seeman tile (ST) origami forms elongated, ordered 2D lattices, which are further rolled into 3D tubes in solution. Imaging structures on a surface by atomic force microscopy reveals ribbon-like structures, with single or double layers of the origami lattice. Further studies of the double-layered structures in a liquid state by confocal microscopy and cryo-TEM revealed elongated tube structures with a relatively uniform width but with a varying length. Through meticulous study, we concluded that the assembly process of these 3D DNA origami tubes is heavily dependent on the concentration of both mono- and divalent cations. In particular, nickel seems to act as a trigger for the formation of the tubular assemblies in liquid.
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Affiliation(s)
- Johannes M Parikka
- University of Jyväskylä, Department of Physics and Nanoscience Center, 40014 University of Jyväskylä, Finland.
| | - Heini Järvinen
- University of Jyväskylä, Department of Physics and Nanoscience Center, 40014 University of Jyväskylä, Finland.
| | - Karolina Sokołowska
- University of Jyväskylä, Department of Physics and Nanoscience Center, 40014 University of Jyväskylä, Finland.
| | - Visa Ruokolainen
- University of Jyväskylä, Department of Biological and Environmental Science and Nanoscience Center, 40014 University of Jyväskylä, Finland
| | - Nemanja Markešević
- University of Jyväskylä, Department of Physics and Nanoscience Center, 40014 University of Jyväskylä, Finland.
| | - Ashwin K Natarajan
- Department of Neuroscience and Biomedical Engineering, Aalto University, 00076 Aalto, Finland
| | - Maija Vihinen-Ranta
- University of Jyväskylä, Department of Biological and Environmental Science and Nanoscience Center, 40014 University of Jyväskylä, Finland
| | - Anton Kuzyk
- Department of Neuroscience and Biomedical Engineering, Aalto University, 00076 Aalto, Finland
| | - Kosti Tapio
- University of Jyväskylä, Department of Physics and Nanoscience Center, 40014 University of Jyväskylä, Finland.
| | - J Jussi Toppari
- University of Jyväskylä, Department of Physics and Nanoscience Center, 40014 University of Jyväskylä, Finland.
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2
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Natarajan AK, Ryssy J, Kuzyk A. A DNA origami-based device for investigating DNA bending proteins by transmission electron microscopy. Nanoscale 2023; 15:3212-3218. [PMID: 36722916 DOI: 10.1039/d2nr05366g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The DNA origami technique offers precise positioning of nanoscale objects with high accuracy. This has facilitated the development of DNA origami-based functional nanomechanical devices that enable the investigation of DNA-protein interactions at the single particle level. Herein, we used the DNA origami technique to fabricate a nanoscale device for studying DNA bending proteins. For a proof of concept, we used TATA-box binding protein (TBP) to evaluate our approach. Upon binding to the TATA box, TBP causes a bend to DNA of ∼90°. Our device translates this bending into an angular change that is readily observable with a conventional transmission electron microscope (TEM). Furthermore, we investigated the roles of transcription factor II A (TF(II)A) and transcription factor II B (TF(II)B). Our results indicate that TF(II)A introduces additional bending, whereas TF(II)B does not significantly alter the TBP-DNA structure. Our approach can be readily adopted to a wide range of DNA-bending proteins and will aid the development of DNA-origami-based devices tailored for the investigation of DNA-protein interactions.
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Affiliation(s)
- Ashwin Karthick Natarajan
- Department of Neuroscience and Biomedical Engineering, Aalto University, School of Science, P.O. Box 12200, FI-00076 Aalto, Finland.
| | - Joonas Ryssy
- Department of Neuroscience and Biomedical Engineering, Aalto University, School of Science, P.O. Box 12200, FI-00076 Aalto, Finland.
| | - Anton Kuzyk
- Department of Neuroscience and Biomedical Engineering, Aalto University, School of Science, P.O. Box 12200, FI-00076 Aalto, Finland.
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3
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Huang Y, Ryssy J, Nguyen MK, Loo J, Hällsten S, Kuzyk A. Measuring the Affinities of RNA and DNA Aptamers with DNA Origami-Based Chiral Plasmonic Probes. Anal Chem 2022; 94:17577-17586. [PMID: 36480745 PMCID: PMC9773176 DOI: 10.1021/acs.analchem.2c04034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Reliable characterization of binding affinities is crucial for selected aptamers. However, the limited repertoire of universal approaches to obtain the dissociation constant (KD) values often hinders the further development of aptamer-based applications. Herein, we present a competitive hybridization-based strategy to characterize aptamers using DNA origami-based chiral plasmonic assemblies as optical reporters. We incorporated aptamers and partial complementary strands blocking different regions of the aptamers into the reporters and measured the kinetic behaviors of the target binding to gain insights on aptamers' functional domains. We introduced a reference analyte and developed a thermodynamic model to obtain a relative dissociation constant of an aptamer-target pair. With this approach, we characterized RNA and DNA aptamers binding to small molecules with low and high affinities.
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Affiliation(s)
- Yike Huang
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076Aalto, Finland,E-mail:
| | - Joonas Ryssy
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076Aalto, Finland
| | - Minh-Kha Nguyen
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076Aalto, Finland,Faculty
of Chemical Engineering, Ho Chi Minh City
University of Technology (HCMUT), 268 Ly Thuong Kiet St., Dist. 10, Ho Chi Minh
City700000, Vietnam,Vietnam
National University Ho Chi Minh City, Linh Trung Ward, Thu Duc Dist., Ho Chi Minh
City700000, Vietnam
| | - Jacky Loo
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076Aalto, Finland
| | - Susanna Hällsten
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076Aalto, Finland
| | - Anton Kuzyk
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076Aalto, Finland,E-mail:
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4
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Elonen A, Natarajan AK, Kawamata I, Oesinghaus L, Mohammed A, Seitsonen J, Suzuki Y, Simmel FC, Kuzyk A, Orponen P. Algorithmic Design of 3D Wireframe RNA Polyhedra. ACS Nano 2022; 16:16608-16616. [PMID: 36178116 PMCID: PMC9620399 DOI: 10.1021/acsnano.2c06035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 09/26/2022] [Indexed: 06/01/2023]
Abstract
We address the problem of de novo design and synthesis of nucleic acid nanostructures, a challenge that has been considered in the area of DNA nanotechnology since the 1980s and more recently in the area of RNA nanotechnology. Toward this goal, we introduce a general algorithmic design process and software pipeline for rendering 3D wireframe polyhedral nanostructures in single-stranded RNA. To initiate the pipeline, the user creates a model of the desired polyhedron using standard 3D graphic design software. As its output, the pipeline produces an RNA nucleotide sequence whose corresponding RNA primary structure can be transcribed from a DNA template and folded in the laboratory. As case examples, we design and characterize experimentally three 3D RNA nanostructures: a tetrahedron, a triangular bipyramid, and a triangular prism. The design software is openly available and also provides an export of the targeted 3D structure into the oxDNA molecular dynamics simulator for easy simulation and visualization.
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Affiliation(s)
- Antti Elonen
- Department
of Computer Science, Aalto University, 00076 Aalto, Finland
| | | | - Ibuki Kawamata
- Department
of Robotics, Graduate School of Engineering, Tohoku University, Sendai 980-8577, Japan
- Natural
Science Division, Faculty of Core Research, Ochanomizu University, Tokyo 112-8610, Japan
| | - Lukas Oesinghaus
- Physics
Department E14, Technical University Munich, 85748 Garching, Germany
| | - Abdulmelik Mohammed
- Department
of Computer Science, Aalto University, 00076 Aalto, Finland
- Department
of Biomedical Engineering, San José
State University, San José, California 95192, United States
| | - Jani Seitsonen
- Department
of Applied Physics and Nanomicroscopy Center, Aalto University, 00076 Aalto, Finland
| | - Yuki Suzuki
- Department
of Robotics, Graduate School of Engineering, Tohoku University, Sendai 980-8577, Japan
- Frontier
Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai 980-8577, Japan
- Division
of Chemistry for Materials, Graduate School of Engineering, Mie University, Tsu 514-8507, Japan
| | - Friedrich C. Simmel
- Physics
Department E14, Technical University Munich, 85748 Garching, Germany
| | - Anton Kuzyk
- Department
of Neuroscience and Biomedical Engineering, Aalto University, 00076 Aalto, Finland
| | - Pekka Orponen
- Department
of Computer Science, Aalto University, 00076 Aalto, Finland
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5
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Ryssy J, Natarajan AK, Wang J, Lehtonen AJ, Nguyen MK, Klajn R, Kuzyk A. Corrigendum: Light‐Responsive Dynamic DNA‐Origami‐Based Plasmonic Assemblies. Angew Chem Int Ed Engl 2022; 61:e202210394. [PMID: 36094309 PMCID: PMC10117912 DOI: 10.1002/anie.202210394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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6
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Ryssy J, Natarajan AK, Wang J, Lehtonen AJ, Nguyen M, Klajn R, Kuzyk A. Berichtigung: Light‐Responsive Dynamic DNA‐Origami‐Based Plasmonic Assemblies. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202210394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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7
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Manuguri S, Nguyen MK, Loo J, Natarajan AK, Kuzyk A. Advancing the Utility of DNA Origami Technique through Enhanced Stability of DNA-Origami-Based Assemblies. Bioconjug Chem 2022; 34:6-17. [PMID: 35984467 PMCID: PMC9853507 DOI: 10.1021/acs.bioconjchem.2c00311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Since its discovery in 2006, the DNA origami technique has revolutionized bottom-up nanofabrication. This technique is simple yet versatile and enables the fabrication of nanostructures of almost arbitrary shapes. Furthermore, due to their intrinsic addressability, DNA origami structures can serve as templates for the arrangement of various nanoscale components (small molecules, proteins, nanoparticles, etc.) with controlled stoichiometry and nanometer-scale precision, which is often beyond the reach of other nanofabrication techniques. Despite the multiple benefits of the DNA origami technique, its applicability is often restricted by the limited stability in application-specific conditions. This Review provides an overview of the strategies that have been developed to improve the stability of DNA-origami-based assemblies for potential biomedical, nanofabrication, and other applications.
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Affiliation(s)
- Sesha Manuguri
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Minh-Kha Nguyen
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland,Faculty
of Chemical Engineering, Ho Chi Minh City
University of Technology (HCMUT), 268 Ly Thuong Kiet St., Dist. 10, Ho Chi Minh
City 70000, Vietnam,Vietnam
National University Ho Chi Minh City, Linh Trung Ward, Thu Duc Dist., Ho Chi Minh
City 756100, Vietnam
| | - Jacky Loo
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Ashwin Karthick Natarajan
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Anton Kuzyk
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland,
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8
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Huang Y, Nguyen MK, Nguyen VH, Loo J, Lehtonen AJ, Kuzyk A. Characterizing Aptamers with Reconfigurable Chiral Plasmonic Assemblies. Langmuir 2022; 38:2954-2960. [PMID: 35212547 PMCID: PMC8908738 DOI: 10.1021/acs.langmuir.1c03434] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/15/2022] [Indexed: 06/14/2023]
Abstract
Aptamers have emerged as versatile affinity ligands and as promising alternatives to protein antibodies. However, the inconsistency in the reported affinities and specificities of aptamers has greatly hindered the development of aptamer-based applications. Herein, we present a strategy to characterize aptamers by using DNA origami-based chiral plasmonic assemblies as reporters and establishing a competitive hybridization reaction-based thermodynamic model. We demonstrate the characterization of several DNA aptamers, including aptamers for small molecules and macromolecules, as well as aptamers with high and low affinities. The presented characterization scheme can be readily adapted to a wide selection of aptamers. We anticipate that our approach will advance the development of aptamer-based applications by enabling reliable and reproducible characterization of aptamers.
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Affiliation(s)
- Yike Huang
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Minh-Kha Nguyen
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
- Faculty
of Chemical Engineering, Ho Chi Minh City
University of Technology (HCMUT), 268 Ly Thuong Kiet Street, Dist. 10, 700000 Ho Chi Minh City, Vietnam
- Vietnam
National University Ho Chi Minh City,
Linh Trung Ward, Thu Duc District, 700000 Ho Chi Minh City, Vietnam
| | - Vu Hoang Nguyen
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Jacky Loo
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Arttu J. Lehtonen
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
- Department
of Electrical Engineering and Automation, School of Electrical Engineering, Aalto University, FI-00076 Aalto, Finland
| | - Anton Kuzyk
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
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9
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Kuzyk A, Zhang C, Parsons L. 636 Factors associated with prolonged wound healing. J Invest Dermatol 2021. [DOI: 10.1016/j.jid.2021.02.665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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10
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Ryssy J, Natarajan AK, Wang J, Lehtonen AJ, Nguyen MK, Klajn R, Kuzyk A. Light-Responsive Dynamic DNA-Origami-Based Plasmonic Assemblies. Angew Chem Int Ed Engl 2021; 60:5859-5863. [PMID: 33320988 PMCID: PMC7986157 DOI: 10.1002/anie.202014963] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Indexed: 12/11/2022]
Abstract
DNA nanotechnology offers a versatile toolbox for precise spatial and temporal manipulation of matter on the nanoscale. However, rendering DNA‐based systems responsive to light has remained challenging. Herein, we describe the remote manipulation of native (non‐photoresponsive) chiral plasmonic molecules (CPMs) using light. Our strategy is based on the use of a photoresponsive medium comprising a merocyanine‐based photoacid. Upon exposure to visible light, the medium decreases its pH, inducing the formation of DNA triplex links, leading to a spatial reconfiguration of the CPMs. The process can be reversed simply by turning the light off and it can be repeated for multiple cycles. The degree of the overall chirality change in an ensemble of CPMs depends on the CPM fraction undergoing reconfiguration, which, remarkably, depends on and can be tuned by the intensity of incident light. Such a dynamic, remotely controlled system could aid in further advancing DNA‐based devices and nanomaterials.
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Affiliation(s)
- Joonas Ryssy
- Department of Neuroscience and Biomedical Engineering, School of Science, Aalto University, 00076, Aalto, Finland
| | - Ashwin K Natarajan
- Department of Neuroscience and Biomedical Engineering, School of Science, Aalto University, 00076, Aalto, Finland
| | - Jinhua Wang
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Arttu J Lehtonen
- Department of Neuroscience and Biomedical Engineering, School of Science, Aalto University, 00076, Aalto, Finland
| | - Minh-Kha Nguyen
- Department of Neuroscience and Biomedical Engineering, School of Science, Aalto University, 00076, Aalto, Finland.,Faculty of Chemical Engineering, HCMC University of Technology, VNU-HCM, Ho Chi Minh City, 700000, Vietnam
| | - Rafal Klajn
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Anton Kuzyk
- Department of Neuroscience and Biomedical Engineering, School of Science, Aalto University, 00076, Aalto, Finland
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11
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Abstract
Understanding how the geometrical property of chirality is transferred into the physical properties of chiral materials is becoming increasingly important in various research fields, including plasmonics. Advances in DNA nanotechnology, especially DNA origami techniques, have enabled routine fabrication of complex chiral plasmonic assemblies. However, most of the work undertaken to date has involved plasmonic enantiomers. The concept of multiple chiral centers in stereochemistry provides simple guidelines for generating multiple chiral configurations beyond enantiomers. In this issue of ACS Nano, Wang et al. report DNA origami-based assembly and characterization of reconfigurable plasmonic chiral stereoisomers with up to three chiral centers. In this Perspective, we explore the implication of these results for further development of functional chiral plasmonic systems.
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Affiliation(s)
- Minh-Kha Nguyen
- Department of Neuroscience and Biomedical Engineering , Aalto University School of Science , P.O. Box 12200, FI-00076 Aalto , Finland
- Faculty of Chemical Engineering , HCMC University of Technology , VNU-HCM, Ho Chi Minh City , Vietnam
| | - Anton Kuzyk
- Department of Neuroscience and Biomedical Engineering , Aalto University School of Science , P.O. Box 12200, FI-00076 Aalto , Finland
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12
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Zhan P, Urban MJ, Both S, Duan X, Kuzyk A, Weiss T, Liu N. DNA-assembled nanoarchitectures with multiple components in regulated and coordinated motion. Sci Adv 2019; 5:eaax6023. [PMID: 31819901 PMCID: PMC6884410 DOI: 10.1126/sciadv.aax6023] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 09/18/2019] [Indexed: 05/21/2023]
Abstract
Coordinating functional parts to operate in concert is essential for machinery. In gear trains, meshed gears are compactly interlocked, working together to impose rotation or translation. In photosynthetic systems, a variety of biological entities in the thylakoid membrane interact with each other, converting light energy into chemical energy. However, coordinating individual parts to carry out regulated and coordinated motion within an artificial nanoarchitecture poses challenges, owing to the requisite control on the nanoscale. Here, we demonstrate DNA-directed nanosystems, which comprise hierarchically-assembled DNA origami filaments, fluorophores, and gold nanocrystals. These individual building blocks can execute independent, synchronous, or joint motion upon external inputs. These are optically monitored in situ using fluorescence spectroscopy, taking advantage of the sensitive distance-dependent interactions between the gold nanocrystals and fluorophores positioned on the DNA origami. Our work leverages the complexity of DNA-based artificial nanosystems with tailored dynamic functionality, representing a viable route towards technomimetic nanomachinery.
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Affiliation(s)
- Pengfei Zhan
- Max Planck Institute for Intelligent Systems, Heisenbergstrasse 3, D-70569 Stuttgart, Germany
| | - Maximilian J. Urban
- Max Planck Institute for Intelligent Systems, Heisenbergstrasse 3, D-70569 Stuttgart, Germany
- Kirchhoff Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, D-69120 Heidelberg, Germany
| | - Steffen Both
- 4th Physics Institute and Stuttgart Research Center of Photonic Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Xiaoyang Duan
- Max Planck Institute for Intelligent Systems, Heisenbergstrasse 3, D-70569 Stuttgart, Germany
- Kirchhoff Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, D-69120 Heidelberg, Germany
| | - Anton Kuzyk
- Department of Neuroscience and Biomedical Engineering, Aalto University, School of Science, P.O. Box 12200, FI-00076 Aalto, Finland
| | - Thomas Weiss
- 4th Physics Institute and Stuttgart Research Center of Photonic Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Na Liu
- Max Planck Institute for Intelligent Systems, Heisenbergstrasse 3, D-70569 Stuttgart, Germany
- Kirchhoff Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, D-69120 Heidelberg, Germany
- Corresponding author.
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13
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Abstract
The inherent addressability of DNA origami structures makes them ideal templates for the arrangement of metal nanoparticles into complex plasmonic nanostructures. The high spatial precision of a DNA origami-templated assembly allows controlling the coupling between plasmonic resonances of individual particles and enables tailoring optical properties of the constructed nanostructures. Recently, chiral plasmonic systems attracted a lot of attention due to the strong correlation between the spatial configuration of plasmonic assemblies and their optical responses (e.g., circular dichroism [CD]). In this protocol, we describe the whole workflow for the generation of DNA origami-based chiral assemblies of gold nanorods (AuNRs). The protocol includes a detailed description of the design principles and experimental procedures for the fabrication of DNA origami templates, the synthesis of AuNRs, and the assembly of origami-AuNR structures. In addition, the characterization of structures using transmission electron microscopy (TEM) and CD spectroscopy is included. The described protocol is not limited to chiral configurations and can be adapted for the construction of various plasmonic architectures.
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Affiliation(s)
- Yike Huang
- Department of Neuroscience and Biomedical Engineering, Aalto University School of Science, Aalto FI-00076;
| | - Minh-Kha Nguyen
- Department of Neuroscience and Biomedical Engineering, Aalto University School of Science, Aalto FI-00076; Faculty of Chemical Engineering, Ho Chi Minh City (HCMC) University of Technology, Vietnam National University - Ho Chi Minh City (VNU-HCM), Ho Chi Minh City 700000
| | - Anton Kuzyk
- Department of Neuroscience and Biomedical Engineering, Aalto University School of Science, Aalto FI-00076;
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14
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Abstract
Accurate and reliable biosensing is crucial for environmental monitoring, food safety, and diagnostics. Spatially reconfigurable DNA origami nanostructures are excellent candidates for the generation of custom sensing probes. Here we present a nanoscale biosensing device that combines the accuracy and precision of the DNA origami nanofabrication technique, unique optical responses of chiral plasmonic assemblies, and high affinity and selectivity of aptamers. This combination enables selective and sensitive detection of targets even in strongly absorbing fluids. We expect that the presented sensing scheme can be adapted to a wide range of analytes and tailored to specific needs.
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Affiliation(s)
- Yike Huang
- Department of Neuroscience and Biomedical Engineering , Aalto University School of Science , Aalto FI-00076 , Finland
| | - Minh-Kha Nguyen
- Department of Neuroscience and Biomedical Engineering , Aalto University School of Science , Aalto FI-00076 , Finland
- Faculty of Chemical Engineering , HCMC University of Technology, VNU-HCM , Ho Chi Minh City 700000 , Vietnam
| | - Ashwin Karthick Natarajan
- Department of Neuroscience and Biomedical Engineering , Aalto University School of Science , Aalto FI-00076 , Finland
| | - Vu Hoang Nguyen
- Department of Neuroscience and Biomedical Engineering , Aalto University School of Science , Aalto FI-00076 , Finland
| | - Anton Kuzyk
- Department of Neuroscience and Biomedical Engineering , Aalto University School of Science , Aalto FI-00076 , Finland
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15
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Affiliation(s)
- Timon Funck
- Department für Physik; Ludwig-Maximilians-Universität; Geschwister-Scholl-Platz 1 80539 München Germany
| | - Francesca Nicoli
- Department für Physik; Ludwig-Maximilians-Universität; Geschwister-Scholl-Platz 1 80539 München Germany
| | - Anton Kuzyk
- Department of Neuroscience and Biomedical Engineering; Aalto University School of Science; P.O. Box 12200 00076 Aalto Finland
| | - Tim Liedl
- Department für Physik; Ludwig-Maximilians-Universität; Geschwister-Scholl-Platz 1 80539 München Germany
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16
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Funck T, Nicoli F, Kuzyk A, Liedl T. Sensing Picomolar Concentrations of RNA Using Switchable Plasmonic Chirality. Angew Chem Int Ed Engl 2018; 57:13495-13498. [DOI: 10.1002/anie.201807029] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Timon Funck
- Department für Physik; Ludwig-Maximilians-Universität; Geschwister-Scholl-Platz 1 80539 München Germany
| | - Francesca Nicoli
- Department für Physik; Ludwig-Maximilians-Universität; Geschwister-Scholl-Platz 1 80539 München Germany
| | - Anton Kuzyk
- Department of Neuroscience and Biomedical Engineering; Aalto University School of Science; P.O. Box 12200 00076 Aalto Finland
| | - Tim Liedl
- Department für Physik; Ludwig-Maximilians-Universität; Geschwister-Scholl-Platz 1 80539 München Germany
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17
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Urban MJ, Both S, Zhou C, Kuzyk A, Lindfors K, Weiss T, Liu N. Gold nanocrystal-mediated sliding of doublet DNA origami filaments. Nat Commun 2018; 9:1454. [PMID: 29654323 PMCID: PMC5899135 DOI: 10.1038/s41467-018-03882-w] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 03/15/2018] [Indexed: 12/21/2022] Open
Abstract
Sliding is one of the fundamental mechanical movements in machinery. In macroscopic systems, double-rack pinion machines employ gears to slide two linear tracks along opposite directions. In microscopic systems, kinesin-5 proteins crosslink and slide apart antiparallel microtubules, promoting spindle bipolarity and elongation during mitosis. Here we demonstrate an artificial nanoscopic analog, in which gold nanocrystals can mediate coordinated sliding of two antiparallel DNA origami filaments powered by DNA fuels. Stepwise and reversible sliding along opposite directions is in situ monitored and confirmed using fluorescence spectroscopy. A theoretical model including different energy transfer mechanisms is developed to understand the observed fluorescence dynamics. We further show that such sliding can also take place in the presence of multiple DNA sidelocks that are introduced to inhibit the relative movements. Our work enriches the toolbox of DNA-based nanomachinery, taking one step further toward the vision of molecular nanofactories. Kinesin, a motor protein, moves along filaments in a walk-like fashion to transport cargo to specific places in the cell. Here, the authors developed an analogous, artificial system consisting of nanoparticles moving along DNA filaments.
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Affiliation(s)
- Maximilian J Urban
- Max Planck Institute for Intelligent Systems, Heisenbergstrasse 3, D-70569, Stuttgart, Germany.,Kirchhoff Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, D-69120, Heidelberg, Germany
| | - Steffen Both
- 4th Physics Institute and Stuttgart Research Center of Photonic Engineering, University of Stuttgart, 70569, Stuttgart, Germany
| | - Chao Zhou
- Max Planck Institute for Intelligent Systems, Heisenbergstrasse 3, D-70569, Stuttgart, Germany. .,Kirchhoff Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, D-69120, Heidelberg, Germany.
| | - 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
| | - Klas Lindfors
- Department of Chemistry, University of Cologne, Luxemburger Strasse 116, 50939, Köln, Germany
| | - Thomas Weiss
- 4th Physics Institute and Stuttgart Research Center of Photonic Engineering, University of Stuttgart, 70569, Stuttgart, Germany
| | - Na Liu
- Max Planck Institute for Intelligent Systems, Heisenbergstrasse 3, D-70569, Stuttgart, Germany. .,Kirchhoff Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, D-69120, Heidelberg, Germany.
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Kuzyk A, Urban MJ, Idili A, Ricci F, Liu N. Selective control of reconfigurable chiral plasmonic metamolecules. Sci Adv 2017; 3:e1602803. [PMID: 28439556 PMCID: PMC5400443 DOI: 10.1126/sciadv.1602803] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 02/16/2017] [Indexed: 05/11/2023]
Abstract
Selective configuration control of plasmonic nanostructures using either top-down or bottom-up approaches has remained challenging in the field of active plasmonics. We demonstrate the realization of DNA-assembled reconfigurable plasmonic metamolecules, which can respond to a wide range of pH changes in a programmable manner. This programmability allows for selective reconfiguration of different plasmonic metamolecule species coexisting in solution through simple pH tuning. This approach enables discrimination of chiral plasmonic quasi-enantiomers and arbitrary tuning of chiroptical effects with unprecedented degrees of freedom. Our work outlines a new blueprint for implementation of advanced active plasmonic systems, in which individual structural species can be programmed to perform multiple tasks and functions in response to independent external stimuli.
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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
- Corresponding author. (A.K.); (F.R.); (N.L)
| | - Maximilian J. Urban
- Max Planck Institute for Intelligent Systems, Heisenbergstrasse 3, D-70569 Stuttgart, Germany
- Kirchhoff Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, D-69120 Heidelberg, Germany
| | - Andrea Idili
- Chemistry Department, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome 00133, Italy
| | - Francesco Ricci
- Chemistry Department, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome 00133, Italy
- Corresponding author. (A.K.); (F.R.); (N.L)
| | - Na Liu
- Max Planck Institute for Intelligent Systems, Heisenbergstrasse 3, D-70569 Stuttgart, Germany
- Kirchhoff Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, D-69120 Heidelberg, Germany
- Corresponding author. (A.K.); (F.R.); (N.L)
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20
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Kuzyk A, Schreiber R, Zhang H, Govorov AO, Liedl T, Liu N. Reconfigurable 3D plasmonic metamolecules. Nat Mater 2014; 13:862-6. [PMID: 24997737 DOI: 10.1038/nmat4031] [Citation(s) in RCA: 397] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 06/09/2014] [Indexed: 05/17/2023]
Abstract
A reconfigurable plasmonic nanosystem combines an active plasmonic structure with a regulated physical or chemical control input. There have been considerable efforts on integration of plasmonic nanostructures with active platforms using top-down techniques. The active media include phase-transition materials, graphene, liquid crystals and carrier-modulated semiconductors, which can respond to thermal, electrical and optical stimuli. However, these plasmonic nanostructures are often restricted to two-dimensional substrates, showing desired optical response only along specific excitation directions. Alternatively, bottom-up techniques offer a new pathway to impart reconfigurability and functionality to passive systems. In particular, DNA has proven to be one of the most versatile and robust building blocks for construction of complex three-dimensional architectures with high fidelity. Here we show the creation of reconfigurable three-dimensional plasmonic metamolecules, which execute DNA-regulated conformational changes at the nanoscale. DNA serves as both a construction material to organize plasmonic nanoparticles in three dimensions, as well as fuel for driving the metamolecules to distinct conformational states. Simultaneously, the three-dimensional plasmonic metamolecules can work as optical reporters, which transduce their conformational changes in situ into circular dichroism changes in the visible wavelength range.
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Affiliation(s)
- Anton Kuzyk
- Max Planck Institute for Intelligent Systems, Heisenbergstrasse 3, D-70569 Stuttgart, Germany
| | - Robert Schreiber
- 1] Fakultät für Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, 80539 München, Germany [2]
| | - Hui Zhang
- Department of Physics and Astronomy, Ohio University, Athens, Ohio 45701, 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, Geschwister-Scholl-Platz 1, 80539 München, Germany
| | - Na Liu
- Max Planck Institute for Intelligent Systems, Heisenbergstrasse 3, D-70569 Stuttgart, Germany
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21
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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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22
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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: 184] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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23
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Scheible MB, Pardatscher G, Kuzyk A, Simmel FC. Single molecule characterization of DNA binding and strand displacement reactions on lithographic DNA origami microarrays. Nano Lett 2014; 14:1627-33. [PMID: 24517269 DOI: 10.1021/nl500092j] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The combination of molecular self-assembly based on the DNA origami technique with lithographic patterning enables the creation of hierarchically ordered nanosystems, in which single molecules are positioned at precise locations on multiple length scales. Based on a hybrid assembly protocol utilizing DNA self-assembly and electron-beam lithography on transparent glass substrates, we here demonstrate a DNA origami microarray, which is compatible with the requirements of single molecule fluorescence and super-resolution microscopy. The spatial arrangement allows for a simple and reliable identification of single molecule events and facilitates automated read-out and data analysis. As a specific application, we utilize the microarray to characterize the performance of DNA strand displacement reactions localized on the DNA origami structures. We find considerable variability within the array, which results both from structural variations and stochastic reaction dynamics prevalent at the single molecule level.
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Affiliation(s)
- Max B Scheible
- Systems Biophysics, Physics Department and ZNN/WSI, Technische Universität München , 85748 Garching, Germany
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24
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Shen X, Zhan P, Kuzyk A, Liu Q, Asenjo-Garcia A, Zhang H, de Abajo FJG, Govorov A, Ding B, Liu N. 3D plasmonic chiral colloids. Nanoscale 2014; 6:2077-2081. [PMID: 24424350 DOI: 10.1039/c3nr06006c] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
3D plasmonic chiral colloids are synthesized through deterministically grouping of two gold nanorod AuNRs on DNA origami. These nanorod crosses exhibit strong circular dichroism (CD) at optical frequencies which can be engineered through position tuning of the rods on the origami. Our experimental results agree qualitatively well with theoretical predictions.
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Affiliation(s)
- Xibo Shen
- National Center for Nanoscience and Technology, No. 11 BeiYiTiao, ZhongGuanCun, Beijing 100190, China.
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25
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Kuzyk A, Schreiber R, Fan Z, Pardatscher G, Roller EM, Högele A, Simmel FC, Govorov AO, Liedl T. 144 Sculpting light with DNA origami. J Biomol Struct Dyn 2013. [DOI: 10.1080/07391102.2013.786386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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26
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Eskelinen AP, Rosilo H, Kuzyk A, Törmä P, Kostiainen MA. Controlling the formation of DNA origami structures with external signals. Small 2012; 8:2016-2020. [PMID: 22508676 DOI: 10.1002/smll.201102697] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Indexed: 05/31/2023]
Abstract
Degradable Newkome-type and polylysine dendrons functionalized with spermine surface units are used to control the formation of DNA origami structures. The intact dendrons form polyelectrolyte complexes with the scaffold strands, therefore blocking the origami formation. Degradation of the dendron with an optical trigger or chemical reduction leads to the release of the DNA scaffold and efficient formation of the desired origami structure. These results provide new insights towards realizing responsive materials with DNA origami.
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27
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Acuna GP, Bucher M, Stein IH, Steinhauer C, Kuzyk A, Holzmeister P, Schreiber R, Moroz A, Stefani FD, Liedl T, Simmel FC, Tinnefeld P. Distance dependence of single-fluorophore quenching by gold nanoparticles studied on DNA origami. ACS Nano 2012; 6:3189-95. [PMID: 22439823 DOI: 10.1021/nn2050483] [Citation(s) in RCA: 175] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
We study the distance-dependent quenching of fluorescence due to a metallic nanoparticle in proximity of a fluorophore. In our single-molecule measurements, we achieve excellent control over structure and stoichiometry by using self-assembled DNA structures (DNA origami) as a breadboard where both the fluorophore and the 10 nm metallic nanoparticle are positioned with nanometer precision. The single-molecule spectroscopy method employed here reports on the co-localization of particle and dye, while fluorescence lifetime imaging is used to directly obtain the correlation of intensity and fluorescence lifetime for varying particle to dye distances. Our data can be well explained by exact calculations that include dipole-dipole orientation and distances. Fitting with a more practical model for nanosurface energy transfer yields 10.4 nm as the characteristic distance of 50% energy transfer. The use of DNA nanotechnology together with minimal sample usage by attaching the particles to the DNA origami directly on the microscope coverslip paves the way for more complex experiments exploiting dye-nanoparticle interactions.
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Affiliation(s)
- Guillermo P Acuna
- Physical and Theoretical Chemistry-NanoBioScience, TU Braunschweig, Hans-Sommer-Strasse 10, 38106 Braunschweig, Germany.
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28
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Kuzyk A, Schreiber R, Fan Z, Pardatscher G, Roller EM, Högele A, Simmel FC, Govorov AO, Liedl T. DNA-based self-assembly of chiral plasmonic nanostructures with tailored optical response. Nature 2012; 483:311-4. [DOI: 10.1038/nature10889] [Citation(s) in RCA: 1606] [Impact Index Per Article: 133.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 01/17/2012] [Indexed: 01/24/2023]
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29
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Abstract
Dielectrophoresis has become a powerful tool for manipulation of various materials, such as metal and semiconducting particles, DNA molecules, nanowires and graphene. This short review is intended to provide the reader with an overview of the recent advances of application of dielectrophoresis at the nanoscale.
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Affiliation(s)
- Anton Kuzyk
- Lehrstuhl für Bioelektronik, Physik-Department und ZNN/WSI, Technische Universität München, Garching, Germany.
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30
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Jungmann R, Scheible M, Kuzyk A, Pardatscher G, Castro CE, Simmel FC. DNA origami-based nanoribbons: assembly, length distribution, and twist. Nanotechnology 2011; 22:275301. [PMID: 21597145 DOI: 10.1088/0957-4484/22/27/275301] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A variety of polymerization methods for the assembly of elongated nanoribbons from rectangular DNA origami structures are investigated. The most efficient method utilizes single-stranded DNA oligonucleotides to bridge an intermolecular scaffold seam between origami monomers. This approach allows the fabrication of origami ribbons with lengths of several micrometers, which can be used for long-range ordered arrangement of proteins. It is quantitatively shown that the length distribution of origami ribbons obtained with this technique follows the theoretical prediction for a simple linear polymerization reaction. The design of flat single layer origami structures with constant crossover spacing inevitably results in local underwinding of the DNA helix, which leads to a global twist of the origami structures that also translates to the nanoribbons.
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Affiliation(s)
- Ralf Jungmann
- Lehrstuhl für Bioelektronik, Physik-Department and ZNN/WSI, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
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31
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Eskelinen AP, Kuzyk A, Kaltiaisenaho TK, Timmermans MY, Nasibulin AG, Kauppinen EI, Törmä P. Assembly of single-walled carbon nanotubes on DNA-origami templates through streptavidin-biotin interaction. Small 2011; 7:746-50. [PMID: 21425460 DOI: 10.1002/smll.201001750] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2010] [Revised: 11/09/2010] [Indexed: 05/17/2023]
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32
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Abstract
DNA is one of the most promising molecules for nanoscale bottom-up fabrication. For both scientific studies and fabrication of devices, it is desirable to be able to manipulate DNA molecules, or self--assembled DNA constructions, at the single unit level. Efficient methods are needed for precisely attaching the single unit to the external measurement setup or the device structure. So far, this has often been too cumbersome to achieve, and consequently most of the scientific studies are based on a statistical analysis or measurements done for a sample containing numerous molecules in liquid or in a dry state. Here, we explain a method for trapping and attaching nanoscale double-stranded DNA (dsDNA) molecules between nanoelectrodes. The method is based on dielectrophoresis and gives a high yield of trapping only single or a few molecules, which enables, for example, transport measurements at the single -molecule level. The method has been used to trap different dsDNA fragments, sizes varying from 27 to 8,416 bp, and also DNA origami constructions. We also explain how confocal microscopy can be used to determine and optimize the trapping parameters.
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Affiliation(s)
- Anton Kuzyk
- Department of Physics, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
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33
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Jungmann R, Steinhauer C, Scheible M, Kuzyk A, Tinnefeld P, Simmel FC. Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami. Nano Lett 2010; 10:4756-61. [PMID: 20957983 DOI: 10.1021/nl103427w] [Citation(s) in RCA: 526] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
DNA origami is a powerful method for the programmable assembly of nanoscale molecular structures. For applications of these structures as functional biomaterials, the study of reaction kinetics and dynamic processes in real time and with high spatial resolution becomes increasingly important. We present a single-molecule assay for the study of binding and unbinding kinetics on DNA origami. We find that the kinetics of hybridization to single-stranded extensions on DNA origami is similar to isolated substrate-immobilized DNA with a slight position dependence on the origami. On the basis of the knowledge of the kinetics, we exploit reversible specific binding of labeled oligonucleotides to DNA nanostructures for PAINT (points accumulation for imaging in nanoscale topography) imaging with <30 nm resolution. The method is demonstrated for flat monomeric DNA structures as well as multimeric, ribbon-like DNA structures.
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Affiliation(s)
- Ralf Jungmann
- Lehrstuhl für Bioelektronik, Physik-Department, Technische Universität München, James-Franck-Strasse 1, 85748 Garching, Germany
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Hakala TK, Linko V, Eskelinen AP, Toppari JJ, Kuzyk A, Törmä P. Field-induced nanolithography for high-throughput pattern transfer. Small 2009; 5:2683-2686. [PMID: 19856328 DOI: 10.1002/smll.200901326] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Affiliation(s)
- Tommi K Hakala
- Nanoscience Center, Department of Physics, University of Jyväskylä, Finland
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35
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Linko V, Paasonen ST, Kuzyk A, Törmä P, Toppari JJ. Characterization of the conductance mechanisms of DNA origami by AC impedance spectroscopy. Small 2009; 5:2382-2386. [PMID: 19637269 DOI: 10.1002/smll.200900683] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Affiliation(s)
- Veikko Linko
- Nanoscience Center, Department of Physics, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
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36
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Hakala TK, Toppari JJ, Kuzyk A, Pettersson M, Tikkanen H, Kunttu H, Törmä P. Vacuum Rabi splitting and strong-coupling dynamics for surface-plasmon polaritons and rhodamine 6G molecules. Phys Rev Lett 2009; 103:053602. [PMID: 19792498 DOI: 10.1103/physrevlett.103.053602] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2009] [Indexed: 05/26/2023]
Abstract
We report on strong coupling between surface-plasmon polaritons (SPP) and Rhodamine 6G (R6G) molecules, with double vacuum Rabi splitting energies up to 230 and 110 meV. In addition, we demonstrate the emission of all three energy branches of the strongly coupled SPP-exciton hybrid system, revealing features of system dynamics that are not visible in conventional reflectometry. Finally, in analogy to tunable-Q microcavities, we show that the Rabi splitting can be controlled by adjusting the interaction time between waveguided SPPs and R6G deposited on top of the waveguide. The interaction time can be controlled with sub-fs precision by adjusting the length of the R6G area with standard lithography methods.
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Affiliation(s)
- T K Hakala
- Nanoscience Center, Department of Physics, University of Jyväskylä, Finland
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37
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Abstract
We describe two general approaches to the utilization of DNA origami structures for the assembly of materials. In one approach, DNA origami is used as a prefabricated template for subsequent assembly of materials. In the other, materials are assembled simultaneously with the DNA origami, i.e. the DNA origami technique is used to drive the assembly of materials. Fabrication of complex protein structures is demonstrated by these two approaches. The latter approach has the potential to be extended to the assembly of multiple materials with single attachment chemistry.
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Affiliation(s)
- Anton Kuzyk
- Nanoscience Center, Department of Physics, University of Jyväskylä, Finland
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Affiliation(s)
- Anton Kuzyk
- Nanoscience Center, Department of Physics, University of Jyväskylä, P.O. Box 35, FIN-40014, Finland.
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Kuzyk A, Pettersson M, Toppari JJ, Hakala TK, Tikkanen H, Kunttu H, Törmä P. Molecular coupling of light with plasmonic waveguides. Opt Express 2007; 15:9908-17. [PMID: 19547341 DOI: 10.1364/oe.15.009908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
We use molecules to couple light into and out of microscale plasmonic waveguides. Energy transfer, mediated by surface plasmons, from donor molecules to acceptor molecules over ten micrometer distances is demonstrated. Also surface plasmon coupled emission from the donor molecules is observed at similar distances away from the excitation spot. The lithographic fabrication method we use for positioning the dye molecules allows scaling to nanometer dimensions. The use of molecules as couplers between far-field and near-field light offers the advantages that no special excitation geometry is needed, any light source can be used to excite plasmons and the excitation can be localized below the diffraction limit. Moreover, the use of molecules has the potential for integration with molecular electronics and for the use of molecular self-assembly in fabrication. Our results constitute a proof-of-principle demonstration of a plasmonic waveguide where signal in- and outcoupling is done by molecules.
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Tuukkanen S, Toppari JJ, Kuzyk A, Hirviniemi L, Hytönen VP, Ihalainen T, Törmä P. Carbon nanotubes as electrodes for dielectrophoresis of DNA. Nano Lett 2006; 6:1339-43. [PMID: 16834407 DOI: 10.1021/nl060771m] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Dielectrophoresis can potentially be used as an efficient trapping tool in the fabrication of molecular devices. For nanoscale objects, however, the Brownian motion poses a challenge. We show that the use of carbon nanotube electrodes makes it possible to apply relatively low trapping voltages and still achieve high enough field gradients for trapping nanoscale objects, e.g., single molecules. We compare the efficiency and other characteristics of dielectrophoresis between carbon nanotube electrodes and lithographically fabricated metallic electrodes, in the case of trapping nanoscale DNA molecules. The results are analyzed using finite element method simulations and reveal information about the frequency-dependent polarizability of DNA.
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Affiliation(s)
- Sampo Tuukkanen
- Nanoscience Center, Department of Physics, University of Jyväskylä, Finland
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