1
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Xing Y, Rottensteiner A, Ciccone J, Howorka S. Functional Nanopores Enabled with DNA. Angew Chem Int Ed Engl 2023; 62:e202303103. [PMID: 37186432 DOI: 10.1002/anie.202303103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/17/2023]
Abstract
Membrane-spanning nanopores are used in label-free single-molecule sensing and next-generation portable nucleic acid sequencing, and as powerful research tools in biology, biophysics, and synthetic biology. Naturally occurring protein and peptide pores, as well as synthetic inorganic nanopores, are used in these applications, with their limitations. The structural and functional repertoire of nanopores can be considerably expanded by functionalising existing pores with DNA strands and by creating an entirely new class of nanopores with DNA nanotechnology. This review outlines progress in this area of functional DNA nanopores and outlines developments to open up new applications.
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Affiliation(s)
- Yongzheng Xing
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H 0AJ, UK
| | - Alexia Rottensteiner
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H 0AJ, UK
| | - Jonah Ciccone
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H 0AJ, UK
| | - Stefan Howorka
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H 0AJ, UK
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2
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Confederat S, Sandei I, Mohanan G, Wälti C, Actis P. Nanopore fingerprinting of supramolecular DNA nanostructures. Biophys J 2022; 121:4882-4891. [PMID: 35986518 PMCID: PMC9808562 DOI: 10.1016/j.bpj.2022.08.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/05/2022] [Accepted: 08/16/2022] [Indexed: 01/07/2023] Open
Abstract
DNA nanotechnology has paved the way for new generations of programmable nanomaterials. Utilizing the DNA origami technique, various DNA constructs can be designed, ranging from single tiles to the self-assembly of large-scale, complex, multi-tile arrays. This technique relies on the binding of hundreds of short DNA staple strands to a long single-stranded DNA scaffold that drives the folding of well-defined nanostructures. Such DNA nanostructures have enabled new applications in biosensing, drug delivery, and other multifunctional materials. In this study, we take advantage of the enhanced sensitivity of a solid-state nanopore that employs a poly-ethylene glycol enriched electrolyte to deliver real-time, non-destructive, and label-free fingerprinting of higher-order assemblies of DNA origami nanostructures with single-entity resolution. This approach enables the quantification of the assembly yields for complex DNA origami nanostructures using the nanostructure-induced equivalent charge surplus as a discriminant. We compare the assembly yield of four supramolecular DNA nanostructures obtained with the nanopore with agarose gel electrophoresis and atomic force microscopy imaging. We demonstrate that the nanopore system can provide analytical quantification of the complex supramolecular nanostructures within minutes, without any need for labeling and with single-molecule resolution. We envision that the nanopore detection platform can be applied to a range of nanomaterial designs and enable the analysis and manipulation of large DNA assemblies in real time.
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Affiliation(s)
- Samuel Confederat
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, United Kingdom; Bragg Centre for Materials Research, Leeds, United Kingdom
| | - Ilaria Sandei
- School of Chemistry, University of Leeds, Leeds, United Kingdom
| | - Gayathri Mohanan
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, United Kingdom; Bragg Centre for Materials Research, Leeds, United Kingdom
| | - Christoph Wälti
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, United Kingdom; Bragg Centre for Materials Research, Leeds, United Kingdom.
| | - Paolo Actis
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, United Kingdom; Bragg Centre for Materials Research, Leeds, United Kingdom.
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3
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Qiao D, Chen Y, Tan H, Zhou R, Feng J. De novo design of transmembrane nanopores. Sci China Chem 2022. [DOI: 10.1007/s11426-022-1354-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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4
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Zeng S, Chinappi M, Cecconi F, Odijk T, Zhang Z. DNA compaction and dynamic observation in a nanopore gated sub-attoliter silicon nanocavity. NANOSCALE 2022; 14:12038-12047. [PMID: 35943364 DOI: 10.1039/d2nr02260e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Confinement of biopolymers inside volumes with micro- or nanoscale lateral dimensions is ubiquitous in nature. Investigating the behavior of biopolymers in a confined environment is essential to improve our basic understanding in life sciences. In this work, we present a nanopore gated sub-attoliter silicon nanocavity device, which allows DNA compaction similar to that in virus capsids. Single DNA molecules can be electrically driven into the nanocavity, and then get compacted inside the nanocavity under certain conditions. The dynamic fluctuations of the compacted DNA can be monitored via ionic current measurements. The mechanism for the DNA compaction is elucidated by varying the DNA length or concentration, voltage polarity, nanocavity dimensions and ionic strength. Furthermore, Brownian dynamics simulations reveal the dynamic fluctuations of the compacted DNA, which are reflected in the measured ionic current. Our nanocavity device is anticipated to provide a controlled environment in extremely small volumes for investigating the physics of confined biopolymers.
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Affiliation(s)
- Shuangshuang Zeng
- Division of Solid-State Electronics, Department of Electrical Engineering, Uppsala University, SE-751 03 Uppsala, Sweden.
| | - Mauro Chinappi
- Dipartimento di Ingegneria Industriale, Università di Roma Tor Vergata, Via del Politecnico 1, 00133 Roma, Italy
| | - Fabio Cecconi
- CNR-Istituto dei Sistemi Complessi, Via dei Taurini 19, 00185 Roma, Italy
- INFN, Unità di Roma 1, 00185, Roma, Italy
| | - Theo Odijk
- Lorentz Institute for Theoretical Physics, University of Leiden, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands
| | - Zhen Zhang
- Division of Solid-State Electronics, Department of Electrical Engineering, Uppsala University, SE-751 03 Uppsala, Sweden.
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5
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Dhanasekar NN, Thiyagarajan D, Bhatia D. DNA origami in the quest for membrane piercing. Chem Asian J 2022; 17:e202200591. [PMID: 35947734 DOI: 10.1002/asia.202200591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 08/07/2022] [Indexed: 11/09/2022]
Abstract
The tool kit for label-free single-molecule sensing, nucleic acid sequencing (DNA, RNA and protein) and other biotechnological applications has been significantly broadened due to the wide range of available nanopore-based technologies. Currently, various sources of nanopores, including biological, fabricated solid-state, hybrid and recently de novo chemically synthesized ion-like channels have put in use for rapid single-molecule sensing of biomolecules and other diagnostic applications. At length scales of hundreds of nanometers, DNA nanotechnology, particularly DNA origami-based devices, enables the assembly of complex and dynamic 3-dimensional nanostructures, including nanopores with precise control over the size/shape. DNA origami technology has enabled to construct nanopores by DNA alone or hybrid architects with solid-state nanopore devices or nanocapillaries. In this review, we briefly discuss the nanopore technique that uses DNA nanotechnology to construct such individual pores in lipid-based systems or coupled with other solid-state devices, nanocapillaries for enhanced biosensing function. We summarize various DNA-based design nanopores and explore the sensing properties of such DNA channels. Apart from DNA origami channels we also pointed the design principles of RNA nanopores for peptide sensing applications.
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Affiliation(s)
- Naresh Niranjan Dhanasekar
- Johns Hopkins University, Chemical and Biomolecular Engineering, 3400 North Charles Street, 21218, Baltimore, UNITED STATES
| | - Durairaj Thiyagarajan
- Helmholtz-Zentrum fur Infektionsforschung GmbH, Pharmacy and Infections, 66123, Saarbrücken, GERMANY
| | - Dhiraj Bhatia
- Indian Institute of Technology Gandhinagar, Biological Engineering, 382355, Gandhi Nagar, INDIA
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6
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Xin Y, Piskunen P, Suma A, Li C, Ijäs H, Ojasalo S, Seitz I, Kostiainen MA, Grundmeier G, Linko V, Keller A. Environment-Dependent Stability and Mechanical Properties of DNA Origami Six-Helix Bundles with Different Crossover Spacings. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2107393. [PMID: 35363419 DOI: 10.1002/smll.202107393] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/14/2022] [Indexed: 05/25/2023]
Abstract
The internal design of DNA nanostructures defines how they behave in different environmental conditions, such as endonuclease-rich or low-Mg2+ solutions. Notably, the inter-helical crossovers that form the core of such DNA objects have a major impact on their mechanical properties and stability. Importantly, crossover design can be used to optimize DNA nanostructures for target applications, especially when developing them for biomedical environments. To elucidate this, two otherwise identical DNA origami designs are presented that have a different number of staple crossovers between neighboring helices, spaced at 42- and 21- basepair (bp) intervals, respectively. The behavior of these structures is then compared in various buffer conditions, as well as when they are exposed to enzymatic digestion by DNase I. The results show that an increased number of crossovers significantly improves the nuclease resistance of the DNA origami by making it less accessible to digestion enzymes but simultaneously lowers its stability under Mg2+ -free conditions by reducing the malleability of the structures. Therefore, these results represent an important step toward rational, application-specific DNA nanostructure design.
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Affiliation(s)
- Yang Xin
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Petteri Piskunen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland
| | - Antonio Suma
- Dipartimento di Fisica, Università di Bari and Sezione INFN di Bari, Bari, 70126, Italy
| | - Changyong Li
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Heini Ijäs
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland
| | - Sofia Ojasalo
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland
| | - Iris Seitz
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland
| | - Guido Grundmeier
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland
| | - Adrian Keller
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
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7
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Gao Y, Chen J, Chen G, Fan C, Liu X. Recent Progress in the Transfer of Graphene Films and Nanostructures. SMALL METHODS 2021; 5:e2100771. [PMID: 34928026 DOI: 10.1002/smtd.202100771] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/13/2021] [Indexed: 06/14/2023]
Abstract
The one-atom-thick graphene has excellent electronic, optical, thermal, and mechanical properties. Currently, chemical vapor deposition (CVD) graphene has received a great deal of attention because it provides access to large-area and uniform films with high-quality. This allows the fabrication of graphene based-electronics, sensors, photonics, and optoelectronics for practical applications. Zero bandgap, however, limits the application of a graphene film as electronic transistor. The most commonly used bottom-up approaches have achieved efficient tuning of the electronic bandgap by customizing well-defined graphene nanostructures. The postgrowth transfer of graphene films/nanostructures to a certain substrate is crucial in utilizing graphene in applicable devices. In this review, the basic growth mechanism of CVD graphene is first introduced. Then, recent advances in various transfer methods of as-grown graphene to target substrates are presented. The fabrication and transfer methods of graphene nanostructures are also provided, and then the transfer-related applications are summarized. At last, the challenging issues and the potential transfer-free approaches are discussed.
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Affiliation(s)
- Yanjing Gao
- School of Chemistry and Chemical Engineering, Frontiers Science Centre for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jielin Chen
- School of Chemistry and Chemical Engineering, Frontiers Science Centre for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Guorui Chen
- Key Laboratory of Artificial Structures and Quantum Control (Ministry of Education), Shenyang National Laboratory for Materials Science, School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Centre for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering, Frontiers Science Centre for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200240, China
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8
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Mohammadi MM, Bavi O. DNA sequencing: an overview of solid-state and biological nanopore-based methods. Biophys Rev 2021; 14:99-110. [PMID: 34840616 PMCID: PMC8609259 DOI: 10.1007/s12551-021-00857-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/14/2021] [Indexed: 12/23/2022] Open
Abstract
The field of sequencing is a topic of significant interest since its emergence and has become increasingly important over time. Impressive achievements have been obtained in this field, especially in relations to DNA and RNA sequencing. Since the first achievements by Sanger and colleagues in the 1950s, many sequencing techniques have been developed, while others have disappeared. DNA sequencing has undergone three generations of major evolution. Each generation has its own specifications that are mentioned briefly. Among these generations, nanopore sequencing has its own exciting characteristics that have been given more attention here. Among pioneer technologies being used by the third-generation techniques, nanopores, either biological or solid-state, have been experimentally or theoretically extensively studied. All sequencing technologies have their own advantages and disadvantages, so nanopores are not free from this general rule. It is also generally pointed out what research has been done to overcome the obstacles. In this review, biological and solid-state nanopores are elaborated on, and applications of them are also discussed briefly.
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Affiliation(s)
- Mohammad M Mohammadi
- Department of Mechanical and Aerospace Engineering, Shiraz University of Technology, Shiraz, 71557-13876 Iran
| | - Omid Bavi
- Department of Mechanical and Aerospace Engineering, Shiraz University of Technology, Shiraz, 71557-13876 Iran
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9
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Schmid S, Stömmer P, Dietz H, Dekker C. Nanopore electro-osmotic trap for the label-free study of single proteins and their conformations. NATURE NANOTECHNOLOGY 2021; 16:1244-1250. [PMID: 34462599 DOI: 10.1038/s41565-021-00958-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
Many strategies have been pursued to trap and monitor single proteins over time to detect the molecular mechanisms of these essential nanomachines. Single-protein sensing with nanopores is particularly attractive because it allows label-free high-bandwidth detection on the basis of ion currents. Here we present the nanopore electro-osmotic trap (NEOtrap) that allows trapping and observing single proteins for hours with submillisecond time resolution. The NEOtrap is formed by docking a DNA-origami sphere onto a passivated solid-state nanopore, which seals off a nanocavity of a user-defined size and creates an electro-osmotic flow that traps nearby particles irrespective of their charge. We demonstrate the NEOtrap's ability to sensitively distinguish proteins on the basis of size and shape, and discriminate between nucleotide-dependent protein conformations, as exemplified by the chaperone protein Hsp90. Given the experimental simplicity and capacity for label-free single-protein detection over the broad bio-relevant time range, the NEOtrap opens new avenues to study the molecular kinetics underlying protein function.
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Affiliation(s)
- Sonja Schmid
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
- NanoDynamicsLab, Laboratory of Biophysics, Wageningen University, Wageningen, The Netherlands
| | - Pierre Stömmer
- Physik Department, Technische Universität München, Garching near Munich, Germany
| | - Hendrik Dietz
- Physik Department, Technische Universität München, Garching near Munich, Germany
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands.
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10
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Gao L, Liu L, Tian Y, Yang Q, Wu P, Fan C, Zhao Q, Li F. Probing the Formation Kinetics and Thermodynamics with Rationally Designed Analytical Tools Enables One-Pot Synthesis and Purification of a Tetrahedral DNA Nanostructure. Anal Chem 2021; 93:7045-7053. [PMID: 33886303 DOI: 10.1021/acs.analchem.1c00363] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The development of robust analytical tools capable of probing the formation kinetics and thermodynamics of DNA nanostructures is a crucial step toward better understanding and manufacturing of diverse DNA-based materials. Herein, we introduce a real-time fluorescence anisotropy assay and rationally designed DNA reaction termination probes (DRTPs) as a set of new tools for exploring the formation mechanisms of DNA nanostructures. We deployed these tools for probing the formation of a classic tetrahedral DNA nanostructure (TDN) as a model system. Our tools revealed that the formation of TDN was dominated by simultaneous hybridization, whereas its undesired side products were caused mainly through step-wise hybridization. An optimal reaction temperature exists that favors the formation of TDN over side products. With insight into the TDN formation mechanism, we further engineered magnetic DRTPs to achieve single-step purification of TDN, enabling 10-fold improvement in the ratio between the targeted TDN and undesired side products without tedious procedures or bulky instruments. Combining the optimal reaction and purification conditions, we finally demonstrated the one-pot synthesis and purification of TDN. The analytical techniques offered in this work may hold potential to find wide applications and inspire new analytical methods for structural DNA nanotechnology.
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Affiliation(s)
- Lu Gao
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, P. R. China
| | - Liying Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunfei Tian
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, P. R. China
| | - Qianfan Yang
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, P. R. China
| | - Peng Wu
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, P. R. China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 201240, China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feng Li
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, P. R. China.,Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, Ontario L2S 3A1, Canada
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11
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Abstract
DNA origami enables the bottom-up construction of chemically addressable, nanoscale objects with user-defined shapes and tailored functionalities. As such, not only can DNA origami objects be used to improve existing experimental methods in biophysics, but they also open up completely new avenues of exploration. In this review, we discuss basic biophysical concepts that are relevant for prospective DNA origami users. We summarize biochemical strategies for interfacing DNA origami with biomolecules of interest. We describe various applications of DNA origami, emphasizing the added value or new biophysical insights that can be generated: rulers and positioning devices, force measurement and force application devices, alignment supports for structural analysis for biomolecules in cryogenic electron microscopy and nuclear magnetic resonance, probes for manipulating and interacting with lipid membranes, and programmable nanopores. We conclude with some thoughts on so-far little explored opportunities for using DNA origami in more complex environments such as the cell or even organisms.
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Affiliation(s)
- Wouter Engelen
- Physik Department, Technische Universität München, 85748 Garching bei München, Germany;
| | - Hendrik Dietz
- Physik Department, Technische Universität München, 85748 Garching bei München, Germany;
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12
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Julin S, Nonappa, Shen B, Linko V, Kostiainen MA. DNA‐Origami‐Templated Growth of Multilamellar Lipid Assemblies. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202006044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Sofia Julin
- Biohybrid Materials Department of Bioproducts and Biosystems Aalto University P. O. Box 16100 00076 Aalto Finland
| | - Nonappa
- HYBER Centre Department of Applied Physics Aalto University P. O. Box 15100 00076 Aalto Finland
- Faculty of Engineering and Natural Sciences Tampere University P. O. Box 541 33101 Tampere Finland
| | - Boxuan Shen
- Biohybrid Materials Department of Bioproducts and Biosystems Aalto University P. O. Box 16100 00076 Aalto Finland
| | - Veikko Linko
- Biohybrid Materials Department of Bioproducts and Biosystems Aalto University P. O. Box 16100 00076 Aalto Finland
- HYBER Centre Department of Applied Physics Aalto University P. O. Box 15100 00076 Aalto Finland
| | - Mauri A. Kostiainen
- Biohybrid Materials Department of Bioproducts and Biosystems Aalto University P. O. Box 16100 00076 Aalto Finland
- HYBER Centre Department of Applied Physics Aalto University P. O. Box 15100 00076 Aalto Finland
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13
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Jung WH, Chen E, Veneziano R, Gaitanaros S, Chen Y. Stretching DNA origami: effect of nicks and Holliday junctions on the axial stiffness. Nucleic Acids Res 2020; 48:12407-12414. [PMID: 33152066 PMCID: PMC7708044 DOI: 10.1093/nar/gkaa985] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/09/2020] [Accepted: 10/15/2020] [Indexed: 12/25/2022] Open
Abstract
The axial stiffness of DNA origami is determined as a function of key nanostructural characteristics. Different constructs of two-helix nanobeams with specified densities of nicks and Holliday junctions are synthesized and stretched by fluid flow. Implementing single particle tracking to extract force–displacement curves enables the measurement of DNA origami stiffness values at the enthalpic elasticity regime, i.e. for forces larger than 15 pN. Comparisons between ligated and nicked helices show that the latter exhibit nearly a two-fold decrease in axial stiffness. Numerical models that treat the DNA helices as elastic rods are used to evaluate the local loss of stiffness at the locations of nicks and Holliday junctions. It is shown that the models reproduce the experimental data accurately, indicating that both of these design characteristics yield a local stiffness two orders of magnitude smaller than the corresponding value of the intact double-helix. This local degradation in turn leads to a macroscopic loss of stiffness that is evaluated numerically for multi-helix DNA bundles.
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Affiliation(s)
- Wei-Hung Jung
- Department of Mechanical Engineering, Johns Hopkins University, USA.,Institute for NanoBioTechnology, Johns Hopkins University, USA.,Center for Cell Dynamics, Johns Hopkins University, USA
| | - Enze Chen
- Department of Civil and Systems Engineering, Johns Hopkins University, USA
| | - Remi Veneziano
- Department of Bioengineering, George Mason University, USA.,Institute for Advanced Biomedical Research, George Mason University, USA
| | - Stavros Gaitanaros
- Department of Civil and Systems Engineering, Johns Hopkins University, USA
| | - Yun Chen
- Department of Mechanical Engineering, Johns Hopkins University, USA.,Institute for NanoBioTechnology, Johns Hopkins University, USA.,Center for Cell Dynamics, Johns Hopkins University, USA
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14
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Julin S, Nonappa, Shen B, Linko V, Kostiainen MA. DNA-Origami-Templated Growth of Multilamellar Lipid Assemblies. Angew Chem Int Ed Engl 2020; 60:827-833. [PMID: 33022870 DOI: 10.1002/anie.202006044] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 07/22/2020] [Indexed: 12/14/2022]
Abstract
Lipids are important building blocks in cellular compartments, and therefore their self-assembly into well-defined hierarchical structures has gained increasing interest. Cationic lipids and unstructured DNA can co-assemble into highly ordered structures (lipoplexes), but potential applications of lipoplexes are still limited. Using scaffolded DNA origami nanostructures could aid in resolving these drawbacks. Here, we have complexed DNA origami together with a cationic lipid 1,2-dioleoly-3-trimethylammonium-propane (DOTAP) and studied their self-assembly driven by electrostatic and hydrophobic interactions. The results suggest that the DNA origami function as templates for the growth of multilamellar lipid structures and that the DNA origami are embedded in the formed lipid matrix. Furthermore, the lipid encapsulation was found to significantly shield the DNA origami against nuclease digestion. The presented complexation strategy is suitable for a wide range of DNA-based templates and could therefore find uses in construction of cell-membrane-associated components.
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Affiliation(s)
- Sofia Julin
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P. O. Box 16100, 00076, Aalto, Finland
| | - Nonappa
- HYBER Centre, Department of Applied Physics, Aalto University, P. O. Box 15100, 00076, Aalto, Finland.,Faculty of Engineering and Natural Sciences, Tampere University, P. O. Box 541, 33101, Tampere, Finland
| | - Boxuan Shen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P. O. Box 16100, 00076, Aalto, Finland
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P. O. Box 16100, 00076, Aalto, Finland.,HYBER Centre, Department of Applied Physics, Aalto University, P. O. Box 15100, 00076, Aalto, Finland
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P. O. Box 16100, 00076, Aalto, Finland.,HYBER Centre, Department of Applied Physics, Aalto University, P. O. Box 15100, 00076, Aalto, Finland
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15
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Zhu L, Zhang Z, Liu Q. Deformation-Mediated Translocation of DNA Origami Nanoplates through a Narrow Solid-State Nanopore. Anal Chem 2020; 92:13238-13245. [PMID: 32872775 DOI: 10.1021/acs.analchem.0c02396] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
With the development in DNA self-assembly technology, DNA origami nanostructures have been widely applied in biomedical research. Solid-state nanopores represent an emerging single-molecule sensing platform for studying nanostructures with arbitrary dimensions and physical characteristics, including DNA origami. Here, we employed relatively narrow silicon nitride nanopores to detect the deformation and translocation of DNA origami nanoplates with dimensions of approximately 60 × 54 nm. We performed translocation experiments using three nanopore diameters that are all smaller than the plat dimensions. Analysis of current blockade signals and the representative events reveals three types of translocation orientations for the nanoplates. Furthermore, by studying the electrical signal characteristics (current change and dwell time) for the different diameter pores, we obtained information about the translocation behaviors for the DNA nanoplates through different constrictions. Our investigation provides an approach to analyze the deformation and translocation of DNA origami structures.
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Affiliation(s)
- Libo Zhu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing 210096, China
| | - Zhen Zhang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing 210096, China
| | - Quanjun Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing 210096, China
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16
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Shen B, Piskunen P, Nummelin S, Liu Q, Kostiainen MA, Linko V. Advanced DNA Nanopore Technologies. ACS APPLIED BIO MATERIALS 2020; 3:5606-5619. [DOI: 10.1021/acsabm.0c00879] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Boxuan Shen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Petteri Piskunen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Sami Nummelin
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Qing Liu
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
- HYBER Centre, Department of Applied Physics, Aalto University, 00076 Aalto, Finland
| | - Mauri A. Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
- HYBER Centre, Department of Applied Physics, Aalto University, 00076 Aalto, Finland
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
- HYBER Centre, Department of Applied Physics, Aalto University, 00076 Aalto, Finland
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17
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Ding T, Yang J, Pan V, Zhao N, Lu Z, Ke Y, Zhang C. DNA nanotechnology assisted nanopore-based analysis. Nucleic Acids Res 2020; 48:2791-2806. [PMID: 32083656 PMCID: PMC7102975 DOI: 10.1093/nar/gkaa095] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 01/29/2020] [Accepted: 02/17/2020] [Indexed: 12/30/2022] Open
Abstract
Nanopore technology is a promising label-free detection method. However, challenges exist for its further application in sequencing, clinical diagnostics and ultra-sensitive single molecule detection. The development of DNA nanotechnology nonetheless provides possible solutions to current obstacles hindering nanopore sensing technologies. In this review, we summarize recent relevant research contributing to efforts for developing nanopore methods associated with DNA nanotechnology. For example, DNA carriers can capture specific targets at pre-designed sites and escort them from nanopores at suitable speeds, thereby greatly enhancing capability and resolution for the detection of specific target molecules. In addition, DNA origami structures can be constructed to fulfill various design specifications and one-pot assembly reactions, thus serving as functional nanopores. Moreover, based on DNA strand displacement, nanopores can also be utilized to characterize the outputs of DNA computing and to develop programmable smart diagnostic nanodevices. In summary, DNA assembly-based nanopore research can pave the way for the realization of impactful biological detection and diagnostic platforms via single-biomolecule analysis.
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Affiliation(s)
- Taoli Ding
- Department of Computer Science and Technology, School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, China.,Department of Biomedical Engineering, College of engineering, Peking University, Beijing 100871, China
| | - Jing Yang
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
| | - Victor Pan
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Emory University School of Medicine, Atlanta, GA 30322, USA.,Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Nan Zhao
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
| | - Zuhong Lu
- Department of Biomedical Engineering, College of engineering, Peking University, Beijing 100871, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Emory University School of Medicine, Atlanta, GA 30322, USA.,Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Cheng Zhang
- Department of Computer Science and Technology, School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, China
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18
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Shen Q, Grome MW, Yang Y, Lin C. Engineering Lipid Membranes with Programmable DNA Nanostructures. ADVANCED BIOSYSTEMS 2020; 4:1900215. [PMID: 31934608 PMCID: PMC6957268 DOI: 10.1002/adbi.201900215] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Indexed: 12/18/2022]
Abstract
Lipid and DNA are abundant biomolecules with critical functions in cells. The water-insoluble, amphipathic lipid molecules are best known for their roles in energy storage (e.g. as triglyceride), signaling (e.g. as sphingolipid), and compartmentalization (e.g. by forming membrane-enclosed bodies). The soluble, highly negatively charged DNA, which stores cells' genetic information, has proven to be an excellent material for constructing programmable nanostructures in vitro thanks to its self-assembling capabilities. These two seemingly distant molecules make contact within cell nuclei, often via lipidated proteins, with proposed functions of modulating chromatin structures. Carefully formulated lipid/DNA complexes are promising reagents for gene therapy. The past few years saw an emerging research field of interfacing DNA nanostructures with lipid membranes, with an overarching goal of generating DNA/lipid hybrid materials that possess novel and controllable structure, dynamics, and function. An arsenal of DNA-based tools has been created to coat, mold, deform, and penetrate lipid bilayers, affording us the ability to manipulate membranes with nanoscopic precision. These membrane engineering methods not only enable quantitative biophysical studies, but also open new opportunities in synthetic biology (e.g. artificial cells) and therapeutics (e.g. drug delivery).
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Affiliation(s)
- Qi Shen
- Department of Cell Biology and Nanobiology Institute, Yale University
| | - Michael W Grome
- Department of Cell Biology and Nanobiology Institute, Yale University
| | - Yang Yang
- Department of Cell Biology and Nanobiology Institute, Yale University
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine
| | - Chenxiang Lin
- Department of Cell Biology and Nanobiology Institute, Yale University
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19
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DNA Nanotechnology for Building Sensors, Nanopores and Ion-Channels. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1174:331-370. [PMID: 31713205 DOI: 10.1007/978-981-13-9791-2_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA nanotechnology has revolutionised the capabilities to shape and control three-dimensional structures at the nanometre scale. Designer sensors, nanopores and ion-channels built from DNA have great potential for both cross-disciplinary research and applications. Here, we introduce the concept of structural DNA nanotechnology, including DNA origami, and give an overview of the work flow from design to assembly, characterisation and application of DNA-based functional systems. Chemical functionalisation of DNA has opened up pathways to transform static DNA structures into dynamic nanomechanical sensors. We further introduce nanopore sensing as a powerful label-free single-molecule technique and discuss how it can benefit from DNA nanotechnology. Especially exciting is the possibility to create membrane-inserted DNA nanochannels that mimic their protein-based natural counterparts in form and function. In this chapter we review the status quo of DNA sensors, nanopores and ion channels, highlighting opportunities and challenges for their future development.
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20
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Synthetic protein-conductive membrane nanopores built with DNA. Nat Commun 2019; 10:5018. [PMID: 31685824 PMCID: PMC6828756 DOI: 10.1038/s41467-019-12639-y] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 09/23/2019] [Indexed: 11/08/2022] Open
Abstract
AbstractNanopores are key in portable sequencing and research given their ability to transport elongated DNA or small bioactive molecules through narrow transmembrane channels. Transport of folded proteins could lead to similar scientific and technological benefits. Yet this has not been realised due to the shortage of wide and structurally defined natural pores. Here we report that a synthetic nanopore designed via DNA nanotechnology can accommodate folded proteins. Transport of fluorescent proteins through single pores is kinetically analysed using massively parallel optical readout with transparent silicon-on-insulator cavity chips vs. electrical recordings to reveal an at least 20-fold higher speed for the electrically driven movement. Pores nevertheless allow a high diffusive flux of more than 66 molecules per second that can also be directed beyond equillibria. The pores may be exploited to sense diagnostically relevant proteins with portable analysis technology, to create molecular gates for drug delivery, or to build synthetic cells.
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21
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Wang W, Yu S, Huang S, Bi S, Han H, Zhang JR, Lu Y, Zhu JJ. Bioapplications of DNA nanotechnology at the solid-liquid interface. Chem Soc Rev 2019; 48:4892-4920. [PMID: 31402369 PMCID: PMC6746594 DOI: 10.1039/c8cs00402a] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
DNA nanotechnology engineered at the solid-liquid interface has advanced our fundamental understanding of DNA hybridization kinetics and facilitated the design of improved biosensing, bioimaging and therapeutic platforms. Three research branches of DNA nanotechnology exist: (i) structural DNA nanotechnology for the construction of various nanoscale patterns; (ii) dynamic DNA nanotechnology for the operation of nanodevices; and (iii) functional DNA nanotechnology for the exploration of new DNA functions. Although the initial stages of DNA nanotechnology research began in aqueous solution, current research efforts have shifted to solid-liquid interfaces. Based on shape and component features, these interfaces can be classified as flat interfaces, nanoparticle interfaces, and soft interfaces of DNA origami and cell membranes. This review briefly discusses the development of DNA nanotechnology. We then highlight the important roles of structural DNA nanotechnology in tailoring the properties of flat interfaces and modifications of nanoparticle interfaces, and extensively review their successful bioapplications. In addition, engineering advances in DNA nanodevices at interfaces for improved biosensing both in vitro and in vivo are presented. The use of DNA nanotechnology as a tool to engineer cell membranes to reveal protein levels and cell behavior is also discussed. Finally, we present challenges and an outlook for this emerging field.
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Affiliation(s)
- Wenjing Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China.
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22
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Ishikawa D, Suzuki Y, Kurokawa C, Ohara M, Tsuchiya M, Morita M, Yanagisawa M, Endo M, Kawano R, Takinoue M. DNA Origami Nanoplate‐Based Emulsion with Nanopore Function. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201908392] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Daisuke Ishikawa
- Department of Computer Science Tokyo Institute of Technology 4259 Nagatsuta-cho Midori-ku, Yokohama Kanagawa 226-8502 Japan
| | - Yuki Suzuki
- Frontier Research Institute for Interdisciplinary Sciences Tohoku University 6-3 Aramaki aza Aoba, Aoba-ku Sendai 980-8578 Japan
| | - Chikako Kurokawa
- Department of Applied Physics Tokyo University of Agriculture and Technology 2-24-6 Naka-cho, Koganei Tokyo 184-8588 Japan
| | - Masayuki Ohara
- Department of Biotechnology and Life Science Tokyo University of Agriculture and Technology 2-24-6 Naka-cho, Koganei Tokyo 184-8588 Japan
| | - Misato Tsuchiya
- Department of Computer Science Tokyo Institute of Technology 4259 Nagatsuta-cho Midori-ku, Yokohama Kanagawa 226-8502 Japan
| | - Masamune Morita
- Department of Computer Science Tokyo Institute of Technology 4259 Nagatsuta-cho Midori-ku, Yokohama Kanagawa 226-8502 Japan
| | - Miho Yanagisawa
- Department of Applied Physics Tokyo University of Agriculture and Technology 2-24-6 Naka-cho, Koganei Tokyo 184-8588 Japan
- Komaba Institute for Science Graduate School of Arts and Sciences The University of Tokyo 3-8-1 Komaba, Meguro Tokyo 153-8902 Japan
| | - Masayuki Endo
- Department of Chemistry Graduate School of Science Kyoto University Yoshida-ushinomiyacho, Sakyo-ku Kyoto 606-8501 Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science Tokyo University of Agriculture and Technology 2-24-6 Naka-cho, Koganei Tokyo 184-8588 Japan
| | - Masahiro Takinoue
- Department of Computer Science Tokyo Institute of Technology 4259 Nagatsuta-cho Midori-ku, Yokohama Kanagawa 226-8502 Japan
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23
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Ishikawa D, Suzuki Y, Kurokawa C, Ohara M, Tsuchiya M, Morita M, Yanagisawa M, Endo M, Kawano R, Takinoue M. DNA Origami Nanoplate-Based Emulsion with Nanopore Function. Angew Chem Int Ed Engl 2019; 58:15299-15303. [PMID: 31411794 DOI: 10.1002/anie.201908392] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Indexed: 11/10/2022]
Abstract
Bio-inspired functional microcapsules have attracted increasing attention in many fields from physical/chemical science to artificial-cell engineering. Although particle-stabilised microcapsules are advantageous for their stability and functionalisation potential, versatile methods for their functionalisation are desired to expand their possibilities. This study reports a water-in-oil microdroplet stabilised with amphiphilic DNA origami nanoplates. By utilising DNA nanotechnology, DNA nanoplates were designed as a nanopore device for ion transportation and to stabilise the oil-water interface. Microscopic examination revealed the microcapsule formed by the accumulation of amphiphilic DNA nanoplates at the oil-water interface. Ion current measurements revealed the nanoplate pores functioned as channel to transport ions. These findings provide a general strategy for the programmable design of microcapsules to engineer artificial cells and molecular robots.
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Affiliation(s)
- Daisuke Ishikawa
- Department of Computer Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
| | - Yuki Suzuki
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramaki aza Aoba, Aoba-ku, Sendai, 980-8578, Japan
| | - Chikako Kurokawa
- Department of Applied Physics, Tokyo University of Agriculture and Technology, 2-24-6 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Masayuki Ohara
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-6 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Misato Tsuchiya
- Department of Computer Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
| | - Masamune Morita
- Department of Computer Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
| | - Miho Yanagisawa
- Department of Applied Physics, Tokyo University of Agriculture and Technology, 2-24-6 Naka-cho, Koganei, Tokyo, 184-8588, Japan.,Komaba Institute for Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-6 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Masahiro Takinoue
- Department of Computer Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
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24
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Wang V, Ermann N, Keyser UF. Current Enhancement in Solid-State Nanopores Depends on Three-Dimensional DNA Structure. NANO LETTERS 2019; 19:5661-5666. [PMID: 31313927 DOI: 10.1021/acs.nanolett.9b02219] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The translocation of double-stranded DNA through a solid-state nanopore may either decrease or increase the ionic current depending on the ionic concentration of the surrounding solution. Below a certain crossover ionic concentration, the current change inverts from a current blockade to current enhancement. In this paper, we show that the crossover concentration for bundled DNA nanostructures composed of multiple connected DNA double-helices is lower than that of double-stranded DNA. Our measurements suggest that counterion mobility in the vicinity of DNA is reduced depending on the three-dimensional structure of the molecule. We further demonstrate that introducing neutral polymers such as polyethylene glycol into the measurement solution reduces electroosmotic outflow from the nanopore, allowing translocation of large DNA structures at low salt concentrations. Our experiments contribute to an improved understanding of ion transport in confined DNA environments, which is critical for the development of nanopore sensing techniques as well as synthetic membrane channels. Our salt-dependent measurements of model DNA nanostructures will guide the development of computational models of DNA translocation through nanopores.
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Affiliation(s)
- Vivian Wang
- Cavendish Laboratory , University of Cambridge , 19 JJ Thomson Avenue , Cambridge CB3 0HE , United Kingdom
| | - Niklas Ermann
- Cavendish Laboratory , University of Cambridge , 19 JJ Thomson Avenue , Cambridge CB3 0HE , United Kingdom
| | - Ulrich F Keyser
- Cavendish Laboratory , University of Cambridge , 19 JJ Thomson Avenue , Cambridge CB3 0HE , United Kingdom
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25
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Yu JS, Lee J, Ju M, Cho OH, Kim HM, Nam KT, Kim KB. DNA translocation through a nanopore in an ultrathin self-assembled peptide membrane. NANOTECHNOLOGY 2019; 30:195602. [PMID: 30721897 DOI: 10.1088/1361-6528/ab0488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Here, we explore the possibility of using peptide-based materials as a membrane in solid-state nanopore devices in an effort to develop a sequence-specific, programmable biological membrane platform. We use a recently developed tyrosine-mediated self-assembly peptide sheet. At the air/water interface, the 5mer peptide YFCFY self-assembles into a uniform and robust two-dimensional (2D) structure, and the peptide sheet is easily transferred to a low-noise glass substrate. The thickness of the peptide membrane can be adjusted to approximately 5 nm (or even to 2 nm) by an etching process, and the diameters of the peptide nanopores can be precisely controlled using a focused electron beam with an attuned spot size. The ionic current noise of the peptide nanopore is comparable to those of typical silicon nitride nanopores or multilayer 2D materials. Using this membrane, we successfully observe translocation of 1000 bp double-stranded DNA with a sufficient signal-to-noise ratio of ∼30 and an elongated translocation speed of ∼1 bp μs-1. Our results suggest that the self-assembled peptide film can be used as a sensitive nanopore membrane and employed as a platform for applying biological functionalities to solid-state substrates.
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Affiliation(s)
- Jae-Seok Yu
- Department of Materials Science and Engineering, Seoul National University, Seoul, 151-742, Republic of Korea
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26
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Zhao H, Ye D, Mao X, Li F, Xu J, Li M, Zuo X. Stepping gating of ion channels on nanoelectrode via DNA hybridization for label-free DNA detection. Biosens Bioelectron 2019; 133:141-146. [PMID: 30925363 DOI: 10.1016/j.bios.2019.03.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/10/2019] [Accepted: 03/17/2019] [Indexed: 12/21/2022]
Abstract
Natural ion channels on cell membrane can gate the transport of ions and molecules by the conformational alteration of transmembrane proteins to regulate the normal physiological activities of cells. Inspired by the similarity of the conformation change under specific stimuli, here we introduce an ion channel gating model on a single nanoelectrode by anchoring DNA-gated switches on the very nanotip of gold nanoelectrode to mimic the response-to-stimulus behaviors of ion channels on bio-membranes. The surface-tethered DNA ion channels can be switched on by the Watson-Crick base pairing, which can alter the conformation of the tethered DNA from lying state to upright state. And these conformational alterations of the anchored DNA switches can effectively gate the transport of potassium ferricyanide onto the electrode interface. By continuously initiating the gates with DNA of different concentrations, we achieved the stepping gating of ion channels on a single nanoelectrode. Further, we demonstrated that the ion gating system on nanoelectrode showed excellent sensing performance. For example, the response kinetic was very fast with the signal saturation time of ~1 min, the reproducibility of the OFF/ON switch was robust enough to sustain for two cycles, and simultaneously, the specificity was high enough to distinguish complementary DNA and noncomplementary DNA. When used for label-free DNA detection, the limit of detection can be as low as 10 pM. This study provides a promising avenue to achieve label free and real-time detection of multiple biomolecules.
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Affiliation(s)
- Haipei Zhao
- NEST Lab, Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, China; Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Dekai Ye
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fan Li
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Jiaqiang Xu
- NEST Lab, Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, China.
| | - Min Li
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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27
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Karawdeniya BI, Bandara YMNDY, Nichols JW, Chevalier RB, Hagan JT, Dwyer JR. Challenging Nanopores with Analyte Scope and Environment. JOURNAL OF ANALYSIS AND TESTING 2019. [DOI: 10.1007/s41664-019-00092-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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28
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Zhao S, Restrepo-Pérez L, Soskine M, Maglia G, Joo C, Dekker C, Aksimentiev A. Electro-Mechanical Conductance Modulation of a Nanopore Using a Removable Gate. ACS NANO 2019; 13:2398-2409. [PMID: 30715850 PMCID: PMC6494462 DOI: 10.1021/acsnano.8b09266] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Ion channels form the basis of information processing in living cells by facilitating the exchange of electrical signals across and along cellular membranes. Applying the same principles to man-made systems requires the development of synthetic ion channels that can alter their conductance in response to a variety of external manipulations. By combining single-molecule electrical recordings with all-atom molecular dynamics simulations, we here demonstrate a hybrid nanopore system that allows for both a stepwise change of its conductance and a nonlinear current-voltage dependence. The conductance modulation is realized by using a short flexible peptide gate that carries opposite electric charge at its ends. We show that a constant transmembrane bias can position (and, in a later stage, remove) the peptide gate right at the most-sensitive sensing region of a biological nanopore FraC, thus partially blocking its channel and producing a stepwise change in the conductance. Increasing or decreasing the bias while having the peptide gate trapped in the pore stretches or compresses the peptide within the nanopore, thus modulating its conductance in a nonlinear but reproducible manner. We envision a range of applications of this removable-gate nanopore system, e.g. from an element of biological computing circuits to a test bed for probing the elasticity of intrinsically disordered proteins.
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Affiliation(s)
- Shidi Zhao
- Center for Biophysics and Quantitative Biology, Department of Physics and Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Laura Restrepo-Pérez
- Department of Bionanoscience, Kavli Institute of Nanoscience , Delft University of Technology , van der Maasweg 9 , 2629 HZ Delft , The Netherlands
| | - Misha Soskine
- Groningen Biomolecular Sciences & Biotechnology Institute , University of Groningen , 9747 AG Groningen , The Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences & Biotechnology Institute , University of Groningen , 9747 AG Groningen , The Netherlands
| | - Chirlmin Joo
- Department of Bionanoscience, Kavli Institute of Nanoscience , Delft University of Technology , van der Maasweg 9 , 2629 HZ Delft , The Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience , Delft University of Technology , van der Maasweg 9 , 2629 HZ Delft , The Netherlands
| | - Aleksei Aksimentiev
- Center for Biophysics and Quantitative Biology, Department of Physics and Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
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29
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Taniguchi M, Ohshiro T. Nanopore Device for Single-Molecule Sensing Method and Its Application. Bioanalysis 2019. [DOI: 10.1007/978-981-13-6229-3_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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30
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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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31
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Lee K, Park KB, Kim HJ, Yu JS, Chae H, Kim HM, Kim KB. Recent Progress in Solid-State Nanopores. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1704680. [PMID: 30260506 DOI: 10.1002/adma.201704680] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 06/08/2018] [Indexed: 05/28/2023]
Abstract
The solid-state nanopore has attracted much attention as a next-generation DNA sequencing tool or a single-molecule biosensor platform with its high sensitivity of biomolecule detection. The platform has advantages of processability, robustness of the device, and flexibility in the nanopore dimensions as compared with the protein nanopore, but with the limitation of insufficient spatial and temporal resolution to be utilized in DNA sequencing. Here, the fundamental principles of the solid-state nanopore are summarized to illustrate the novelty of the device, and improvements in the performance of the platform in terms of device fabrication are explained. The efforts to reduce the electrical noise of solid-state nanopore devices, and thus to enhance the sensitivity of detection, are presented along with detailed descriptions of the noise properties of the solid-state nanopore. Applications of 2D materials including graphene, h-BN, and MoS2 as a nanopore membrane to enhance the spatial resolution of nanopore detection, and organic coatings on the nanopore membranes for the addition of chemical functionality to the nanopore are summarized. Finally, the recently reported applications of the solid-state nanopore are categorized and described according to the target biomolecules: DNA-bound proteins, modified DNA structures, proteins, and protein oligomers.
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Affiliation(s)
- Kidan Lee
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kyeong-Beom Park
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyung-Jun Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jae-Seok Yu
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hongsik Chae
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyun-Mi Kim
- Research Institute of Advanced Materials, Seoul National University, Seoul, 08826, Republic of Korea
| | - Ki-Bum Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
- Research Institute of Advanced Materials, Seoul National University, Seoul, 08826, Republic of Korea
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32
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Ren YA, Gao H, Ouyang X. Advances in DNA Origami Nanopores: Fabrication, Characterization and Applications. CHINESE J CHEM 2018. [DOI: 10.1002/cjoc.201800173] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Yong-An Ren
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education of China, Key Laboratory of Modern Separation Science in Shaanxi Province, College of Chemistry & Material Science; Northwest University; Xi'an Shaanxi 710127 China
| | - Han Gao
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education of China, Key Laboratory of Modern Separation Science in Shaanxi Province, College of Chemistry & Material Science; Northwest University; Xi'an Shaanxi 710127 China
| | - Xiangyuan Ouyang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education of China, Key Laboratory of Modern Separation Science in Shaanxi Province, College of Chemistry & Material Science; Northwest University; Xi'an Shaanxi 710127 China
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33
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Nummelin S, Kommeri J, Kostiainen MA, Linko V. Evolution of Structural DNA Nanotechnology. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1703721. [PMID: 29363798 DOI: 10.1002/adma.201703721] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 09/17/2017] [Indexed: 05/24/2023]
Abstract
The research field entitled structural DNA nanotechnology emerged in the beginning of the 1980s as the first immobile synthetic nucleic acid junctions were postulated and demonstrated. Since then, the field has taken huge leaps toward advanced applications, especially during the past decade. This Progress Report summarizes how the controllable, custom, and accurate nanostructures have recently evolved together with powerful design and simulation software. Simultaneously they have provided a significant expansion of the shape space of the nanostructures. Today, researchers can select the most suitable fabrication methods, and design paradigms and software from a variety of options when creating unique DNA nanoobjects and shapes for a plethora of implementations in materials science, optics, plasmonics, molecular patterning, and nanomedicine.
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Affiliation(s)
- Sami Nummelin
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076, Aalto, Finland
| | - Juhana Kommeri
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076, Aalto, Finland
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076, Aalto, Finland
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076, Aalto, Finland
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34
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Ketterer P, Ananth AN, Laman Trip DS, Mishra A, Bertosin E, Ganji M, van der Torre J, Onck P, Dietz H, Dekker C. DNA origami scaffold for studying intrinsically disordered proteins of the nuclear pore complex. Nat Commun 2018; 9:902. [PMID: 29500415 PMCID: PMC5834454 DOI: 10.1038/s41467-018-03313-w] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/02/2018] [Indexed: 11/09/2022] Open
Abstract
The nuclear pore complex (NPC) is the gatekeeper for nuclear transport in eukaryotic cells. A key component of the NPC is the central shaft lined with intrinsically disordered proteins (IDPs) known as FG-Nups, which control the selective molecular traffic. Here, we present an approach to realize artificial NPC mimics that allows controlling the type and copy number of FG-Nups. We constructed 34 nm-wide 3D DNA origami rings and attached different numbers of NSP1, a model yeast FG-Nup, or NSP1-S, a hydrophilic mutant. Using (cryo) electron microscopy, we find that NSP1 forms denser cohesive networks inside the ring compared to NSP1-S. Consistent with this, the measured ionic conductance is lower for NSP1 than for NSP1-S. Molecular dynamics simulations reveal spatially varying protein densities and conductances in good agreement with the experiments. Our technique provides an experimental platform for deciphering the collective behavior of IDPs with full control of their type and position.
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Affiliation(s)
- Philip Ketterer
- Physik Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, Garching bei München, D-85748, Germany
| | - Adithya N Ananth
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Diederik S Laman Trip
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Ankur Mishra
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Eva Bertosin
- Physik Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, Garching bei München, D-85748, Germany
| | - Mahipal Ganji
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Jaco van der Torre
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Patrick Onck
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Hendrik Dietz
- Physik Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, Garching bei München, D-85748, Germany.
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands.
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35
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Henning-Knechtel A, Knechtel J, Magzoub M. DNA-assisted oligomerization of pore-forming toxin monomers into precisely-controlled protein channels. Nucleic Acids Res 2017; 45:12057-12068. [PMID: 29088457 PMCID: PMC5716084 DOI: 10.1093/nar/gkx990] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 10/11/2017] [Indexed: 01/12/2023] Open
Abstract
We have developed a novel approach for creating membrane-spanning protein-based pores. The construction principle is based on using well-defined, circular DNA nanostructures to arrange a precise number of pore-forming protein toxin monomers. We can thereby obtain, for the first time, protein pores with specifically set diameters. We demonstrate this principle by constructing artificial alpha-hemolysin (αHL) pores. The DNA/αHL hybrid nanopores composed of twelve, twenty or twenty-six monomers show stable insertions into lipid bilayers during electrical recordings, along with steady, pore size-dependent current levels. Our approach successfully advances the applicability of nanopores, in particular towards label-free studies of single molecules in large nanoscaled biological structures.
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Affiliation(s)
- Anja Henning-Knechtel
- Biology Program, Division of Science, New York University Abu Dhabi, PO Box 129188, Saadiyat Island, Abu Dhabi, UAE
| | - Johann Knechtel
- Division of Engineering, New York University Abu Dhabi, PO Box 129188, Saadiyat Island, Abu Dhabi, UAE
| | - Mazin Magzoub
- Biology Program, Division of Science, New York University Abu Dhabi, PO Box 129188, Saadiyat Island, Abu Dhabi, UAE
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36
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Kroener F, Heerwig A, Kaiser W, Mertig M, Rant U. Electrical Actuation of a DNA Origami Nanolever on an Electrode. J Am Chem Soc 2017; 139:16510-16513. [PMID: 29111693 DOI: 10.1021/jacs.7b10862] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Development of electrically powered DNA origami nanomachines requires effective means to actuate moving origami parts by externally applied electric fields. We demonstrate how origami nanolevers on an electrode can be manipulated (switched) at high frequency by alternating voltages. Orientation switching is long-time stable and can be induced by applying low voltages of 200 mV. The mechanical response time of a 100 nm long origami lever to an applied voltage step is less than 100 μs, allowing dynamic control of the induced motion. Moreover, through voltage assisted capture, origamis can be immobilized from folding solution without purification, even in the presence of excess staple strands. The results establish a way for interfacing and controlling DNA origamis with standard electronics, and enable their use as moving parts in electro-mechanical nanodevices.
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Affiliation(s)
- Felix Kroener
- Technische Universitaet Dresden , 01069 Dresden, Germany.,Dynamic Biosensors GmbH , 82152 Planegg, Germany
| | - Andreas Heerwig
- Kurt-Schwabe-Institut fuer Mess- und Sensortechnik Meinsberg e.V. , 04736 Waldheim, Germany
| | | | - Michael Mertig
- Technische Universitaet Dresden , 01069 Dresden, Germany.,Kurt-Schwabe-Institut fuer Mess- und Sensortechnik Meinsberg e.V. , 04736 Waldheim, Germany
| | - Ulrich Rant
- Dynamic Biosensors GmbH , 82152 Planegg, Germany
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37
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Alibakhshi MA, Halman JR, Wilson J, Aksimentiev A, Afonin KA, Wanunu M. Picomolar Fingerprinting of Nucleic Acid Nanoparticles Using Solid-State Nanopores. ACS NANO 2017; 11:9701-9710. [PMID: 28841287 PMCID: PMC5959297 DOI: 10.1021/acsnano.7b04923] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Nucleic acid nanoparticles (NANPs) are an emerging class of programmable structures with tunable shape and function. Their promise as tools for fundamental biophysics studies, molecular sensing, and therapeutic applications necessitates methods for their detection and characterization at the single-particle level. In this work, we study electrophoretic transport of individual ring-shaped and cube-shaped NANPs through solid-state nanopores. In the optimal nanopore size range, the particles must deform to pass through, which considerably increases their residence time within the pore. Such anomalously long residence times permit detection of picomolar amounts of NANPs when nanopore measurements are carried out at a high transmembrane bias. In the case of a NANP mixture, the type of individual particle passing through nanopores can be efficiently determined from analysis of a single electrical pulse. Molecular dynamics simulations provide insight into the mechanical barrier to transport of the NANPs and corroborate the difference in the signal amplitudes observed for the two types of particles. Our study serves as a basis for label-free analysis of soft programmable-shape nanoparticles.
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Affiliation(s)
| | - Justin R. Halman
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - James Wilson
- Department of Physics, University of Illinois at Urbana—Champaign, Urbana, Illinois 61801, United States
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana—Champaign, Urbana, Illinois 61801, United States
| | - Kirill A. Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- The Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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38
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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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39
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Mathur D, Medintz IL. Analyzing DNA Nanotechnology: A Call to Arms For The Analytical Chemistry Community. Anal Chem 2017; 89:2646-2663. [DOI: 10.1021/acs.analchem.6b04033] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Divita Mathur
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
- Center
for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Code 6900, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center
for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Code 6900, Washington, D.C. 20375, United States
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40
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Barati Farimani A, Dibaeinia P, Aluru NR. DNA Origami-Graphene Hybrid Nanopore for DNA Detection. ACS APPLIED MATERIALS & INTERFACES 2017; 9:92-100. [PMID: 28004567 DOI: 10.1021/acsami.6b11001] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
DNA origami nanostructures can be used to functionalize solid-state nanopores for single molecule studies. In this study, we characterized a nanopore in a DNA origami-graphene heterostructure for DNA detection. The DNA origami nanopore is functionalized with a specific nucleotide type at the edge of the pore. Using extensive molecular dynamics (MD) simulations, we computed and analyzed the ionic conductivity of nanopores in heterostructures carpeted with one or two layers of DNA origami on graphene. We demonstrate that a nanopore in DNA origami-graphene gives rise to distinguishable dwell times for the four DNA base types, whereas for a nanopore in bare graphene, the dwell time is almost the same for all types of bases. The specific interactions (hydrogen bonds) between DNA origami and the translocating DNA strand yield different residence times and ionic currents. We also conclude that the speed of DNA translocation decreases due to the friction between the dangling bases at the pore mouth and the sequencing DNA strands.
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Affiliation(s)
- Amir Barati Farimani
- Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Payam Dibaeinia
- Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Narayana R Aluru
- Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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41
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Xu J, Wu ZS, Chen Y, Zheng T, Le J, Jia L. Collapse of chain anadiplosis-structured DNA nanowires for highly sensitive colorimetric assay of nucleic acids. Analyst 2017; 142:613-620. [DOI: 10.1039/c6an02526a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In this work, we have proposed a chain anadiplosis-structured DNA nanowire by using two well-defined assembly strands (AS1 and AS2).
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Affiliation(s)
- Jianguo Xu
- Cancer Metastasis Alert and Prevention Center, and Biopharmaceutical Photocatalysis
- State Key Laboratory of Photocatalysis on Energy and Environment
- Fuzhou University
- Fuzhou 350002
- China
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, and Biopharmaceutical Photocatalysis
- State Key Laboratory of Photocatalysis on Energy and Environment
- Fuzhou University
- Fuzhou 350002
- China
| | - Yanru Chen
- Cancer Metastasis Alert and Prevention Center, and Biopharmaceutical Photocatalysis
- State Key Laboratory of Photocatalysis on Energy and Environment
- Fuzhou University
- Fuzhou 350002
- China
| | - Tingting Zheng
- Cancer Metastasis Alert and Prevention Center, and Biopharmaceutical Photocatalysis
- State Key Laboratory of Photocatalysis on Energy and Environment
- Fuzhou University
- Fuzhou 350002
- China
| | - Jingqing Le
- Cancer Metastasis Alert and Prevention Center, and Biopharmaceutical Photocatalysis
- State Key Laboratory of Photocatalysis on Energy and Environment
- Fuzhou University
- Fuzhou 350002
- China
| | - Lee Jia
- Cancer Metastasis Alert and Prevention Center, and Biopharmaceutical Photocatalysis
- State Key Laboratory of Photocatalysis on Energy and Environment
- Fuzhou University
- Fuzhou 350002
- China
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42
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Krishnan S, Ziegler D, Arnaut V, Martin TG, Kapsner K, Henneberg K, Bausch AR, Dietz H, Simmel FC. Molecular transport through large-diameter DNA nanopores. Nat Commun 2016; 7:12787. [PMID: 27658960 PMCID: PMC5036142 DOI: 10.1038/ncomms12787] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 08/02/2016] [Indexed: 01/10/2023] Open
Abstract
DNA-based nanopores are synthetic biomolecular membrane pores, whose geometry and chemical functionality can be tuned using the tools of DNA nanotechnology, making them promising molecular devices for applications in single-molecule biosensing and synthetic biology. Here we introduce a large DNA membrane channel with an ≈4 nm diameter pore, which has stable electrical properties and spontaneously inserts into flat lipid bilayer membranes. Membrane incorporation is facilitated by a large number of hydrophobic functionalizations or, alternatively, streptavidin linkages between biotinylated channels and lipids. The channel displays an Ohmic conductance of ≈3 nS, consistent with its size, and allows electrically driven translocation of single-stranded and double-stranded DNA analytes. Using confocal microscopy and a dye influx assay, we demonstrate the spontaneous formation of membrane pores in giant unilamellar vesicles. Pores can be created both in an outside-in and an inside-out configuration. Artificial DNA membrane channels are promising molecular devices for biotechnology but suffer from low affinity for lipid bilayers. Here, the authors report a large DNA nanopore that spontaneously inserts into a flat lipid membrane, driven by engineered hydrophobic or streptavidin-biotin interactions.
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Affiliation(s)
- Swati Krishnan
- Physik-Department E14, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany.,Zentrum für Nanotechnologie und Nanomaterialien/WSI, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
| | - Daniela Ziegler
- Physik-Department E14, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany.,Zentrum für Nanotechnologie und Nanomaterialien/WSI, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
| | - Vera Arnaut
- Physik-Department E14, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany.,Zentrum für Nanotechnologie und Nanomaterialien/WSI, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
| | - Thomas G Martin
- Zentrum für Nanotechnologie und Nanomaterialien/WSI, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany.,Physik-Department E69, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
| | - Korbinian Kapsner
- Physik-Department E14, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany.,Zentrum für Nanotechnologie und Nanomaterialien/WSI, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
| | - Katharina Henneberg
- Physik-Department E27, Technische Universität München, James-Franck-Straße 1, 85748 Garching, Germany
| | - Andreas R Bausch
- Physik-Department E27, Technische Universität München, James-Franck-Straße 1, 85748 Garching, Germany
| | - Hendrik Dietz
- Zentrum für Nanotechnologie und Nanomaterialien/WSI, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany.,Physik-Department E69, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
| | - Friedrich C Simmel
- Physik-Department E14, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany.,Zentrum für Nanotechnologie und Nanomaterialien/WSI, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
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43
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Ayub M, Bayley H. Engineered transmembrane pores. Curr Opin Chem Biol 2016; 34:117-126. [PMID: 27658267 DOI: 10.1016/j.cbpa.2016.08.005] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 08/09/2016] [Accepted: 08/10/2016] [Indexed: 12/15/2022]
Abstract
Today, hundreds of researchers are working on nanopores, making an impact in both basic science and biotechnology. Proteins remain the most versatile sources of nanopores, based on our ability to engineer them with sub-nanometer precision. Recent work aimed at the construction and discovery of novel pores has included unnatural amino acid mutagenesis and the application of selection techniques. The diversity of structures has now been increased through the development of helix-based pores as well as the better-known β barrels. New developments also include truncated pores, which pierce bilayers through lipid rearrangement, and hybrid pores, which do away with bilayers altogether. Pore dimers, which span two lipid bilayers, have been constructed and pores based on DNA nanostructures are gaining in importance. While nanopore DNA sequencing has received enthusiastic attention, protein pores have a wider range of potential applications, requiring specifications that will require engineering efforts to continue for years to come.
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Affiliation(s)
- Mariam Ayub
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom.
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44
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Linko V, Eerikäinen M, Kostiainen MA. A modular DNA origami-based enzyme cascade nanoreactor. Chem Commun (Camb) 2016; 51:5351-4. [PMID: 25594847 DOI: 10.1039/c4cc08472a] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In this communication, we present a nanoscale reactor assembled from tuneable and spatially addressable tubular DNA origami units. We can controllably combine separate origami units equipped with glucose oxidase (GOx) and horseradish peroxidase (HRP), and demonstrate efficient GOx/HRP enzyme cascade reaction inside the tube. The reactor could be utilized as a nanoscale diagnostic tool, and modularity of the proposed system would further enable more complex reactions.
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Affiliation(s)
- Veikko Linko
- Biohybrid Materials, Department of Biotechnology and Chemical Technology, Aalto University, FI-00076 Aalto, Finland.
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45
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Affiliation(s)
- Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
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46
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Heerema SJ, Dekker C. Graphene nanodevices for DNA sequencing. NATURE NANOTECHNOLOGY 2016; 11:127-36. [PMID: 26839258 DOI: 10.1038/nnano.2015.307] [Citation(s) in RCA: 292] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 11/23/2015] [Indexed: 05/24/2023]
Abstract
Fast, cheap, and reliable DNA sequencing could be one of the most disruptive innovations of this decade, as it will pave the way for personalized medicine. In pursuit of such technology, a variety of nanotechnology-based approaches have been explored and established, including sequencing with nanopores. Owing to its unique structure and properties, graphene provides interesting opportunities for the development of a new sequencing technology. In recent years, a wide range of creative ideas for graphene sequencers have been theoretically proposed and the first experimental demonstrations have begun to appear. Here, we review the different approaches to using graphene nanodevices for DNA sequencing, which involve DNA passing through graphene nanopores, nanogaps, and nanoribbons, and the physisorption of DNA on graphene nanostructures. We discuss the advantages and problems of each of these key techniques, and provide a perspective on the use of graphene in future DNA sequencing technology.
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Affiliation(s)
- Stephanie J Heerema
- Kavli Institute of Nanoscience Delft, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Cees Dekker
- Kavli Institute of Nanoscience Delft, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
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Wang L, Sun Y, Li Z, Wu A, Wei G. Bottom-Up Synthesis and Sensor Applications of Biomimetic Nanostructures. MATERIALS (BASEL, SWITZERLAND) 2016; 9:E53. [PMID: 28787853 PMCID: PMC5456561 DOI: 10.3390/ma9010053] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 01/05/2016] [Accepted: 01/07/2016] [Indexed: 12/21/2022]
Abstract
The combination of nanotechnology, biology, and bioengineering greatly improved the developments of nanomaterials with unique functions and properties. Biomolecules as the nanoscale building blocks play very important roles for the final formation of functional nanostructures. Many kinds of novel nanostructures have been created by using the bioinspired self-assembly and subsequent binding with various nanoparticles. In this review, we summarized the studies on the fabrications and sensor applications of biomimetic nanostructures. The strategies for creating different bottom-up nanostructures by using biomolecules like DNA, protein, peptide, and virus, as well as microorganisms like bacteria and plant leaf are introduced. In addition, the potential applications of the synthesized biomimetic nanostructures for colorimetry, fluorescence, surface plasmon resonance, surface-enhanced Raman scattering, electrical resistance, electrochemistry, and quartz crystal microbalance sensors are presented. This review will promote the understanding of relationships between biomolecules/microorganisms and functional nanomaterials in one way, and in another way it will guide the design and synthesis of biomimetic nanomaterials with unique properties in the future.
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Affiliation(s)
- Li Wang
- College of Chemistry, Jilin Normal University, Haifeng Street 1301, Siping 136000, China.
| | - Yujing Sun
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Renmin Street 5625, Changchun 130022, China.
| | - Zhuang Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Renmin Street 5625, Changchun 130022, China.
| | - Aiguo Wu
- Key Laboratory of Magnetic Materials and Devices & Division of Functional Materials and Nanodevices, Ningbo Institute of Material Technology and Engineering, Chinese Academy Sciences, Ningbo 315201, China.
| | - Gang Wei
- Faculty of Production Engineering, University of Bremen, Am Fallturm 1, D-28359 Bremen, Germany.
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Linko V, Shen B, Tapio K, Toppari JJ, Kostiainen MA, Tuukkanen S. One-step large-scale deposition of salt-free DNA origami nanostructures. Sci Rep 2015; 5:15634. [PMID: 26492833 PMCID: PMC4616047 DOI: 10.1038/srep15634] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 09/28/2015] [Indexed: 01/13/2023] Open
Abstract
DNA origami nanostructures have tremendous potential to serve as versatile platforms in self-assembly -based nanofabrication and in highly parallel nanoscale patterning. However, uniform deposition and reliable anchoring of DNA nanostructures often requires specific conditions, such as pre-treatment of the chosen substrate or a fine-tuned salt concentration for the deposition buffer. In addition, currently available deposition techniques are suitable merely for small scales. In this article, we exploit a spray-coating technique in order to resolve the aforementioned issues in the deposition of different 2D and 3D DNA origami nanostructures. We show that purified DNA origamis can be controllably deposited on silicon and glass substrates by the proposed method. The results are verified using either atomic force microscopy or fluorescence microscopy depending on the shape of the DNA origami. DNA origamis are successfully deposited onto untreated substrates with surface coverage of about 4 objects/mm(2). Further, the DNA nanostructures maintain their shape even if the salt residues are removed from the DNA origami fabrication buffer after the folding procedure. We believe that the presented one-step spray-coating method will find use in various fields of material sciences, especially in the development of DNA biochips and in the fabrication of metamaterials and plasmonic devices through DNA metallisation.
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Affiliation(s)
- Veikko Linko
- Aalto University, Department of Biotechnology and Chemical Technology, Biohybrid Materials, Espoo, P.O. Box 16100, FI-00076 Aalto, Finland
| | - Boxuan Shen
- University of Jyvaskyla, Department of Physics, Nanoscience Center, Jyväskylä, P.O. Box 35, FI-40014 University of Jyväskylä, Finland
| | - Kosti Tapio
- University of Jyvaskyla, Department of Physics, Nanoscience Center, Jyväskylä, P.O. Box 35, FI-40014 University of Jyväskylä, Finland
| | - J. Jussi Toppari
- University of Jyvaskyla, Department of Physics, Nanoscience Center, Jyväskylä, P.O. Box 35, FI-40014 University of Jyväskylä, Finland
| | - Mauri A. Kostiainen
- Aalto University, Department of Biotechnology and Chemical Technology, Biohybrid Materials, Espoo, P.O. Box 16100, FI-00076 Aalto, Finland
| | - Sampo Tuukkanen
- Tampere University of Technology, Department of Automation Science and Engineering, Tampere, P.O. Box 692, FI-33101, Finland
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Mallik L, Dhakal S, Nichols J, Mahoney J, Dosey AM, Jiang S, Sunahara RK, Skiniotis G, Walter NG. Electron Microscopic Visualization of Protein Assemblies on Flattened DNA Origami. ACS NANO 2015; 9:7133-41. [PMID: 26149412 PMCID: PMC5835357 DOI: 10.1021/acsnano.5b01841] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
DNA provides an ideal substrate for the engineering of versatile nanostructures due to its reliable Watson-Crick base pairing and well-characterized conformation. One of the most promising applications of DNA nanostructures arises from the site-directed spatial arrangement with nanometer precision of guest components such as proteins, metal nanoparticles, and small molecules. Two-dimensional DNA origami architectures, in particular, offer a simple design, high yield of assembly, and large surface area for use as a nanoplatform. However, such single-layer DNA origami were recently found to be structurally polymorphous due to their high flexibility, leading to the development of conformationally restrained multilayered origami that lack some of the advantages of the single-layer designs. Here we monitored single-layer DNA origami by transmission electron microscopy (EM) and discovered that their conformational heterogeneity is dramatically reduced in the presence of a low concentration of dimethyl sulfoxide, allowing for an efficient flattening onto the carbon support of an EM grid. We further demonstrated that streptavidin and a biotinylated target protein (cocaine esterase, CocE) can be captured at predesignated sites on these flattened origami while maintaining their functional integrity. Our demonstration that protein assemblies can be constructed with high spatial precision (within ∼2 nm of their predicted position on the platforms) by using strategically flattened single-layer origami paves the way for exploiting well-defined guest molecule assemblies for biochemistry and nanotechnology applications.
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Affiliation(s)
- Leena Mallik
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Soma Dhakal
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Joseph Nichols
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jacob Mahoney
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Anne M. Dosey
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Shuoxing Jiang
- The Biodesign Institute and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Roger K. Sunahara
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Georgios Skiniotis
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Nils G. Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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Shen B, Linko V, Tapio K, Kostiainen MA, Toppari JJ. Custom-shaped metal nanostructures based on DNA origami silhouettes. NANOSCALE 2015; 7:11267-72. [PMID: 26066528 DOI: 10.1039/c5nr02300a] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The DNA origami technique provides an intriguing possibility to develop customized nanostructures for various bionanotechnological purposes. One target is to create tailored bottom-up-based plasmonic devices and metamaterials based on DNA metallization or controlled attachment of nanoparticles to the DNA designs. In this article, we demonstrate an alternative approach: DNA origami nanoshapes can be utilized in creating accurate, uniform and entirely metallic (e.g. gold, silver and copper) nanostructures on silicon substrates. The technique is based on developing silhouettes of the origamis in the grown silicon dioxide layer, and subsequently using this layer as a mask for further patterning. The proposed method has a high spatial resolution, and the fabrication yields can approach 90%. The approach allows a cost-effective, parallel, large-scale patterning on a chip with fully tailored metallic nanostructures; the DNA origami shape and the applied metal can be specifically chosen for each conceivable implementation.
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Affiliation(s)
- Boxuan Shen
- University of Jyvaskyla, Department of Physics, Nanoscience Center, P.O. Box 35, FI-40014. and University of Jyväskylä, Finland.
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