1
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Sytu MRC, Cho DH, Hahm JI. Self-Assembled Block Copolymers as a Facile Pathway to Create Functional Nanobiosensor and Nanobiomaterial Surfaces. Polymers (Basel) 2024; 16:1267. [PMID: 38732737 PMCID: PMC11085100 DOI: 10.3390/polym16091267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
Block copolymer (BCP) surfaces permit an exquisite level of nanoscale control in biomolecular assemblies solely based on self-assembly. Owing to this, BCP-based biomolecular assembly represents a much-needed, new paradigm for creating nanobiosensors and nanobiomaterials without the need for costly and time-consuming fabrication steps. Research endeavors in the BCP nanobiotechnology field have led to stimulating results that can promote our current understanding of biomolecular interactions at a solid interface to the never-explored size regimes comparable to individual biomolecules. Encouraging research outcomes have also been reported for the stability and activity of biomolecules bound on BCP thin film surfaces. A wide range of single and multicomponent biomolecules and BCP systems has been assessed to substantiate the potential utility in practical applications as next-generation nanobiosensors, nanobiodevices, and biomaterials. To this end, this Review highlights pioneering research efforts made in the BCP nanobiotechnology area. The discussions will be focused on those works particularly pertaining to nanoscale surface assembly of functional biomolecules, biomolecular interaction properties unique to nanoscale polymer interfaces, functionality of nanoscale surface-bound biomolecules, and specific examples in biosensing. Systems involving the incorporation of biomolecules as one of the blocks in BCPs, i.e., DNA-BCP hybrids, protein-BCP conjugates, and isolated BCP micelles of bioligand carriers used in drug delivery, are outside of the scope of this Review. Looking ahead, there awaits plenty of exciting research opportunities to advance the research field of BCP nanobiotechnology by capitalizing on the fundamental groundwork laid so far for the biomolecular interactions on BCP surfaces. In order to better guide the path forward, key fundamental questions yet to be addressed by the field are identified. In addition, future research directions of BCP nanobiotechnology are contemplated in the concluding section of this Review.
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Affiliation(s)
- Marion Ryan C. Sytu
- Department of Chemistry, Georgetown University, 37th & O Sts. NW., Washington, DC 20057, USA
| | - David H. Cho
- National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA;
| | - Jong-in Hahm
- Department of Chemistry, Georgetown University, 37th & O Sts. NW., Washington, DC 20057, USA
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2
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Ranasinghe DR, Doerk G, Aryal BR, Pang C, Davis RC, Harb JN, Woolley AT. Block copolymer self-assembly to pattern gold nanodots for site-specific placement of DNA origami and attachment of nanomaterials. NANOSCALE 2023; 15:2188-2196. [PMID: 36633155 DOI: 10.1039/d2nr05045e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Directed placement of DNA origami could play a key role in future integrated nanoelectronic devices. Here we demonstrated the site-selective attachment of DNA origami on gold dots formed using a pattern transfer method through block copolymer self-assembly. First, a random copolymer brush layer is grafted on the Si surface and then poly (styrene-b-methylmethacrylate) block copolymer is spin-coated to give a hexagonal nanoarray after annealing. UV irradiation followed by acetic acid etching is used to remove the PMMA, creating cylindrical holes and then oxygen plasma etching removes the random copolymer layer inside those holes. Next, metal evaporation, followed by lift-off creates a gold dot array. We evaluated different ligand functionalization of Au dots, as well as DNA hybridization to attach DNA origami to the nanodots. DNA-coated Au nanorods are assembled on the DNA origami as a step towards creating nanowires and to facilitate electron microscopy characterization of the attachment of DNA origami on these Au nanodots. The DNA hybridization approach showed better DNA attachment to Au nanodots than localization by electrostatic interaction. This work contributes to the understanding of DNA-templated assembly, nanomaterials, and block copolymer nanolithography. Furthermore, the work shows potential for creating DNA-templated nanodevices and their placement in ordered arrays in future nanoelectronics.
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Affiliation(s)
| | - Gregory Doerk
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, USA
| | - Basu R Aryal
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA.
| | - Chao Pang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA.
| | - Robert C Davis
- Department of Physics and Astronomy, Brigham Young University, Provo, UT, USA
| | - John N Harb
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Adam T Woolley
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA.
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3
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Marrs J, Lu Q, Pan V, Ke Y, Hihath J. Structure-Dependent Electrical Conductance of DNA Origami Nanowires. Chembiochem 2023; 24:e202200454. [PMID: 36342926 DOI: 10.1002/cbic.202200454] [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: 08/08/2022] [Revised: 10/27/2022] [Indexed: 11/09/2022]
Abstract
Exploring the structural and electrical properties of DNA origami nanowires is an important endeavor for the advancement of DNA nanotechnology and DNA nanoelectronics. Highly conductive DNA origami nanowires are a desirable target for creating low-cost self-assembled nanoelectronic devices and circuits. In this work, the structure-dependent electrical conductance of DNA origami nanowires is investigated. A silicon nitride (Si3 N4 ) on silicon semiconductor chip with gold electrodes was used for collecting electrical conductance measurements of DNA origami nanowires, which are found to be an order of magnitude less electrically resistive on Si3 N4 substrates treated with a monolayer of hexamethyldisilazane (HMDS) (∼1013 ohms) than on native Si3 N4 substrates without HMDS (∼1014 ohms). Atomic force microscopy (AFM) measurements of the height of DNA origami nanowires on mica and Si3 N4 substrates reveal that DNA origami nanowires are ∼1.6 nm taller on HMDS-treated substrates than on the untreated ones indicating that the DNA origami nanowires undergo increased structural deformation when deposited onto untreated substrates, causing a decrease in electrical conductivity. This study highlights the importance of understanding and controlling the interface conditions that affect the structure of DNA and thereby affect the electrical conductance of DNA origami nanowires.
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Affiliation(s)
- Jonathan Marrs
- Department of Electrical and Computer Engineering, University of California, Davis, Davis, California, 95616, USA
| | - Qinyi Lu
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, 30322, USA
| | - Victor Pan
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, 30322, USA
| | - Yonggang Ke
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, 30322, USA
| | - Joshua Hihath
- Department of Electrical and Computer Engineering, University of California, Davis, Davis, California, 95616, USA.,Biodesign Center for Bioelectronics, School of Electrical, Computer, and Energy Engineering, Arizona State University, Tempe, AZ 85287, USA
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4
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Rahman MM, Tolbert CL, Saha P, Halpern JM, Hill CM. On-Demand Electrochemical Fabrication of Ordered Nanoparticle Arrays using Scanning Electrochemical Cell Microscopy. ACS NANO 2022; 16:21275-21282. [PMID: 36399100 DOI: 10.1021/acsnano.2c09336] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Well-ordered nanoparticle arrays are attractive platforms for a variety of analytical applications, but the fabrication of such arrays is generally challenging. Here, it is demonstrated that scanning electrochemical cell microscopy (SECCM) can be used as a powerful, instantly reconfigurable tool for the fabrication of ordered nanoparticle arrays. Using SECCM, Ag nanoparticle arrays were straightforwardly fabricated via electrodeposition at the interface between a substrate electrode and an electrolyte-filled pipet. By dynamically monitoring the currents flowing in an SECCM cell, individual nucleation and growth events could be detected and controlled to yield individual nanoparticles of controlled size. Characterization of the resulting arrays demonstrate that this SECCM-based approach enables spatial control of nanoparticle location comparable with the terminal diameter of the pipet employed and straightforward control over the volume of material deposited at each site within an array. These results provide further evidence for the utility of probe-based electrochemical techniques such as SECCM as tools for surface modification in addition to analysis.
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Affiliation(s)
- Md Maksudur Rahman
- Department of Chemistry, University of Wyoming, 1000 East University Avenue, Laramie, Wyoming82071, United States
| | - Chloe L Tolbert
- Department of Chemistry, University of Wyoming, 1000 East University Avenue, Laramie, Wyoming82071, United States
| | - Partha Saha
- Department of Chemistry, University of Wyoming, 1000 East University Avenue, Laramie, Wyoming82071, United States
| | - Jeffrey M Halpern
- Department of Chemical Engineering and the Materials Science and Engineering Program, University of New Hampshire, 33 Academic Way, Durham, New Hampshire03824, United States
| | - Caleb M Hill
- Department of Chemistry, University of Wyoming, 1000 East University Avenue, Laramie, Wyoming82071, United States
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5
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Pang C, Aryal BR, Ranasinghe DR, Westover TR, Ehlert AEF, Harb JN, Davis RC, Woolley AT. Bottom-Up Fabrication of DNA-Templated Electronic Nanomaterials and Their Characterization. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:1655. [PMID: 34201888 PMCID: PMC8306176 DOI: 10.3390/nano11071655] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 11/30/2022]
Abstract
Bottom-up fabrication using DNA is a promising approach for the creation of nanoarchitectures. Accordingly, nanomaterials with specific electronic, photonic, or other functions are precisely and programmably positioned on DNA nanostructures from a disordered collection of smaller parts. These self-assembled structures offer significant potential in many domains such as sensing, drug delivery, and electronic device manufacturing. This review describes recent progress in organizing nanoscale morphologies of metals, semiconductors, and carbon nanotubes using DNA templates. We describe common substrates, DNA templates, seeding, plating, nanomaterial placement, and methods for structural and electrical characterization. Finally, our outlook for DNA-enabled bottom-up nanofabrication of materials is presented.
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Affiliation(s)
- Chao Pang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA; (C.P.); (B.R.A.); (D.R.R.); (A.E.F.E.)
| | - Basu R. Aryal
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA; (C.P.); (B.R.A.); (D.R.R.); (A.E.F.E.)
| | - Dulashani R. Ranasinghe
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA; (C.P.); (B.R.A.); (D.R.R.); (A.E.F.E.)
| | - Tyler R. Westover
- Department of Physics and Astronomy, Brigham Young University, Provo, UT 84602, USA; (T.R.W.); (R.C.D.)
| | - Asami E. F. Ehlert
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA; (C.P.); (B.R.A.); (D.R.R.); (A.E.F.E.)
| | - John N. Harb
- Department of Chemical Engineering, Brigham Young University, Provo, UT 84602, USA;
| | - Robert C. Davis
- Department of Physics and Astronomy, Brigham Young University, Provo, UT 84602, USA; (T.R.W.); (R.C.D.)
| | - Adam T. Woolley
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA; (C.P.); (B.R.A.); (D.R.R.); (A.E.F.E.)
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6
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Xin Y, Shen B, Kostiainen MA, Grundmeier G, Castro M, Linko V, Keller A. Scaling Up DNA Origami Lattice Assembly. Chemistry 2021; 27:8564-8571. [PMID: 33780583 PMCID: PMC8252642 DOI: 10.1002/chem.202100784] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Indexed: 12/31/2022]
Abstract
The surface-assisted hierarchical assembly of DNA origami nanostructures is a promising route to fabricate regular nanoscale lattices. In this work, the scalability of this approach is explored and the formation of a homogeneous polycrystalline DNA origami lattice at the mica-electrolyte interface over a total surface area of 18.75 cm2 is demonstrated. The topological analysis of more than 50 individual AFM images recorded at random locations over the sample surface showed only minuscule and random variations in the quality and order of the assembled lattice. The analysis of more than 450 fluorescence microscopy images of a quantum dot-decorated DNA origami lattice further revealed a very homogeneous surface coverage over cm2 areas with only minor boundary effects at the substrate edges. At total DNA costs of € 0.12 per cm2 , this large-scale nanopatterning technique holds great promise for the fabrication of functional surfaces.
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Affiliation(s)
- Yang Xin
- Technical and Macromolecular ChemistryPaderborn UniversityWarburger Str. 10033098PaderbornGermany
| | - Boxuan Shen
- Biohybrid MaterialsDepartment of Bioproducts and BiosystemsAalto UniversityP. O. Box 1610000076AaltoFinland
| | - Mauri A. Kostiainen
- Biohybrid MaterialsDepartment of Bioproducts and BiosystemsAalto UniversityP. O. Box 1610000076AaltoFinland
| | - Guido Grundmeier
- Technical and Macromolecular ChemistryPaderborn UniversityWarburger Str. 10033098PaderbornGermany
| | - Mario Castro
- Grupo Interdisciplinar de Sistemas Complejos and Instituto de Investigación TecnológicaUniversidad Pontificia Comillas de MadridMadrid28015Spain
| | - Veikko Linko
- Biohybrid MaterialsDepartment of Bioproducts and BiosystemsAalto UniversityP. O. Box 1610000076AaltoFinland
| | - Adrian Keller
- Technical and Macromolecular ChemistryPaderborn UniversityWarburger Str. 10033098PaderbornGermany
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7
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Gopinath A, Thachuk C, Mitskovets A, Atwater HA, Kirkpatrick D, Rothemund PWK. Absolute and arbitrary orientation of single-molecule shapes. Science 2021; 371:371/6531/eabd6179. [DOI: 10.1126/science.abd6179] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/14/2020] [Indexed: 11/02/2022]
Abstract
DNA origami is a modular platform for the combination of molecular and
colloidal components to create optical, electronic, and biological devices.
Integration of such nanoscale devices with microfabricated connectors and circuits
is challenging: Large numbers of freely diffusing devices must be fixed at desired
locations with desired alignment. We present a DNA origami molecule whose energy
landscape on lithographic binding sites has a unique maximum. This property
enabled device alignment within 3.2° on silica surfaces. Orientation was absolute
(all degrees of freedom were specified) and arbitrary (the orientation of every
molecule was independently specified). The use of orientation to optimize device
performance was shown by aligning fluorescent emission dipoles within
microfabricated optical cavities. Large-scale integration was demonstrated with an
array of 3456 DNA origami with 12 distinct orientations that indicated the
polarization of excitation light.
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Affiliation(s)
- Ashwin Gopinath
- Department of Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Chris Thachuk
- Department of Computing and Mathematical Science, California Institute of Technology, Pasadena, CA 91125, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA
| | - Anya Mitskovets
- Department of Applied Physics and Materials Science, California Institute of Technology, Pasadena, CA 91125, USA
| | - Harry A. Atwater
- Department of Applied Physics and Materials Science, California Institute of Technology, Pasadena, CA 91125, USA
| | - David Kirkpatrick
- Department of Computer Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Paul W. K. Rothemund
- Department of Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
- Department of Computing and Mathematical Science, California Institute of Technology, Pasadena, CA 91125, USA
- Computation and Neural Systems, California Institute of Technology, Pasadena, CA 91125, USA
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8
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Zhang H, Kinnear C, Mulvaney P. Fabrication of Single-Nanocrystal Arrays. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1904551. [PMID: 31576618 DOI: 10.1002/adma.201904551] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/10/2019] [Indexed: 05/17/2023]
Abstract
To realize the full potential of nanocrystals in nanotechnology, it is necessary to integrate single nanocrystals into addressable structures; for example, arrays and periodic lattices. The current methods for achieving this are reviewed. It is shown that a combination of top-down lithography techniques with directed assembly offers a platform for attaining this goal. The most promising of these directed assembly methods are reviewed: capillary force assembly, electrostatic assembly, optical printing, DNA-based assembly, and electrophoretic deposition. The last of these appears to offer a generic approach to fabrication of single-nanocrystal arrays.
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Affiliation(s)
- Heyou Zhang
- ARC Centre of Excellence in Exciton Science, School of Chemistry, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Calum Kinnear
- CSIRO Manufacturing, Ian Wark Laboratories, Bayview Avenue, Clayton, VIC, 3168, Australia
| | - Paul Mulvaney
- ARC Centre of Excellence in Exciton Science, School of Chemistry, University of Melbourne, Parkville, VIC, 3010, Australia
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9
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Hu H, Wang S, Feng X, Pauly M, Decher G, Long Y. In-plane aligned assemblies of 1D-nanoobjects: recent approaches and applications. Chem Soc Rev 2020; 49:509-553. [DOI: 10.1039/c9cs00382g] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
One-dimensional (1D) nanoobjects have strongly anisotropic physical properties which are averaged out and cannot be exploited in disordered systems. We reviewed the in plane alignment approaches and potential applications with perspectives shared.
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Affiliation(s)
- Hebing Hu
- School of Materials Science and Engineering
- Nanyang Technological University
- Singapore
- Singapore-HUJ Alliance for Research and Enterprise (SHARE)
- Nanomaterials for Energy and Energy-Water Nexus (NEW)
| | - Shancheng Wang
- School of Materials Science and Engineering
- Nanyang Technological University
- Singapore
- Singapore-HUJ Alliance for Research and Enterprise (SHARE)
- Nanomaterials for Energy and Energy-Water Nexus (NEW)
| | - Xueling Feng
- Key Laboratory of Science and Technology of Eco-Textile
- Ministry of Education
- College of Chemistry
- Chemical Engineering and Biotechnology
- Donghua University
| | - Matthias Pauly
- Université de Strasbourg
- CNRS
- Institut Charles Sadron
- F-67000 Strasbourg
- France
| | - Gero Decher
- Université de Strasbourg
- CNRS
- Institut Charles Sadron
- F-67000 Strasbourg
- France
| | - Yi Long
- School of Materials Science and Engineering
- Nanyang Technological University
- Singapore
- Singapore-HUJ Alliance for Research and Enterprise (SHARE)
- Nanomaterials for Energy and Energy-Water Nexus (NEW)
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10
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Nanoengineering of Gold Nanoparticles: Green Synthesis, Characterization, and Applications. CRYSTALS 2019. [DOI: 10.3390/cryst9120612] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The fundamental aspects of the manufacturing of gold nanoparticles (AuNPs) are discussed in this review. In particular, attention is devoted to the development of a simple and versatile method for the preparation of these nanoparticles. Eco-friendly synthetic routes, such as wet chemistry and biosynthesis with the aid of polymers, are of particular interest. Polymers can act as reducing and/or capping agents, or as soft templates leading to hybrid nanomaterials. This methodology allows control of the synthesis and stability of nanomaterials with novel properties. Thus, this review focus on a fundamental study of AuNPs properties and different techniques to characterize them, e.g., Transmission Electron Microscopy (TEM), Atomic Force Microscopy (AFM), UV-Visible spectroscopy, Dynamic Light Scattering (DLS), X-Ray Diffraction (XRD), X-Ray Photoelectron Spectroscopy, Small-angle X-Ray Scattering (SAXS), and rheology. Recently, AuNPs obtained by “green” synthesis have been applied in catalysis, in medicine, and as antibacterials, sensors, among others.
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11
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Kielar C, Ramakrishnan S, Fricke S, Grundmeier G, Keller A. Dynamics of DNA Origami Lattice Formation at Solid-Liquid Interfaces. ACS APPLIED MATERIALS & INTERFACES 2018; 10:44844-44853. [PMID: 30501167 DOI: 10.1021/acsami.8b16047] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The self-organized formation of regular patterns is not only a fascinating topic encountered in a multitude of natural and artificial systems, but also presents a versatile and powerful route toward large-scale nanostructure assembly and materials synthesis. The hierarchical, interface-assisted assembly of DNA origami nanostructures into regular, 2D lattices represents a particularly promising example, as the resulting lattices may exhibit an astonishing degree of order and can be further utilized as masks in molecular lithography. Here, we thus investigate the development of order in such 2D DNA origami lattices assembled on mica surfaces by employing in situ high-speed atomic force microscopy imaging. DNA origami lattice formation is found to resemble thin-film growth in several aspects. In particular, the Na+/Mg2+ ratio controls DNA origami adsorption, surface diffusion, and desorption, and is thus equivalent in its effects to substrate temperature which controls adatom dynamics in thin-film deposition. Consequently, we observe a pronounced dependence of lattice order on Na+ concentration. At low Na+ concentrations, lattice formation resembles random deposition and results in unordered monolayers, whereas very high Na+ concentrations are accompanied by rapid diffusion and especially DNA origami desorption, which prevent lattice formation. At intermediate Na+ concentrations, highly ordered DNA origami lattices are obtained that display an intricate symmetry, stemming from the complex shape of the employed Rothemund triangle. Nevertheless, even under such optimized conditions, the lattices display a considerable number of defects, including grain boundaries, point and line defects, and screw-like dislocations. By monitoring the dynamics of selected lattice defects, we identify mechanisms that limit the obtainable degree of lattice order. Possible routes toward further increasing lattice order by postassembly annealing are discussed.
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Affiliation(s)
- Charlotte Kielar
- Technical and Macromolecular Chemistry , Paderborn University , Warburger Str. 100 , 33098 Paderborn , Germany
| | - Saminathan Ramakrishnan
- Technical and Macromolecular Chemistry , Paderborn University , Warburger Str. 100 , 33098 Paderborn , Germany
| | - Sebastian Fricke
- Technical and Macromolecular Chemistry , Paderborn University , Warburger Str. 100 , 33098 Paderborn , Germany
| | - Guido Grundmeier
- Technical and Macromolecular Chemistry , Paderborn University , Warburger Str. 100 , 33098 Paderborn , Germany
| | - Adrian Keller
- Technical and Macromolecular Chemistry , Paderborn University , Warburger Str. 100 , 33098 Paderborn , Germany
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12
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Brassat K, Ramakrishnan S, Bürger J, Hanke M, Doostdar M, Lindner JKN, Grundmeier G, Keller A. On the Adsorption of DNA Origami Nanostructures in Nanohole Arrays. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14757-14765. [PMID: 29754490 DOI: 10.1021/acs.langmuir.8b00793] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
DNA origami nanostructures are versatile substrates for the controlled arrangement of molecular capture sites with nanometer precision and thus have many promising applications in single-molecule bioanalysis. Here, we investigate the adsorption of DNA origami nanostructures in nanohole arrays which represent an important class of biosensors and may benefit from the incorporation of DNA origami-based molecular probes. Nanoholes with well-defined diameter that enable the adsorption of single DNA origami triangles are fabricated in Au films on Si wafers by nanosphere lithography. The efficiency of directed DNA origami adsorption on the exposed SiO2 areas at the bottoms of the nanoholes is evaluated in dependence of various parameters, i.e., Mg2+ and DNA origami concentrations, buffer strength, adsorption time, and nanohole diameter. We observe that the buffer strength has a surprisingly strong effect on DNA origami adsorption in the nanoholes and that multiple DNA origami triangles with 120 nm edge length can adsorb in nanoholes as small as 120 nm in diameter. We attribute the latter observation to the low lateral mobility of once adsorbed DNA origami on the SiO2 surface, in combination with parasitic adsorption to the Au film. Although parasitic adsorption can be suppressed by modifying the Au film with a hydrophobic self-assembled monolayer, the limited surface mobility of the adsorbed DNA origami still leads to poor localization accuracy in the nanoholes and results in many DNA origami crossing the boundary to the Au film even under optimized conditions. We discuss possible ways to minimize this effect by varying the composition of the adsorption buffer, employing different fabrication conditions, or using other substrate materials for nanohole array fabrication.
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13
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Marcovici A, Le Saux G, Bhingardive V, Rukenstein P, Flomin K, Shreteh K, Golan R, Mokari T, Schvartzman M. Directed Assembly of Au-Tipped 1D Inorganic Nanostructures via Nanolithographic Docking. ACS NANO 2018; 12:10016-10023. [PMID: 30252443 DOI: 10.1021/acsnano.8b04443] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Controlled assembly of nanostructures is a key challenge in nanotechnology. In this work, we introduce an approach for the controlled assembly of 1D nanodumbbells-Au-tipped semiconductor nanorods-into arbitrary 2D higher architectures, by their chemical docking to nanopatterned functionalities. We realized the docking functionalities via nanoimprinted metallic nanodots functionalized with an organic monolayer, whose terminal thiol groups chemically bind the nanodumbbell tips. We demonstrated that the functional nanopattern encodes the nanodumbbell assembly and can be designed to deterministically position nanodumbbells in two possible modes. In the single-docking mode, the nanodot arrays are designed with a spacing that exceeds the nanodumbbell length, restricting each nanodumbbell to dock with one edge and physically connect with its free edge to one of the neighboring nanodumbbells. Alternatively, in the double-docking mode, the nanodots are spaced to exactly fit the nanodumbbell length, allowing nanodumbbell docking with both edges. We found that the docking kinetics can be described by a random attachment model, and verified that for the used docking chemistry, nanodumbbells that are docked to the same dot do not interact with each other. Our work demonstrates the possibility for massively parallel positioning of sub-100 nm 1D semiconductor nanostructures, and can potentially enable their future integration into functional nanodevices and nanosystems.
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14
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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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15
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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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16
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Cai H, Wolfenson H, Depoil D, Dustin ML, Sheetz MP, Wind SJ. Molecular Occupancy of Nanodot Arrays. ACS NANO 2016; 10:4173-83. [PMID: 26966946 PMCID: PMC5337305 DOI: 10.1021/acsnano.5b07425] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Single-molecule nanodot arrays, in which a biomolecule of choice (protein, nucleic acid, etc.) is bound to a metallic nanoparticle on a solid substrate, are becoming an increasingly important tool in the study of biomolecular and cellular interactions. We have developed an on-chip measurement protocol to monitor and control the molecular occupancy of nanodots. Arrays of widely spaced nanodots and nanodot clusters were fabricated on glass surfaces by nanolithography and functionalized with fluorescently labeled proteins. The molecular occupancy was determined by monitoring individual fluorophore bleaching events, while accounting for fluorescence quenching effects. We found that the occupancy can be interpreted as a packing problem, and depends on nanodot size and binding ligand concentration, where the latter is easily adjusted to compensate the flexibility of dimension control in nanofabrication. The results are scalable with nanodot cluster size, extending to large area close packed arrays. As an example, the nanoarray platform was used to probe the geometric requirement of T-cell activation at the single-molecule level.
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Affiliation(s)
- Haogang Cai
- Department of Mechanical Engineering, Columbia University, New York, New York 10027, United States
| | - Haguy Wolfenson
- Department of Biological Sciences, Columbia University, New York, New York 10027, United States
| | - David Depoil
- The Kennedy Institute of Rheumatology, University of Oxford, Oxford, OX3 7FY, United Kingdom
| | - Michael L. Dustin
- The Kennedy Institute of Rheumatology, University of Oxford, Oxford, OX3 7FY, United Kingdom
| | - Michael P. Sheetz
- Department of Biological Sciences, Columbia University, New York, New York 10027, United States
| | - Shalom J. Wind
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, United States
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17
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Angelin A, Weigel S, Garrecht R, Meyer R, Bauer J, Kumar RK, Hirtz M, Niemeyer CM. Multiscale Origami Structures as Interface for Cells. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201509772] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Alessandro Angelin
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann‐von‐Helmholtz‐Platz, 76344 Eggenstein‐Leopoldshafen (Germany)
| | - Simone Weigel
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann‐von‐Helmholtz‐Platz, 76344 Eggenstein‐Leopoldshafen (Germany)
| | - Ruben Garrecht
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann‐von‐Helmholtz‐Platz, 76344 Eggenstein‐Leopoldshafen (Germany)
| | - Rebecca Meyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann‐von‐Helmholtz‐Platz, 76344 Eggenstein‐Leopoldshafen (Germany)
| | - Jens Bauer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann‐von‐Helmholtz‐Platz, 76344 Eggenstein‐Leopoldshafen (Germany)
| | - Ravi Kapoor Kumar
- Karlsruhe Institute of Technology (KIT), Institute for Nanotechnology (INT) & Karlsruhe Nano Micro Facility (KNMF), Hermann‐von‐Helmholtz‐Platz, 76344 Eggenstein‐Leopoldshafen (Germany)
| | - Michael Hirtz
- Karlsruhe Institute of Technology (KIT), Institute for Nanotechnology (INT) & Karlsruhe Nano Micro Facility (KNMF), Hermann‐von‐Helmholtz‐Platz, 76344 Eggenstein‐Leopoldshafen (Germany)
| | - Christof M. Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann‐von‐Helmholtz‐Platz, 76344 Eggenstein‐Leopoldshafen (Germany)
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18
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Angelin A, Weigel S, Garrecht R, Meyer R, Bauer J, Kumar RK, Hirtz M, Niemeyer CM. Multiscale Origami Structures as Interface for Cells. Angew Chem Int Ed Engl 2015; 54:15813-7. [DOI: 10.1002/anie.201509772] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 11/12/2015] [Indexed: 01/07/2023]
Affiliation(s)
- Alessandro Angelin
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann‐von‐Helmholtz‐Platz, 76344 Eggenstein‐Leopoldshafen (Germany)
| | - Simone Weigel
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann‐von‐Helmholtz‐Platz, 76344 Eggenstein‐Leopoldshafen (Germany)
| | - Ruben Garrecht
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann‐von‐Helmholtz‐Platz, 76344 Eggenstein‐Leopoldshafen (Germany)
| | - Rebecca Meyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann‐von‐Helmholtz‐Platz, 76344 Eggenstein‐Leopoldshafen (Germany)
| | - Jens Bauer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann‐von‐Helmholtz‐Platz, 76344 Eggenstein‐Leopoldshafen (Germany)
| | - Ravi Kapoor Kumar
- Karlsruhe Institute of Technology (KIT), Institute for Nanotechnology (INT) & Karlsruhe Nano Micro Facility (KNMF), Hermann‐von‐Helmholtz‐Platz, 76344 Eggenstein‐Leopoldshafen (Germany)
| | - Michael Hirtz
- Karlsruhe Institute of Technology (KIT), Institute for Nanotechnology (INT) & Karlsruhe Nano Micro Facility (KNMF), Hermann‐von‐Helmholtz‐Platz, 76344 Eggenstein‐Leopoldshafen (Germany)
| | - Christof M. Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann‐von‐Helmholtz‐Platz, 76344 Eggenstein‐Leopoldshafen (Germany)
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19
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Teschome B, Facsko S, Gothelf KV, Keller A. Alignment of Gold Nanoparticle-Decorated DNA Origami Nanotubes: Substrate Prepatterning versus Molecular Combing. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:12823-12829. [PMID: 26522180 DOI: 10.1021/acs.langmuir.5b02569] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
DNA origami has become an established technique for designing well-defined nanostructures with any desired shape and for the controlled arrangement of functional nanostructures with few nanometer resolution. These unique features make DNA origami nanostructures promising candidates for use as scaffolds in nanoelectronics and nanophotonics device fabrication. Consequently, a number of studies have shown the precise organization of metallic nanoparticles on various DNA origami shapes. In this work, we fabricated large arrays of aligned DNA origami decorated with a high density of gold nanoparticles (AuNPs). To this end, we first demonstrate the high-yield assembly of high-density AuNP arrangements on DNA origami adsorbed to Si surfaces with few unbound background nanoparticles by carefully controlling the concentrations of MgCl2 and AuNPs in the hybridization buffer and the hybridization time. Then, we evaluate two methods, i.e., hybridization to prealigned DNA origami and molecular combing in a receding meniscus, with respect to their potential to yield large arrays of aligned AuNP-decorated DNA origami nanotubes. Because of the comparatively low MgCl2 concentration required for the efficient immobilization of the AuNPs, the prealigned DNA origami become mobile and displaced from their original positions, thereby decreasing the alignment yield. This increased mobility, on the other hand, makes the adsorbed origami susceptible to molecular combing, and a total alignment yield of 86% is obtained in this way.
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Affiliation(s)
- Bezu Teschome
- Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf , 01328 Dresden, Germany
- Technische Universität Dresden, Mommsenstraße 13, 01069 Dresden, Germany
| | - Stefan Facsko
- Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf , 01328 Dresden, Germany
| | - Kurt V Gothelf
- Danish National Research Foundation: Centre for DNA Nanotechnology (CDNA) at Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University , 8000 Aarhus C, Denmark
| | - Adrian Keller
- Technical and Macromolecular Chemistry, University of Paderborn , Warburger Str. 100, 33098 Paderborn, Germany
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20
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Kopielski A, Csaki A, Fritzsche W. Surface Mobility and Ordered Rearrangement of Immobilized DNA Origami. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:12106-12110. [PMID: 26488367 DOI: 10.1021/acs.langmuir.5b03137] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The immobilization of DNA nanostructures on a surface is a key step for the integration of DNA-based material in nanotechnology for electronic or sensorial applications. Thereby the arrangement and distribution at the substrate surface is of growing interest. Top-down approaches such as lithography have been reported, but show certain limitations regarding costs and/or throughput. Here we present a self-assembly effect observed when already immobilized and dried origami preparations were again rehydrated under certain conditions, resulting in a certain ordering of densely packed origami structures. We investigate the influence of different parameters in order to reveal the underlying mechanisms, and find that subsequent droplet formation and interfacial tension during the droplet drying play a role. Further adjustment of these parameters could develop the introduced effect to an additional tool for controlled integration of DNA nanostructures.
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Affiliation(s)
- Andreas Kopielski
- Leibniz Institute of Photonic Technology (IPHT) Jena , 07745 Jena, Germany
| | - Andrea Csaki
- Leibniz Institute of Photonic Technology (IPHT) Jena , 07745 Jena, Germany
| | - Wolfgang Fritzsche
- Leibniz Institute of Photonic Technology (IPHT) Jena , 07745 Jena, Germany
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21
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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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22
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Gopinath A, Rothemund PWK. Optimized assembly and covalent coupling of single-molecule DNA origami nanoarrays. ACS NANO 2014; 8:12030-40. [PMID: 25412345 DOI: 10.1021/nn506014s] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Artificial DNA nanostructures, such as DNA origami, have great potential as templates for the bottom-up fabrication of both biological and nonbiological nanodevices at a resolution unachievable by conventional top-down approaches. However, because origami are synthesized in solution, origami-templated devices cannot easily be studied or integrated into larger on-chip architectures. Electrostatic self-assembly of origami onto lithographically defined binding sites on Si/SiO2 substrates has been achieved, but conditions for optimal assembly have not been characterized, and the method requires high Mg2+ concentrations at which most devices aggregate. We present a quantitative study of parameters affecting origami placement, reproducibly achieving single-origami binding at 94±4% of sites, with 90% of these origami having an orientation within ±10° of their target orientation. Further, we introduce two techniques for converting electrostatic DNA-surface bonds to covalent bonds, allowing origami arrays to be used under a wide variety of Mg2+-free solution conditions.
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Affiliation(s)
- Ashwin Gopinath
- Departments of †Bioengineering, ‡Computer Science, and §Computation & Neural Systems, California Institute of Technology , Pasadena, California 91125, United States
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23
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Trasobares J, Vaurette F, François M, Romijn H, Codron JL, Vuillaume D, Théron D, Clément N. High speed e-beam lithography for gold nanoarray fabrication and use in nanotechnology. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2014; 5:1918-25. [PMID: 25383303 PMCID: PMC4222405 DOI: 10.3762/bjnano.5.202] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 09/30/2014] [Indexed: 05/26/2023]
Abstract
E-beam lithography has been used for reliable and versatile fabrication of sub-15 nm single-crystal gold nanoarrays and led to convincing applications in nanotechnology. However, so far this technique was either too slow for centimeter to wafer-scale writing or fast enough with the so-called dot on the fly (DOTF) technique but not optimized for sub-15 nm dots dimension. This prevents use of this technology for some applications and characterization techniques. Here, we show that the DOTF technique can be used without degradation in dots dimension. In addition, we propose two other techniques. The first one is an advanced conventional technique that goes five times faster than the conventional one. The second one relies on sequences defined before writing which enable versatility in e-beam patterns compared to the DOTF technique with same writing speed. By comparing the four different techniques, we evidence the limiting parameters for the writing speed. Wafer-scale fabrication of such arrays with 50 nm pitch allowed XPS analysis of a ferrocenylalkyl thiol self-assembled monolayer coated gold nanoarray.
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Affiliation(s)
- Jorge Trasobares
- Institut d’Electronique Microélectronique et Nanotechnologie (IEMN) CNRS, Avenue Poincaré, 59652, Villeneuve d’Ascq, France
| | - François Vaurette
- Institut d’Electronique Microélectronique et Nanotechnologie (IEMN) CNRS, Avenue Poincaré, 59652, Villeneuve d’Ascq, France
| | - Marc François
- Institut d’Electronique Microélectronique et Nanotechnologie (IEMN) CNRS, Avenue Poincaré, 59652, Villeneuve d’Ascq, France
| | - Hans Romijn
- Vistec Lithography BV, De Dintel 27a, 5684 PS Best, The Netherlands
| | - Jean-Louis Codron
- Institut d’Electronique Microélectronique et Nanotechnologie (IEMN) CNRS, Avenue Poincaré, 59652, Villeneuve d’Ascq, France
| | - Dominique Vuillaume
- Institut d’Electronique Microélectronique et Nanotechnologie (IEMN) CNRS, Avenue Poincaré, 59652, Villeneuve d’Ascq, France
| | - Didier Théron
- Institut d’Electronique Microélectronique et Nanotechnologie (IEMN) CNRS, Avenue Poincaré, 59652, Villeneuve d’Ascq, France
| | - Nicolas Clément
- Institut d’Electronique Microélectronique et Nanotechnologie (IEMN) CNRS, Avenue Poincaré, 59652, Villeneuve d’Ascq, France
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24
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Gates EP, Dearden AM, Woolley AT. DNA‐templated lithography and nanofabrication for the fabrication of nanoscale electronic circuitry. Crit Rev Anal Chem 2014; 44:354-70. [DOI: 10.1080/10408347.2014.910636] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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25
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Wang X, Berger R, Ramos JI, Wang T, Koynov K, Liu G, Butt HJ, Wu S. Nanopatterns of polymer brushes for understanding protein adsorption on the nanoscale. RSC Adv 2014. [DOI: 10.1039/c4ra07623k] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Nanopatterns of polymer brushes enable us to directly image protein adsorption/desorption processes on the polymer brushes by atomic force microscopy (AFM).
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Affiliation(s)
- Xiaowen Wang
- Max Planck Institute for Polymer Research
- 55128 Mainz, Germany
- Hefei National Laboratory for Physical Sciences at the Microscale
- Department of Chemical Physics
- University of Science and Technology of China
| | - Rüdiger Berger
- Max Planck Institute for Polymer Research
- 55128 Mainz, Germany
| | | | - Tao Wang
- Hefei National Laboratory for Physical Sciences at the Microscale
- Department of Chemical Physics
- University of Science and Technology of China
- Hefei 230026, P. R. China
| | - Kaloian Koynov
- Max Planck Institute for Polymer Research
- 55128 Mainz, Germany
| | - Guangming Liu
- Hefei National Laboratory for Physical Sciences at the Microscale
- Department of Chemical Physics
- University of Science and Technology of China
- Hefei 230026, P. R. China
| | | | - Si Wu
- Max Planck Institute for Polymer Research
- 55128 Mainz, Germany
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26
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Zhang X, Rahman M, Neff D, Norton ML. DNA origami deposition on native and passivated molybdenum disulfide substrates. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2014; 5:501-506. [PMID: 33708460 PMCID: PMC7879407 DOI: 10.3762/bjnano.5.58] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 04/03/2014] [Indexed: 05/14/2023]
Abstract
Maintaining the structural fidelity of DNA origami structures on substrates is a prerequisite for the successful fabrication of hybrid DNA origami/semiconductor-based biomedical sensor devices. Molybdenum disulfide (MoS2) is an ideal substrate for such future sensors due to its exceptional electrical, mechanical and structural properties. In this work, we performed the first investigations into the interaction of DNA origami with the MoS2 surface. In contrast to the structure-preserving interaction of DNA origami with mica, another atomically flat surface, it was observed that DNA origami structures rapidly lose their structural integrity upon interaction with MoS2. In a further series of studies, pyrene and 1-pyrenemethylamine, were evaluated as surface modifications which might mitigate this effect. While both species were found to form adsorption layers on MoS2 via physisorption, 1-pyrenemethylamine serves as a better protective agent and preserves the structures for significantly longer times. These findings will be beneficial for the fabrication of future DNA origami/MoS2 hybrid electronic structures.
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Affiliation(s)
- Xiaoning Zhang
- Department of Chemistry, Marshall University, One John Marshall Drive, Huntington, West Virginia 25755, United States
| | - Masudur Rahman
- Department of Chemistry, Marshall University, One John Marshall Drive, Huntington, West Virginia 25755, United States
| | - David Neff
- Department of Chemistry, Marshall University, One John Marshall Drive, Huntington, West Virginia 25755, United States
| | - Michael Louis Norton
- Department of Chemistry, Marshall University, One John Marshall Drive, Huntington, West Virginia 25755, United States
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27
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Teshome B, Facsko S, Keller A. Topography-controlled alignment of DNA origami nanotubes on nanopatterned surfaces. NANOSCALE 2014; 6:1790-1796. [PMID: 24352681 DOI: 10.1039/c3nr04627c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The controlled positioning of DNA nanostructures on technologically relevant surfaces represents a major goal along the route toward the full-scale integration of DNA-based materials into nanoelectronic and sensor devices. Previous attempts to arrange DNA nanostructures into defined arrays mostly relied on top-down lithographic patterning techniques combined with chemical surface functionalization. Here we combine two bottom-up techniques for nanostructure fabrication, i.e., self-organized nanopattern formation and DNA origami self-assembly, in order to demonstrate the electrostatic self-alignment of DNA nanotubes on topographically patterned silicon surfaces. Self-organized nanoscale ripple patterns with periodicities ranging from 20 nm to 50 nm are fabricated by low-energy ion irradiation and serve as substrates for DNA origami adsorption. Electrostatic interactions with the charged surface oxide during adsorption direct the DNA origami nanotubes to the ripple valleys and align them parallel to the ripples. By optimizing the pattern dimensions and the Debye length of the adsorption buffer, we obtain an alignment yield of ∼70%. Since this novel and versatile approach does not rely on any chemical functionalization of the surface or the DNA nanotubes, it can be applied to virtually any substrate material and any top-down or bottom-up nanopatterning technique. This technique thus may enable the wafer-scale fabrication of ordered arrays of functional DNA-based nanowires.
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Affiliation(s)
- Bezuayehu Teshome
- Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf, 01328 Dresden, Germany.
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28
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Ethirajan A, Punniyakoti S, D'Olieslaeger M, Wagner P, Boyen HG. Ultrafast Self-Assembly Using Ultrasound: A Facile Route to the Rapid Fabrication of Well-Ordered Dense Arrays of Inorganic Nanostructures. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201301980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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29
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Ethirajan A, Punniyakoti S, D'Olieslaeger M, Wagner P, Boyen HG. Ultrafast Self-Assembly Using Ultrasound: A Facile Route to the Rapid Fabrication of Well-Ordered Dense Arrays of Inorganic Nanostructures. Angew Chem Int Ed Engl 2013; 52:9709-13. [DOI: 10.1002/anie.201301980] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 06/09/2013] [Indexed: 11/10/2022]
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30
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Howorka S. DNA nanoarchitectonics: assembled DNA at interfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:7344-7353. [PMID: 23373872 DOI: 10.1021/la3045785] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
DNA is a powerful biomaterial for creating rationally designed and functionally enhanced nanostructures. DNA nanoarchitectures positioned at substrate interfaces can offer unique advantages leading to improved surface properties relevant to biosensing, nanotechnology, materials science, and cell biology. This Perspective highlights the benefits and challenges of using assembled DNA as a nanoscale building block for interfacial layers and surveys their applications in three areas: homogeneous dense surface coatings, bottom-up nanopatterning, and 3D nanoparticle lattices. Possible future research developments are discussed at the end of the Perspective.
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Affiliation(s)
- Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London, England, United Kingdom.
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31
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Pearson AC, Linford MR, Harb JN, Davis RC. Dual patterning of a poly(acrylic acid) layer by electron-beam and block copolymer lithographies. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:7433-7438. [PMID: 23342948 DOI: 10.1021/la304486x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We show the controllable patterning of palladium nanoparticles in both one and two dimensions using electron-beam lithography and reactive ion etching of a thin film of poly(acrylic acid) (PAA). After the initial patterning of the PAA, a monolayer of polystyrene-b-poly-2-vinylpyridine micelles is spun cast onto the surface. A short reactive ion etch is then used to transfer the micelle pattern into the patterned poly(acrylic acid). Finally, PdCl2 is loaded from solution into the patterned poly(acrylic acid) features, and a reactive-ion etching process is used to remove the remaining polymer and form Pd nanoparticles. This method yields location-controlled patches of nanoparticles, including single- and double-file lines and nanoparticle pairs. A locational accuracy of 9 nm or less in one direction was achieved by optimizing the size of the PAA features.
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Affiliation(s)
- Anthony C Pearson
- Department of Physics and Astronomy, Brigham Young University, Provo, Utah, USA
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Roy S, Olesiak M, Shang S, Caruthers MH. Silver Nanoassemblies Constructed from Boranephosphonate DNA. J Am Chem Soc 2013; 135:6234-41. [DOI: 10.1021/ja400898s] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Subhadeep Roy
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, United
States
| | - Magdalena Olesiak
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, United
States
| | - Shiying Shang
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, United
States
| | - Marvin H. Caruthers
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, United
States
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Pearson AC, Liu J, Pound E, Uprety B, Woolley AT, Davis RC, Harb JN. DNA origami metallized site specifically to form electrically conductive nanowires. J Phys Chem B 2012; 116:10551-60. [PMID: 22578334 DOI: 10.1021/jp302316p] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA origami is a promising tool for use as a template in the design and fabrication of nanoscale structures. The ability to engineer selected staple strands on a DNA origami structure provides a high density of addressable locations across the structure. Here we report a method using site-specific attachment of gold nanoparticles to modified staple strands and subsequent metallization to fabricate conductive wires from DNA origami templates. We have modified DNA origami structures by lengthening each staple strand in select regions with a 10-base nucleotide sequence and have attached DNA-modified gold nanoparticles to the lengthened staple strands via complementary base-pairing. The high density of extended staple strands allowed the gold nanoparticles to pack tightly in the modified regions of the DNA origami, where the measured median gap size between neighboring particles was 4.1 nm. Gold metallization processes were optimized so that the attached gold nanoparticles grew until gaps between particles were filled and uniform continuous nanowires were formed. Finally, electron beam lithography was used to pattern electrodes in order to measure the electrical conductivity of metallized DNA origami, which showed an average resistance of 2.4 kΩ per metallized structure.
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Affiliation(s)
- Anthony C Pearson
- Department of Physics and Astronomy, Brigham Young University, Provo, Utah 84602, United States
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Zeng L, Li Q, Tang D, Chen G, Wei M. Metal platinum-wrapped mesoporous carbon for sensitive electrochemical immunosensing based on cyclodextrin functionalized graphene nanosheets. Electrochim Acta 2012. [DOI: 10.1016/j.electacta.2012.02.045] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Biswas A, Bayer IS, Biris AS, Wang T, Dervishi E, Faupel F. Advances in top-down and bottom-up surface nanofabrication: techniques, applications & future prospects. Adv Colloid Interface Sci 2012; 170:2-27. [PMID: 22154364 DOI: 10.1016/j.cis.2011.11.001] [Citation(s) in RCA: 301] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 11/02/2011] [Accepted: 11/08/2011] [Indexed: 02/02/2023]
Abstract
This review highlights the most significant advances of the nanofabrication techniques reported over the past decade with a particular focus on the approaches tailored towards the fabrication of functional nano-devices. The review is divided into two sections: top-down and bottom-up nanofabrication. Under the classification of top-down, special attention is given to technical reports that demonstrate multi-directional patterning capabilities less than or equal to 100 nm. These include recent advances in lithographic techniques, such as optical, electron beam, soft, nanoimprint, scanning probe, and block copolymer lithography. Bottom-up nanofabrication techniques--such as, atomic layer deposition, sol-gel nanofabrication, molecular self-assembly, vapor-phase deposition and DNA-scaffolding for nanoelectronics--are also discussed. Specifically, we describe advances in the fabrication of functional nanocomposites and graphene using chemical and physical vapor deposition. Our aim is to provide a comprehensive platform for prominent nanofabrication tools and techniques in order to facilitate the development of new or hybrid nanofabrication techniques leading to novel and efficient functional nanostructured devices.
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Affiliation(s)
- Abhijit Biswas
- Center for Nano Science and Technology (NDnano), Department of Electrical Engineering, University of Notre Dame, Notre Dame, IN 46556, USA.
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Onses MS, Pathak P, Liu CC, Cerrina F, Nealey PF. Localization of multiple DNA sequences on nanopatterns. ACS NANO 2011; 5:7899-7909. [PMID: 21899356 DOI: 10.1021/nn2021277] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
DNA oligonucleotides of different sequences were patterned at the nanoscale. Areas of positive charge were generated by exposure of insulating substrates, spin-on hydrogen silsesquioxane or vapor-deposited SiO(2) on Si, with ionizing radiation sources used in electron beam and extreme ultraviolet lithography. Au nanoparticles (NPs) with a diameter of 15 nm, carrying covalently bound negatively charged single-stranded DNA oligonucleotides, were site specifically immobilized directly on the exposed regions and presented oligonucleotides for subsequent hybridization. Repeated exposure and deposition of NPs allowed for patterning multiple DNA sequences. Patterns with dimensions as small as 15 nm were fabricated using electron beam lithography. The use of DNA-functionalized NPs rather than just DNA facilitates metrology in scanning electron microscopy and improves the hybridization efficiency of the oligonucleotides on the surface.
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Affiliation(s)
- M Serdar Onses
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Wisconsin 53706, United States
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