DNA origami: The bridge from bottom to top

Over the last decade, DNA origami has matured into one of the most powerful bottom-up nanofabrication techniques. It enables both the fabrication of nanoparticles of arbitrary two-dimensional or three-dimensional shapes, and the spatial organization of any DNA-linked nanomaterial, such as carbon nanotubes, quantum dots, or proteins at ∼5-nm resolution. While widely used within the DNA nanotechnology community, DNA origami has yet to be broadly applied in materials science and device physics, which now rely primarily on top-down nanofabrication. In this article, we first introduce DNA origami as a modular breadboard for nanomaterials and then present a brief survey of recent results demonstrating the unique capabilities created by the combination of DNA origami with existing top-down techniques. Emphasis is given to the open challenges associated with each method, and we suggest potential next steps drawing inspiration from recent work in materials science and device physics. Finally, we discuss some near-term applications made possible by the marriage of DNA origami and top-down nanofabrication.

[1]  J. Michaelis,et al.  Bottom-Up Fabrication of Nanopatterned Polymers on DNA Origami by In Situ Atom-Transfer Radical Polymerization. , 2016, Angewandte Chemie.

[2]  T. Wilk,et al.  Single-Atom Single-Photon Quantum Interface , 2007, Science.

[3]  M. Y. Simmons,et al.  A single atom transistor , 2012, 2012 IEEE Silicon Nanoelectronics Workshop (SNW).

[4]  Ryan J. Kershner,et al.  Placement and orientation of individual DNA shapes on lithographically patterned surfaces. , 2009, Nature nanotechnology.

[5]  Kuan-Neng Chen,et al.  Wafer-to-Wafer Alignment for Three-Dimensional Integration: A Review , 2011, Journal of Microelectromechanical Systems.

[6]  Philip Tinnefeld,et al.  Fluorescence Enhancement at Docking Sites of DNA-Directed Self-Assembled Nanoantennas , 2012, Science.

[7]  J. Reif,et al.  DNA-Templated Self-Assembly of Protein Arrays and Highly Conductive Nanowires , 2003, Science.

[8]  A. Kuzyk,et al.  Reconfigurable 3D plasmonic metamolecules. , 2014, Nature materials.

[9]  John Hickey,et al.  Metallization of branched DNA origami for nanoelectronic circuit fabrication. , 2011, ACS nano.

[10]  J. Goodenough JAHN-TELLER PHENOMENA IN SOLIDS , 1998 .

[11]  Fengnian Xia,et al.  Tunable phonon-induced transparency in bilayer graphene nanoribbons. , 2013, Nano letters (Print).

[12]  Hao Yan,et al.  Interconnecting gold islands with DNA origami nanotubes. , 2010, Nano letters.

[13]  Erik Winfree,et al.  Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates. , 2010, Nature nanotechnology.

[14]  Mikael T. Björk,et al.  Integration of Colloidal Nanocrystals into Lithographically Patterned Devices , 2004 .

[15]  Tim Liedl,et al.  DNA origami-templated growth of arbitrarily shaped metal nanoparticles. , 2011, Small.

[16]  Wael Mamdouh,et al.  Single-molecule chemical reactions on DNA origami. , 2010, Nature nanotechnology.

[17]  James E. Martin,et al.  Control of the Interparticle Spacing in Gold Nanoparticle Superlattices , 2000 .

[18]  Paul W K Rothemund,et al.  Optimized assembly and covalent coupling of single-molecule DNA origami nanoarrays. , 2014, ACS nano.

[19]  Stefan Diez,et al.  Toward Self-Assembled Plasmonic Devices: High-Yield Arrangement of Gold Nanoparticles on DNA Origami Templates. , 2016, ACS nano.

[20]  N. Seeman,et al.  Crystalline two-dimensional DNA-origami arrays. , 2011, Angewandte Chemie.

[21]  Igal Brener,et al.  Observation of Fano resonances in all-dielectric nanoparticle oligomers. , 2013, Small.

[22]  P. Rothemund,et al.  Engineering and mapping nanocavity emission via precision placement of DNA origami , 2016, Nature.

[23]  Hao Yan,et al.  Controlled delivery of DNA origami on patterned surfaces. , 2009, Small.

[24]  F. Simmel,et al.  Surface-assisted large-scale ordering of DNA origami tiles. , 2014, Angewandte Chemie.

[25]  H. Dietz,et al.  Placing molecules with Bohr radius resolution using DNA origami. , 2016, Nature nanotechnology.

[26]  Yifang Chen,et al.  Nanofabrication and coloration study of artificial Morpho butterfly wings with aligned lamellae layers , 2015, Scientific Reports.

[27]  Zhipeng Huang,et al.  Metal‐Assisted Chemical Etching of Silicon: A Review , 2011, Advanced materials.

[28]  P. Rothemund,et al.  Programmable molecular recognition based on the geometry of DNA nanostructures. , 2011, Nature chemistry.

[29]  Xing Zhu,et al.  Active tunable absorption enhancement with graphene nanodisk arrays. , 2014, Nano letters.

[30]  Z. Li,et al.  Nanoscale patterning of self-assembled monolayers using DNA nanostructure templates. , 2016, Chemical communications.

[31]  Tim Liedl,et al.  Hot spot-mediated non-dissipative and ultrafast plasmon passage , 2017, Nature Physics.

[32]  Gregg M. Gallatin,et al.  Nanomanufacturing with DNA Origami: Factors Affecting the Kinetics and Yield of Quantum Dot Binding , 2012 .

[33]  Wei Sun,et al.  Nanoscale growth and patterning of inorganic oxides using DNA nanostructure templates. , 2013, Journal of the American Chemical Society.

[34]  N. Seeman Nanomaterials based on DNA. , 2010, Annual review of biochemistry.

[35]  Raluca Tiron,et al.  DNA Origami Mask for Sub-Ten-Nanometer Lithography. , 2016, ACS nano.

[36]  Katerina Busuttil,et al.  Transfer of a protein pattern from self-assembled DNA origami to a functionalized substrate. , 2013, Chemical communications.

[37]  Martha A Grover,et al.  Folding and imaging of DNA nanostructures in anhydrous and hydrated deep-eutectic solvents. , 2015, Angewandte Chemie.

[38]  Dong Wang,et al.  Programmably Shaped Carbon Nanostructure from Shape-Conserving Carbonization of DNA. , 2016, ACS nano.

[39]  Emre H. Discekici,et al.  Simple Benchtop Approach to Polymer Brush Nanostructures Using Visible-Light-Mediated Metal-Free Atom Transfer Radical Polymerization. , 2016, ACS macro letters.

[40]  H. Sugiyama,et al.  Lipid-bilayer-assisted two-dimensional self-assembly of DNA origami nanostructures , 2015, Nature Communications.

[41]  Zheng Yan,et al.  Growth of graphene from solid carbon sources , 2010, Nature.

[42]  Tim Liedl,et al.  Sculpting light by arranging optical components with DNA nanostructures , 2017, MRS bulletin.

[43]  Bai Yang,et al.  Colloidal Self‐Assembly Meets Nanofabrication: From Two‐Dimensional Colloidal Crystals to Nanostructure Arrays , 2010, Advanced materials.

[44]  Michael Krueger,et al.  Sequence-Specific Molecular Lithography on Single DNA Molecules , 2002, Science.

[45]  S. Howorka,et al.  Self-assembled DNA nanopores that span lipid bilayers. , 2013, Nano letters.

[46]  P. Rothemund Folding DNA to create nanoscale shapes and patterns , 2006, Nature.

[47]  P. Yin,et al.  DNA Nanostructures-Mediated Molecular Imprinting Lithography. , 2017, ACS nano.

[48]  Shichao Zhao,et al.  Molecular lithography through DNA-mediated etching and masking of SiO2. , 2011, Journal of the American Chemical Society.

[49]  N. Yu,et al.  Flat optics with designer metasurfaces. , 2014, Nature materials.

[50]  Qinghua Xu,et al.  Single-Particle Spectroscopic Study on Fluorescence Enhancement by Plasmon Coupled Gold Nanorod Dimers Assembled on DNA Origami. , 2015, The journal of physical chemistry letters.

[51]  Lulu Qian,et al.  Programmable disorder in random DNA tilings. , 2017, Nature nanotechnology.

[52]  David J. Mooney,et al.  Oligolysine-based coating protects DNA nanostructures from low-salt denaturation and nuclease degradation , 2017, Nature Communications.

[53]  Lei Liu,et al.  Routing of individual polymers in designed patterns. , 2015, Nature nanotechnology.

[54]  Michael Matthies,et al.  Block Copolymer Micellization as a Protection Strategy for DNA Origami. , 2017, Angewandte Chemie.