Self-assembly of highly ordered DNA origami lattices at solid-liquid interfaces by controlling cation binding and exchan
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2020, 13(11): 3142–3150
ISSN 1998-0124 CN 11-5974/O4 https://doi.org/10.1007/s12274-020-2985-4
Self-assembly of highly ordered DNA origami lattices at solidliquid interfaces by controlling cation binding and exchange Yang Xin1, Salvador Martinez Rivadeneira1, Guido Grundmeier1, Mario Castro2, and Adrian Keller1 () 1 2
Technical and Macromolecular Chemistry, Paderborn University, Paderborn 33098, Germany Grupo Interdisciplinar de Sistemas Complejos and Instituto de Investigación Tecnológica, Universidad Pontificia Comillas de Madrid, Madrid 28015, Spain
© The Author(s) 2020 Received: 9 June 2020 / Revised: 11 July 2020 / Accepted: 12 July 2020
ABSTRACT The surface-assisted hierarchical self-assembly of DNA origami lattices represents a versatile and straightforward method for the organization of functional nanoscale objects such as proteins and nanoparticles. Here, we demonstrate that controlling the binding and exchange of different monovalent and divalent cation species at the DNA–mica interface enables the self-assembly of highly ordered DNA origami lattices on mica surfaces. The development of lattice quality and order is quantified by a detailed topological analysis of high-speed atomic force microscopy (HS-AFM) images. We find that lattice formation and quality strongly depend on the monovalent cation species. Na+ is more effective than Li+ and K+ in facilitating the assembly of high-quality DNA origami lattices, because it is replacing the divalent cations at their binding sites in the DNA backbone more efficiently. With regard to divalent cations, Ca2+ can be displaced more easily from the backbone phosphates than Mg2+ and is thus superior in guiding lattice assembly. By independently adjusting incubation time, DNA origami concentration, and cation species, we thus obtain a highly ordered DNA origami lattice with an unprecedented normalized correlation length of 8.2. Beyond the correlation length, we use computer vision algorithms to compute the time course of different topological observables that, overall, demonstrate that replacing MgCl2 by CaCl2 enables the synthesis of DNA origami lattices with drastically increased lattice order.
KEYWORDS DNA origami, self-assembly, lattice formation, high-speed atomic force microscopy, topological analysis
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Introduction
Regular macroscopic structures with controllable nanoscale features are attracting increasing attention in the fields of nanoscience and materials science owing to their remarkable properties [1–5]. DNA molecules are widely used as a building material for the programmable self-assembly of nanostructures and functional molecular devices [6–12]. In particular, the DNA origami technique allows for the high-yield assembly of almost arbitrary nanoscale shapes [13–16]. Surface-assisted hierarchical self-assembly of DNA origami nanostructures offers a simple yet efficient route for scaling up the total structure size, yielding regular DNA origami lattices over large surface areas that can be utilized as molecular lithography masks for the controlle
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