Self-assembly of highly ordered DNA origami lattices at solid- liquid interfaces by controlling cation binding and exchange

Yang Xin; Salvador Martinez Rivadeneira; Guido Grundmeier; Mario Castro; Adrian Keller

doi:10.1007/s12274-020-2985-4

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Research Article | Open Access

Self-assembly of highly ordered DNA origami lattices at solid- liquid interfaces by controlling cation binding and exchange

Yang Xin^¹, Salvador Martinez Rivadeneira^¹, Guido Grundmeier^¹, Mario Castro^², Adrian Keller^¹(

)

1 Technical and Macromolecular Chemistry, Paderborn University, Paderborn 33098, Germany

2 Grupo Interdisciplinar de Sistemas Complejos and Instituto de Investigación Tecnológica, Universidad Pontificia Comillas de Madrid, Madrid 28015, Spain

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Graphical Abstract

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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Nano Research

Volume 13 Issue 11,
November 2020

Pages 3142-3150

DOI: 10.1007/s12274-020-2985-4

Cite this article:

Xin Y, Rivadeneira SM, Grundmeier G, et al. Self-assembly of highly ordered DNA origami lattices at solid- liquid interfaces by controlling cation binding and exchange. Nano Research, 2020, 13(11): 3142-3150. https://doi.org/10.1007/s12274-020-2985-4

Topics:

Atomic force microscopy Chlorine compounds DNA Magnesium compounds Positive ions Self assembly Topology

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Received: 09 June 2020

Revised: 11 July 2020

Accepted: 12 July 2020

Published: 22 August 2020

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