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Nano Research 2020, 13(11): 3142-3150 https://doi.org/10.1007/s12274-020-2985-4
Research Article | Open Access | Issue | Published: 22 August 2020

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

Show Author's Information Yang Xin1,  Salvador Martinez Rivadeneira1,  Guido Grundmeier1,  Mario Castro2,  Adrian Keller1( )
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
Keywords:
self-assembly, DNA origami, lattice formation, high-speed atomic force microscopy, topological analysis
Topics:
Atomic force microscopyChlorine compoundsDNA Magnesium compoundsPositive ionsSelf assemblyTopology
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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
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Abstract Full text Electronic supplementary material About this article

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.


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About this article

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

Show Author's information Yang Xin1, Salvador Martinez Rivadeneira1, Guido Grundmeier1, Mario Castro2, Adrian Keller1( )
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

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: self-assembly, DNA origami, lattice formation, high-speed atomic force microscopy, topological analysis

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Publication history

Received: 09 June 2020
Revised: 11 July 2020
Accepted: 12 July 2020
Published: 22 August 2020
Issue date: November 2020

Copyright

© The Author(s) 2020

Acknowledgements

We thank David Contreras for his helpful discussions and comments. This research has been partially funded by the Spanish Ministerio de Ciencia, Innovacion y Universidades- FEDER funds of the European Union support, under projects FIS2016-78883-C2-2-P and PID2019-106339GB-I00 (M.C.).

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