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Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability

DNA origami nanostructures are widely employed in various areas of fundamental and applied research. Due to the tremendous success of the DNA origami technique in the academic field, considerable efforts currently aim at the translation of this technology from a laboratory setting to real-world appl...

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Autores principales: Kielar, Charlotte, Xin, Yang, Xu, Xiaodan, Zhu, Siqi, Gorin, Nelli, Grundmeier, Guido, Möser, Christin, Smith, David M., Keller, Adrian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6680526/
https://www.ncbi.nlm.nih.gov/pubmed/31315177
http://dx.doi.org/10.3390/molecules24142577
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author Kielar, Charlotte
Xin, Yang
Xu, Xiaodan
Zhu, Siqi
Gorin, Nelli
Grundmeier, Guido
Möser, Christin
Smith, David M.
Keller, Adrian
author_facet Kielar, Charlotte
Xin, Yang
Xu, Xiaodan
Zhu, Siqi
Gorin, Nelli
Grundmeier, Guido
Möser, Christin
Smith, David M.
Keller, Adrian
author_sort Kielar, Charlotte
collection PubMed
description DNA origami nanostructures are widely employed in various areas of fundamental and applied research. Due to the tremendous success of the DNA origami technique in the academic field, considerable efforts currently aim at the translation of this technology from a laboratory setting to real-world applications, such as nanoelectronics, drug delivery, and biosensing. While many of these real-world applications rely on an intact DNA origami shape, they often also subject the DNA origami nanostructures to rather harsh and potentially damaging environmental and processing conditions. Furthermore, in the context of DNA origami mass production, the long-term storage of DNA origami nanostructures or their pre-assembled components also becomes an issue of high relevance, especially regarding the possible negative effects on DNA origami structural integrity. Thus, we investigated the effect of staple age on the self-assembly and stability of DNA origami nanostructures using atomic force microscopy. Different harsh processing conditions were simulated by applying different sample preparation protocols. Our results show that staple solutions may be stored at −20 °C for several years without impeding DNA origami self-assembly. Depending on DNA origami shape and superstructure, however, staple age may have negative effects on DNA origami stability under harsh treatment conditions. Mass spectrometry analysis of the aged staple mixtures revealed no signs of staple fragmentation. We, therefore, attribute the increased DNA origami sensitivity toward environmental conditions to an accumulation of damaged nucleobases, which undergo weaker base-pairing interactions and thus lead to reduced duplex stability.
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spelling pubmed-66805262019-08-09 Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability Kielar, Charlotte Xin, Yang Xu, Xiaodan Zhu, Siqi Gorin, Nelli Grundmeier, Guido Möser, Christin Smith, David M. Keller, Adrian Molecules Article DNA origami nanostructures are widely employed in various areas of fundamental and applied research. Due to the tremendous success of the DNA origami technique in the academic field, considerable efforts currently aim at the translation of this technology from a laboratory setting to real-world applications, such as nanoelectronics, drug delivery, and biosensing. While many of these real-world applications rely on an intact DNA origami shape, they often also subject the DNA origami nanostructures to rather harsh and potentially damaging environmental and processing conditions. Furthermore, in the context of DNA origami mass production, the long-term storage of DNA origami nanostructures or their pre-assembled components also becomes an issue of high relevance, especially regarding the possible negative effects on DNA origami structural integrity. Thus, we investigated the effect of staple age on the self-assembly and stability of DNA origami nanostructures using atomic force microscopy. Different harsh processing conditions were simulated by applying different sample preparation protocols. Our results show that staple solutions may be stored at −20 °C for several years without impeding DNA origami self-assembly. Depending on DNA origami shape and superstructure, however, staple age may have negative effects on DNA origami stability under harsh treatment conditions. Mass spectrometry analysis of the aged staple mixtures revealed no signs of staple fragmentation. We, therefore, attribute the increased DNA origami sensitivity toward environmental conditions to an accumulation of damaged nucleobases, which undergo weaker base-pairing interactions and thus lead to reduced duplex stability. MDPI 2019-07-16 /pmc/articles/PMC6680526/ /pubmed/31315177 http://dx.doi.org/10.3390/molecules24142577 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Kielar, Charlotte
Xin, Yang
Xu, Xiaodan
Zhu, Siqi
Gorin, Nelli
Grundmeier, Guido
Möser, Christin
Smith, David M.
Keller, Adrian
Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability
title Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability
title_full Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability
title_fullStr Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability
title_full_unstemmed Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability
title_short Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability
title_sort effect of staple age on dna origami nanostructure assembly and stability
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6680526/
https://www.ncbi.nlm.nih.gov/pubmed/31315177
http://dx.doi.org/10.3390/molecules24142577
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