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Salting-Out of DNA Origami Nanostructures by Ammonium Sulfate

DNA origami technology enables the folding of DNA strands into complex nanoscale shapes whose properties and interactions with molecular species often deviate significantly from that of genomic DNA. Here, we investigate the salting-out of different DNA origami shapes by the kosmotropic salt ammonium...

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Autores principales: Hanke, Marcel, Hansen, Niklas, Chen, Ruiping, Grundmeier, Guido, Fahmy, Karim, Keller, Adrian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8911265/
https://www.ncbi.nlm.nih.gov/pubmed/35269959
http://dx.doi.org/10.3390/ijms23052817
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author Hanke, Marcel
Hansen, Niklas
Chen, Ruiping
Grundmeier, Guido
Fahmy, Karim
Keller, Adrian
author_facet Hanke, Marcel
Hansen, Niklas
Chen, Ruiping
Grundmeier, Guido
Fahmy, Karim
Keller, Adrian
author_sort Hanke, Marcel
collection PubMed
description DNA origami technology enables the folding of DNA strands into complex nanoscale shapes whose properties and interactions with molecular species often deviate significantly from that of genomic DNA. Here, we investigate the salting-out of different DNA origami shapes by the kosmotropic salt ammonium sulfate that is routinely employed in protein precipitation. We find that centrifugation in the presence of 3 M ammonium sulfate results in notable precipitation of DNA origami nanostructures but not of double-stranded genomic DNA. The precipitated DNA origami nanostructures can be resuspended in ammonium sulfate-free buffer without apparent formation of aggregates or loss of structural integrity. Even though quasi-1D six-helix bundle DNA origami are slightly less susceptible toward salting-out than more compact DNA origami triangles and 24-helix bundles, precipitation and recovery yields appear to be mostly independent of DNA origami shape and superstructure. Exploiting the specificity of ammonium sulfate salting-out for DNA origami nanostructures, we further apply this method to separate DNA origami triangles from genomic DNA fragments in a complex mixture. Our results thus demonstrate the possibility of concentrating and purifying DNA origami nanostructures by ammonium sulfate-induced salting-out.
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spelling pubmed-89112652022-03-11 Salting-Out of DNA Origami Nanostructures by Ammonium Sulfate Hanke, Marcel Hansen, Niklas Chen, Ruiping Grundmeier, Guido Fahmy, Karim Keller, Adrian Int J Mol Sci Article DNA origami technology enables the folding of DNA strands into complex nanoscale shapes whose properties and interactions with molecular species often deviate significantly from that of genomic DNA. Here, we investigate the salting-out of different DNA origami shapes by the kosmotropic salt ammonium sulfate that is routinely employed in protein precipitation. We find that centrifugation in the presence of 3 M ammonium sulfate results in notable precipitation of DNA origami nanostructures but not of double-stranded genomic DNA. The precipitated DNA origami nanostructures can be resuspended in ammonium sulfate-free buffer without apparent formation of aggregates or loss of structural integrity. Even though quasi-1D six-helix bundle DNA origami are slightly less susceptible toward salting-out than more compact DNA origami triangles and 24-helix bundles, precipitation and recovery yields appear to be mostly independent of DNA origami shape and superstructure. Exploiting the specificity of ammonium sulfate salting-out for DNA origami nanostructures, we further apply this method to separate DNA origami triangles from genomic DNA fragments in a complex mixture. Our results thus demonstrate the possibility of concentrating and purifying DNA origami nanostructures by ammonium sulfate-induced salting-out. MDPI 2022-03-04 /pmc/articles/PMC8911265/ /pubmed/35269959 http://dx.doi.org/10.3390/ijms23052817 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/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 (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Hanke, Marcel
Hansen, Niklas
Chen, Ruiping
Grundmeier, Guido
Fahmy, Karim
Keller, Adrian
Salting-Out of DNA Origami Nanostructures by Ammonium Sulfate
title Salting-Out of DNA Origami Nanostructures by Ammonium Sulfate
title_full Salting-Out of DNA Origami Nanostructures by Ammonium Sulfate
title_fullStr Salting-Out of DNA Origami Nanostructures by Ammonium Sulfate
title_full_unstemmed Salting-Out of DNA Origami Nanostructures by Ammonium Sulfate
title_short Salting-Out of DNA Origami Nanostructures by Ammonium Sulfate
title_sort salting-out of dna origami nanostructures by ammonium sulfate
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8911265/
https://www.ncbi.nlm.nih.gov/pubmed/35269959
http://dx.doi.org/10.3390/ijms23052817
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