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Using ultraviolet absorption spectroscopy to study nanoswitches based on non-canonical DNA structures

Non-canonical forms of DNA are attracting increasing interest for applications in nanotechnology. It is frequently convenient to characterize DNA molecules using a label-free approach such as ultraviolet absorption spectroscopy. In this paper we present the results of our investigation into the use...

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Detalles Bibliográficos
Autores principales: McCarte, Blair, Yeung, Owen T., Speakman, Alexander J., Elfick, Alistair, Dunn, Katherine E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9167695/
https://www.ncbi.nlm.nih.gov/pubmed/35677630
http://dx.doi.org/10.1016/j.bbrep.2022.101293
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author McCarte, Blair
Yeung, Owen T.
Speakman, Alexander J.
Elfick, Alistair
Dunn, Katherine E.
author_facet McCarte, Blair
Yeung, Owen T.
Speakman, Alexander J.
Elfick, Alistair
Dunn, Katherine E.
author_sort McCarte, Blair
collection PubMed
description Non-canonical forms of DNA are attracting increasing interest for applications in nanotechnology. It is frequently convenient to characterize DNA molecules using a label-free approach such as ultraviolet absorption spectroscopy. In this paper we present the results of our investigation into the use of this technique to probe the folding of quadruplex and triplex nanoswitches. We confirmed that four G-quartets were necessary for folding at sub-mM concentrations of potassium and found that the wrong choice of sequence for the linker between G-tracts could dramatically disrupt folding, presumably due to the presence of kinetic traps in the folding landscape. In the case of the triplex nanoswitch we examined, we found that the UV spectrum showed a small change in absorbance when a triplex was formed. We anticipate that our results will be of interest to researchers seeking to design DNA nanoswitches based on quadruplexes and triplexes.
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spelling pubmed-91676952022-06-07 Using ultraviolet absorption spectroscopy to study nanoswitches based on non-canonical DNA structures McCarte, Blair Yeung, Owen T. Speakman, Alexander J. Elfick, Alistair Dunn, Katherine E. Biochem Biophys Rep Research Article Non-canonical forms of DNA are attracting increasing interest for applications in nanotechnology. It is frequently convenient to characterize DNA molecules using a label-free approach such as ultraviolet absorption spectroscopy. In this paper we present the results of our investigation into the use of this technique to probe the folding of quadruplex and triplex nanoswitches. We confirmed that four G-quartets were necessary for folding at sub-mM concentrations of potassium and found that the wrong choice of sequence for the linker between G-tracts could dramatically disrupt folding, presumably due to the presence of kinetic traps in the folding landscape. In the case of the triplex nanoswitch we examined, we found that the UV spectrum showed a small change in absorbance when a triplex was formed. We anticipate that our results will be of interest to researchers seeking to design DNA nanoswitches based on quadruplexes and triplexes. Elsevier 2022-06-04 /pmc/articles/PMC9167695/ /pubmed/35677630 http://dx.doi.org/10.1016/j.bbrep.2022.101293 Text en © 2022 Published by Elsevier B.V. https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Research Article
McCarte, Blair
Yeung, Owen T.
Speakman, Alexander J.
Elfick, Alistair
Dunn, Katherine E.
Using ultraviolet absorption spectroscopy to study nanoswitches based on non-canonical DNA structures
title Using ultraviolet absorption spectroscopy to study nanoswitches based on non-canonical DNA structures
title_full Using ultraviolet absorption spectroscopy to study nanoswitches based on non-canonical DNA structures
title_fullStr Using ultraviolet absorption spectroscopy to study nanoswitches based on non-canonical DNA structures
title_full_unstemmed Using ultraviolet absorption spectroscopy to study nanoswitches based on non-canonical DNA structures
title_short Using ultraviolet absorption spectroscopy to study nanoswitches based on non-canonical DNA structures
title_sort using ultraviolet absorption spectroscopy to study nanoswitches based on non-canonical dna structures
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9167695/
https://www.ncbi.nlm.nih.gov/pubmed/35677630
http://dx.doi.org/10.1016/j.bbrep.2022.101293
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