DNA dynamics and computation based on toehold-free strand displacement

We present a simple and effective scheme of a dynamic switch for DNA nanostructures. Under such a framework of toehold-free strand displacement, blocking strands at an excess amount are applied to displace the complementation of specific segments of paired duplexes. The functional mechanism of the s...

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Autores principales: Kang, Hong, Lin, Tong, Xu, Xiaojin, Jia, Qing-Shan, Lakerveld, Richard, Wei, Bryan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8371076/
https://www.ncbi.nlm.nih.gov/pubmed/34404799
http://dx.doi.org/10.1038/s41467-021-25270-7
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author Kang, Hong
Lin, Tong
Xu, Xiaojin
Jia, Qing-Shan
Lakerveld, Richard
Wei, Bryan
author_facet Kang, Hong
Lin, Tong
Xu, Xiaojin
Jia, Qing-Shan
Lakerveld, Richard
Wei, Bryan
author_sort Kang, Hong
collection PubMed
description We present a simple and effective scheme of a dynamic switch for DNA nanostructures. Under such a framework of toehold-free strand displacement, blocking strands at an excess amount are applied to displace the complementation of specific segments of paired duplexes. The functional mechanism of the scheme is illustrated by modelling the base pairing kinetics of competing strands on a target strand. Simulation reveals the unique properties of toehold-free strand displacement in equilibrium control, which can be leveraged for information processing. Based on the controllable dynamics in the binding of preformed DNA nanostructures, a multi-input-multi-output (MIMO) Boolean function is controlled by the presence of the blockers. In conclusion, we implement two MIMO Boolean functions (one with 4-bit input and 2-bit output, and the other with 16-bit input and 8-bit output) to showcase the controllable dynamics.
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spelling pubmed-83710762021-09-02 DNA dynamics and computation based on toehold-free strand displacement Kang, Hong Lin, Tong Xu, Xiaojin Jia, Qing-Shan Lakerveld, Richard Wei, Bryan Nat Commun Article We present a simple and effective scheme of a dynamic switch for DNA nanostructures. Under such a framework of toehold-free strand displacement, blocking strands at an excess amount are applied to displace the complementation of specific segments of paired duplexes. The functional mechanism of the scheme is illustrated by modelling the base pairing kinetics of competing strands on a target strand. Simulation reveals the unique properties of toehold-free strand displacement in equilibrium control, which can be leveraged for information processing. Based on the controllable dynamics in the binding of preformed DNA nanostructures, a multi-input-multi-output (MIMO) Boolean function is controlled by the presence of the blockers. In conclusion, we implement two MIMO Boolean functions (one with 4-bit input and 2-bit output, and the other with 16-bit input and 8-bit output) to showcase the controllable dynamics. Nature Publishing Group UK 2021-08-17 /pmc/articles/PMC8371076/ /pubmed/34404799 http://dx.doi.org/10.1038/s41467-021-25270-7 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Kang, Hong
Lin, Tong
Xu, Xiaojin
Jia, Qing-Shan
Lakerveld, Richard
Wei, Bryan
DNA dynamics and computation based on toehold-free strand displacement
title DNA dynamics and computation based on toehold-free strand displacement
title_full DNA dynamics and computation based on toehold-free strand displacement
title_fullStr DNA dynamics and computation based on toehold-free strand displacement
title_full_unstemmed DNA dynamics and computation based on toehold-free strand displacement
title_short DNA dynamics and computation based on toehold-free strand displacement
title_sort dna dynamics and computation based on toehold-free strand displacement
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8371076/
https://www.ncbi.nlm.nih.gov/pubmed/34404799
http://dx.doi.org/10.1038/s41467-021-25270-7
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