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Investigating the dynamics of surface-immobilized DNA nanomachines

Surface-immobilization of molecules can have a profound influence on their structure, function and dynamics. Toehold-mediated strand displacement is often used in solution to drive synthetic nanomachines made from DNA, but the effects of surface-immobilization on the mechanism and kinetics of this r...

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Autores principales: Dunn, Katherine E., Trefzer, Martin A., Johnson, Steven, Tyrrell, Andy M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937388/
https://www.ncbi.nlm.nih.gov/pubmed/27387252
http://dx.doi.org/10.1038/srep29581
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author Dunn, Katherine E.
Trefzer, Martin A.
Johnson, Steven
Tyrrell, Andy M.
author_facet Dunn, Katherine E.
Trefzer, Martin A.
Johnson, Steven
Tyrrell, Andy M.
author_sort Dunn, Katherine E.
collection PubMed
description Surface-immobilization of molecules can have a profound influence on their structure, function and dynamics. Toehold-mediated strand displacement is often used in solution to drive synthetic nanomachines made from DNA, but the effects of surface-immobilization on the mechanism and kinetics of this reaction have not yet been fully elucidated. Here we show that the kinetics of strand displacement in surface-immobilized nanomachines are significantly different to those of the solution phase reaction, and we attribute this to the effects of intermolecular interactions within the DNA layer. We demonstrate that the dynamics of strand displacement can be manipulated by changing strand length, concentration and G/C content. By inserting mismatched bases it is also possible to tune the rates of the constituent displacement processes (toehold-binding and branch migration) independently, and information can be encoded in the time-dependence of the overall reaction. Our findings will facilitate the rational design of surface-immobilized dynamic DNA nanomachines, including computing devices and track-based motors.
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spelling pubmed-49373882016-07-13 Investigating the dynamics of surface-immobilized DNA nanomachines Dunn, Katherine E. Trefzer, Martin A. Johnson, Steven Tyrrell, Andy M. Sci Rep Article Surface-immobilization of molecules can have a profound influence on their structure, function and dynamics. Toehold-mediated strand displacement is often used in solution to drive synthetic nanomachines made from DNA, but the effects of surface-immobilization on the mechanism and kinetics of this reaction have not yet been fully elucidated. Here we show that the kinetics of strand displacement in surface-immobilized nanomachines are significantly different to those of the solution phase reaction, and we attribute this to the effects of intermolecular interactions within the DNA layer. We demonstrate that the dynamics of strand displacement can be manipulated by changing strand length, concentration and G/C content. By inserting mismatched bases it is also possible to tune the rates of the constituent displacement processes (toehold-binding and branch migration) independently, and information can be encoded in the time-dependence of the overall reaction. Our findings will facilitate the rational design of surface-immobilized dynamic DNA nanomachines, including computing devices and track-based motors. Nature Publishing Group 2016-07-08 /pmc/articles/PMC4937388/ /pubmed/27387252 http://dx.doi.org/10.1038/srep29581 Text en Copyright © 2016, Macmillan Publishers Limited http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
Dunn, Katherine E.
Trefzer, Martin A.
Johnson, Steven
Tyrrell, Andy M.
Investigating the dynamics of surface-immobilized DNA nanomachines
title Investigating the dynamics of surface-immobilized DNA nanomachines
title_full Investigating the dynamics of surface-immobilized DNA nanomachines
title_fullStr Investigating the dynamics of surface-immobilized DNA nanomachines
title_full_unstemmed Investigating the dynamics of surface-immobilized DNA nanomachines
title_short Investigating the dynamics of surface-immobilized DNA nanomachines
title_sort investigating the dynamics of surface-immobilized dna nanomachines
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937388/
https://www.ncbi.nlm.nih.gov/pubmed/27387252
http://dx.doi.org/10.1038/srep29581
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