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Handhold-mediated strand displacement: a nucleic acid-based mechanism for generating far-from-equilibrium assemblies through templated reactions

View ORCID ProfileJavier Cabello-Garcia, View ORCID ProfileWooli Bae, View ORCID ProfileGuy-Bart V. Stan, View ORCID ProfileThomas E. Ouldridge
doi: https://doi.org/10.1101/2020.05.22.108571
Javier Cabello-Garcia
Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, London, U.K.
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Wooli Bae
Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, London, U.K.
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Guy-Bart V. Stan
Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, London, U.K.
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Thomas E. Ouldridge
Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, London, U.K.
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  • ORCID record for Thomas E. Ouldridge
  • For correspondence: t.ouldridge@imperial.ac.uk
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Abstract

Toehold-mediated strand displacement (TMSD) is a nucleic acid-based reaction wherein an invader strand (I) replaces an incumbent strand (N) in a duplex with a target strand (T). TMSD is driven by toeholds, overhanging single-stranded domains in T recognised by I. Although TMSD is responsible for the outstanding potential of dynamic DNA nanotechnology1, 2, TMSD cannot implement templating, the central mechanism by which biological systems generate complex, far-from equilibrium assemblies like RNA or proteins3, 4. Therefore, we introduce handhold-mediated strand displacement (HMSD). Handholds are toehold analogues located in N and capable of implementing templating. We measure the kinetics of 98 different HMSD systems to demonstrate that handholds can accelerate the rate of invader-target (IT) binding by more than 4 orders of magnitude. Furthermore, handholds of moderate length accelerate reactions whilst allowing detachment of the product IT from N. We are thus able to experimentally demonstrate the use of HMSD-based templating to produce highly-specific far-from-equilibrium DNA duplexes.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Reference 17 was incomplete. Erase reference to supplementary material present in Nature nanotechnology web page (not yet).

  • https://zenodo.org/record/3832588

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted May 23, 2020.
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Handhold-mediated strand displacement: a nucleic acid-based mechanism for generating far-from-equilibrium assemblies through templated reactions
Javier Cabello-Garcia, Wooli Bae, Guy-Bart V. Stan, Thomas E. Ouldridge
bioRxiv 2020.05.22.108571; doi: https://doi.org/10.1101/2020.05.22.108571
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Handhold-mediated strand displacement: a nucleic acid-based mechanism for generating far-from-equilibrium assemblies through templated reactions
Javier Cabello-Garcia, Wooli Bae, Guy-Bart V. Stan, Thomas E. Ouldridge
bioRxiv 2020.05.22.108571; doi: https://doi.org/10.1101/2020.05.22.108571

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