Modelling DNA-strand displacement reactions in the presence of base-pair mismatches
File(s)Merged-20200609-090046.pdf (4.25 MB)
Accepted version
Author(s)
Irmisch, P
Ouldridge, TE
Seidel, R
Type
Journal Article
Abstract
Toehold-mediated strand displacement is the most abundantly used method to achieve dynamic switching in DNA-based nanotechnology. An ‘invader’ strand binds to the ‘toehold’ overhang of a target strand and replaces a target-bound ’incumbent’ strand. Hereby, complementarity of the invader to the single-stranded toehold provides the energetic bias of the reaction. Despite the widespread use of strand displacement reactions for realizing dynamic DNA nanostructures, variants on the basic motif have not been completely characterized. Here we introduce a simple thermodynamic model, which is capable of quantitatively describing the kinetics of strand displacement reactions in the presence of mismatches, using a minimal set of parameters. Furthermore, our model highlights that base pair fraying and internal loop formation are important mechanisms when involving mismatches in the displacement process. Our model should provide a helpful tool for the rational design of strand-displacement reaction networks.
Date Issued
2020-07-01
Date Acceptance
2020-06-01
ISSN
0002-7863
Publisher
American Chemical Society (ACS)
Start Page
11451
End Page
11463
Journal / Book Title
Journal of the American Chemical Society
Volume
142
Copyright Statement
© 2020 American Chemical Society. This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of the American Chemical Society, after peer review and technical editing by the publisher. To access the final edited and published work see https://doi.org/10.1021/jacs.0c03105
Sponsor
The Royal Society
Identifier
https://pubs.acs.org/doi/10.1021/jacs.0c03105
Grant Number
UF150067
Subjects
General Chemistry
03 Chemical Sciences
Publication Status
Published
Article Number
jacs.0c03105
Date Publish Online
2020-06-04