Journal
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
Volume 142, Issue 26, Pages 11451-11463Publisher
AMER CHEMICAL SOC
DOI: 10.1021/jacs.0c03105
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Funding
- European Research Council [724863]
- Royal Society University Research Fellowship
- European Research Council (ERC) [724863] Funding Source: European Research Council (ERC)
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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. Here, the complementarity of the invader to the single-stranded toehold provides the free energy 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.
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