Abstract
The tweezers demonstrate the possibility of using DNA hybridization and toehold-mediated strand displacement to perform mechanical operations. As such, they have inspired the growing field of DNA nanodevices, as outlined in Chapter.
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Notes
- 1.
The existence of a dip in free energy at (5,11) is the only significant difference between this work and Ref. [2], which used an earlier version of the model that lacked coaxial stacking.
- 2.
If Fig. 7.3b is analyzed closely, one finds that the final step is actually less favourable for the inert hairpin than the normal system. This is because there is some tendency for the two single-stranded tails of \(\bar{\text{ f}}\) and \(\alpha \) to transiently bind at this point (lowering the free energy), which is obviously impossible for the inert tail.
- 3.
It is plausible that the destabilizing effect of electrostatics could account for the population of partially open tweezers inferred from the single-molecule FRET analysis of tweezers performed by the Simmel group [8].
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Ouldridge, T.E. (2012). Modelling DNA Tweezers. In: Coarse-Grained Modelling of DNA and DNA Self-Assembly. Springer Theses. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-30517-7_7
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