Abstract
The feet are intended to bind to adjacent sites on a single-stranded track. The binding sites overlap, meaning that the feet compete for binding to the track. As a consequence, a single-stranded region of one foot or the other is always exposed. A fuel strand that is also present in solution can bind to either exposed toehold.
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Notes
- 1.
Throughout this chapter, the terms back or backwards are defined by the \(5^\prime \) direction of the track, and front or forwards by the \(3^\prime \) direction.
- 2.
In fact, it is not clear that the fuel must completely detach before the foot rebinds to the track—the possible consequences of this will be discussed in Sect. 8.1.5.
- 3.
Unbiased VMMC simulations performed at the same temperature demonstrate similar behaviour, suggesting that these results are not overly dependent on the details of the simulation technique. Although statistics are fairly poor, the VMMC simulations appear to give a somewhat higher probability of any misbonds melting before they are displaced—nevertheless, binding through displacement is still observed.
- 4.
Using the parameters of Ref. [2], I calculate melting temperatures of 316 K, 311.7 K and 312.8 K at 0.000336 M for strands carrying the motifs causing misbonds in Fig. 8.2d–h respectively. This should be compared to that of an ‘average’ 6-bp duplex with two dangling ends, which has a \(T_m\) of 309.4 K.
- 5.
There is no evidence from my simulations that being attached to the body of the walker causes a significant unpeeling tension on the end of the front foot/track duplex. The presence of explicit electrostatics, however, would tend to generate some repulsion between the walker body and the foot/track duplex. This would favour conformations in which they are separated by a greater distance, perhaps providing some tendency for the foot/track duplex to peel from its front end.
- 6.
8 bp between fuel and foot was found to be a metastable minimum of free energy. At this point, the fuel has repaired the two mismatches between track and foot, which is favourable, but forming any more base pairs is geometrically difficult without melting the fuel/toehold duplex (see Fig. 8.9).
References
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D.Y. Zhang and E. Winfree. Control of DNA strand displacement kinetics using toehold exchange. J. Am. Chem. Soc., 131(47):17303–17314, 2009.
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Ouldridge, T.E. (2012). Modelling a DNA Walker. 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_8
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