Fig. 2: The position of an eliminated mismatch affects strand-displacement rate.
a Mismatch-elimination TMSD: an invader I displaces an output strand O from an OT duplex containing a mismatch. O subsequently participates in a secondary displacement reaction that liberates a fluorophore-bearing strand from a quenching duplex. In this example, complex OT has a cytosine–cytosine mismatch at position 7, counting from the beginning of the displacement domain. The three-base-pair mismatch motif (dashed rectangle) is the same for all mismatch positions. b Experimentally obtained TMSD rate constant as a function of mismatch position relative to k0 = 2.6 × 103 M−1s−1 for a mismatch-free system (squares). Fluorescence data and fit for position 7 is shown inset. Triangles show corresponding relative rate constants obtained from oxDNA simulations, showing a similar non-monotonic relationship between reaction rate and mismatch location. Error bars show standard error on the mean (2 ≤ n ≤ 6 for experiment, n = 6 for simulation); there is also an error that systematically effects all relative rates due to the error in determination of no-mismatch rate constant k0 of ±15% for experimental points (n = 7) and ±11% for simulated points (n = 6).
