Fig. 2: TMSD for DNA and RNA.
From: Single-molecule force spectroscopy of toehold-mediated strand displacement
A Representative force-extension curves (stretching: black, relaxation: gray) in the absence of trigger strands. The colored curves correspond to fits of a WLC model to the data for the different intermediate states. The inset shows unfolding transitions in more detail. B Analogous for RNA. C Passive mode trace of a DNA (upper trace with zoom) and RNA hairpin (lower trace) when moving from buffer to trigger channel. Binding of a trigger occurs after a lag time of ≈ 2 s, followed by toehold-mediated strand invasion, which is observed as the force drops. An exponential fit was used to determine the invasion time (black dashed line). In contrast, RNA invasion times are significantly longer (2 ms as obtained from the time between the two dotted lines), and an intermediate state is populated during the invasion process. An exponential fit to the part after the intermediate still gives longer invasion times compared to DNA (black dashed line). D Plots of invasion time vs. force. Gray crosses: system response time (see Methods for details, N = 20). To guide the eye, we used an exponential function to fit these data points (gray line). Blue circles: DNA hairpin with DNA trigger (N = 20). Dark green circles: RNA hairpin with RNA trigger (N = 3). Dark green triangles: RNA hairpin with an RNA trigger with two proximal mismatches (see Supplementary Fig. 1 for sequence details, N = 46). Dark green squares: RNA hairpin with RNA trigger without magnesium (N = 5). Invasion times via fitting the part after the intermediate. Light green circles: RNA hairpin with RNA trigger (N = 3). Light green triangles: RNA hairpin with an RNA trigger with two proximal mismatches (N = 46). Light green squares: RNA hairpin with RNA trigger without magnesium (N = 5). Data are presented as mean values ± standard deviation (s.d.). E Representative force-extension curves after TMSD. Colored curves correspond to WLC fits: toehold bound (TB), fully invaded (FI) and fully invaded as well as fully unfolded state (FU) state. Source data are provided as a Source Data file.
