Extended Data Fig. 6: Hinge properties of simulations.
From: A rhythmically pulsing leaf-spring DNA-origami nanoengine that drives a passive follower
(a) Calculated spring constant of each design at 23 °C and 37 °C. Only NS with an intact dsDNA-t show a substantial difference between 23 °C and 37 °C, demonstrating the influence of stable secondary structures on angle distribution. (b) Angle-distribution simulations (n = 3). At higher temperatures, simulations with secondary structures in the flexure resulted in a slightly increased average angle, while simulations showed a slight decrease when secondary structures were prevented. Presumably, secondary structures limit the opening angle of the structures, while the extended single strands behave more like entropic springs that become more flexible with increasing temperature (nNE_23: n = 5666, min=30.24, max=79.33 median = 54.35; nNE_37: n = 6000, min=26.56, max=81.57, median = 58.42; nNE_NS_23: n = 6000, min=49.62, max=89.42, median = 76.27; nNE_NS_37: n = 6000, min=50.28, max=88.75, median = 74.51; NE_23: n = 6000, min=25.98, max=76.02, median = 49.16; NE_37: n = 6000, min=27.79, max=77.43, median = 53.49; NE_NS_23: n = 6000, min=51.32, max=86.30, median = 73.90; NE_NS_37: n = 6000, min=46.39, max=86.39, median = 72.05,; NTS_23: n = 18000, min=13.09, max=86.33, median = 46.40; NTS_37: n = 5971, min=28.91, max=81.70, median = 55.62; NTS_NS_23: n = 6000, min=68.62, max=120.99, median = 95.14; NTS_NS_37: n = 6000, min=49.34, max=107.45, median = 80.01. (c) Estimation of spring constants of individual (nicked-)nanoengines at 37 °C based on the modelling studies, obtained either by taking the average and S.D. (n = 3) or by bootstrapping with 1,000 re-samplings of the combined data of the three replicates. (d,e) Experimental angle distributions of the nicked-nanoengine (red, n = 5135, 189 micrographs) and NTS (cyan, n = 1382, 28 micrographs) are highly comparable (p = 0.6, two-tailed, heteroscedastic t-test). (e) NTS: n = 1382, 63.84° ± 18.77°, min=1.68° max=164.00° median = 66.40; nNE: n = 5135, 64.13° ± 20.04°, min=0.00° max=161.11° median = 67.03°. (f) Relaxation of the nicked-nanoengine in simulation indicates that the origami arms bend out of plane showing a longitudinal twist in 18 HBs. Reference lines illustrate the amount of bending (green: designed structure, left; red: simulated structure, middle). Right: snapshot from a simulation of the nicked-nanoengine. (g) 2D-Averages of nicked-nanoengine top-views. One arm does not overlap the more resolved one, consistent with its simulation-predicted out-of-plane bending. The distortion of surface-deposited nicked-nanoengine likely explains the systematic difference in angle distributions between TEM imaging and simulation. Box-plot edges: 25th and 75th percentiles. Box lines: 50th percentile. Whisker size: 1.5× the IQR, grey dots: outliers. Error ranges: mean and S.D. Glossary - nNE: nicked-nanoengine, nNE_23: nicked-nanoengine at 23 °C, nNE_37: nicked-nanoengine at 37 °C, nNE_NS_23: non-structured nicked-nanoengine at 23 °C, nNE_NS_37: non-structured nicked-nanoengine at 37 °C, NE_23: nanoengine at 23 °C, NE_37: nanoengine at 37 °C, NE_NS_23: non-structured nanoengine at 23 °C, NE_NS_37: non-structured nanoengine at 37 °C, NTS_23: origami lacking the dsDNA-t at 23 °C, NTS_37: origami lacking the dsDNA-t 37 °C, NTS_NS_23: non-structured origami lacking the dsDNA-t at 23 °C, NTS_NS_37: non-structured origami lacking the dsDNA-t at 37 °C; NE: nanongine, NE_NS: non-structured nanongine nNE: nicked-nanoengine, nNE_NS: non-structured nicked-nanoengine, NTS: hinge_origami_NTS, NTS_NS: non-structured hinge_origami_NTS.
