Fig. 5: oxDNA simulations were performed to determine the dynamic structural properties of the nanoengine.
From: A rhythmically pulsing leaf-spring DNA-origami nanoengine that drives a passive follower
a, Mean structure of an equilibrium sampling simulation of an nNE represented in oxDNA. b, Equilibrium angle distribution of six designs during oxDNA simulation. Regions where base pairing was turned off for single-stranded regions of the flexure to isolate the effect of secondary structures forming in the flexure are flagged with NS (no structure). nNE: n = 6,000, min = 26.6, max = 81.6, median = 58.4; nNE_NS: n = 6,000 min = 50.3, max = 88.8, median = 74.5; NTS: n = 5,971, min = 28.9, max = 81.7, median = 55.6; NTS_NS: n = 6,000, min = 49.3, max = 107.4, median = 80.0; nNE: n = 6,000, min = 26.6, max = 81.6, median = 58.4; nNE_NS: n = 6,000, min = 50.3, max = 88.8, median = 74.5; NE: n = 6,000, min = 27.8, max = 77.4, median = 53.5; NE_NS: n = 6,000, min = 46.4, max = 86.4, median = 72.0. c, Simulation-determined closing rates from pulling simulations relative to nNE. No significant difference in rate was observed. n = 10 for all boxes. nNE: min = −1.5, max = −0.6, median = −1.0; nNE_NS: min = −1.8, max = −0.5, median = −1.1; NE: min = −1.5, max = −0.1 median = −1.0; NE_NS: min = −1.7, max = −0.6, Q2 = −0.9 d, Simulation-determined opening rates relative to nNE from relaxation simulations where the forces from the pulling simulations were released and the structure allowed to open again. There is a trend toward higher opening rates in the NS simulations; however, NE and NE_NS are the only pair of corresponding structures where the difference is significant (*P < 0.05, calculated with a two-tailed Komogorov–Smirnov test). n = 10 for all boxes. nNE: min = 0.25, max = 1.65, median = 0.93; nNE_NS: min = 0.80 max = 2.63, median = 1.52; NTS: min = −0.17, max = 1.52, median = 0.66; NTS_NS: min = 0.45, max = 1.89, median = 1.15; NE: min = 0.09, max = 1.61, median = 0.87; NE_NS: min = 1.27, max = 2.36, median = 1.58. NE, nanoengine; NE_NS, non-structured nanoengine; nNE, nicked-nanoengine; nNE_NS, non-structured nicked-nanoengine; NTS, origami lacking dsDNA-t; NTS_NS, non-structured origami lacking dsDNA-t.
