Fig. 2: Structural characterization by bulk transcription experiments.
From: A rhythmically pulsing leaf-spring DNA-origami nanoengine that drives a passive follower
a–d, Transcriptional rates were determined from the linear fit during the linear growth phase of fluorescence increase due to MB binding to the transcribed RNA (Supplementary Dataset 4 and Supplementary Fig. 2b,c). All rates relate to the transcriptional rate of the nanoengine. a, Column I, NTS; column II, intermolecular transcription rate from the dsDNA-t incubated with HT–T7RNAP; column III, nanoengine lacking the chloroalkane linker; column IV, nanoengine (I: n = 14, −0.06 ± 0.12, min = −0.38, max = 0.04, median = 0.00; II: n = 32; 0.16 ± 0.15, min = −0.14, max = 1.48, median= 0.16; III: n = 38, 0.19 ± 0.26, min = −0.42, max = 0.70, median = 0.18; IV: n = 40, 1.00 ± 0.12, min = 0.52, max = 1.48 median = 1.00. ***P = 3.0 × 10−23). b, Transcription rates of the nanoengine (column IV) compared with the nNE (column V) (IV: n = 40; 1.00 ± 0.12, min = 0.52, max = 1.48, median = 1.00; V: n = 14, 2.12 ± 0.69, min = 1.45, max = 3.30, median = 1.89. ***P = 3.9 × 10−5). c, Column IIIa, nNE lacking the chloroalkane linker; column VI, nNE + HT–T7RNAP preincubated with 1 equiv. of the chloroalkane linker; columns VIIa–c, nNE in the presence of 1 (VIIa), 2 (VIIb) and 5 (VIIc) equiv. of the chloroalkane linker; column V, nNE (IIIa: n = 14, 0.08 ± 0.04, min = 0.01, max = 0.15, median = 0.09; VI: n = 12, 0.65 ± 0.40, min = 0.16, max = 1.30, median = 0.63; VIIa: n = 14, 2.03 ± 0.53, min = 1.35, max = 3.13, median = 1.91; VIIb, n = 8, 1.89 ± 0.55, min = 1.03, max = 2.64, median = 1.87; VIIc: n = 12, 1.77 ± 0.44, min = 0.95, max = 2.49, median = 1.82; V: n = 56, 2.12 ± 0.32, min = 1.04, max = 3.19, median = 2.12; ***1P = 0.0005, ***2P = 9.6 × 10−8, ***3P = 1.6 × 10−6); column VIII: nNE lacking the T7 promoter (n = 8, 0.05 ± 0.04, min = −0.01, max = 0.10, median = 0.05). d, Transcription rates of constructs with different attachments of dsDNA-t to the origami: column IX, nNE with dsDNA-t not connected next to HT–T7RNAP; column X, nNE with dsDNA-t connected only next to HT–T7RNAP (both dsDNA-t have a nick at the single attachment site); column IV, nanoengine; column V, nNE (IX: n = 8, 0.06 ± 0.14, min = −0.07, max = 0.27, median = 0.02; X: n = 20, 1.15 ± 0.43, min = 0.50, max = 1.83, median = 1.08; IV: n = 40; 1.00 ± 0.12, min = 0.52, max = 1.48, median = 1.00; V: n = 70, 2.12 ± 0.41, min = 1.04, max = 3.30, median = 2.09; ***1P = 1.6 × 10−21, ***2P = 7.8 × 10−10). P values were obtained with a two-tailed, heteroscedastic t-test. Box-plot edges, 25th and 75th percentiles; box lines, 50th percentiles; whisker sizes, 1.5 × interquartile range (IQR); red dots, single datapoints. Error ranges are mean and s.d.
