Fig. 3: Design and characterization of cytoskeleton-like RNA origami nanotubes.
From: Genetic encoding and expression of RNA origami cytoskeletons in synthetic cells
a, In silico design of RNA origami nanotubes. The nanotube-forming RNA origami tiles assemble co-transcriptionally from a single RNA strand, forming 3 duplexes with α = 120° intrinsic curvature. The 180° external kissing loops (KLs) for nanotube assembly are paired corner-to-corner (a–a′ and b–b′). b, AFM micrograph of WT RNA origami nanotubes. The height profile is plotted along the black line. c, Confocal image of iSpi RNA origami nanotubes after 12 h of in vitro transcription. Fluorescence visualization was achieved by including an iSpinach aptamer and DFHBI-1T dye (λex = 488 nm). d, oxRNA MD simulations of WT, iSpi and dsOV RNA origami tiles. e, oxRNA MD simulation of a 300-tile assembly (here WT). Panels d and e show the centroid structures from simulation. Each nucleotide is coloured by its RMSF. f,g, Persistence length of the RNA origami nanotubes calculated from AFM images (mean ± s.e. of fit; Methods; f) and simulations (300-tile nanotubes during the final 10% of the time steps, mean ± propagated s.e. of fit, n = 603 simulation frames; Supplementary Note 1; g). h, AFM micrograph (error signal mode) of bundled dsOV RNA origami nanotubes upon addition of Mg2+ as a crosslinker. The corresponding height image is shown in Supplementary Fig. 18. i, Width of non-bundled and bundled dsOV RNA origami nanotubes (mean ± s.d., n = 8 and 11 nanotubes, respectively).
