Fig. 1: Design principles and simulations of the pH-responsive origami switch for ligand pattern hiding and display.
From: A DNA robotic switch with regulated autonomous display of cytotoxic ligand nanopatterns
a, A three-dimensional origami has a head part with a cavity that physically hides six peptide ligands conjugated to DNA strands. b, Illustration of the mechanism of how a peptide ligand hides inside the head cavity via the entropic spring imparted by the random coiling of the TFO. c, When the pH drops, the TFO of the peptide–DNA conjugate forms a tsDNA that forces the six peptides that were originally hidden in the cavity to get displayed as a hexagonal pattern on the top surface of the origami. d, Close-ups of the tsDNA. e, The mean structure of the head part and cavity (the whole mean structure is shown in Supplementary Fig. 2), calculated as an average from multiple oxDNA simulations. TFOs are coloured in cyan, and their 5′ termini are in orange. The top (left) and side (right) views are presented. f, Schematic of how the distance from the TFO terminus or the peptide to the origami surface plane is defined by two vectors. g, Real-time distances, from the TFO terminus (dots in orange) or from the peptide surface to the origami surface (dots in magenta, recalculated from the dataset of orange points via inclusion of the orientation information of the TFO terminus and the physical diameter of the peptide), along the simulation. h,j, Distance frequency histograms of the 5′ termini (h) or peptides (j) of the six TFOs to the origami surface. i,k, Probability that multiple 5′ termini (i) or peptides (k) of the six TFOs are simultaneously outside the origami. For g, h and j, positive values indicate that the tracked points are at the origami side of the defined plane (inside the origami cavity), while negative values mean that the tracked points are on the opposite side (outside the cavity).
