Fig. 1
Design of three quasi-independent DNA origami domains. a In presence of magnesium ions, the Holliday junction (HJ) displays two isoforms, characterized by pairwise coaxial stacking of arms into a right-handed antiparallel stacked X-structure, with arms I/IV and III/II stacked in iso I and II/I, IV/III stacked in iso II. The interconversion between the two isomers passes through a less stable open intermediate, where the four helical arms point towards the corners of a square. Global iso I (b) and iso II (c) conformation of the HJs constituting a DNA origami domain and corresponding to the canonical (c) and isomerized (i) shape of the structure. In the iso I isomer the lateral loops are 32 nt- and 22 nt-long, respectively, at the left- and right-side of each domain, whereas 24 nt-long stretches of the unpaired scaffold are located at the top and bottom of each domain (e(−) construct). In the iso II form, instead, every domain adopts an “inverted” configuration, in which the HJs of the core (blue and orange strands) are flanked by lateral stretches and vertical loops of the unpaired scaffold (c). Note the last row of staples on the right-side of each domain (cyan strands): Although forming 32 bp-long duplexes, their secondary structure is partially constrained into a loop by a parallel stretch of unpaired scaffold that is 10 nt shorter. Both the left- and right-side of each domain have been addressed with three types of edges (yellow strands, in the e(0), e(1), and e(2) constructs), differing in the mechanical strain applied at the points of scaffold inversion. Circular symbols indicate the relative orientations of the bases at the helical edges (scaffold and staple bases are in gray and yellow, respectively). The angular displacement from the ideal situation in which the two scaffold bases are aligned and face each other (0°) denotes the degree of torsional stress generated by the hybridization of edge staples
