The CanDo origami simulation tool was used to model the confirmation of the structure. The tool assumes 10.5 bp / turn.
Twist correction
As it can be seen in the side by side comparison below, the structure's twist was corrected. This was achieved by introducing skips in the structure at a rate of 1 skip every 48 bp. This number is justified as follows: the target bp/turn for a flat 2D lattice is 10.44. The CADNano square lattice assumes a 10.66 bp/turn. This implies that we need to incur a 0.22/10.44 = 0.02 = 2% reduction in bp / turn. We chose to round that off to 1 per 48bp because the square lattice has a unit length of 8bp, thus converting to 1 bp skip every 6 unit lengths. This was implemented in the CADNano design, a screenshot of which is available here, where skips are represented by the red crosses.
No Correction
Skip corrected
Linker placement calculation
The structure was modeled in SolidWorks on a 2x106:1 scale (pic 1). Using that model, the linkers were placed in such a way as to avoid any cross-hybridisation between them while allowing for new structures to hybridize (pic 2).
The origami lattice is then modeled in Maya via the CADNano plugin (pic 3). The scaled model is then used to pinpoint the positions of the linkers and replace the affected oligos with linker strands of the appropriate lengths. These linker oligos should be ordered HPLC purified as it has been shown to be necessary to their selective binding efficiency.
The structure was modeled in SolidWorks on a 2x106:1 scale (pic 1). Using that model, the linkers were placed in such a way as to avoid any cross-hybridisation between them while allowing for new structures to hybridize (pic 2).