DNA origami is a method of using DNA as a construction material to create two- and three-dimensional structures at the nanoscale. This method involves taking a long single strand of DNA as a base material and using many smaller "staple" strands to fold the long strand in specific places. This technique was published in 2006 by Paul W.K. Rothemund at Caltech, and has since grown into a popular and easy to use method for building structures at the nanometer scale.
The Autodesk A
The Bio/Nano Group at Autodesk Research are working with world-class researchers and industry experts to create the next generation of CAD tools to enable the design and manufacturing of these incredible nanoscale structures. In order to better understand the barriers faced by researchers trying to advance this field of science, the Bio/Nano Research group at Pier 9 set out to ‘Imagine, Design, and Create’ the Autodesk ‘A’ in the nanoscale.
Standard DNA Origami is designed in a program called cadnano.
cadnano simplifies and enhances the process of designing three-dimensional DNA origami nanostructures. Through its user-friendly 2D and 3D interfaces it accelerates the creation of arbitrary designs. The embedded rules within cadnano paired with the finite element analysis performed by cando, provide relative certainty of the stability of the structures.
In order to demonstrate the complete process of design to assembly and verification, we elected to construct a DNA Origami nanostructure of the Autodesk Logo.
The target design was constructed in cadnano version 2. The design is composed of 39 rows of a single scaffold arranged in 1 column on a square array.
The design was exported as a cadnano .json file containing the structure information and a .csv file containing the staple strand sequence data for ordering.
A scaffold length of 3818 nucleotides was needed for this design, so we used the M13mp18 viral ssDNA as the scaffold sequence. While this sequence is 7249 nucleotides, the unused portion should not interfere with the construction though we realized later that it would be better to use it completely. The scaffold was routed through the design using the mid-seam auto-scaffold method with the mid-seam located between position  and . The length of the Autodesk logo ribbon was set to ~40-50 basepairs. The mid-seam of the design divided in half to create the division in the A and the scaffold of each ribbon is therefore composed in the raster style. Because the scaffold is composed in a single column, the only scaffold crossovers occur in the proceeding and following cell of the square grid.
111 staple strands were generated through the cadnano auto staple function and manual editing. The auto staple function is used initially and produced staples with long lengths. These staples were broken up manually using the cadnano nick function to produce staples between 20-50 basepairs with at least 4 bound basepairs adjacent to crossovers. After these operations, we ended up with staple strands with an average length of 36.5 basepairs with a minimum length of 18 basepairs and a maximum length of 50 basepairs. In order to avoid stacking interactions at the outer edges of the construct, four nucleotide basepair tails were created using a poly-T sequence. Due to the cadnano design lattice corresponding to a particular orientation of the DNA helices, it was necessary to adjust where to place the entire raster design on that lattice in order to optimize the number of staple cross overs and thus increasing the stability. We found that for this design, setting the midpoint of the construct to position  worked well.