PERDIX (Programmed Eulerian Routing for DNA Designs using X-overs) is a free, open-source resource for the fully autonomous design of arbitrary 2D scaffolded DNA origami nanostructures.

DNA can be programmed to robustly self-assemble into pre-defined nanoscale structures of nearly arbitrary 2D and 3D shape using the principle of scaffolded DNA origami, invented by Dr. Paul Rothemund in 2006. This website offers a free online portal to the PERDIX design software that automatically converts any 2D polygonal mesh file specified using simple Computer-Aided Design (CAD) into the synthetic DNA sequences needed to synthesize the target object. In short, PERDIX offers the ability to “print” your 2D nanometer-scale geometry using DNA.

Pre-compiled Executables

• For Microsoft Windows without a MATLAB license, download here
  • Requirements: MATLAB Compiler Runtime 2015 and Python 2.7 and Shapely 1.6.4

   

• For Microsoft Windows with MATLAB installed, download here
  • Requirements: MATLAB, Python 2.7 and Shapely 1.6.4 python package

   

• For Mac OS X, download here
  • Requirements: Python 2.7 and Python packages, Shapely 1.6.4 and PyDistMesh 1.2

For more information on our approach, please see this accompanying article by Jun et al., Science Advances, 2019 and the About page.