PERDIX

This free online resource is developed and maintained by the Laboratory for Computational Biology & Biophysics at MIT, which is directed by Professor Mark Bathe.

With this software, you may render nearly any target 2D geometry as scaffolded DNA origami by providing only an input CAD (Computer Aided Design) file of your lattice. The common CAD file format IGES (“Initial Graphics Exchange Specification”) is used to represent the target 2D lattice, which PERDIX translates to the necessary scaffold and staple sequences that will self-assemble into, using the principle of scaffolded DNA origami. The specific outputs of the program are:

  • A list of synthetic staple strand sequences. These oligonucleotide staple strands, when combined with your scaffold strand (M13 by default in PERDIX or provided by you), will self-assemble into your scaffolded DNA origami 2D surface by following the standard annealing protocol provided in our work.
  • A PDB file of your 2D surface. This PDB (“Protein Data Bank”) file provides a 3D structural model of the coordinates of every atom in your folded DNA 2D surface, as predicted by PERDIX’s rigid-duplex model.

The goal of PERDIX is to cross disciplines and democratize the usage of structured DNA assemblies by offering a fully autonomous, CAD geometry-based sequence design algorithm. We hope that you can use PERDIX to explore the capabilities of the powerful molecular design paradigm of scaffolded DNA origami for applications of your own interest.

The Laboratory for Computational Biology & Biophysics is grateful to its sponsors for financial support of that enabled this work including the Office of Naval Research and the National Science Foundation.

Google Groups Forum

Please post your questions related to use of PERDIX to this Google Groups forum, where you can also find answers to some commonly asked questions.

Open Source Software Packages

PERDIX is freely available under the GNU General Public License, version 3 (GPL-3.0). Source code is available in Fortran. The source code is available for download through GitHub