DAEDALUS (DNA Origami Sequence Design Algorithm for User-defined Structures)
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 3D geometry as a scaffolded DNA origami nanoparticle by providing only an input CAD (Computer Aided Design) file of your object. The common CAD file format PLY (“Polygon File Format”) is used to represent the target 3D geometry, which DAEDALUS will generate the necessary DNA sequences to fold using the principle of scaffolded DNA origami. The specific outputs of the program are:
- A list of synthetic staple strand sequences. These staple strands, when combined with your scaffold strand (generated by default by DAEDALUS or provided by you), will self-assemble into your scaffolded DNA origami nanoparticle by following the standard annealing protocol provided in our work (Veneziano, Ratanalert, Zhang, et al., Science doi 10.1126/science.aaf4388 (2016)).
- A PDB file of your nanoparticle. This PDB (“Protein Data Bank”) file provides a 3D structural model of the coordinates of every atom in your folded DNA nanoparticle, as predicted by DAEDALUS’ rigid-duplex model described in detail in our work (Veneziano, Ratanalert, Zhang, et al., Science doi 10.1126/science.aaf4388 (2016)).
The goal of DAEDALUS is to broaden the participation of non-experts in the design and synthesis of structured DNA assemblies by offering a fully autonomous, CAD geometry-based sequence design algorithm. We hope that you can use DAEDALUS to explore the capabilities of the powerful molecular design paradigm of scaffolded DNA origami for applications of your own interest. In doing so, we kindly request that you cite the following article when publishing work that utilized this resource: Veneziano, Ratanalert, Zhang, et al., Science doi 10.1126/science.aaf4388 (2016).
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, the National Science Foundation, and the Human Frontier Science Program.
Google Groups Forum
Please post your questions related to use of DAEDALUS to this Google Groups forum, where you can also find answers to some commonly asked questions.
Open Source Software Packages for Python and MATLAB
DAEDALUS is freely available under the GNU General Public License, version 2 (GPL-2.0). Source code is available in both MATLAB and Python. The software package for MATLAB (R2015a or R2016a) with complete documentation is available for download here. The software package for Python is available for download here.