DNA origami design software

The software package distributes a sequence editor with a set of tools for designing DNA origami structures:

Bitmap reader - import any shape as design object.
DNA origami fold - automatically finds a folding path through a shape.
3D generator - automatically generates a 3D atomic model of your design.
Oligotrack - accepts any sequence to be integrated in your design and outputs an oligo list for ordering.

Download:

The program currently runs on Mac and Linux
The program might be ported for Windows some time in the future, but for the moment here is a protocol on how to run SARSE in Virtualbox on Windows.
Click here to download SARSE - DNA origami v1.1
P.S. The earlier download file was dysfunctional.

Get started:

For usage please cite:

Andersen et al. DNA Origami Design of Dolphin-Shaped Structures with Flexible Tails. ACS nano (2008)

Contact:

Please send an email to This e-mail address is being protected from spambots. You need JavaScript enabled to view it marked "SARSE mailinglist" if you want to stay informed about updates of the SARSE - DNA origami package or marked "SARSE comment" if you have any questions or suggestions.

Related software:

CDNA highlights

March 2, 2010

Single-molecule chemical reactions on DNA origami

Researchers at the Danish National Research Foundation’s Centre for DNA Nanotechnology (CDNA) at iNANO demonstrate that it is possible to control chemical reactions on DNA nanostructures and generate images of reactions of individual molecules. The results were published on 28 February in Nature Nanotechnology. The article is available here

CDNA news

elena February 12, 2010

Electrochemical assay for attomole detection of DNA

The project was carried out in collaboration between CDNA and DTI. We combined a magnetic bead sandwich hybridization capture assay used for pre-concentration and bioseparation of target DNA, with a lipase-based amplification and electrochemical readout system. The signal amplification in the DNA assay is based on the catalytic activity of a lipase enzyme, and this “electrochemical blotting” concept is principally new. The use of this hydrolytic enzyme allowed for close to few-molecule detection of lipase-labeled DNAs at the electrode surface, due to accumulation of the catalysis product (ester bond cleavage and removal of the redox label from the zone of electrochemical reaction). The developed electrochemical lipase- and magnetic beads-based sandwich hybridization assay represents a fundamentally new electrochemical approach for sensitive DNA detection.

ChemComm link