Input Your DNA Origami Design

To get started, you need to input your origami design into the scaffoldselector.

The scaffoldselector works with origamis specified as a contact map. This is a simple CSV format specifying how staple bases are hybridised with scaffold bases in the target origami design.

Origami CAD designs in scadnano, oxDNA or caDNAno can be easily converted to a contact map as described below.

scadnano to Contact Map

  1. Move your scadnano design file to e.g. origami/contactmap/_assets/myorigami.sc.

  2. Run:

    cd origami
source venv/bin/activate
cd contactmap
python3 scadnano2contact.py myorigami

  3. The contact map is created at origami/contactmap/_assets/myorigami.csv.

oxDNA to Contact Map

  1. Move your oxDNA topology and configuration files to the origami/contactmap/_assets/ directory. For example myorigami.top and myorigami.dat (or myorigami.oxdna).

Note

The oxDNA files must be freshly-exported from a design tool and they must not be relaxed. Note that many oxDNA designs in nanobase are already relaxed and thus are not suitable.

  1. Run:

    cd origami
source venv/bin/activate
cd contactmap
python3 oxdna2contact.py myorigami

  2. The contact map is created at origami/contactmap/_assets/myorigami.csv.

caDNAno to Contact Map

Designs in caDNAno can either be imported into scadnano and exported as .sc files, or they can be converted to oxDNA files via tacoxDNA. Then the steps above can be applied.

Note

Conversion of designs via tacoxDNA. assigns random sequences to the scaffold and staples. When a contact map has been produced, its sequences can be changed by using utilities of the contact map module.

Circularising Scaffold

If an origami specified as a contact map has a linear scaffold strand which requires to be joined into a circle, this can be accomplished via the contact map module:

  1. Move the contact map of your origami design to e.g. origami/contactmap/_assets/myorigami.csv.

  2. Run:

    cd origami
source venv/bin/activate
cd contactmap
python3 contactutils.py circ myorigami

  3. The contact map at origami/contactmap/_assets/myorigami.csv is modified to have a circular scaffold strand.

Many other operations on origami contact maps can also be performed: see the contact map module documentation.