ligation

You can download the script here.

Ligates two strands in an origami and prints out the new configuration and topology file.

Usage:

python ligation.py conf_file top_file virt2nuc ligate_file

Args:

• conf_file: configuration file
• top_file: topology file
• virt2nuc: virt2nuc file (can be generated from cadnano_interface.py with a cadnano json file)
• ligate_file: file containing which nucleotide to ligate (details described below)

Notes:

This script works for multiple ligations in a single structure, but none of the ligations should be performed on the same strand, otherwise the script does not give correct results.

If you want to connect the 5’ end nucleotide of strand 1 to the 3’ end nucleotide of strand 2, you should put the former nucleotide before the latter in the ligate_file.

An example ligate_file is shown below:

1 16 stap 0 39 scaf

1 31 scaf 1 31 stap

This ligates the staple nucleotide at (vh, vb) = (1, 16) to the scaffold nucleotide at (vh, vb) = (0, 39), as well as the scaffold nucleotide at (vh, vb) = (1, 31) to the staple nucleotide at (1, 31). vh and vb stands for virtual base index and virtual helix index in cadnano. (Apparently this does not make any sense. It only serves as an example.)