`origamiUROP`

Autonomous generation of DNA Origami nanostructures

origamiUROP is a Python Library which can currently be used for generating a system comprised of ssDNA/dsDNA strands. Using a set of vertices, lines (edges) are generated which act as centrelines for single/double strands of DNA. It is modelled using the oxDNA model and can be exported in this format.

The end goal of the package is to autonomously generate many possible DNA origami scaffold configurations and subsequently their complimentary staple strands for a given 2D shape.

📃 Features

Polygon

Generate a polygon, given its verticies, where every edge is individually accessible
Write the polygon to .STL and .PLY file formats

oxDNA

Create an oxDNA system with tools to control the length, sequence, base-pairs/nucleotides per 2π turn and more.
Export to oxDNA file format or LAMMPS data format
Read oxDNA and LAMMPS data and dump formats

Lattice

Create a lattice within a polygon
Allocate a route for a strand of DNA to take to fill the polygon
Create an oxDNA system of the scaffold strand which follows the route

📆 Upcoming

Staple the scaffold strand together
More IO (e.g. CanDo)
Vibrational Mode analysis

🔋 Installation

At the time of writing it is only possible to manually install the package. This requires the following prerequisites:

numpy
pandas
matplotlib
meshio
shapely

To install, run the following commands:

git clone https://github.com/shanilpanara/origamiUROP
cd origamiUROP
pip install .

And to test:

pytest

✍️ Example

We can create an Edge object which will act as the centreline ssDNA/dsDNA. Then by creating and adding DNA strands to a system, it allows us to write out a file in an oxDNA format.

from origamiUROP.oxdna import Strand, System
from origamiUROP.polygons import Edge
import numpy as np

# Create two `Edge` objects, with a length of 6.5 and 14 units, respectively
edge_1 = Edge(np.array([-5.5, 0.0, 0.0]), np.array([1.0, 0.0, 0]))
edge_2 = Edge(np.array([1.0, 0.0, 0.0]), np.array([15.0, 0.0, 0.0]))

# Create a single stranded DNA object with 6 nucleotides (rounded down from length of Edge)
# a random sequence will be assigned
strand_ssDNA = edge_1.strand()

# Create a double stranded DNA object with 14 base pairs and assign a sequence for one
# of the strands (a complementary sequence will be assigned to the second strand)
strand_dsDNA = edge_2.strand(double=True, sequence="CCAAGGTTCAGTCA")
print("ssDNA: ", strand_ssDNA[0], "\ndsDNA: ", strand_dsDNA[0], strand_dsDNA[1])

# Create system, add strands and write oxDNA files
system = System(np.array([20.0, 20.0, 20.0]))
strands_to_add = strand_ssDNA + strand_dsDNA
system.add_strands(strands_to_add)

# Creates 2 files -> oxdna.out.top & oxdna.out.conf
system.write_oxDNA('out')

# View pandas dataframe
system.dataframe

System can be visualised using Ovito

🎉 Acknowledgements

oxDNA system inspired by code from https://github.com/lorenzo-rovigatti/oxDNA/

shanilpanara / origamiUROP