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 (.conf and .top files).

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

• Generate a polygon, given its verticies, where every edge is individually accessible
• Write the polygon to .STL and .PLY file formats
• Create an oxDNA system with tools to control the length, sequence, base-pairs/nucleotides per 2π turn and more.
• Write the oxDNA system to .conf and .top formats

📆 Upcoming

• Write the oxDNA system to a LAMMPS configuration file
• Read in oxDNA .conf and .top files
• Read in LAMMPS dump files
• Rasterisation algorithm(s) for autonomous scaffold generation

🔋 Installation

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

• numpy
• pandas
• matplotlib
• meshio

To install, run the following commands:

    git clone https://github.com/shanilpanara/origamiUROP.git
    cd origamiUROP.git
    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()

# View pandas dataframe
system.dataframe

system can be visualised using Ovito

🎉 Acknowledgements

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