circDNA

This repository contains a Python3 script and examples used to generate a circular fragment model of DNA.

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Question: What makes it a "circle"?

A circular model of DNA is defined as being "covalently closed". DNA has two antiparallel chains: the 'coding' strand and the 'complementary' or 'anti-coding' strand. Both strands are read from the 5' to 3' direction, where the prime-notation refers to the carbon atoms on the deoxyribose sugars that are attached to phosphate groups along the chains.

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How to Use this Repo

This repository is designed to be a training site. Therefore, I would not suggest forking this directory; rather just download the files and directories locally and use from there.

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Getting Started

This work is done with Python3 in a terminal or command line application.

• Downloading: Download the Python3 script located in the circle_generator_script directory.

  • You can make a single copy in one standard directory or make multiple copies and place them in directories as you need them.
  • In order to use this script, you must have the following modules locally downloaded: os, argparse, numpy, scipy. You can also use the circdna.yml conda environment file with all packages ready for you to install on your own local Conda environment.
  • For instructions, visit https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#activating-an-environment
    • From the (base) conda environment:
      • conda env create -f circdna.yml
      • For standardization, NEVER update this environment unless stated in this repo. This build specifically uses Python3 3.10 (as of 26 Jun 2024).

• Execution: From within your desired directory, open a terminal and execute the script. Note: if you are planning on using the circdna conda environment, make sure to activate it now: $ conda activate circdna CLI commands & flags:

  • long: $ python3 planar_circle_generator.py --length ... --rise ... --bp-per-turn ... --seq ... --output-name ...
  • shortened: $ python3 planar_circle_generator.py -l ... -r ... -t ... -s ... -o ...
  • note not all commands are required. The seq, rise, and bp-per-turn flags default to all dA residues, 3.400-Å, and 10.5-bp/turn, respectively. For example: $ python3 planar_circle_generator.py --length 100 --output-name test_circ

• File conversion: You may note the files produced have a .par file extension. You can use an online web server to generate an all-atom .pdf file.

  • Visit http://web.x3dna.org/
  • Select the 'Rebuilding' tab at top.
  • Select the 'Customized base-pair step/nucleotide parameters' blue button.
  • Look for text "Upload a base-pair parameter file" found under a grayed-out text input box. Select the "Choose File" button and locate/upload your .par file.
  • Deselect the "Backbone geometry optimization" radial button found to the right of the blue "Build Model" button.
  • Select the "Build Model" button.
  • Under the top 2D image select the "Download the rebuild PDB file" hyperlink.
  • (optional) Locate this downloaded file and rename/move as needed. You can also verify your output with the files located in "assets/initial_test_files".

• Result: Below should be a 100-bp planar circle generated from the web3DNA server.

Congrats! Now you can make more circles as needed. You can customize using software such as emDNA[https://nicocvn.github.io/emDNA/].

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Common Software used

The software and web servers used includes:

• Python3.X (here, 3.10)
• Jupyter Notebooks (use of IDEs such as Visual Studio Code will also work)
• PyMol 2.X
• web3DNA [http://web.x3DNA.org]
• emDNA [https://nicocvn.github.io/emDNA/]

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Reference

If you are interested in additional detail, you may read over the 'Appendix' of my Physics Masters Thesis (Rutgers University, Jan 2022) found in the assets directory.

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