caDNAno Design Validation Tool

Note: Curently this tool is run from the terminal/cmd, but the eventual goal of this project will implement a GUI, also providing more informatics such as suggested thermal annealing ramp, basic staple stand statistics etc.

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Prerequisites

This documentation assumes basic knowledge of caDNAno2, and DNA origami concepts including thermodynamics, structure, design etc.
Users should be familiar with the caDNAno2 interface and the representations of staple/scaffold strands.

Introduction

caDNAno is a very popular tool for computer-aided DNA origami design. This project aims to analyze caDNAno design files (.json), identifying potentially problematic staple strands such as 'kinetic traps', or 'sandwich strands', a term coined by Dr.Stephanie Lauback. The inclusion of such strands in the design are thought to affect parameters of the DNA origami structure formed in the lab such as stability and formation yield. This tool was developed for the DNA origami design pipeline at UBC BIOMOD.

Usage

Dependencies

numpy >= 1.23.0

Workflow

After users have a design file exported from caDNAno2, users can analyze their designs for staple strands which may be potentially problematic to the formation of the structure in vitro. These strands are explained in the Background section below.

First Steps

Users should first clone or download the repository. To get the full functionality of this program, users should complete the following two steps.

1. Setup SciTools API access and get their own IDT API access credentials - learn how here.
2. Input IDT API credentials into idt_api_credentials_template.json and rename the file to idt_api_credentials.json.

To make an IDT (Integrated DNA Technologies) account and set up API access, follow the link to the SciTools Plus API Overview Docs here. Once the SciTools API access is set up, users should edit the idt_api_credentials_template.json file with their API access details, and rename that file to idt_api_credentials.json. Program functionality relevant to staple strand melting temperature will not work if the above has not been completed.

Users should run the following command from the location where this program is downloaded. Replace "download_location" with the path where this repository is downloaded.

C:\Users\username\download_location> python mainscript.py path\to\design\file.json
username@macos download_location ~ % python3 mainscript.py path/to/design/file.json
username@ubuntu download_location ~ $ python3 mainscript.py path/to/design/file.json

Providing the path to the caDNAno design file when running the script from terminal is optional. If it is not provided, the script will display a prompt where users can browse through their filesystem to search for the design file to analyze.

C:\Users\username\download_location> python mainscript.py
username@macos download_location ~ % python3 mainscript.py
username@ubuntu ~ $ python3 mainscript.py

Once the analysis is complete, users can reopen the design file on caDNAno2, and will see that the problematic strands are colored red, while the others are colored green. The script also outputs a text file name_of_design_file_summary.txt, with the date and time of the analysis, along with the coordinates fo the problematic strands provided in the format "helix_number[longitudinal_index]". Sample analyses files and results are available in the Examples folder.

Additionally, a histogram of the melting temperatures of staple strands in 1^oC wide bins will be saved.

Background

DNA Origami nanostructures are formed typically using one long 'scaffold' DNA strand (3000 - 8000 bp) and hundreds of smaller 'staple' DNA strands (24 - 64 bp) which bind to specific regions of the scaffold strand, holding it in a programmable structure/conformation.

An important concept in the formation of DNA origami structures are 'cross overs'. This is when a single DNA strand in a double-stranded DNA (dsDNA) double helix crosses over from one dsDNA helix to another, resulting in one DNA strand being a part of two or more double helices.