DNA Sequence Analysis & Removal of Restriction Sites

This is a solution of team NULL 404 (Arman Bolatov, Daniil Filimonov, Polina Rakhalskaya, Darina Mukhamejanova) for BioHackathon 2021 organized by IGEM.

Table of contents

• Problem statement
• Technologies
• Key features
• Project structure
• How to use
• Naming conventions

Problem statement

The DNA contains specific base order which can correspond to restriction sites. A restriction site is a sequence of approximately 6–8 base pairs of DNA that binds to a given restriction enzyme. For example EcoRI restriction site:

These sites allow restriction enzymes to cut DNA strands into two pieces. In synthetic biology, this cut allows the insertion of a specific gene. However, some restriction sites in DNA can be redundant when it is used in a laboratory.

The IGEM competition has a specific DNA design submission standard where some restriction sites are unacceptable. According to IGEM, this is done to allow future users of submitted DNA to use them without facing problems from those restriction sites. There are two standards: RFC-10 and Type IIS RFC-1000. Hence the illegal restriction sites are:

Base sequence (5' → 3')	GAATTC	TCTAGA	ACTAGT	CTGCAG	GCGGCCGC	GCTCTTC	GGTCTC
Base name	EcoRI	XbaI	SpeI	PstI	NotI	SapI	BsaI

Apart from these standards, other standards can be followed but are not mandated by IGEM.

Therefore, one base change should “hide” the restriction site. If these restriction sites are in the coding region, the restriction sites should be removed without changing the amino acid sequence. This process should be similar to silent mutation.

The task is:

• To create a program that can detect and alter restriction sites of user's choosing.
• The program should not alter the amino acid sequence in the coding region.
• Indicated are only few examples of restriction enzymes, try to make your algorithm useful for any researcher if they wish to "hide" their restriction enzymes.
• Think about other ways you can make your project of use for researchers.

Technologies

Project is created with:

• Python version: 3.7
• PySimpleGUI version: 4.51.6
• Pandas version: 1.3.4

Key features

1. The main feature of this program is that it not only determines the precise location of prohibited restriction sites according to IGEM standards, but also allows the user to hide these sites by altering the minimum number of nucleotides.

2. The algorithms are versatile and adaptable, so the researcher may add new restriction sites into the table and/or delete previous ones, so we are not limited with those provided by default.

3. An intuitive interface visually shows the restriction sites within the DNA sequence and annotates the precise name and position of the restriction site.

4. While the user enters DNA sequence for 5’-3’ direction, they receive the similar data output for the second strand with reversed direction.

5. The program makes sure that DNA alteration is similar to silent mutation and amino acids sequence encoded in coding frame remains the same.

6. Works perfectly for all bacterial genomes.

Project structure

.
├── dictionaries.py              # Converts amino-acids to codons and vice-versa
├── help_text.txt                # The text of the help window
├── help.py                      # The help window with instructions
├── init_rest.py                 # Initializes a pickle file with restriction sites
├── main.py                      # The main window with input fields
├── messages.py                  # Texts of error messages
├── requirements.txt             # A list of dependencies
├── restrictions.pickle          # The dictionary of restriction sites
├── result.py                    # The result window with the program output
├── sequence_algorithms.py       # Algorithms to analyze DNA strands and hide restriction sites
└── README.md

How to use

To clone and run this program, you'll need Git and Python installed on your computer. From your command line:

# Clone this repository
$ git clone https://github.com/armanbolatov/dna_analysis
# Go into the repository
$ cd dna_analysis
# Install the dependencies
$ pip install -r requirements.txt
# Run the program
$ python main.py

By clicking the "Help" button you can find further details on how to use the program properly.

Naming conventions

Here naming conventions should be described:

1. Amino Acids. Source: www.hgmd.cf.ac.uk
2. Restriction Sites (from 5' to 3'). Source: www.sciencedirect.com