Create your own recognition site for your own made-up restriction enzyme. What type of
cut does it produce?
To create a recognition site for a made-up restriction enzyme and determine the type of cut it produces, you'll need to define the sequence of the enzyme's recognition site and then analyze the specific DNA sequence to determine the type of cut it creates. Here are the steps to follow:
1. Define the recognition site sequence: Design a specific sequence of bases that the restriction enzyme will recognize and cut. For example, let's use the recognition sequence "GAATTC", which corresponds to the EcoRI restriction enzyme recognition site.
2. Analyze the DNA sequence: Take a DNA molecule of your choice, such as a plasmid or a fragment of genomic DNA. Ensure that this DNA sequence actually contains the recognition site you designed.
3. Use a bioinformatics tool: To determine if your restriction enzyme recognition site is present in the target DNA sequence, you can use online bioinformatics tools. Tools like NEBcutter (https://www.neb.com/tools-and-resources/interactive-tools/nebcutter-restriction-enzyme-tool) or RestrictionMapper (https://www.restrictionmapper.org/) allow you to input the DNA sequence and search for the presence of a specific recognition site.
4. Analyze the cut type: Based on the recognition site sequence, you can determine the type of cut the restriction enzyme will produce. There are three types of cuts:
- Blunt end: The enzyme cuts the DNA sequence straight across, resulting in two fragments with blunt ends.
- 5' overhang: The enzyme cuts the DNA sequence, leaving a single-stranded extension (overhang) of bases on the 5' end of one fragment.
- 3' overhang: The enzyme cuts the DNA sequence, leaving a single-stranded extension (overhang) of bases on the 3' end of one fragment.
By visually inspecting the target DNA sequence with the recognition site, or using additional tools like SnapGene or ApE (both free software), you can determine which type of cut is produced. The cut type depends on the specific sequence you designed for your restriction enzyme recognition site.
Remember, this process assumes you have already created a hypothetical restriction enzyme and that the recognition site sequence has been defined.