Visualizing PAM Recognition Sequences

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  User Interface: After Populating Nucleotides and Complement

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  User Interface: Before Populating Nucleotides and Complement

Inspiration

Project: Visualizing PAM recognitions sequences

To conduct CRISPR experiments, guide RNA/DNA constructs need to be made for the correct gene to be targeted. These sequences have been found to have off-target effects which vary based on the sequence itself. Since sequences high in G and C are found to be more accurate, we wanted to create a visual interface to visualize PAM identifying sequences and their complements.

What it does

Allows user to build off of one of the PAM recognition sequences for E. coli (WGG) which is commonly used to build sgRNA constructs. Here we allow the user to build the DNA strand that the CAS9 protein complex would recognize, bind to and cut in CRISPR experiments. The user is able to select the nucleotide of choice, and then produce the complement strand as well.

How we built it

We created a list of objects for the user to select and interact with. Based upon the list of objects populated for the recognition sequence, the builder uses nucleotide base pairings to create the complement strand.

Challenges we ran into

Allowing easy access with an intuitive interface. The objective of the project is relatively simple but the primary product assessment is ease of use and interpretability. We've also never used Windows MR and are almost completely unfamiliar with Unity prior to beginning the project, so the learning curve was another challenge we had to overcome.

Accomplishments that we're proud of

This is our first Unity project as a team. We are only a team of 2 and neither of us have worked in Unity before. We went through the entire learning curve for downloading, learning and creating a Unity project in 36 hours. We are really proud of having a final product and everything we learned.

What we learned

A lot. We learned the entire Unity interface starting this weekend. We went from not knowing where to write our code to having a functional product with the complement strand builder which was an extra functionality we had intially abandoned.

What's next for Visualizing PAM Recognition Sequences

We would like to fix the code such that the complement strand always repopulates correctly, even if the nucleotides are added after creating the complement strand. Furthermore, we would like to allow input such that the user can visualize computer generated sgRNA and DNA constructs to further maximize CRISPR efficiency and minimize off-target effects.

Special thanks to Justin Park, Tracy Nguyen and Connor, and the rest of TritonXR

Built With

• unity