DNA Origami Education/Tutorials
In our experience, DNA origami can sometimes be a confusing area to get started in, especially due to the lack of user-friendly tutorials and resources that explain the basic design principles of DNA origami. This is why we made a series of video tutorials about DNA origami for our Contribution to future teams. This series of 4 videos explains how DNA origami works, how to design a simple DNA origami structure in caDNAno, and some free online resources that can be used to simulate a DNA origami structure. We hope you enjoy and learn from these videos!
How Does DNA Origami Work?
Creating a Scaffold in caDNAno
Creating Staple Strands in caDNAno
Simulating Your DNA Origami Structure
AAIndex Function in Python
During our model design, we found that we had to use Python to run our model. However, Interpol was necessary for our pipeline, but was an R exclusive package. We originally used RPy2 to run R through Python. However, since our model was running thousands of iterations, the program would take 20+ hours to run. Therefore, we needed a program to accomplish the task of converting the amino acid sequences to the desired AAIndex values locally in Python. As such, we created a script to do just that. As we were working, we felt like this is something that could possibly be used by future iGEM teams. We hope that this expedites future works and allows them to complete a successful project. The link to this function is here, along with the necessary file. Instructions to use it are in the Github repository. Additionally, the link to the Interpol site can be found here.