In 2017, I met some very cool people from the Toronto iGem team. In their entry project, they wanted to fine-tune the CRISPR-Cas9 system via a light-sensitive switch. This is where I first learned how you can turn a molecular network into logical functional units. As I researched for a molecular topic to illustrate for Derek’s molecular vis course, I read about how researchers have constructed the largest living circuits in yeast cells. The coolest part of the biggest yeast genetic circuit was that you only need a single type of logic gate, i.e., a single transcription cascade, to compute multiple logic functions and produce multiple genetic products to control how a cell functions.
The early draft focused more on the individual elements of the circuit. For example, to complete the circuit, you must keep the output of the circuit, a strand of guide RNA, inside the nucleus. By nature, RNA wants to exit the nucleus. How do we keep that RNA inside the nucleus? You flank the RNA export signal with two self-cleaving ribozymes. As the ribozymes cut themselves free from the guide RNA, they take the export signals with them leaving the guide RNA to roam inside the nucleus until it’s picked up by its Cas9 counterpart.
––– Spoilers, the ribozyme part did not make it into the final draft, neither did the ominous looking polymerase. After a few rounds of peer review, everyone points out that I need to include the application of the molecular gates to complete the narrative. The focus of this piece is not the molecular construct, but the possibility it inspires.
Making a molecule inside a cell has become pretty standard. But with advanced synthetic tools like CRISPR, we could add some logic to this production process. Say, let’s only make that molecule during special circumstances. I decided to describe the gene circuit in the context of cancer. The gene circuit detects cancer using some logic; such as, am I in a cancer cell, or am I in a normal cell? If the cell is in a cancer cell, we don’t make the molecule. If we are in a normal cell, we will make that molecule that kills the cell.
Coming up with a scenario got me very excited. Inspired the initial 8-bit font choice, I changed all the schematic elements into 8-bit representations after looking up tutorials on creating pixel art (WARNING, this is addictive).
The graphic itself is a composite of several renders. The models are retrieved from the protein data bank by the epmv plugin, and rendered using Maxon Cinema 4D. The long DNA strand is taken from DNA strands associated with the protein themselves, and short segments I built using epmv.
If you have a molecular biology or biochemistry background, Derek’s course will definitely be the highlight of your semester. The amount of tools you learn within 5 weeks is INSANE.