Tag a gene with CRISPR
The last stretch of a gene, drawn letter by letter. Find a place where Cas9 can land near the stop sign, then choose how to write a small tag into the gene.
What this simulates
What you do
You see the end of a gene as two strands of DNA letters, finishing in a stop sign. First you click a landing spot near the stop: any letter followed by two Gs. If you pick a letter that isn't a landing spot, or one too far from the stop for this game, the game says why and lets you try again.
Then you choose a tool. With Cas9 and a patch, the strands are cut and a donor patch carrying the tag drops in. With prime editing, one strand is nicked and the new letters are written in from a template. Either way, the FLAG tag ends up just before the stop. Afterwards you can go back and try the other tool at the same landing spot.
The real technique
This is epitope tagging, a common way to follow a protein when you can't pick it out directly. The landing spot is a PAM, the short motif that Cas9 needs next to its target. For the commonly used Cas9 it is any letter followed by two Gs, and Cas9 cuts a few letters upstream of it. With the Cas9 route you supply a donor patch carrying the tag, and the cell can use the matching ends to repair the break and insert it. CETCh-seq, which tags proteins so they can be mapped on DNA, uses this approach.
Prime editing does not cut both strands. It nicks one strand and copies new letters from an RNA template into it, so a planned break through both strands can be avoided. Success depends on the edit and on the cells, so the DNA still has to be checked afterwards. The FLAG tag is eight amino acids long (DYKDDDDK), and an antibody that binds it can be used to collect the tagged protein.
The gene sequence in the game is invented. Only the FLAG tag sequence is real.
What you learn
Why a protein needs a handle before you can map where it sits on DNA, what a PAM is and why the cut site depends on it, and how the two routes differ: a cut and a patch, or a nick and a rewrite. You also see why a tag has to be checked afterwards, both in the DNA and for any change to how the protein works.