DNA Nanostructures

Week 12 > Learn about the genetic circuit responsible for reporting PAM binding and introduce various CRISPR-Cas9 enzymes into bacterial cells.

Scroll down

In this assignment, we evaluated the PAM binding of different Cas9 enzymes. We implemented a previously-developed positive selection bacterial screen based on green fluorescent protein (GFP) expression conditioned on PAM binding, termed PAM-SCANR. Then, we learneds about the design of the genetic circuit responsible for reporting PAM binding, and introduced various Cas9 enzymes into bacterial cells, already containing the reporter and guide RNA plasmids. On the following day we sumbited for Sanger sequencing.

The CRISPR-Cas9 system has been successfully harnessed for various genome editing applications, which have a wide range of implications in fields such as medicine, agriculture, bioenergy, and food security. CRISPR systems contain two components: a guide RNA (gRNA) and a CRISPR-associated (Cas) endonuclease. The gRNA is a short synthetic RNA composed of a scaffold sequence necessary for Cas-binding and a user-defined ∼20 nucleotide spacer that defines the genomic target to be modified. Thus, one can change the genomic target of the Cas protein by simply changing the target sequence present in the gRNA. To access specific targets, however, these enzymes require a protospacer adjacent motif (PAM), which is determined by DNA-protein interactions, to immediately follow the DNA sequence specified by the gRNA. The PAM sequence is essential for target binding, but the exact sequence depends on which Cas protein you use. For example, the standardly used Cas9 derived from Streptococcus pyogenes bacteria (SpCas9), for example, requires an 5'-NGG-3’ motif.

Next Week's Assignment

Short description of next week's assignment.