CRISPR (Clustered regularly interspaced short palindromic repeats) is a technology that can be used to edit the DNA in cells of organisms which can allow scientists to fix genetic diseases, improve crops, and defeat viruses. In Anatomy & Physiology 12, we have been spending this unit on learning about DNA, RNA and protein synthesis. To expand on our knowledge and apply it to real-life practices, we used paper models to represent the process of how CRISPR allows scientists to edit genetic information. CRISPR (Clustered regularly interspaced short palindromic repeats) refers to specific sequences of DNA found in bacteria. These DNA sequences are part of the bacterial immune system, helping them recognize and fight off viruses. CRISPR-Cas9 refers to specific process that involves the Cas9 protein.

CRISPR-Cas9 involves 2 parts:

Guide RNA: A small piece of RNA that directs the system to a specific DNA sequence that scientists want to target. 

Cas9 Protein: A separate molecule (an enzyme) that acts like scissors to cut the DNA at the targeted spot. 

The Cas9 enzyme

CRISPR uses guide RNA to find a specific gene in a cell. Each gene in our DNA sequence codes for a protein and by changing the DNA sequence scientists can change the function of that protein. The guide RNA is designed to match the exact sequence of DNA that scientists want to change. 

Once the guide RNA finds its target, the protein Cas9 binds to the DNA and cuts it at that exact spot. To do this, it first recognizes a 3-nucletotide sequence called PAM which occurs throughout the genome. An example of a PAM sequence is highlighted yellow on the model.  After, if the guide RNA matches the DNA sequence, it will bind to the strand. Once the RNA is bound to the DNA, the DNA-cutting (cleaving) ability of the Cas9 enzyme is activated. Cas9 begins cleaving both strands 3 nucleotides upstream.  

The DNA is cut by the Cas9 enzyme

After the DNA is cut, the cell naturally tries to repair it. Scientists can then either allow the cell to make changes on its own (which might deactivate a gene) or they can insert new pieces of DNA to edit the gene in a specific way. 

Nonhomologous end joining (NHEJ) is what happens when a cell tries to repair the cut DNA. It is an error-prone repair mechanism, which is why scientists allow NHEJ to happen in order to deactivate a target gene. Scientists use NHEJ when they are attempting to knock out a gene.

The gene is deactivated after random nucleotides are inserted from the cell to repair the damage done by Cas9

When scientists want to be more precise, they can edit a target gene using homology-directed repair (HDR) which instead of using random nucleotides, uses template DNA. Scientists can provide a donor DNA as a template to trick the cell into using HDR. This method is used for editing genes, such as inserting or correcting specific sequences.  

The gene is precisely edited by scientists due to the insertion of template DNA

Editing DNA is a powerful ability and can be used to better humanity in ways such as correcting genetic disorders, treating cancer, and developing disease-resistant crops with higher yield, nutritional value and longer shelf life. 

The model was mostly accurate in modeling the process of how CRISPR-Cas9 is used to edit and deactivate target genes. It allowed us to visualize each component during the editing/deactivating process in 2D with colors. 

The paper model was accurate showing that Cas9 binds to PAM sequence, which was highlighted in yellow, although it did not do a good job of showing how Cas9 binds to it. The model also accurately represented how the guide RNA binds to DNA and how Cas9 cleaves DNA through the actual cutting of the paper. The most accurate and understandable components of the paper model were the addition of random nucleotide and template DNA. Being able to attach the paper parts and visualize the final DNA strand made for a clear and simple explanation. 

Despite being a useful tool, sometimes models can be misleading and misrepresent the process. For example, our paper models attempted to represent the process in 2D, oversimplifying it to a point where we could not see or understand the complex 3D structure of the molecules involved. In addition, the paper modelling is static, which makes it difficult to visualize the processes in motion.

I think models are a great way to visualize a concept as well as add tactile involvement to educate the public. Models are good at simplifying concepts and creating an opportunity to engage in them, but it is important to note any possible inaccuracies in the model and inform the public of it. Using models to communicate science is effective as long as educators and communicators are aware of the limitations. Models are powerful tools to promote active learning and break down complex topics into simpler ones, but they must be accompanied by careful explanations to avoid oversimplification or misconceptions.  

 

Works Cited

Bio-Rad Laboratories. “CRISPR-Cas Gene Editing Teaching Resources.” Bio-Rad, www.bio-rad.com/en-ca/applications-technologies/crispr-cas-gene-editing-teaching-resources?ID=Q58I0DWDLBV5. Accessed 18 Oct. 2024.

CRISPR Therapeutics. “Gene Editing.” CRISPR Therapeutics, www.crisprtx.com/gene-editing. Accessed 18 Oct. 2024.