An Incoming Genetic Revolution

Gene therapy is ascending to new heights with the development of prime editing

Allen Wang
7 min readMay 24, 2020

We’re all guilty of having envied the characteristics of our friends. Whether it be their eye color, height, or muscular build, we can all agree there are features of our friends that we wished we possessed. Alas, we’ve been raised into a world where we’re born with traits that are unalterable, determined by our complex and rigid genetics. But wait.

What if there was a way we could alter our genes, to become the perfect version of ourselves that we’ve long wished for?

That’s where gene editing comes in. Though we may still be a ways away, fully genetically engineering humans is now closer than ever with the arrival of prime editing, a new way of genetic modification.

A new way? What did we have before?

Before prime editing, we had a system known as CRISPR, short for clustered regularly interspaced short palindromic repeats. In order to understand prime editing, we must first take a look at the CRISPR system.

This system was adapted from bacterial immune systems defending against invading viruses. When new viruses enter a bacteria cell, the CRISPR system creates a class 1 Cas protein that breaks apart the viral DNA, and stores a piece of the DNA segment into the CRISPR arrays. This essentially allows the immune system to “memorize” this type of virus DNA.

In the event that viruses assault once more, a Cas enzyme complex searches for the virus’s DNA match in the CRISPR array. From this located DNA, an RNA section, known as CRISPR RNA (crRNA), is produced and used by the complex to kill the viral DNA.

CRISPR Locus example. The spacer DNAs are the viral DNAs the bacteria have encountered, with the repeats separating the different viral DNAs. The CAS genes are what produces the enzymes, the Cas enzyme complex and the class 1 Cas protein. The leader is simply a segment of DNA that holds the two parts together.

It seems to me that you’re talking an awful lot about immune systems… where does the gene-editing stuff come in?

Scientists observed this phenomenon occurring in bacteria, and some attempted to adapt and utilize this system to our advantage. The most famous adaptation was CRISPR-Cas9.

This system contains only one Cas9 protein (unlike the bacterial system which used two different ones), as well as something known as guide RNA (gRNA). The gRNA has a predesigned sequence that matches a section of the DNA segment, which helps the Cas9 protein locate the targeted part of DNA. After the Cas9 protein locates the DNA segment, the Cas9 protein nuclease is used to cut the DNA into two parts. This ensures that the genome is cut at the correct location.

The Cas9 protein is the white structure and the gRNA is the gray strand with blue dots. The red strand is the targeted DNA segment. The two edges of the Cas9 protein nuclease on the DNA segment is used to separate the DNA into two pieces.

Now, since the Cas9 protein complex has cut and separated the DNA, scientists are able to put their desired DNA addition between the two separated pieces of DNA. This effectively modifies the genetic code, and can be used to treat a variety of genetic problems, such as cystic fibrosis or hemophilia.

Wow! This CRISPR-Cas9 system sounds great! Why do we need a new system?

Yes, the CRISPR-Cas9 tool does sound like the ultimate gene-editing tool, at least in theory. However, as scientists have discovered, the CRISPR-Cas9 tool is prone to many errors and unintended effects. Because it cuts through both strands of DNA, the repair process of the DNA segment can introduce dangerous mutations, as the DNA repair systems are likely to insert random insertions or deletions when repairing the genome.

How is prime editing able to fix this?

In order to understand prime editing, you need to understand where the idea came from. Prime editing originated from the idea of CRISPR base editors. In the base editor system, the Cas-9 protein doesn’t cut through the DNA strands, which reduces the occurrences of unwanted mutations. It still uses the original CRISPR targeting system, but converts only a single nucleotide into another, instead of a whole strand of DNA. Though safer than the traditional CRISPR-Cas9 cut and paste system, it has heavy limitations on the genetic diseases it can treat. Thus, scientists raced to find a better alternative.

That’s where prime editing comes in. Prime editing ensures not only safety but also offers treatment to a wide range of genetic diseases.

Prime editing differs from the traditional CRISPR system by using an altered version of both the Cas-9 protein and gRNA. This method uses a Cas-9 nickase fused with a reverse transcriptase, known as the prime editor. The new guide, known as pegRNA, now contains an additional RNA template as well as a primer binding sequence (PBS). The RNA template is used by the reverse transcriptase to create the desired DNA segment, and the PBS is used to bind the pegRNA onto the DNA segment after it has been snipped (not to be confused with the gRNA target sequence).

*Image by Synthego

How does this new prime editing system work?

Similarly to before, the PE:pegRNA complex first locates the target DNA segment. However, the Cas9 nickase nicks only one of the strands loose, creating a flap of DNA that the PBS can bind to and hold in place. This allows the reverse transcriptase to attach to the flap and create a new genetic sequence by reverse transcribing the edited RNA template, which replaces the original flap on the DNA strand. The prime editor now removes the flap’s corresponding segment that is on the opposite strand of the original DNA, which is still unedited at this time. This triggers the repair system to fix the damage by using the newly placed, synthesized gene as a template. Thus, both strands of DNA are effectively edited at the end of this process.

The blue section is the PBS that binds and holds the reverse transcriptase to the DNA flap. The yellow shape is the reverse transcriptase that reads the desired RNA segment(red) and creates the new, synthesized DNA (purple). The new DNA (purple) eventually replaces the original(green flap) in filling the open section of the original DNA segment. The unedited strand is then removed, which causes it to be repaired by using the new DNA segment as a template. *Image by Synthego

Why is this method better than before?

As previously mentioned, prime editing works by nicking one strand of DNA while the original CRISPR system cuts through both strands. Cutting only one strand prevents the DNA from automatically activating its repair system, which reduces the chance of genetic mutations.

Additionally, the prime editing (PE) system requires three pairing events to operate, as opposed to the single pairing system used in CRISPR-Cas9. This allows for increased accuracy and reliability when replacing the gene sequence. In fact, prime editing’s reduced off-target effects compared to the traditional CRISPR-Cas9 system allows it to make single-nucleotide edits in DNA that even base editors are unable to.

Besides being more accurate and less prone to errors, the PE system has much more versatile applications. Its edits now include 12 possible combinations of single base replacements against the 4 that base editing is capable of. This new system can now swap DNA letters into any other, as well as delete or insert letters in a genome, doing so with minimal damage to the DNA strands.

Another benefit of this new editing tool is its ability to operate in cells that can’t divide, something that the traditional CRISPR system has been unable to do. This allows PE to correct genetic mutations caused in cells that don’t divide, such as those in the nervous system.

Sooo…what’s the impact of all this?

Prime editing provides us with a tremendous advantage that base editing and CRISPR cannot. With the PE system’s more precise replacement technique and smaller error rate, scientists are able to better control their DNA replacement segments than the original CRISPR-Cas9. The additional versatility also allows the prime editing system to target more types of genetic diseases that both CRISPR and base editing are unable to fix successfully.

All this has led scientists to believe that prime printing can theoretically correct at least 89% of all human genetic diseases. If properly developed, the PE system could eventually cut and replace the cancer markers in DNA, and become the long-awaited cure for cancer.

Moreover, prime editing will be able to do all these new treatments at a much lower cost. For instance, cancer treatments that often drain a patient’s financial state could later be treated using a (relatively) cheap treatment of prime editing. PE could also treat long-term disabilities such as those with Alzheimer’s or special needs, thus reducing and maybe even removing the costs needed to take care of them altogether. This new editing technique could lead to an enormous decrease in healthcare costs, effectively redefining how the healthcare system works.

Wow! We’re basically invincible now!

Not quite. Though it has lots of potential, prime editing is still in its early stages, with much more testing needed to validate usage. So far, prime editing has only been tested in a small number of genetic diseases, while CRISPR has been proven through years of clinical research. In addition, prime editing has thus far been unable to edit larger sections of genetic material, which are needed for conditions such as hereditary heart disease, so the CRISPR system is still necessary for those types of diseases.

However, in due time and with lots more tests, prime editing may very well become the future of all genetic disease treatment plans. With the ability to accurately modify genetic structure with minimal risks, the technique has the potential to provide limitless treatments to genetic diseases, and eventually even address therapeutic treatments for medical conditions. Providing all this at a cheaper cost, the method of medical care will have to be re-evaluated in the coming years. As such, prime printing may well become the start of a genetic revolution.

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Allen Wang

Hey! I'm an 18 year old that is passionate about emerging tech, especially AI! Nice to have you here :)