Prime Editing: A Powerful Innovation on the Forefront of Genome Editing
Imagine a world where one’s genetic disease could be cured before they were even born. Given that nearly 6 out of 10 people are affected by illnesses that have some sort of genetic background, you’d think that I was lying when I say that we don’t need to imagine. Soon, we may be able to see these fictional ideas become a feasible reality — thanks to a revolutionary biotechnology tool, Prime Editing!
In simple words, gene editing refers to a method that allows scientists to change the DNA of living organisms, which includes us, humans! Since 1981, when the first genome editing methods were discovered, scientists have been working towards attempting to change and have more control over our DNA. Until recently, CRISPR-Cas9 was the main technology used to edit our genes but it had a lot of limitations to it.
Now, this is exactly where Prime Editing comes in! The new improvements made to the original CRISPR tool have allowed for a future where gene editing is more precise, efficient and most importantly, safe.
I’m sure you’re eager to learn more, but before we get into the specifics of Prime Editing, it’s important that you understand DNA and RNA!
DNA and RNA: What Are They?
Have you ever wondered why you have the colour of eyes that you do? Or why certain plants have more leaves than another? Well, it’s all because of DNA! Deoxyribonucleic acid, aka DNA, is a molecule that acts as the set of instructions for our bodies. It’s what makes us so unique. From the colour of our eyes to our chances of hereditary diseases, DNA is responsible for choosing all of it.
Our DNA is structurally a double helix shape — or you could say they are 2 strands that are bonded to each other in a ladder-like shape that’s twisted. Every one of these strands contains nucleotides, which act as the building blocks of DNA. In each nucleotide, we have 4 bases that act as our bodies’ code: Adenine, Thymine, Cytosine and Guanine! We use letters A, T, C and G to represent them.
Note: Each type of nucleotide does not bond with each other so you can only have them bonding with specific nucleotides.
- A + T
- C + G
These are known as our base pairs!
Now, the order of these are very important as they form your genetic code, which are basically the instructions for our lives. Depending on the sequence of the nucleotides, the gene will encode for a different protein. For example, one gene codes for the protein, insulin, which is a hormone that helps control the levels of sugar in our blood. Though, if you changed up the order of these letters, you would change what the gene would express as well.
Let’s say you changed the spelling of “fried” to “fired”. Even though you switched around one letter, the meaning of the word changes completely, right? So, if you were to change the sequence of nucleotides, you’d change its meaning as well. In this case, it means the strand will encode for a completely different protein.
This is referred to as a mutation in scientific terms. Most of the time, mutations are harmless and have no effect on the organism. Though, it’s important to be careful of the risks involved as well because harmful mutations can cause genetic disorders and cancer.
Now, ribonucleic acid, aka RNA, is a molecule that is very similar to DNA. It’s also made up of nucleotides but instead of Thymine, it has Uracil to bond with A. Also, instead of two strands in a double helix shape, an RNA molecule is one strand. In terms of roles, DNA provides the code for the cell’s activities whereas the RNA converts the code into proteins to carry out the functions of the cell. Though, the coolest part about RNA is that it can bond with unfolded pieces of DNA, in a process called transcription!
Now that you have a better understanding of DNA, RNA and their main functions, let’s explore Prime Editing!
What is Prime Editing: Let’s Learn The Basics
Dr. David Liu and his team at the Broad Institute of MIT and Harvard have developed a new CRISPR gene-editing tool that can potentially correct 89% of known disease-causing genetic abnormalities. This emerging technology is referred to as Prime Editing, also known as CRISPR 2.0, and it is a “search and replace” genome editing tool.
Let’s say you’ve been writing on Microsoft Word and mid-way through, you realized one of the words you’re using doesn’t make sense. In that case, instead of searching for them individually and risking that you’ll miss one, you’ll simply Ctrl + H to target the text and then replace all of them. Prime Editing is exactly like that — but instead of words on a screen, you’re modifying the letters in the genome of actual living organisms!
CRISPR 2.0 has the power to change how we treat inherited diseases, many of which also have no cure. Using CRISPR 2.0, scientists are able to locate mutations within our DNA to edit and replace it! Remember how we talked about DNA, specifically nucleotides, earlier? Well, the human genome contains six billion DNA letters — which we know are A, C, G and T.
CRISPR is able to change one of these letters at a time without breaking the DNA structure — which can tackle thousands of potential mutations.
So, how does Prime Editing actually work? How are we able to see successful results through this gene-editing tool?
CRISPR 2.0 consists of 3 main components that work together in allowing it to be successful: Cas9 nickase enzyme and a reverse transcriptase enzyme combined together as a protein along with prime editing guide RNA (pegRNA).
Each of these components are extremely important to editing the genome. Think of the Cas9 enzyme as the “scissors” of the tool — it’s been modified to target and pick only one strand of DNA. The reverse transcriptase’s purpose is to create new DNA from an RNA template, which is known as the guideRNA — a template that is engineered by scientists to help the Cas9 identify specific gene sequences. Finally, there is the pegRNA, which encodes for DNA editing. This simply implies that it will prepare to have additional DNA letters added to it.
From here, let’s take a look at the specific procedure of the Prime Editing procedure!
In the beginning, scientists will have to engineer a pegRNA that will act as the guide or template for the Cas9 nickase. From there, they will need to build the Prime Editing Complex — which will be done through binding the pegRNA to a “Cas9 nickase + reverse transcriptase complex.”
When we go to use CRISPR 2.0, the pegRNA will identify and send the editor to the nucleotide that’s being targeted. The Cas9 nickase will nick the appropriate DNA sequence here. The reverse transcriptase will then read the DNA letter templates encoded by the pegRNA and attach them to the end of the nicked DNA. From here, the old nucleotides are removed and the new letters are added into the genome. Another enzyme called endonuclease will naturally remove the old segment of DNA and seal the new letters into the genome.
Now, when you do this, you will initially get a mismatch as your DNA will have one edited strand and one unedited strand. These can also be called a “target strand” or “non-target strand.”
Think about it this way: Both of these strands are competing for a spot in the genome. Our cells will recognize this discrepancy and try to fix it immediately, either by replacing the base pair on the non-target strand (which is good) OR replace the base pair on the target strand (which isn’t what we want).
To solve this, scientists will apply a different guideRNA to instruct the primary editor to nick the unedited strand as well. By doing this, they can trick the cell into perceiving the non-target strand as unhealthy, so it’ll rush to replace that instead! This will finish the edit by remaking the unedited strand using the edited strand as a template.
The Difference Between CRISPR 1.0 and CRISPR 2.0: How is Prime Editing an Evolved Version of Base Editing
In less than 5 years, CRISPR has accomplished significant improvements in gene editing. However the question typically arises: What differentiates Prime Editing from the original CRISPR tool?
You’d assume they’re very similar because the CRISPR-Cas9 system also employs the Cas9 enzyme to make edits — which is true to some extent — but there are other differences that make Prime Editing much better!
Remember how we explored reverse transcriptase and pegRNA, both of which are key components in Prime Editing? Well, these are only a part of CRISPR 2.0. The reason why they’re so significant to Prime Editing is because it’s what allows CRISPR 2.0 to be so precise while eliminating the high risks associated with gene editing.
CRISPR’s targeted cutting action is its defining feature, yet there is a significant risk connected with cutting an organism’s DNA; cells are prone to creating mistakes rather than correcting genetic diseases. Thankfully, in Prime Editing, the Cas9 nickase has been modified to cut only one DNA nucleotide at a time. In doing so, we can modify the genome while avoiding the limitations of the original CRISPR tool.
The way I like to think of it is: Our DNA is a book that we’re trying to edit — CRISPR is like ripping our pages and adding in a completely different page whereas CRISPR 2.0 is similar to simply editing one word on a page!
Which method would you prefer to edit your book? Personally, I think that the best method is to tweak a single word on a page since it doesn’t ruin the book — exactly like Prime Editing!
Overall, CRISPR 2.0’s precision, efficiency and reliability give us a far better chance of safely fixing genetic conditions.
A Groundbreaking Discovery: Why is Prime Editing So Significant?
If you had time before an essay was due to remove all your spelling errors, would you do it or not? I know that I would — I mean if it lets me remove the possibility of a lower grade, I’d do it!
Now, consider this: If you had the chance to remove or replace mutations in a human’s DNA before they were born, so they wouldn’t have to deal with genetic abnormalities, you would do it right?
Unfortunately, genetic disorders are prevalent in the human population — Down Syndrome, Cystic Fibrosis and Sickle Cell Anemia are some of the most common examples. They can occur for a variety of reasons and result in a range of genetic illnesses; nonetheless, they are always caused by harmful mutations. Even though some genetic conditions may not cause any symptoms, others can cause severe, life-lasting problems for both the child and family.
Luckily, the right tool to solve this widespread issue is in front of us — Prime Editing!
Using this genome-editing technology, we can locate and identify any mutations in the DNA and quickly replace them with the editor.
The best thing about all this is… it’s already happened using CRISPR! Imagine how many more changes we could make in the world when we have a much more precise and efficient tool, Prime-Editing.
The Future of Prime Editing: What’s Next?
Without a doubt, Prime Editing has a promising future ahead of it as scientists continue to focus on its advancements. CRISPR 2.0’s wide flexibility, efficiency and high degree of precision allows it to hold a great level of potential for the future.
Till this day, companies such as Beam Therapeutics and Prime Medicine have incorporated prime editing into their laboratory research. Prime Medicine, in specific, is a biotech startup that has raised $315 million to fuel the “search-and-replace” genome editing tool.
“It only makes the correction you’re aiming to make, and it doesn’t make corrections elsewhere in the genome.” — Keith Gottesdiener, CEO of Prime Medicine
Though, it’s important to note that Prime Editing is still in its early stages. Even if we’ve been exposed to the idea of limiting hereditary diseases through removing mutations, prime editing technology is still at its early phase of development — it hasn’t been experimented heavily to the point where the general public is secure with the idea of editing our DNA.
Despite significant developments in the CRISPR-Cas9 system, it still has technical limitations and requires further research. Nonetheless, once that is completed, Prime Editing, an efficient and precise tool, has the potential to revolutionize the world and make it a better place.
- Prime Editing is able to edit our DNA as easily as we can “Ctrl + H” on Microsoft Word to limit diseases that are genetic-based!
- Prime Editing works by using the Cas9 nickase enzyme and a reverse transcriptase enzyme combined together to target our DNA using a gRNA. A mismatch will initially be created, but the CRISPR 2.0 technology helps that issue by nicking the non-target strand to replace it — which will complete the edit.
- Prime Editing is an evolved version of Base Editing and has the potential to change the way we tackle genetic diseases!
Thank you so much for reading! I hope that through reading this article you were able to learn something new about the world of gene-editing 😁