Prime Editing

Varsha Prasad
6 min readJul 27, 2020


Cancer is the second leading cause of death globally, accounting for an estimated 9.6 million deaths, or one in six deaths and is constantly growing and caused by a genetic mutation.

Our DNA is not perfect and it forms many mutations that are passed down to the next generation. This is how people have different eye colours and hair colour but this can also cause detrimental conditions like diseases and disabilities. When a machine is not working or has an issue, we find what part is causing the problem and replace it. This is what Prime Editing is accomplishing but on a genetic level.

Prime Editing is a ‘search and replace’ a genome editing technology that alters different genes in living organisms. It uses a fusion protein that consists of catalytically impaired Cas9 endonuclease fused to an engineered reverse transcriptase with a prime editing guide RNA (pegRNA) that finds that DNA and rewrites it. Prime Editing allows scientists to add, remove or alter specific locations in the genome.

Background Information

DNA(deoxyribonucleic acid)is a molecule, located in the nucleus of a cell, shaped like a spiral staircase (double helix), which is a blueprint for all living things. Genes are strands of DNA and each strand is made of millions of particles called nucleotides. Genes are segments of deoxyribonucleic acid (DNA) that contain the code for a specific protein that functions. The genetic code enables a cell to translate the nucleotide language of DNA into the amino acid language of proteins. The strands are a sequence of nucleotides and each sequence forms a different shape.

Nucleotides have a sugar part, a phosphate part and a base. The nitrogenous base is the part that holds the genetic information and has four types(Adenine, Thymine, Cytosine and Guanine). Amino acids are the building blocks that follow the instructions of the DNA. The amino acids come in twenty different types and make proteins. Genes are contained in chromosomes, which are in the cell nucleus. Chromosomes are made of DNA and protein and a human being has 46 (23 pairs). As an atom is the fundamental unit of matter, a gene is the fundamental unit of heredity.

Let’s think of this process in an analogy so we can understand it better. The nucleus is the engineers and they fax a small copy of the DNA which are instructions to build a product. The copy that they made is called RNA. The RNA goes to ribosomes through the pores of the nucleus. The ribosomes are the construction workers that make proteins by reading the instructions three letters at a time. The instructions in the RNA are nucleotides put into different sequences that represent different shapes. The construction worker will take blocks of amino acids and will have the final product of a protein. Proteins are important as they make up living cells and fix the damage.

Prime Editing has three major segments:

  1. The RNA editing guide(pegRNA) finds the target nucleotide sequence and encodes it with the new genetic information.
  2. The Cas9 endonuclease is responsible for nicking the selected part of the DNA.
  3. The engineered reverse transcriptase produces DNA from a single-stranded RNA template.


The cell is first transfected with the pegRNA and the fusion protein. It gets into a cell using a vector which is like a vehicle that carries foreign genetic material into a cell.

The prime editing guide identifies the target DNA sequence that needs to be cut. The fusion protein cleaves the targetted area and starts the reverse transcription of the RT template. In simpler words, this is when they make the edited sequence that needs to be inserted. Then, they insert the edited sequence(Y) into the DNA strand and the original sequence is completely cut off. Later the same process happens to the non-edited side.


CRISPR-Cas9 is another type of genome technology that was discovered before Prime Editing(in 2012) but it had flaws. The CRISPR-Cas9 cut both strands of DNA and relied on the cell’s recovery system to fix itself. When both the strands are cut, there is more space for more insertions. Since they are trusting the cell’s recovery system, there are lots of chances for more mutations where the DNA was cut. Additionally, this was not reliable because sometimes it cleaves the wrong strand.

Prime Editing can insert or delete specific sequences at exact locations making it more precise. Since it is only nicking one of the strands, there is less collateral damage. Both the technologies use the Cas9 enzymes but prime editing uses another enzyme to reduce errors. The enzyme reverse transcriptase makes the edits so there are very low chances of unwanted edits. When the CRISPR-Cas9 makes an unwanted edit, it has lots of damage without creating anything.

Another disadvantage of CRISPR-Cas9 was that it relied on the ability of the cell division to make the changes. This is bad because if there are diseases with cells that do not divide, like the cells in the nervous system, will not be treated. Since Prime Editing does not rely on cell division, it has fewer limitations on what it can treat. Some medical conditions that are caused by mutations in genes in those cells are Parkinson’s and Huntington’s diseases.

The Importance of Prime Editing

If we get rid of the mutations in all people who have a disease, we can get rid of most of that disease in the world. This will make sure the next generation has fewer diseases. Some disabilities are also because of genetic mutations and although it has not been done yet, I believe they can also be corrected with Prime Editing.

Genome Mapping can figure out if diseases have been transmitted from parent to child. This is because those diseases are linked to genes that provide information on which chromosomes contain and where the gene is on the chromosome. When people figure out they have diseases, they may have to sacrifice a lot but with Prime Editing, they could sacrifice a lot less.

For example, Angelina Jolie had genome mapping done and figured out she had a high risk of developing breast cancer due to the mutation of the BRCA1 gene. She did not want any chance of having this cancer so she had her breasts removed. If Prime Editing had been advanced enough then, they could have edited the genes that were causing this problem and she would not have gotten a mastectomy done.

The Future of Prime Editing

Prime Editing is still in its early stages and has not been used in many diseases. Researchers have had success in correcting the main causes of sickle cell disease and Tay-Sachs disease. In the future, Prime Editing will play a leading role in plant biology and crop improvement which will help greatly with the health of people and starvation.

For medical conditions, scientists have estimated that at least 89 percent of known disease-linked genetic mutations could theoretically be corrected using prime editing. If gone hand-in-hand with genome mapping, it could have many more uses.

Prime Editing has very few limitations and is an extremely precise tool that can be used in very great ways in the future. When scientists learn and understand more about Prime Editing, it could be one of the biggest revolutions in health for the world.

Key Takeaways:

  • Prime Editing is beneficial to get rid of diseases that are caused by genetic mutations.
  • Prime Editing is more efficient and beneficial than CRISPR-Cas9 as it is more precise and has less collateral damage.
  • Although this technology has been used in a few diseases, more research is needed to improve the technology so that is can clinically solve all the genetically related diseases.