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You may have seen it in the news recently: a baby in Pennsylvania with a rare genetic disorder was healed with a personalized treatment that repaired his specific genetic mutation. The treatment was created using a form of gene editing called base editing —a method created by Alexis Komor when she was a postdoctoral scholar in molecular biologist David Liu’s group at Harvard University.

Since that work was published in 2016, Komor, who is now an associate professor of chemistry and biochemistry at the University of California San Diego, has continued to study base-editing tools to better understand and further develop their capabilities. Her latest research, published in Nature Communications, outlines the way certain DNA repair proteins can be manipulated to produce desired outcomes.

Our genomic DNA is comprised of four bases — cytosine (C), thymine (T), guanine (G) and adenosine (A). These bases join together into approximately 3 billion different base pairs, arranged in a double-helix structure.

Humans are 99.9% identical in their genetic makeup, while the remaining 0.1% accounts for any difference between one person and another. Where one person has a C base, another person might have a T base. There are millions of genetic variations possible between any two people, and although many are harmless, others can lead to debilitating or terminal genetic diseases.

For many people with genetic diseases, gene editing is their only hope of a cure.

Gene editing is traditionally done using CRISPR-Cas9 to make a physical change in the DNA. A guide RNA directs the Cas9 protein to a specific DNA location, where Cas9 completely severs the DNA — called a double stranded break. There are many proteins within the cell that can detect DNA damage and then fix it through a process called a repair pathway.

Normally these pathways take the two broken ends of the DNA and fuse them back together, called a ligation. With CRISPR-Cas9, as the number of breaks and repairs increases, so do unwanted insertions and deletions, called indels. When this happens, the DNA strand no longer matches the original and the editing process ends.

The basics of base editing/h3>

As a postdoc, Komor found a way to achieve gene-editing with higher efficiencies and a lower incidence of indels by avoiding double-stranded breaks. She called this new class of tools “base editing” because it chemically changes a DNA base one letter at a time.

“With base editing, not only do we achieve a better outcome, but the steps leading to the outcome are also improved,” stated Komor. “Double-stranded breaks can be toxic and can cause cell death. They can also cause larger-scale genomic rearrangements because you’re physically cutting up the DNA. Base editors avoid that.”

Komor developed two tools, an adenine base editor (ABE), which converts an A base to G base, and a cytosine base editor (CBE), which converts a C base to a T base. Base editors make conversions through an intermediary. In the case of CBEs, the cytosine is first converted to uracil, a nucleic acid found in RNA. During repair, the DNA reads the uracil as thymine.

Although there’s no double-stranded break, base editors do create a nick in one strand. An enzyme is attached to the Cas9 and chemically changes the base. CBEs can have a 90-95% conversion rate with minimal unwanted byproducts.

We know the base editor works, but how? That’s the main question Komor’s group wanted to answer. They wondered how the uracil was being handled by the cell. What role does the nick play? How do all of the different proteins in the cell affect the editing outcomes?