New CRISPR technique called prime editing could make gene editing safer and better

The CRISPR genome-editing technique revolutionizing biology just got a major upgrade. A new variant, called prime editing, should be even better at correcting disease-causing mutations.

This approach, devised by Andrew Anzalone at the Broad Institute in Massachusetts makes it possible to add or delete short DNA sequences, or change one DNA letter to another, with fewer unwanted side effects. The findings were published in the journal, Nature.

The technique gets closer to the ideal form of genome editing, which would work like the “find and replace” command in a writing app. Use of CRISPR has grown rapidly since it was devised in 2012 because it made the “find” part far cheaper and easier.

CRISPR exploits a protein called Cas9, which hooks up with a piece of guide RNA and seeks out matching DNA sequences in a cell’s genome. Because it is easy to make custom RNAs, Cas9 can be programmed to find any desired sequence.

The “replace” part is more problematic. Cas9 is usually used only to introduce mutations that can disable a gene, by cutting the cell’s DNA. If an extra piece of DNA is added at the same time, it sometimes gets spliced into the cut site, but this typically works in less than one in 10 cells.

That is why many biologists are trying to improve CRISPR. Anzalone and his colleagues have altered the Cas9 protein and fused it with another to make it work in a different way.

DNA’s double-stranded structure helps cells repair some forms of damage: because the two strands are complementary, the cell can sometimes fix an error in one by referencing the other. But Cas9 cuts both strands, meaning the cell usually makes mistakes during repairs, introducing mutations that can disable a gene.

Anzalone’s hybrid protein is programmed with an extra segment added to the guide RNA, which adds a single strand of DNA to the target site. The protein then cuts the opposite strand, prompting the cell to repair the DNA using the added strand as the template.

In effect, Anzalone has made CRISPR fully programmable. The sequence of the guide RNA determines both the site of an edit and the change to be made.

The team has already used the new method to correct mutations in human cells. “What we observed was remarkable,” says team leader David Liu, whose “base editing” approach inspired Anzalone. There are fewer off-target edits, he says, because editing now involves three steps rather than just one.

The limitation is that only short sequences can be changed – the biggest addition so far was 44 DNA letters long, and the biggest deletion 80.

Source: New Scientist, Nature