Scientists develop technology that brings new precision to genome editing

The FDA’s approval of the first CRISPR-Cas9–based gene therapy marked a major milestone in biomedicine, validating genome editing as a promising treatment strategy for disorders like sickle cell disease, muscular dystrophy, and certain cancers.

CRISPR-Cas9, often likened to “molecular scissors,” allows scientists to cut DNA at targeted sites to snip, repair, or replace genes. But despite its power, Cas9 poses a critical safety risk: the active enzyme can linger in cells and cause unintended DNA breaks—so-called off-target effects—which may trigger harmful mutations in healthy genes.

Now, researchers in the labs of Ronald Raines and Amit Choudhary, both associate members in the Broad Institute’s Chemical Biology and Therapeutics Science Program, have engineered a precise way to turn Cas9 off after its job is done—significantly reducing off-target effects and improving the clinical safety of gene editing.

Their findings are detailed in the Proceedings of the National Academy of Sciences (PNAS).

“To ‘turn off’ Cas9 after it achieves its intended genome-editing outcome, we developed the first cell-permeable anti-CRISPR protein system,” said Raines, who is the Roger and Georges Firmenich Professor of Natural Products Chemistry at MIT.

“Our technology reduces the off-target activity of Cas9 and increases its genome-editing specificity and clinical utility.”

The new tool—called LF_N-Acr/PA—uses a protein-based delivery system to ferry anti-CRISPR proteins into human cells rapidly and efficiently. While natural Type II anti-CRISPR proteins (Acrs) are known to inhibit Cas9, their use in therapy has been limited: they’re often too bulky or charged to enter cells, and conventional delivery methods are too slow or ineffective.

LF_N-Acr/PA overcomes these hurdles using a component derived from anthrax toxin to introduce Acrs into cells within minutes. Even at picomolar concentrations, the system shuts down Cas9 activity with remarkable speed and precision—boosting genome-editing specificity of up to 40%.

MIT chemistry professor Bradley Pentelute, an expert on the anthrax delivery system, is also an author of the PNAS paper. Choudhary is an assistant professor of medicine at Harvard Medical School

The implications of this advance are wide-ranging. With patent applications filed, LF_N-Acr/PA represents a faster, safer, and more controllable means of harnessing CRISPR-Cas9, opening the door to more refined gene therapies with fewer unintended consequences.