Supercomputer-Powered CRISPR Simulation Lights Path to Better DNA Editing

By Oliver Peckham

May 5, 2021

CRISPR-Cas9 – mostly just known as CRISPR – is a powerful genome editing tool that uses an enzyme (Cas9) to slice off sections of DNA and a guide RNA to repair and modify the DNA as desired, opening the door for cures to diseases like Huntington’s disease, sickle cell anemia, polycystic kidney disease and others. CRISPR, however, is still new tech, and in its current form can sometimes err, causing unintended DNA changes – a serious risk. Researchers from the University of California Riverside used supercomputing to run simulations of CRISPR, illuminating ways to make the tool more accurate and avoid major side effects.

The UC Riverside team, which includes a pair of post-doctoral researchers and a pair of students, sought to understand the motions that the Cas9 protein exhibited when docking to and severing a slice of DNA. Specifically, the team was interested in the severing; they had already used other supercomputers to simulate the binding process, led by the REC1 and REC2 domains of Cas9, but had failed to observe the cutting process, led by the HNH domain.

The HNH domain – which remained in an inactive state in the binding simulations – appeared to require much more simulated time if the researchers wanted to observe its motions. So the researchers designed a 16 microsecond simulation: 40 times longer than the previous 16-microsecond simulations. To run this more powerful simulation, the team turned to the Pittsburgh Supercomputing Center (PSC), which provided its 128-node Anton 2 supercomputer for the research. 

Through the much longer CRISPR simulation, the team was indeed able to observe the HNH domain activating and severing the DNA at the atomic level. What’s more, subsequent cryo-electron microscopy research has validated the in silico research.

“If Anton wouldn’t have been available, I think that this amount of sampling wouldn’t have been possible,” said Giulia Palermo, an assistant professor at UC Riverside, in an interview with PSC’s Ken Chiacchia. “Using earlier simulations, based on a novel Gaussian accelerated molecular dynamics method, we saw some movements that actually told us that this would have been possible to simulate. However, perhaps without Anton we wouldn’t have been able to observe the full conformational activation in a timely fashion.”

Now, the team is moving forward using Anton 2 (alongside other HPC resources) to further delve into the errors that are occasionally produced by this cleaving process and investigate other CRISPR-related proteins.

To learn more about this research, read Ken Chiacchia’s article here or read the research papers here and here.

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