You may have heard of CRISPR, a technique whose unparalleled ability to edit DNA has revolutionized the field of biology. But what exactly is CRISPR?

CRISPR, which stands for Clustered Regularly Interspersed Short Palindromic Repeats, is a powerful tool that researchers can use to both disable genes and increase their expression.

CRISPR-Cas9, as the name suggests, uses the Cas9 enzyme, which was first synthesized from a bacterium. (Cas standing for CRISPR associated protein – all Cas proteins are involved with CRISPR).

Dr. Megan Hochstrasser, who is the scientific communications manager for the Innovative Genomics Initiative and received her Ph.D. in the Berkeley Doudna lab, one of the first labs to use the CRISPR-Cas9 system in research, describes CRISPR-Cas9 as having been adapted from a “bacterial immune system.”

“Bacteria can be infected by viruses just like you and I can,” Dr. Hochstrasser said. “It’s evolutionarily advantageous for the bacteria to develop some way to defend against these viruses. And the way that they did it is they developed the CRISPR system, which lets them capture these little segments of DNA from viruses and integrate them into their own genome, so the bacterial host genome is full of these little snippets of viruses.”

Somewhere in its genetic sequence, the bacterium will have a series of short, repeated DNA segments called repeats broken up by variable DNA segments, called spacers. These spacers are part of the DNA sequence of a bacteriophage, a virus with a bacterial host cell.

The bacterium can use this sort of “rogues’ gallery” to protect the bacterium from infection. The bacterium transcribes excerpts of spacers into RNA and gives it to the Cas9 enzyme. The Cas9 enzyme then tries to find a match of the given guide RNA to a DNA sequence. Upon finding one, it promptly cuts the DNA, deactivating it.

“The cell will remember what the virus looks like, what sequence it has in its DNA, so that if [the virus] comes back, [the bacterium] can destroy the virus by finding the matching sequence and then cutting it so the virus can’t replicate,” Dr. Hochstrasser said.

What this amounts to is that the Cas9 enzyme can use the bacterium’s records to identify bacteriophage DNA and destroy it before it becomes integrated into the bacterium.

Researchers have adapted the Cas9 enzyme for research. As any sequence of RNA can be used as the guide, the Cas9 enzyme can be “programmed” to seek a target sequence of the researcher’s choice.

“The first thing when CRISPR came out is this idea we can now edit the genome,” said Rajiv Movva (11), who worked with CRISPR on a research project over the summer. “What that means is that we have a certain sequence in the genome—we know where it is, we know what the sequence is and basically we can take out that sequence and replace it with whatever we want.”

This ease of use is unprecedented in the field of biology. Marie La Russa, a Ph.D. candidate at the Stanford Stanley Qi lab, which has done much research into CRISPR, says that CRISPR’s facility results from the fact that it uses RNA rather than proteins.

“We know how DNA bases will pair up with each other, and it’s a very simple rule system, and it’s very similar to RNA-DNA interaction,” La Russa said. “It’s very easy to change the target sequence that you look at. With older technologies, they targeted DNA through protein-DNA interactions, and those are much more complicated to engineer because when you want to target a new site, you have to do very complicated protein engineering.”

While CRISPR has already made waves in the field of research, many are excited about its potential applications in the field of medicine, as it could be used to treat genetic diseases by correcting patients’ genomes. However, current technology is insufficient for effective therapeutic use.

“One of the big challenges of using CRISPR for medicine is delivering it specifically to the cell type that you want—not just targeting the gene region that you want, but also making sure that that the CRISPR Cas9 system is only delivered to [the desired target cells],” La Russa said. “But it’s very exciting; there’s a lot of potential.”

Some worry about the potential ethical implications of editing the human genome.

“If we’re talking about preventing disease in an embryo, for example, by doing germ line editing, you introducing CRISPR into a fertilized egg or embryo without the consent of the embryo before it’s born, you don’t really know how you’re affecting that organism, which will eventually become a person,” Dr. Hochstrasser said. “They can’t say whether or not they want this to happen, we don’t know yet whether the protein will cut somewhere unintentionally.”

Regardless of your moral stance, one thing is indisputable: CRISPR has already significantly augmented the capabilities of research and will only continue to influence science in the years to come.

Gallery • 3 Photos

Derek Yen