A Crisp(r) Explanation of Biology’s Coolest New Tool

[En español]

If perusing the headlines is a regular part of your daily routine, you’ve probably noticed that one acronym has been exceedingly popular in the Science and Technology section for last couple of years: CRISPR. Even once you figure out what CRISPR stands for – Clustered Regularly Interspaced Short Palindromic Repeats – it’s not immediately clear what this technology does, let alone why it has earned a spotlight in so many headlines and has biologists everywhere buzzing with excitement.

What is CRISPR?

CRISPR – also referred to as CRISPR/Cas9 – is a DNA editing system. This natural system was first identified in bacteria. Scientists noticed short sequences of DNA were repeated in the bacterial genome. We call these CRISPR sequences: they appear in Clusters, they are Regularly Interspaced, they are Short Palindromes, and they are Repeated in several places. These CRISPR sequences flank unique sequences that aren’t found anywhere else in the bacterial genome. Scientists would later identify these unique sequences as viral DNA. If you’re a little bacterium, viruses are your enemy. Just like a human immune system generates antibodies to fight off the invaders that make you sick, these bacteria had found a way to identify foreign viruses that were trying to harm them – they put a DNA sequence that could identify the virus in between two CRISPR bookends, like a molecular wanted poster.


Apparently I’m not the first one to think of this metaphor.

This is where the Cas9 part of the system comes in. Cas refers to a group of enzymes – CRISPR-associated proteins – that interact with CRISPR sequences to delete foreign DNA. If the CRISPR sequences are your wanted posters, the enzyme Cas9 is your sheriff. It picks up the wanted poster, which is in the form of a guide RNA that contains the identifying code that was flanked by CRISPR sequences. Once Cas9 has found a match, it neutralizes the threat by cutting up the target sequence. In the laboratory, Cas9 uses a guide RNA that a scientist designs to find and edit a specific sequence; it’s our very own customizable gene editor.

Why is CRISPR so often making headlines??

This is super cool and all, but scientists have been editing DNA for a long time now. Why would an apparent extension of extant technological ability make its way to the headlines – especially those of nonscientific publications – so many times over the course of years?

Turns out, there’s a whole bunch of reasons.

CRISPR is way more efficient.

DNA editing is a much faster and more precise process now that we have CRISPR. Once you’ve designed your guide RNA (that molecular wanted poster), you can order it online and have it at your laboratory door about as easily and quickly as you’d order 1500 live ladybugs from Amazon (unfortunately, neither ladybugs nor guide RNAs are Prime eligible or anything, but it’s still pretty quick).

Once your guide RNA has arrived, your experiments will move much more quickly, too. Say you want to breed a mouse model of a human disease, and to do so you need to alter their DNA to include a certain mutation. Back in “the day,” breeding these genetically modified mice could easily take over a year. You often needed several generations of mice before you’d start to get mice with the genes you were looking for in the numbers that you needed for your experiment. With CRISPR, you need only one generation of mice to get your model!

Another awesome CRISPR feature is that it’s a potentially universal system of DNA editing. It used to be that scientists would be somewhat limited in terms of what kinds of organisms they could use because we only knew how to manipulate the genomes of certain species. This is part of why animals like mice and fruit flies are so common in biomedical research – we know how to edit their DNA to create our models. CRISPR, however, is theoretically capable of editing the DNA of any animal. As a result…



CRISPR opens up a world of innovative possibilities.

If we can edit the DNA of anything, where do we even start to assess the potential gains? You can really let your imagination loose to explore wild ideas with this one. I’m talking bring back the extinct wild. But if a world full of woolly mammoths isn’t on your list of priorities, CRISPR is still a game changer when it comes to generating practical solutions for some of our greatest collective problems.

Let’s start with a global problem that we all would love to solve – hunger. CRISPR carries huge implications for the global hunger crisis. In the realm of agriculture, CRISPR is already being used to generate crops that are resistant to common pests and diseases that can wipe out important food supplies. It can also bolster animal-based food sources. For example, a transgenic type of salmon that grows to full size more quickly than wild salmon was approved for human consumption by the FDA. It was an exciting development since sustainability is a significant problem in the world of commercial fishing. However, there were concerns that these transgenic salmon could escape their fisheries and then breed with wild salmon, which could have a negative ecological impact. Rather than scrap these valuable, fast-growing salmon, CRISPR has been employed to sterilize the transgenic salmon, so that even if they do escape, they’re not a threat to the environmental balance. Win-Win!

The use of CRISPR to modify animal genomes could also help us to slow or even stop the spread of serious diseases if we can spread the modification throughout populations of mosquitoes or other carriers of infectious disease. To this end, researchers have been using CRISPR to develop systems known as gene drives. With gene drives, genomes are edited so that certain genes become more likely to be passed onto future generations. So in mosquitoes for example, a gene drive for a malaria-resistance gene could be used to quickly spread malaria resistance throughout entire populations of mosquitoes. Like the sustainable salmon solution, a gene drive could also be used to spread a gene that sterilizes the mosquitoes, which is another intriguing method of curbing infectious diseases.

There is also a lot of excitement surrounding the idea that CRISPR could edit the DNA of humans. This is not some futuristic sci-fi fantasy; scientists in China have already been able to edit the DNA of human embryos using CRISPR. With this technology, we could edit the genomes of the human immune system to create stronger immune cells specifically designed to attack cancer. That is just one incredible opportunity if CRISPR was approved for use in humans. That said, there are a lot of ethical concerns associated with opening the can of worms that is editing the human genome. Its potential for both positive and negative innovation renders it worthy of intense scrutiny and debate. As such, we won’t go into that in this tiny paragraph – instead, we’ll cover it in much more detail in a later post.

Oh, and then there’s the legal drama.

I’d be remiss to ignore that there’s one other reason you may have noticed CRISPR populating your news feeds. There’s been some legal drama regarding who exactly owns CRISPR. (To be clear, “owning” is a bit of an overstatement; it’s a patent dispute, but all of us scientists can start using CRISPR right now if we want to without having to get involved in messy patent law). If you’re like me, the question seems like it would be straightforward – who did it first? That person should own it.

Well, it turns out that’s not that easy of a question.

The first published use of CRISPR was in the journal Science in 2012. That paper came from Drs. Jennifer Doudna and Emmanuelle Charpentier. The University of California filed for a patent based on their work in 2012, but it was quickly followed by another patent application from MIT that same year. That application was born out of the work of Dr. Feng Zhang, which extended the use of CRISPR into higher-order cells, like the cells of mammals. This is where the dispute comes in; many would claim that use in mammals is an obvious extension of the original pioneering work. So, does MIT’s patent interfere with the University of California’s? According to a recent opinion by the US Patent Office – no. The ruling claims that the work done by Drs. Doudna and Charpentier did not make its application to higher-order cells obvious enough for MIT’s patent to interfere.

This is a hotly debated topic in the science world, and for good reason. Beyond the finer points of patent law, this case could also decide how history remembers the creation of a revolutionary technology, and in particular who was the driving force behind it. Rather than get into the nitty gritty legal details, here is a starting point if you’d like to dig into this and decide for yourself who deserves the glory.

Possibly the most exciting thing about CRISPR (at least in my opinion) is that this is just the beginning. The coming years are poised to bring outstanding innovation to various scientific fields, all thanks to our ability to recognize the grand potential of a system that little bacteria have been benefitting from for a long time. The legal drama isn’t over yet either, so there will be interesting developments with that, too, if you’re into that sort of thing. If you’re as excited to watch this story continue unfold as I am, I strongly recommend checking out this Radiolab episode, which delves deeper into the mechanisms, history, and potential future of CRISPR.