Just How Easy Is It to Edit DNA?

11:18 minutes

A model of a DNA strand, via Shutterstock
A model of a DNA strand, via Shutterstock

Several years ago, a new DNA-editing technique called CRISPR-Cas9 swept through biotech labs around the world. The technology, borrowed from a bacterial defense system, uses a pair of molecular scissors to snip DNA within a host cell at predetermined spots. A new gene can then be subbed into the vacant spot. It’s incredibly powerful technology, with huge potential—and sometimes scary consequences.

But too often, says synthetic biologist Karmella Haynes, CRISPR-Cas9 is described in the media as an easy fix for gene editing, when in reality it often fails dozens of times before working. That’s because the system evolved in bacteria, which have much simpler DNA. It’s much harder, she says, to perform Cas9-mediated genetic surgery on the tightly coiled DNA of animals and plants. In this segment, Haynes explains the challenges posed by the technique, the subject of her latest paper in ACS Synthetic Biology.

Segment Guests

Karmella Haynes

Karmella Haynes is an assistant professor in the School of Biological and Health Systems Engineering at Arizona State University in Tempe, Arizona.

Segment Transcript

IRA FLATOW: This is Science Friday. I’m Ira Flatow. One of the most powerful tools biologists use today is not some new DNA sequencer. It’s not a gene printer, either. In fact, it’s not something we humans invented at all.

It’s something we borrowed from bacteria, a sophisticated self-defense they have, a molecular machine that chops up invading viruses to stop an infection. The tool is called CRISPR-cas9, and it allow scientists to edit DNA, to modify or delete genes and add new ones, too. It’s already being used to develop new drugs. And its versatility is not without controversy.

Like, should you use CRISPR to edit the genes in a human embryo? Should you use it to modify mosquitoes so they can’t transmit malaria? Lots of big questions.

But before we get ahead of ourselves, my next guest says this gene editing technology, well, it’s not as easy to use or as much of a guaranteed home run as we have been led to believe. Carmela Haynes is an Assistant Professor in the School of Biology and Health Systems Engineering at Arizona State University in Tempe. Welcome back to Science Friday.

CARMELA HAYNES: Hi, Ira. It’s great to be here. Thank you.

IRA FLATOW: You’re welcome. We’ve been reading sort of a challenge about how easy CRISPR is to use. Rudolf Jaenisch of MIT said quote, “any idiot could do it”. And that’s been sort of put to the test and found out that any idiot could really not do it that easily.

CARMELA HAYNES: Right, yeah, definitely. So our lab spends a lot of time studying a system that is unique to any living thing that is basically made up of more than one cell. And so sort of the catch there is that any idiot could do it assuming that there are no roadblocks or special things about how the DNA is coiled up inside of the cell that would prevent the CRISPR– I guess a sort of scissors-like machinery to get in and actually access the target gene.

IRA FLATOW: So for example, in human embryos, those cells are pretty well coiled up?

CARMELA HAYNES: Indeed, yes. And so the thing about the CRISPR machinery is that, I mean it is fantastic. It’s very good at what it does. But over the millions of years that it’s evolved, it’s operated inside bacteria in a space where we don’t see the same, quite the same type of DNA coiling and packaging that we see in a cell like cell in a human embryo.

So the DNA in embryonic cells, in particular, has a lot of interactions deep inside the nucleus that sort of package and separate certain genes away from the rest of the environment. So this actually poses a bit of a molecular challenge to the CRISPR machinery in terms of accessing the target that you’re going after.

CARMELA HAYNES: Whenever– we talk about CRISPR, a lot on the show because it is such a cutting edge technology and one that is fraught with ethical decisions. And the more I talk to people around, they say, you know it sounds pretty easy.

But what you don’t hear of are a lot of failed attempts at using it. A lot of trial and error, and so on. Would you agree with that?

CARMELA HAYNES: I would definitely agree with that. So when scientists publish what get higher priority are those success stories. So if there’s a particular gene that has a lot of importance in medical research, there is a lot of work that’s put into picking just the right spot on that gene that through trial and error, we find that CRISPR is very good at cutting. So what you’ll see in a lot of the publications are examples of where it works.

But due to the way that publications are structured, and our general culture around reporting on successes and not so much failures, there’s a lot of information out in the body of scientific knowledge that tells us that it doesn’t always work quite as well as we expect it to.

IRA FLATOW: It’s CRISPR itself, the whole connection to bacteria is just, it’s so fascinating, isn’t it? That bacteria have been fighting this fight with viruses, every bacteria has a virus that wants to eat it, and has come up with this mechanism to stave it off. And then here we are sort of adopting it.

CARMELA HAYNES: Oh, yes definitely. That is a fascinating aspect of the use of the system. I think that when scientists started figuring out how the system worked, they immediately started thinking about applications. There are things that are similar in the research community, like things called restriction enzymes that are also derived from bacteria that are very good at cutting up DNA.

But I think that another– speaking of defense mechanisms, the cells of higher organisms, as it were, have a system that doesn’t necessarily rely on cutting invading DNA. What cells like human cells like to do is sort of after the DNA finds its way into the nucleus, what has happened in a lot of cases or at least we have a lot of evidence for this is that special proteins that co-exist with the DNA inside of a cell nucleus will take the DNA and package and wrap it in a very tight structure. So that those invading pieces of DNA can’t replicate and excise themselves and move around and sort of mess up our genetic code. So human cells have their own defense mechanism that I think that, in the early stages of developing CRISPR as a tool, we hadn’t quite started to address that challenge just yet.

IRA FLATOW: But you think it is an addressable challenge?

CARMELA HAYNES: Oh definitely. So a little over, just about two years ago, my grad student and I– so a fantastic grad student, Renee Dare, we’d worked with some other professors to start teaching a course on synthetic biology. So that’s my field. We think of ways to put together borrowed bits and pieces from biology and make very useful tools.

So we set out to develop a course at Cold Spring Harbor Laboratory. And we decided to focus on teaching about CRISPR for aspiring synthetic biologists. So we sat down and thought about how to set up this lesson. And we wanted to make it very interesting.

So we started looking in the CRISPR, and we got very curious– since our specialty is in DNA packaging and how to engineer that– we started asking ourselves, well, you know since CRISPR comes from a bacterial system. It’s evolved in an environment where it hasn’t really been exposed to all of these complex packaging machineries. What if we actually challenged CRISPR with a packaged system?

So we happened to have a very nice engineered, human cultured cell line that we use in the lab to probe questions about engineering DNA packaging. And what we did was that we did a pretty simple experiment where we packaged, artificially packaged a target sequence inside the cells. And then introduced CRISPR and measured how good it was at cutting.

And we found that in some cases, you can completely eliminate or completely block CRISPR cutting altogether, if that target gene is packaged. One of the neat things about our artificial system is that it is built around the same machinery that stem cells use to shut down activity of certain genes that are involved in converting the stem cell into a specialized cell like a muscle cell or a nerve cell. So our artificial system, although it is artificial, it overlaps. It uses a lot of the same protein bits and pieces that stem cells use to make their genes inaccessible. Yeah, we think that our finding, which we just published in ACS Synthetic Biology is extremely relevant to sort of looking deeper, more deeply into the challenges facing practical use of CRISPR as a tool.

IRA FLATOW: Let me see if I can get a quick phone call in before we have to go. Let’s go to Panama City, Florida. Matthew, welcome to Science Friday.

MATTHEW: Gosh, thank you, Ira. So how many idiots are using this around the world? To get my mind around it, like there are hundreds of laboratories, are there thousands of laboratories?

IRA FLATOW: Hey, is that a fair– thanks, thanks for the call. Is that a fair question to ask, Carmela?

CARMELA HAYNES: Well, I think the right way to think about that is thinking about the steps involved in using CRISPR yourself. So it is– I do agree that the technology itself is very accessible, like tomorrow if I decided to change my lesson plan here at ASU, I could come up with, I could develop a tutorial that would allow students to look at a publicly available human DNA sequence online at a website like NCBI, and look at a sequence. Teach them a couple of basic rules about how to target CRISPR to a site and give them instructions on how to design a CRISPR.

So this is a customizable system where you can change nucleotide sequences that are associated with the CRISPR machinery to match the target that you wanted to go after and edit. So I could certainly teach those students how it works on paper. We could even walk through, OK, well, how would you order the DNA from a company, a DNA synthesis company to build your own customized CRISPR tool?

But then the huge barrier– you can map everything out on paper. You can run algorithms to look for just the right target, but then when it comes to actually taking cells or an organism and then expressing it and getting what you want, there are a lot of complicated steps involved. So while CRISPR may be accessible to everyone, and it’s easy to learn how to use it, actually implementing it is quite a challenge.

IRA FLATOW: So we’re not going to see a home CRISPR kit for your living room just quite yet. But you never know how soon. Yeah, exactly.


IRA FLATOW: Dr. Haynes, thank you for taking time to be with us today. Carmela Haynes is an Assistant Professor in the School of Biological and Health Systems Engineering at Arizona State University in Tempe, Arizona.

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